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The numbering goes left to right, top to bottom: Block 1 = top-left, Block 2 = top-right, Block 3 = bottom-left, Block 4 = bottom-right.", "mask_path": "forgery/copy_move/60101210_FG_02/mask/60101210_FG_02_4_20_mask.png", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["forgery/copy_move/60101210_FG_02/panel/60101210_FG_02_4_20.png"], "tampered": true, "paper_ids": ["60101210"], "panel_ids": ["60101210_FG_02_4_20.png"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "forgery/copy_move/62317423_FG_02/panel/62317423_FG_02_1_14.png", "question_id": "forgery_555", "fraud_type": "forgery", "fraud_sub_types": ["copy-move"], "ground_truth": ["B"], "mask_indices": [1, 2, 3, 4], "mask_caption": "The image was divided into a 2-row by 2-column equal-area grid, resulting in 4 blocks. The numbering goes left to right, top to bottom: Block 1 = top-left, Block 2 = top-right, Block 3 = bottom-left, Block 4 = bottom-right.", "mask_path": "forgery/copy_move/62317423_FG_02/mask/62317423_FG_02_1_14_mask.png", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["forgery/copy_move/62317423_FG_02/panel/62317423_FG_02_1_14.png"], "tampered": true, "paper_ids": ["62317423"], "panel_ids": ["62317423_FG_02_1_14.png"], "figure_ids": ["None"], "scenario": "Micrograph"}} {"file_name": "forgery/copy_move/62011665_FG_02/panel/62011665_FG_02_4_48.png", "question_id": "forgery_556", "fraud_type": "forgery", "fraud_sub_types": ["copy-move"], "ground_truth": ["B"], "mask_indices": [1, 2, 3, 4], "mask_caption": "The image was divided into a 2-row by 2-column equal-area grid, resulting in 4 blocks. The numbering goes left to right, top to bottom: Block 1 = top-left, Block 2 = top-right, Block 3 = bottom-left, Block 4 = bottom-right.", "mask_path": "forgery/copy_move/62011665_FG_02/mask/62011665_FG_02_4_48_mask.png", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["forgery/copy_move/62011665_FG_02/panel/62011665_FG_02_4_48.png"], "tampered": true, "paper_ids": ["62011665"], "panel_ids": ["62011665_FG_02_4_48.png"], "figure_ids": ["None"], "scenario": "Micrograph"}} {"file_name": "forgery/copy_move/62324201_FG_02/panel/62324201_FG_02_0_4.png", "question_id": "forgery_557", "fraud_type": "forgery", "fraud_sub_types": ["copy-move"], "ground_truth": ["B"], "mask_indices": [1, 2, 3, 4], "mask_caption": "The image was divided into a 2-row by 3-column equal-area grid, resulting in 6 blocks. The numbering goes left to right, top to bottom: Block 1 = first row, left; Block 2 = first row, middle; Block 3 = first row, right; Block 4 = second row, left; Block 5 = second row, middle; Block 6 = second row, right.", "mask_path": "forgery/copy_move/62324201_FG_02/mask/62324201_FG_02_0_4_mask.png", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["forgery/copy_move/62324201_FG_02/panel/62324201_FG_02_0_4.png"], "tampered": true, "paper_ids": ["62324201"], "panel_ids": ["62324201_FG_02_0_4.png"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "forgery/copy_move/60865970_FG_02/panel/60865970_FG_02_3_15.png", "question_id": "forgery_558", "fraud_type": "forgery", "fraud_sub_types": ["copy-move"], "ground_truth": ["B"], "mask_indices": [1, 2], "mask_caption": "The image was divided into a 2-row by 2-column equal-area grid, resulting in 4 blocks. The numbering goes left to right, top to bottom:\nBlock 1 = top-left\nBlock 2 = top-right\nBlock 3 = bottom-left\nBlock 4 = bottom-right", "mask_path": "forgery/copy_move/60865970_FG_02/mask/60865970_FG_02_3_15_mask.png", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["forgery/copy_move/60865970_FG_02/panel/60865970_FG_02_3_15.png"], "tampered": true, "paper_ids": ["60865970"], "panel_ids": ["60865970_FG_02_3_15.png"], "figure_ids": ["None"], "scenario": "Micrograph"}} {"file_name": "forgery/copy_move/62073207_FG_02/panel/62073207_FG_02_14_8.png", "question_id": "forgery_559", "fraud_type": "forgery", "fraud_sub_types": ["copy-move"], "ground_truth": ["B"], "mask_indices": [1, 3], "mask_caption": "The image was divided into a 2-row by 2-column equal-area grid, resulting in 4 blocks. The numbering goes left to right, top to bottom: Block 1 = top-left, Block 2 = top-right, Block 3 = bottom-left, Block 4 = bottom-right.", "mask_path": "forgery/copy_move/62073207_FG_02/mask/62073207_FG_02_14_8_mask.png", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["forgery/copy_move/62073207_FG_02/panel/62073207_FG_02_14_8.png"], "tampered": true, "paper_ids": ["62073207"], "panel_ids": ["62073207_FG_02_14_8.png"], "figure_ids": ["None"], "scenario": "Micrograph"}} {"file_name": "forgery/copy_move/60182179_FG_02/panel/60182179_FG_02_5_0.png", "question_id": "forgery_560", "fraud_type": "forgery", "fraud_sub_types": ["copy-move"], "ground_truth": ["B"], "mask_indices": [1, 2], "mask_caption": "The image was divided into a 2-row by 2-column equal-area grid, resulting in 4 blocks. The numbering goes left to right, top to bottom:\nBlock 1 = top-left\nBlock 2 = top-right\nBlock 3 = bottom-left\nBlock 4 = bottom-right", "mask_path": "forgery/copy_move/60182179_FG_02/mask/60182179_FG_02_5_0_mask.png", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["forgery/copy_move/60182179_FG_02/panel/60182179_FG_02_5_0.png"], "tampered": true, "paper_ids": ["60182179"], "panel_ids": ["60182179_FG_02_5_0.png"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "forgery/copy_move/62425877_FG_02/panel/62425877_FG_02_3_2.png", "question_id": "forgery_561", "fraud_type": "forgery", "fraud_sub_types": ["copy-move"], "ground_truth": ["B"], "mask_indices": [1, 2, 3, 4], "mask_caption": "The image was divided into a 2-row by 2-column equal-area grid, resulting in 4 blocks. The numbering goes left to right, top to bottom: Block 1 = top-left, Block 2 = top-right, Block 3 = bottom-left, Block 4 = bottom-right.", "mask_path": "forgery/copy_move/62425877_FG_02/mask/62425877_FG_02_3_2_mask.png", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["forgery/copy_move/62425877_FG_02/panel/62425877_FG_02_3_2.png"], "tampered": true, "paper_ids": ["62425877"], "panel_ids": ["62425877_FG_02_3_2.png"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "forgery/copy_move/60205464_FG_02/panel/60205464_FG_02_3_9.png", "question_id": "forgery_562", "fraud_type": "forgery", "fraud_sub_types": ["copy-move"], "ground_truth": ["B"], "mask_indices": [1, 2], "mask_caption": "The image was divided into a 2-row by 2-column equal-area grid, resulting in 4 blocks. The numbering goes left to right, top to bottom:\nBlock 1 = top-left\nBlock 2 = top-right\nBlock 3 = bottom-left\nBlock 4 = bottom-right", "mask_path": "forgery/copy_move/60205464_FG_02/mask/60205464_FG_02_3_9_mask.png", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["forgery/copy_move/60205464_FG_02/panel/60205464_FG_02_3_9.png"], "tampered": true, "paper_ids": ["60205464"], "panel_ids": ["60205464_FG_02_3_9.png"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "forgery/copy_move/60866570_FG_02/panel/60866570_FG_02_1_38.png", "question_id": "forgery_563", "fraud_type": "forgery", "fraud_sub_types": ["copy-move"], "ground_truth": ["B"], "mask_indices": [1, 3], "mask_caption": "The image was divided into a 2-row by 2-column equal-area grid, resulting in 4 blocks. The numbering goes left to right, top to bottom: Block 1 = top-left, Block 2 = top-right, Block 3 = bottom-left, Block 4 = bottom-right.", "mask_path": "forgery/copy_move/60866570_FG_02/mask/60866570_FG_02_1_38_mask.png", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["forgery/copy_move/60866570_FG_02/panel/60866570_FG_02_1_38.png"], "tampered": true, "paper_ids": ["60866570"], "panel_ids": ["60866570_FG_02_1_38.png"], "figure_ids": ["None"], "scenario": "Micrograph"}} {"file_name": "forgery/copy_move/60919629_FG_02/panel/60919629_FG_02_26_0.png", "question_id": "forgery_564", "fraud_type": "forgery", "fraud_sub_types": ["copy-move"], "ground_truth": ["B"], "mask_indices": [1], "mask_caption": "The image was divided into a 2-row by 2-column equal-area grid, resulting in 4 blocks. 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The numbering goes left to right, top to bottom: Block 1 = top-left, Block 2 = top-right, Block 3 = bottom-left, Block 4 = bottom-right.", "mask_path": "forgery/copy_move/60267270_FG_02/mask/60267270_FG_02_4_7_mask.png", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["forgery/copy_move/60267270_FG_02/panel/60267270_FG_02_4_7.png"], "tampered": true, "paper_ids": ["60267270"], "panel_ids": ["60267270_FG_02_4_7.png"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "forgery/copy_move/61982938_FG_02/panel/61982938_FG_02_1_0.png", "question_id": "forgery_566", "fraud_type": "forgery", "fraud_sub_types": ["copy-move"], "ground_truth": ["B"], "mask_indices": [4, 5, 6], "mask_caption": "The image was divided into a 2-row by 3-column equal-area grid, resulting in 6 blocks. The numbering goes left to right, top to bottom: Block 1 = first row, left; Block 2 = first row, middle; Block 3 = first row, right; Block 4 = second row, left; Block 5 = second row, middle; Block 6 = second row, right.", "mask_path": "forgery/copy_move/61982938_FG_02/mask/61982938_FG_02_1_0_mask.png", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["forgery/copy_move/61982938_FG_02/panel/61982938_FG_02_1_0.png"], "tampered": true, "paper_ids": ["61982938"], "panel_ids": ["61982938_FG_02_1_0.png"], "figure_ids": ["None"], "scenario": "Micrograph"}} {"file_name": "forgery/copy_move/60785756_FG_02/panel/60785756_FG_02_3_1.png", "question_id": "forgery_567", "fraud_type": "forgery", "fraud_sub_types": ["copy-move"], "ground_truth": ["B"], "mask_indices": [1, 2, 4], "mask_caption": "The image was divided into a 2-row by 2-column equal-area grid, resulting in 4 blocks. The numbering goes left to right, top to bottom: Block 1 = top-left, Block 2 = top-right, Block 3 = bottom-left, Block 4 = bottom-right.", "mask_path": "forgery/copy_move/60785756_FG_02/mask/60785756_FG_02_3_1_mask.png", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["forgery/copy_move/60785756_FG_02/panel/60785756_FG_02_3_1.png"], "tampered": true, "paper_ids": ["60785756"], "panel_ids": ["60785756_FG_02_3_1.png"], "figure_ids": ["None"], "scenario": "Micrograph"}} {"file_name": "forgery/copy_move/60866570_FG_02/panel/60866570_FG_02_6_14.png", "question_id": "forgery_568", "fraud_type": "forgery", "fraud_sub_types": ["copy-move"], "ground_truth": ["B"], "mask_indices": [1, 2], "mask_caption": "The image was divided into a 2-row by 2-column equal-area grid, resulting in 4 blocks. The numbering goes left to right, top to bottom: Block 1 = top-left, Block 2 = top-right, Block 3 = bottom-left, Block 4 = bottom-right.", "mask_path": "forgery/copy_move/60866570_FG_02/mask/60866570_FG_02_6_14_mask.png", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["forgery/copy_move/60866570_FG_02/panel/60866570_FG_02_6_14.png"], "tampered": true, "paper_ids": ["60866570"], "panel_ids": ["60866570_FG_02_6_14.png"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "forgery/copy_move/60156018_FG_02/panel/60156018_FG_02_6_9.png", "question_id": "forgery_569", "fraud_type": "forgery", "fraud_sub_types": ["copy-move"], "ground_truth": ["B"], "mask_indices": [1, 2, 3, 4], "mask_caption": "The image was divided into a 2-row by 3-column equal-area grid, resulting in 6 blocks. 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The numbering goes left to right, top to bottom: Block 1 = top-left, Block 2 = top-right, Block 3 = bottom-left, Block 4 = bottom-right.", "mask_path": "forgery/copy_move/60813470_FG_02/mask/60813470_FG_02_5_11_mask.png", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["forgery/copy_move/60813470_FG_02/panel/60813470_FG_02_5_11.png"], "tampered": true, "paper_ids": ["60813470"], "panel_ids": ["60813470_FG_02_5_11.png"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "forgery/copy_move/62340571_FG_02/panel/62340571_FG_02_2_0.png", "question_id": "forgery_571", "fraud_type": "forgery", "fraud_sub_types": ["copy-move"], "ground_truth": ["B"], "mask_indices": [1, 3, 5], "mask_caption": "The image was divided into a 3-row by 2-column equal-area grid, resulting in 6 blocks. The numbering goes left to right, top to bottom: Block 1 = first row, left; Block 2 = first row, right; Block 3 = second row, left; Block 4 = second row, right; Block 5 = third row, left; Block 6 = third row, right.", "mask_path": "forgery/copy_move/62340571_FG_02/mask/62340571_FG_02_2_0_mask.png", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["forgery/copy_move/62340571_FG_02/panel/62340571_FG_02_2_0.png"], "tampered": true, "paper_ids": ["62340571"], "panel_ids": ["62340571_FG_02_2_0.png"], "figure_ids": ["None"], "scenario": "Micrograph"}} {"file_name": "forgery/copy_move/2010073196_FG_02/panel/2010073196_FG_02_4_15.png", "question_id": "forgery_572", "fraud_type": "forgery", "fraud_sub_types": ["copy-move"], "ground_truth": ["B"], "mask_indices": [1], "mask_caption": "The image was divided into a 1-row by 2-column equal-area grid, resulting in 2 blocks. 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"panel_ids": ["61727468_4_2"], "figure_ids": ["None"], "scenario": "Physical Object"}} {"file_name": "text_image_inconsistency/numerical/2010027936_TII_01/figure/2010027936_TII_01_8.png", "question_id": "consistency_1", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "EDS analysis at the grain boundaries of Fe-6.5 wt % Si steel strip samples: (a) 1.0 wt % Cu, (b) 1.5 wt % Cu, and (c) 2.0 wt % Cu.", "figure_related_sentences": "Further SEM microstructural examination revealed that Cu rich precipitates were absent in the 1.5 wt % Cu specimen (Figure 8a), but became visible in the 1.5 wt % Cu specimen (Figure 8b). The precipitates in the 1.5 wt % Cu specimen were tiny, few, and irregularly scattered at grain boundaries. Cu-rich precipitates were continuous or semicontinuous at grain boundaries as the Cu dosage was raised to 1.0 wt %, as shown in Figure 8c.", "inconsistent_part": "related_sentences", "tampered_sentences": ["Further SEM microstructural examination revealed that Cu rich precipitates were absent in the 1.5 wt % Cu specimen (Figure 8a),", "Cu-rich precipitates were continuous or semicontinuous at grain boundaries as the Cu dosage was raised to 1.0 wt %,"], "golden_sentences": ["Further SEM microstructural examination revealed that Cu rich precipitates were absent in the 1.0 wt % Cu specimen (Figure 8a),", "Cu-rich precipitates were continuous or semicontinuous at grain boundaries as the Cu dosage was raised to 2.0 wt %,"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010027936_TII_01/figure/2010027936_TII_01_8.png"], "tampered": true, "paper_ids": ["2000000143"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010000860_TII_01/figure/2010000860_TII_01_1.png", "question_id": "consistency_2", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2. BcR stimulation downregulates cathepsin S activity in IIA1.6 cells. (A)Accumulation of the p10 invariant chain fragment in BcR-stimulated IIA1.6 cells. IIA1.6 cells were incubated for the times indicated with anti–mouse IgG antibodies, as described in Materials and Methods. The p10 fragment was detected with a rabbit antiserum specific for the cytoplasmic tail of the invariant chain. The same blot was incubated with an anti-IA chain antiserum and then with an antitubulin antibody (left). In the right panel, the p10 signal is normalized with the MHC class II signal obtained for the same lane and these p10 signals are expressed in arbitrary units.These results are representative of three independent experiments. (B) IIA1.6 cells were left unstimulated or were stimulated for various times with anti–mouse IgG antibodies and membranes were prepared to assess cathepsin S (top) hexosaminidase (bottom right), and cathepsin B/L (bottom left) activities in fluorometric assays. Cathepsin S activity was tested at pH 7.0, because cathepsin S is functional at neutral pH, with (white bars) or without (back bars) LHVS, a cathepsin S inhibitor. Error bars correspond to the mean of three experiments. (C) Detection of cathepsin S with an iodinated peptide that binds to the active site of cathepsin S. Stimulated or unstimulated cells were incubated for 1 h with I-Mu-Tyr-Ala-CH2F, with or without LHVS, and cell lysates were then subjected to electrophoresis in 12% polyacrylamide gels. Cathepsin S was detected as a 26-kD band. The labeling of this protein was inhibited by adding LHVS. LHVS did not inhibit the labeling of an higher molecular weight band in the gel at 32 kD, which was identified as cathepsin L. Rat basophilic leukemia cell line cells,which do not produce cathepsin S, were used as a negative control. In the bottom panel, each band was quantified with a PhosphorImager™. Cathepsin S labeling was normalized against labeling of the 32-kD band for each lane and cathepsin S labeling was quantified in arbitrary units.", "figure_related_sentences": "BcR stimulation, showed an increase in the amount of p10 invariant chain fragment detected with a rabbit antiserum specific for the cytosolic domain of the invariant chain,whereas MHC class II and tubulin levels remained constant (Fig. 2 A). The effect of BcR stimulation on invariant chain degradation depended on the MHC class II allele; the effect was strongest in IIA1.6 cells–expressing IA. In parental IIA1.6 cells expressing IAd, p10 levels doubled (data not shown), whereas they increased by a factor of 5 in IAk-transfected IIA1.6 cells (Fig. 2 A) and in IIA1.6 cells expressing IAb (data not shown). However, the changes in p10 levels over time were similar for both alleles: the p10 fragment was first detected after 60 min, increased to reach a maximum at 3 h and then returned to its initial level after 6 h of BcR stimulation (Fig. 2 A). No change in de novo MHC class II synthesis was observed in pulse-chase experiments (data not shown). Although MHC class II–peptide complexes were detected in dense fractions after BcR stimulation, the increase in p10 invariant chain fragment levels and the detection of invariant chain, together with MHC class II, in late endosomal compartments after BcR cross-linking suggests that the proteolytic degradation of invariant chain was inhibited during B cell activation. Therefore, we assessed various proteolytic activities during BcR-induced cell activation. IIA1.6 cells were stimulated for various times as described above, and the activities of cathepsin S, cathepsin L/B, and hexosaminidase were assessed on the same membrane preparations by means of fluorometric assays (23). Cathepsin S activity was measured at pH 7.0 (Fig. 2 B) in membrane preparations of B cells because cathepsin S is active at this pH, whereas cathepsinB is not. We demonstrated that the activity measured corresponded to cathepsin S by adding low concentrations of LHVS. Such low concentrations (1 nM) of LHVS inhibit cathepsin S, but not cathepsin B. Higher concentrations of LHVS (30 nM) are required to inhibit cathepsin B (24). Cathepsin S activity decreased after BcR cross-linking: maximal inhibition (75%) occurred at 3 h, with cathepsin Sactivity progressively increasing thereafter and returning to initial values after 6 h; 18 h after BcR cross-linking, 15%inhibition of cathepsin activity was still observed. No change in hexosaminidase activity was detected in the same samples, whereas cathepsin L/B activity decreased slightly (Fig. 2 B). We directly measured cathepsin S activity in B cells by labeling stimulated and unstimulatedIIA1.6 cells with an iodinated peptide that bound specifically to the active site of cathepsin S (22). A 26-kD protein,presumably cathepsin S, was specifically labeled in these conditions and this labeling was inhibited in the presence of LHVS peptide. This assay gave similar results to the original assay, as 80% inhibition of cathepsin S labeling was ob-served after 3 h and this inhibition was partially reversible after 18 h (Fig. 2 C). No changes in the amounts of cathepsin S and cystatin C proteins present were detected by Western blotting (data not shown). These results demon-strate that BcR-induced B cell activation downregulated cathepsin S activity, accounting for the transient accumulation of MHC class II–invariant chain complexes in lyso-somes. The changes in MIIC composition induced by B cell activation suggest that BcR stimulation may trigger morphological changes in processing compartments.First, higher levels of transient intracellular accumulation of MHC class II and p10 fragment were observed in IIA1.6 cells expressing class II alleles with a strong affinity for invariant chain such IAk (Fig. 2 A and data not shown).", "inconsistent_part": "related_sentences", "tampered_sentences": ["the p10 fragment was first detected after 60 min, increased to reach a maximum at 3 h and then returned to its initial level after 6 h of BcR stimulation (Fig. 2 A)."], "golden_sentences": ["the p10 fragment was first detected after 30 min, increased to reach a maximum at 3 h and then returned to its initial level after 6 h of BcR stimulation (Fig. 2 A)."], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010000860_TII_01/figure/2010000860_TII_01_1.png"], "tampered": true, "paper_ids": ["2010000104"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010064544_TII_01/figure/2010064544_TII_01_4.png", "question_id": "consistency_3", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 5. Summary of genome-wide STAT5 binding sites at L1. (A) The Venn diagram shows the number of identified STAT5A and STAT5B sites (peaks) in AABB tissue and STAT5B sites in BB tissue. (B) Average peak heights of STAT5A and STAT5B in AABB and BB tissues were estimated after library size normalization (RPM, reads per 10 million, input subtracted). (C) Mean fold changes of STAT5A and STAT5B target genes in AABB tissue and STAT5B target genes in BB tissue were calculated. The genes containing STAT5 peaks within ±1 kb around TSSs were regarded as STAT5 target genes. (D) Normalized tag counts (RPM) of STAT5A, RNA polII and H3K4me3 from 200 bp around STAT5A peak centers at L1 were calculated and compared between AABB and BB. Log2-transformed values were used (x and y axes). (E) Normalized tags of H3K4me3 at positions 1 kb upstream and 2 kb downstream of TSS were summed up and divided by the size (3 kb) and then quantile normalized for comparison (top). The scatter plot shows the fold change (x-axis) and difference (y-axis) of H3K4me3 average enrichment between genes (spot) in AABB and BB. Cutoffs for significant changes were set as follows: 1.5-fold change (x-axis, AABB/BB) and four average tag difference (y-axis, AABB/BB). Among the genes showing significant changes of H3K4me3 enrichment, the number of STAT5 target and non-target genes was counted (bottom). (F) Genome browser views represent three gene loci (Wap, Csn1s2a and Stap1) showing changes of H3K4me3 level and one housekeeping gene locus (Actb).", "figure_related_sentences": "Totals of 26,231 STAT5A and 6,969 STAT5B peaks in wild type (AABB) and 2,574 STAT5B peaks in Stat5a-null (BB) were identified as STAT5 binding sites (Figure 5). For visualization, total number of reads in each sample was normalized to 10 million. The ChIP-seq data are deposited in GEO under accession number GSE40930. In total, more than 26,000 STAT5A peaks were identified in control but not in Stat5a-null mammary tissue (Figure 5). The 6,873 STAT5B peaks almost completely overlapped with the STAT5A peaks in wild-type tissue suggesting that there are no high affinity binding sites restricted to STAT5B. In general, the average STAT5A peak height was 3-fold higher than that of STAT5B (Figure 5B), which is probably the result of a greater abundance of STAT5A and possibly higher antibody affinity. The 2,395 STAT5B binding sites in Stat5a-null and 6,873 STAT5B binding sites in wild-type mammary tissues, which probably reflect high affinity STAT5 binding sites, were a better predictor for gene activation. Indeed, mean expression fold changes of the genes targeted by STAT5B in Stat5a-null mammary tissue were higher than those of the others (Figure 5C). The level of STAT5 binding was positively correlated with the enrichment level of RNA PolII and H3K4me3 near promoter regions (Supplementary Figure S7). Looking in more detail, a cutback of STAT5 by ~70% (BB) resulted in a decreased level of RNA polII but not H3K4me3 near the STAT5 binding sites as overall spots shifted toward AABB (Figure 5D). However, comparison of H3K4me3 enrichment on promoter regions between AABB and BB tissues revealed that some STAT5 target and non-target genes showed a significant decrease of H3K4me3 in BB tissue (Figure 5E; Supplementary Table S4). Manual evaluation of several loci including STAT5 target genes (Wap and Csn1s2a), and a non-STAT5 target gene (Stap1) confirmed the decrease of H3K4me3 marks, which did not occur over the housekeeping gene, Actb (Figure 5F).", "inconsistent_part": "related_sentences", "tampered_sentences": ["In general, the average STAT5A peak height was 3-fold higher than that of STAT5B (Figure 5B)"], "golden_sentences": ["In general, the average STAT5A peak height was 5-fold higher than that of STAT5B (Figure 5B)"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010064544_TII_01/figure/2010064544_TII_01_4.png"], "tampered": true, "paper_ids": ["2010000117"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010065447_TII_01/figure/2010065447_TII_01_3.png", "question_id": "consistency_4", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 4. Editing and ADAR2-binding reduces splicing efficiency at the Gria2 R/G site. (A) RT-PCR shows a gradual reduction of splicing in the presence of a strong (+/+), intermediate (+/−) or weak (−/−) polypyrimidine tract in wildtype (wt) or pre-edited (pre-ed) versions of a Gria2 exon 13 minigene. Pre-mRNA and mRNA are indicated at the right side of the panel. M = size standard. bp = basepairs. A white asterisk marks an aberrant splicing product. (B) The relative splicing efficiency––measured from the gel in panel A––is given as % unspliced product. Pre-editing reduces splicing efficiency. Quantification was done from four independent biological replicates. (* P-value < 0.05; n.s. not significant). Dark gray = wt, light gray = pre-edited at position -2-3. (C) RT-PCR of Gria2 reporter transcripts in the presence (y) or absence (n) of ADAR2 indicate a strong reduction in splicing in the presence of ADAR2. Pre-mRNA and mRNA are indicated at the right side of the panel. M = size standard. bp = basepairs. (D) The splicing efficiency––deduced from the gel in panel (C)––in percent unspliced transcript is given. The presence of ADAR2 reduces splicing efficiency. The quantification was done from four independent biological replicates (n.s. not significant, * P-value < 0.05; ** P-value < 0.01).", "figure_related_sentences": "One of the Gria2 minigenes (+/−; Supplementary Figure S2). An even stronger accumulation of pre-mRNA was observed for the pre-edited -2-3 constructs in context with the strongest and weakest branch points (Figure 4A and B). This demonstrates that guanosines and therefore most likely also inosines introduced by editing can interfere with splicing of the Gria2 minigene. Surprisingly, when we transfected the Gria2 minigene (+/+) without the addition of the ADAR2 plasmid we observed a strong reduction in pre-mRNA (Figure 4C and D). Conversely, an increase in pre-mRNA accumulation was observed when the pre-edited -2 version of Gria2 was cotransfected with ADAR2. It thus appears that ADAR2 binding alone impairs splicing, even when editing cannot take place.", "inconsistent_part": "caption", "tampered_sentences": ["The quantification was done from four independent biological replicates", "Quantification was done from four independent biological replicates"], "golden_sentences": ["The quantification was done from three independent biological replicates", "Quantification was done from three independent biological replicates"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010065447_TII_01/figure/2010065447_TII_01_3.png"], "tampered": true, "paper_ids": ["2010000124"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010065498_TII_01/figure/2010065498_TII_01_0.png", "question_id": "consistency_5", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. Cdc48 and ubiquitin ligases affect the distribution pattern of ribosome-associated ubiquitinated species. Sucrose gradient sedimentation analysis of ribosomes extracted from the wild-type RS1158 strain (A) and its derivative strain harboring a tetracycline-repressible PTET-O7-CDC48 allele (B). Cells were grown in the presence of doxycycline (Dox) for 20 h. Cell lysates were centrifuged through 15%–45% sucrose gradients and fractionated with the continuous measurement of absorbance at 254 nm to visualize ribosomal peaks. Proteins isolated from individual fractions were separated on 10% SDS-acrylamide gels and the same membrane was probed with anti-ubiquitin (top) and anti-Rpl3 (bottom) antibodies. (C) and (D) The same analysis performed in PTET-O7-CDC48 cells lacking either LTN1 or NOT4. All gradients were run at least five times, representative blots are shown; see Supplemental Figure S1 for additional controls. (E) Hygromycin B (HygB) treatment induces accumulation of Ltn1-ubiquitinated 60S products. Where indicated, cells were treated with 100 µg/mL hygromycin for 2 h. Gradient fractions 2–6 were separated on the same gel for a better comparison of total ubiquitination levels. (F) Lack of LTN1 makes cells hypersensitive to hygromycin. Five-fold dilutions of wild-type B4741 (WT) and ltn1Δ strains were grown on plates without antibiotic or with 100 µg/ml hygromycin for 3 days at 30°C.", "figure_related_sentences": "RESULTS Gradient analysis of ubiquitinated polypeptides associated with ribosomes in Cdc48-depleted cells To examine how endogenous targets of cotranslational protein QC are distributed among different subpopulations of ribosomes in yeast cells, we fractionated cytoplasmic lysates by sedimentation through sucrose gradients. We observed a smear of ubiquitinated translation products in fractions containing polysomes and 80S monosomes in wild-type cells (Figure 1A, Supplementary Figure S1A), consistent with the previously described ubiquitination of ribosome-associated NCs (3,4). Previous studies have shown that loss of Cdc48 function increases accumulation of ubiquitinated NCs associated with ribosomes (2–4). To better define this effect, we analyzed yeast strains in which CDC48 is placed under the control of a tetracycline-regulatable promoter (PTET-O7-CDC48) (39). Depletion of Cdc48 by addition of doxycycline (Dox) to growing yeast cultures significantly increased the intensity of the ubiquitin signal in these cells (Figure 1B, Supplementary Figure S1A-D), as expected from stabilization of ubiquitinated NCs that normally undergo Cdc48-assisted degradation by the proteasome (4). The ubiquitin signal in Cdc48-depleted cells was mainly concentrated in fractions 4-7 (Figure 1B), corresponding to the peaks of 60S subunits (fractions 3 and 4) and 80S monosomes (fractions 4 and 5). In this and other experiments, the equivalent separation of ribosomal fractions on gradients was controlled by comparing alignment of A260 traces of the gradients, gel analysis of rRNA from the same fractions that were used for protein isolation, Ponceau S staining to control protein transfer, and probing with antibodies against ribosomal protein Rpl3 (Supplementary Figure S1A). When it was necessary to compare absolute levels of ubiquitinated species between different strains, we analyzed fractions side by side on the same gel to rule out variations between processing of individual membranes (Supplementary Figure S1D). Notably, the increase in ubiquitination of the 80S fraction was not due to redistribution of ribosomes from polysomes to the 80S monosome form in Cdc48-depleted cells, as shift of wild-type cells to medium lacking glucose (a condition known to inhibit translation initiation) resulted in elevated 80S levels comparable to those in Dox-treated PTET-O7-CDC48 cells, but did not cause accumulation of polyubiquitinated peptides in the 60S–80S fractions (Supplementary Figure S1E). Thus, Cdc48 depletion leads to increased accumulation of ubiquitinated polypeptides associated predominantly with 60S and 80S ribosomes. We next examined the distribution of ubiquitin-conjugated species in the 60S–80S fractions of PTET-O7-CDC48 strains containing additional deletions in genes of E3 ligases implicated in cotranslational QC. Consistent with previous findings obtained with model substrates (4,14,15,40), an ltn1Δ deletion completely abrogated the accumulation of ubiquitin-modified NCs in fractions that contained free 60S subunits, but not in the 80S fraction (Figure 1C). In contrast, a Cdc48-depleted strain lacking Not4, part of the Ccr4-Not deadenylase complex reported to ubiquitinate polypeptides associated with stalled ribosomes (19,27), showed a diminished intensity of the ubiquitin signal in the 80S fraction, whereas accumulation of ubiquitinated products in the 60S fraction remained constitutively high (Figure 1D). These results support the notion (2,10,14,15) that Ltn1 is a primary, and possibly unique, E3 ligase responsible for ubiquitin tagging of the 60S-associated NCs, a process necessary for Cdc48 recruitment and polypeptide degradation. To further investigate whether the observed accumulation of 60S-associated products ubiquitinated by Ltn1 is related to aberrant polypeptide synthesis during translation, we treated cells for 2 h with hygromycin B, an aminoglycoside that causes decoding errors, stop codon readthrough and ribosomal stalling (41–43). In wild-type cells, hygromycin treatment significantly increased the amount of polyubiquitinated products present in the 60S–80S fractions (Figure 1E). Similarly to PTET-O7-CDC48 ltn1Δ cells, deletion of LTN1 abrogated the accumulation of ubiquitinated products in the 60S, but not 80S fraction in the hygromycin-treated cells (Figure 1E). Consistent with a role of Ltn1 in resolving translation errors caused by hygromycin, ltn1Δ cells are hypersensitive to this antibiotic (Figure 1F). These results support the idea that the Ltn1-Cdc48-mediated QC mechanism can capture a variety of defective translational products that remain associated with the large ribosomal subunit after splitting of the ribosome. We found that the ubiquitin signal in the 60S fraction was greatly reduced compared to wild-type cells, although these cells continued to display the robust accumulation of ubiquitinated 80S complexes, resembling the effect of the ltn1Δ deletion (compare Figure 4B, right with Figure 1C).", "inconsistent_part": "related_sentences", "tampered_sentences": ["The ubiquitin signal in Cdc48-depleted cells was mainly concentrated in fractions 4-7 (Figure 1B)"], "golden_sentences": ["The ubiquitin signal in Cdc48-depleted cells was mainly concentrated in fractions 3–5 (Figure 1B)"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010065498_TII_01/figure/2010065498_TII_01_0.png"], "tampered": true, "paper_ids": ["2010000139"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010065537_TII_02/figure/2010065537_TII_02_4.png", "question_id": "consistency_6", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 5. Increased U12-dependent intron retention in SMA mice. (A) qPCR validation of U12-dependent intron retention at PND1 and PND5 in spinal cord. (B) qPCR validation of U12-dependent intron retention at PND1 and PND5 in brain. (C) qPCR validation of U12-dependent intron retention at PND1 and PND5 in liver. (D) qPCR validation of U12-dependent intron retention at PND1 and PND5 in muscle. Error bars indicate SEM, n ≥ 3, ***P-value < 0.001, **P-value < 0.01, *P-value < 0.05. White bars indicate heterozygous control mice, gray bars indicate SMA-like mice. Spl = spliced, Unspl = unspliced/retained intron.", "figure_related_sentences": "We validated the decrease in retention of the U12-dependent intron and the decrease of the levels of spliced Rasgrp3 by specific qPCR assays in all tissues, at both PND1 and PND5 (Figure 5 and 6). Since retention of the intron could lead to degradation of the transcript via the NMD pathway due to a premature termination codon (PTC) in the U12-dependent intron (Supplementary Figure S10), our observations point out that aberrant retention of the U12-dependent intron in the Rasgrp3 gene might be an underlying mechanism contributing to deregulation of the cell cycle in SMA mice. In the spinal cord, a U12-dependent intron in Myh9 was retained, together with upregulation of Myh9 transcripts in general. As in the case of Rasgrp3, this may be due to a PTC being present within the U12-dependent intron (Supplementary Figure S13). Validation with qPCR confirmed the downregulation of spliced Myh9 and upregulation of unspliced Myh9 in both spinal cord and brain (Figure 5A and B), whereas there was increased retention of the U12-dependent intron in liver and muscle (Figure 5C and D). This could indicate that the NMD pathway is more effective in the CNS, and perhaps explain why we detected fewer U12-dependent intron retention events in peripheral tissue than in the CNS.", "inconsistent_part": "related_sentences", "tampered_sentences": ["We validated the decrease in retention of the U12-dependent intron and the decrease of the levels of spliced Rasgrp3 by specific qPCR assays in all tissues,", "together with upregulation of Myh9 transcripts in general.", "and perhaps explain why we detected fewer U12-dependent intron retention events in peripheral tissue than in the CNS."], "golden_sentences": ["We validated the increase in retention of the U12-dependent intron and the decrease of the levels of spliced Rasgrp3 by specific qPCR assays in all tissues,", "together with downregulation of Myh9 transcripts in general.", "and perhaps explain why we detected more U12-dependent intron retention events in peripheral tissue than in the CNS."], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010065537_TII_02/figure/2010065537_TII_02_4.png"], "tampered": true, "paper_ids": ["2010000141"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010065559_TII_02/figure/2010065559_TII_02_0.png", "question_id": "consistency_7", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. BRD4 is required for osteoblast differentiation. (A and B) Alkaline Phosphatase staining of hFOBs differentiated into the osteoblast lineage following DMSO or JQ1 (250nM) (upper panel) and siCNTR or siBRD4 (SmartPool) (lower panel) treatments (A). The stained areas were quantified and displayed as percentage of whole area. Mean ± SD, n = 2 (B). Student’s t-test was performed for statistical analysis where ***P < 0.001, **P < 0.01, *P < 0.05 (C). The relative expression of osteoblast marker genes in hFOBs in undifferentiated (UND) and differentiated (DIF) state following siBRD4 or JQ1 treatment was evaluated via qRT-PCR and normalized to expression level of RPLP0 and the expression in the undifferentiated state. Mean ± SD, n = 3. One-way ANOVA followed by Turkey’s test was performed for statistical analysis where ***P < 0.001, **P < 0.01, *P < 0.05. (D and E). Mouse IDG-SW3 osteocyte cells were differentiated for 14 and 26 days following DMSO or JQ1 treatment and stained with alizarin red for detection of mineralized.", "figure_related_sentences": "RESULTS BRD4 promotes osteoblast differentiation. To examine the function of BRD4 during lineage specification and maintenance, we examined the effects of BETi on the differentiation of hFOBs (32). Perturbation of BRD4 function by BETi (JQ1) treatment or siRNA-mediated knockdown (Supplementary Figure S1A and B) resulted in a significant decrease of differentiation-induced alkaline phosphatase activity (Figure 1A and B; Supplementary Figure S1C and D). Gene expression analyses confirmed these findings and showed a reduced expression of the osteoblast-specific genes RUNX2, TNFRSF11B (Osteoprotegerin) and ALPL following JQ1 treatment or BRD4 knockdown (Figure 1C). To investigate whether this effect was limited to early stages of lineage-specification, we also tested the effect of BRD4 inhibition on IDG-SW3 mouse osteocytes. Despite their advanced stage of differentiation, mineralization was significantly impaired following JQ1 treatment (Figure 1D and E). Consistently, BETi treatment resulted in reduced expression of the osteoblast/osteocyte-specific genes Mepe, Bglap and Dmp1 (Figure 1F). The role of BET proteins in controlling osteoblast differentiation was differentiation-stage independent since similar effects were also observed in multipotent hMSC, where knockdown or inhibition of BRD4 also potently affected the expression of osteoblast lineage-specific genes (ALPL, COL1A1 and BGLAP; Supplementary Figure S1E and F). In order to gain a more complete overview of the effects of BRD4 on the regulation of lineage-specific gene expression, we performed transcriptome-wide mRNA-seq analyses following BRD4 depletion or JQ1 treatment in hFOB cells (Supplementary Figure S1G). Inhibition of BRD4 by JQ1 resulted in the differential regulation of a selected subset of genes. Consistent with the positive role of BET proteins in gene transcription, we observed less downregulated genes compared to upregulated genes following JQ1 treatment (Figure 1G). Interestingly, a large fraction of BETi-regulated genes were also differentially regulated during osteoblast differentiation, further supporting a lineage-specific function of BRD4 (Figure 1G–I). Consistent with the fact that JQ1 targets all BET proteins including BRD2, -3 and -4 (56) and the potential differences induced by inhibition of bromodomain-mediated protein-protein interactions versus effects observed following a complete loss of BRD4 protein expression, the effects of JQ1 and BRD4 knockdown were not identical (Figure 1G–I). However, both treatments showed a similar effect of preferential downregulation of differentiation-induced genes (Figure 1I). Moreover, GSEA on siBRD4-downregulated genes indicated a significant enrichment for pathways associated with extracellular matrix, collagen and skeletal development (Figure 1J). JQ1-downregulated genes were similarly enriched for developmental pathways (Supplementary Figure S1H). Taken together, these results suggest a role of BRD4 in maintaining and directing osteoblast-specific lineage gene expression. Interestingly, some ‘Segment 3+4’ regions showed co-occupancy of all TFs (Supplementary Figure S6A) while some osteoblast-specific BRD4 target genes such as TNFRSF11B (Figure 1C), ELN and DCN (Supplementary Figure S5C) showed distinct occupancy of the identified TFs at putative enhancer sites located within 50 kb of the genes (Figure 5K; Supplementary Figure S6B and E).", "inconsistent_part": "related_sentences", "tampered_sentences": ["we observed less downregulated genes compared to upregulated genes following JQ1 treatment (Figure 1G)"], "golden_sentences": ["we observed more downregulated genes compared to upregulated genes following JQ1 treatment (Figure 1G)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010065559_TII_02/figure/2010065559_TII_02_0.png"], "tampered": true, "paper_ids": ["2010000145"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010104206_TII_02/figure/2010104206_TII_02_1.png", "question_id": "consistency_8", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2. Increased blood glucose in Kir6.1-GOF mice. (A–C, left) Representative intrinsic GFP fluorescence in freshly isolated islets from transgenic mice. High fluorescence in transgenic islets indicates the presence of the Kir6.1 transgene (Kir6.1[x], Control), and loss of fluorescence in transgenic β cells within islets after Cre-recombination (Rip-Kir6.1[x]) indicates actual expression of the transgene specifically in these cells. Bars, 10 µm. (right) Fed blood glucose over time after weaning in Rip-Kir6.1[WT] (A, black), single mutant Rip-Kir6.1[GD] (B, green), and double mutant Rip-Kir6.1[GD,QR] (C, red) with respect to their control littermates (white). Data represent mean ± SEM, n = 8–10 animals in each group. Significant differences (*, P < 0.05) between transgenic and control littermate mice are indicated (t test).", "figure_related_sentences": "To study the effects of Kir6.1 subunits of the KATP channel in vivo, we have generated novel mice that express either the Kir6.1 WT (Kir6.1[WT]) or a Kir6.1-GOF, single mutant G343D (Kir6.1[GD]) or double mutant G343D/Q53R (Kir6.1[GD,QR]) transgenes under Cre-recombinase control (Li et al., 2013). Global Cx1 Kir6.1[WT], Kir6.1[GD], and Kir6.1[GD,QR] mice express GFP fluorescence ubiquitously in the whole body, but after tissue-specific Cre-recombination, these mice lose fluorescence only in the tissue of interest (Li et al., 2013). Specific expression in pancreatic β cells was achieved by crossing Kir6.1 transgenic mice with Rip-Cre mice. Fig. 2 shows marked gain of fluorescence in pancreatic islets from double transgenic Rip-Kir6.1[WT] (A), Rip-Kir6.1[GD] (B), and Rip-Kir6.1[GD,QR] (C; as an indication of transgene expression), compared with bright fluorescent islets from single Kir6.1[WT], Kir6.1[GD], and Kir6.1[GD,QR] transgenic mice (lacking recombination and absence of transgene expression). Littermate control mice in all experiments below include pooled WT, single transgenic Rip-Cre, and single transgenic Kir6.1[GD] or Kir6.1[GD,QR] mice. In each case, no significant differences were found between these genotypes when independently tested. Diabetes in Kir6.1-GOF mutant mice GOF mutations in the Kir6.1 subunit of the KATP channel result in either glucose intolerance (Rip-Kir6.1[GD]) or frank diabetes (Rip-Kir6.1[GD,QR]), mimicking the consequences of weak or more significant expression of Kir6.2-GOF transgenes (Koster et al., 2000, 2005; Remedi et al., 2009). 7-wk-old double transgenic Rip-Kir6.1[GD] mice showed higher fed glucose than littermate control mice (Fig. 2 B). They also demonstrate increased fasting blood glucose and a mildly impaired glucose tolerance, accompanied by reduced circulating plasma insulin after glucose challenge with respect to control littermates (Fig. 3 B). Importantly, however, 2 out of 10 Rip-Kir6.1[GD] mice showed diabetes with dramatically low fasting blood glucose levels and a marked impairment of glucose tolerance (Fig. 2 B). Strikingly, all Rip-Kir6.1[GD,QR] mice developed severe diabetes (Fig. 2 C) with markedly impaired glucose tolerance, as the result of significantly reduced plasma insulin levels in response to glucose challenge (Fig. 3 C). Importantly, however, and as expected, overexpression of WT Kir6.1 subunits in Rip-Kir6.1[WT] mice did not result in increased blood glucose or glucose intolerance (Figs. 2 A and 3A), suggesting that impaired glucose tolerance and diabetes are promoted by Kir6.1-GOF and are not an artifactual consequence of overexpressed transgenic protein levels perse.", "inconsistent_part": "related_sentences", "tampered_sentences": [" Fig. 2 shows marked gain of fluorescence in pancreatic islets from double transgenic Rip-Kir6.1[WT] (A)", "1[GD] mice showed diabetes with dramatically low fasting blood glucose levels and a marked impairment of glucose tolerance (Fig."], "golden_sentences": [" Fig. 2 shows marked loss of fluorescence in pancreatic islets from double transgenic Rip-Kir6.1[WT] (A)", "1[GD] mice showed diabetes with dramatically high fasting blood glucose levels and a marked impairment of glucose tolerance (Fig."], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010104206_TII_02/figure/2010104206_TII_02_1.png"], "tampered": true, "paper_ids": ["2010000148"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010105100_TII_01/figure/2010105100_TII_01_1.png", "question_id": "consistency_9", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2Id-immunized mice are protected against MM cells that produce complete myeloma protein while they succumb to FLC MM cells. (A–H) BALB/c mice were immunized i.m./EP with 50µg CCL3-scFv315 or NaCl and challenged 14 days later with MOPC315.BM.Luc.IgAλ2 cells (2×105) that produce complete M315, (left panel), (A–D) or MOPC315.BM.λ2 cells (2×105) that produce only free λ2 L chains (right panel), (E–H). (A, E) Images of whole body bioluminescence (BLI) showing mean±SEM, (B, F) representative ventral images, (C, G) serum M315 on days 0, 21 and 35 in individual mice, and (D, H) survival. End point was paraplegia. n=5–8 mice/group. Statistics: Two-way ANOVA with Bonferroni correction (A, C, E, G) and Mantel Cox Log-Rank test for survival (D, H). *p<0.05, **p<0.01, ****p<0.0001. ANOVA, analysis of variance; MM, multiple myeloma; ND, not detected; ns, not significant.", "figure_related_sentences": "The phenomenon was confirmed in experiments using luciferase-labeled MOPC315.BM.Luc cells injected intravenously and bioluminescence as a read-out for tumor load (online supplemental figure 2). Thus, while radiance and M315 levels correlated strongly in the CCL3-scFvA20-immunized mice, there was no such correlation in the CCL3-scFv315-immunized mice. Immunized mice are protected against MOPC315.BM.Luc.IgAλ2 while they succumb to the FLC variant. Having developed cloned MOPC315.BM cell lines that either secrete H+L myeloma protein (MOPC315.BM.Luc.IgAλ2) or only free λ2 L chains (MOPC315.BM.Luc.λ2), we tested these two cell lines in challenge experiments. Mice were immunized with CCL3-scFv315 and challenged 14 days later with either of the two variants. NaCl was used as a negative control. Six out of eight immunized mice were protected against cells that produced complete M315 (MOPC315.BM.Luc.IgAλ2), as measured by bioluminescence imaging (BLI) (figure 2A,B), serum M315 (figure 2C) and survival (figure 2D). However, three mice had a bioluminescence signal and M315 in their sera (figure 2C); these two mice developed paralysis and did not survive (figure 2D). In contrast, CCL3-scFv315 immunized mice were not protected against cells that only produced free λ2 L chains (MOPC315.BM.Luc.λ2) measured either by BLI (figure 2E–F) or by survival (figure 2H). As would be expected, none of the mice challenged with the FLC MM cells had detectable serum levels of M315 throughout the experiment (figure 2G). These results indicate that H chain-expression by MOPC315 MM cells is required for CCL3-scFv315 immunization to have a protective effect. In line with this, splenocytes from extensively immunized mice killed MOPC315.BM.Luc.IgAλ2 cells more efficiently than MOPC315.BM.Luc.λ2 cells, in vitro (online supplemental figure 6).", "inconsistent_part": "related_sentences", "tampered_sentences": ["three mice had a bioluminescence signal and M315 in their sera"], "golden_sentences": ["two mice had a bioluminescence signal and M315 in their sera"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010105100_TII_01/figure/2010105100_TII_01_1.png"], "tampered": true, "paper_ids": ["2010000149"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010010059_TII_01/figure/2010010059_TII_01_10.png", "question_id": "consistency_10", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Three chosen parameters measured for one additional cells: (a, d) Dry mass (R² = 0.9344 for the upper graph and R² = 0.8961 for the lower graph); (b, e) Phase skewness (R² = 0.87 for the upper graph and R² = 0.8471 for the lower graph); (c) Phase variance (R² = 0.9801 for the upper graph and R² = 0.954 for the lower graph).", "figure_related_sentences": "Figure 11 presents the measured values for two additional HeLa cells. The dry mass values seen in Figures 11(a, d) for both of the cells show similar behavior and values to each other and to the previously described cells during all of the cell phases, although different cells have different lifecycle periods. The lifecycle phase classification was established based on the dry mass values combined with the statistical parameters as described before. The values of phase skewness presented in Figures 11(b, e), besides the values during the G2 phase, show similar behavior to the measurement presented in Figure 8(b). We assume that the differences during the G2 phase are due to the influence of the apoptosis of the cell. Nevertheless, the result shows that the G1 and S phases can be distinguished by the phase skewness. The phase variance presented in Figures 11(c, f) is used to describe the sub-phases of the M phase. Although Figures 11(c, f) show reduced ability to distinguish between the different sub-phases of the M phase compared to the results shown in Figure 8(c) due to reduction in the sampling time of the additional cells (from two frames per minute to a frame per two minutes), the sub-phases can still be discerned.", "inconsistent_part": "caption", "tampered_sentences": ["Three chosen parameters measured for one additional cells: (a,"], "golden_sentences": ["Three chosen parameters measured for two additional cells: (a,"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010010059_TII_01/figure/2010010059_TII_01_10.png"], "tampered": true, "paper_ids": ["2010000163"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010010376_TII_01/figure/2010010376_TII_01_5.png", "question_id": "consistency_11", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "qPCR validation of PUNCH-P results. (A, top panel) Polysome profiles of HeLa cells synchronized to S and M phase by double-thymidine block. (Bottom panel) Total RNA extracted from each of the polysomal fractions visualized by ethidium bromide staining. (B, C) Polysomal association of nonfluctuating mRNAs encoding for CALR (B) and CYCS (C). (D) Polysomal association of mRNAs encoding for proteins that were elevated in S phase according to PUNCH-P. (E) Polysomal association of mRNAs encoding for proteins that were elevated in M phase according to PUNCH-P. Graphs show mean ± SD of qPCR replicates for one of three independent experiments with similar results. (C–E) represent qPCR results normalized to CALR.", "figure_related_sentences": "To validate some of these results and provide further evidence for the potential of PUNCH-P to measure differences in translation of specific mRNAs, we analyzed the polysome association of selected mRNAs in S and M phase. We chose two proteins whose PUNCH-P expression remained stable throughout the cell cycle and six proteins whose expression fluctuated between S and M phase. Such fluctuations at the protein level can result from differences in total mRNA abundance, translation efficiency, or both. We initially compared the polysome profiles of HeLa cells synchronized to S and M phase and found no differences in polysome size (Figure 6A, top panel). Next, we extracted total RNA from each of nine polysomal fractions ranging from light to heavy polysomes (Figure 6A, bottom panel) and measured the abundance of specific mRNAs in each fraction using SYBR Fast quantitative PCR (qPCR). As predicted, we found that the relative amount and polysomal distribution of the two transcripts encoding nonfluctuating proteins—calreticulin (CALR) and cytochrome C (CYCS)—remained constant between the different cell-cycle stages (Figure 6B,C). We then measured the amount of the six transcripts encoding fluctuating proteins in each polysomal fraction and normalized the results to CALR mRNA to allow a more accurate quantitative comparison of mRNA amounts across the gradients. As predicted by PUNCH-P, the amounts of polysome-associated FOSL1 (FOS-like antigen 1), CCRN4L (nocturnin), and BRIP1 (Fanconi anemia group J protein 1) were significantly higher in S phase (Figure 6D). Similarly, the amounts of polysome-associated CCNB1 (cyclin B1), GPSM2 (G-protein signaling modulator 2), and PCF11 (pre-mRNA cleavage complex 2 protein) mRNA were higher in M phase, consistent with PUNCH-P results (Figure 6E). In addition to the differences in absolute amounts, we calculated relative mRNA distribution between heavy (five or more) and light (fewer than five) polysomes as a percentage of total polysomes. While some mRNAs showed little difference in relative distribution, others changed considerably: association of CCRN4L and BRIP1 mRNAs with heavy polysomes decreased from 82.4 % and 43.3 % in S phase to 73.5 % and 29.2 % in M phase, respectively. Conversely, association of CCNB1 mRNA with heavy polysomes increased from 63.8 % in S phase to 84.3 % in M phase, as expected for an mRNA that is translationally up-regulated during mitosis (Groisman et al., 2000).", "inconsistent_part": "related_sentences", "tampered_sentences": ["we extracted total RNA from each of nine polysomal fractions ranging from light to heavy polysomes (Figure 6A, bottom panel) and measured the abundance of specific mRNAs in each fraction using SYBR Fast quantitative PCR (qPCR)"], "golden_sentences": ["we extracted total RNA from each of seven polysomal fractions ranging from light to heavy polysomes (Figure 6A, bottom panel) and measured the abundance of specific mRNAs in each fraction using SYBR Fast quantitative PCR (qPCR)"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010010376_TII_01/figure/2010010376_TII_01_5.png"], "tampered": true, "paper_ids": ["2010000169"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010010402_TII_02/figure/2010010402_TII_02_3.png", "question_id": "consistency_12", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "MeRIP-seq analysis of four RNAs tested for m⁶A status in this work. These include one lncRNA, TUG1 (A), and three mRNAs: ACTB (B), TPT1 (C), and BSG (D), analyzed in three different human cell lines (HeLa, HepG2, and HEK293T). SCARLET-tested sites are marked with bold arrows. Sites that tested positive for m⁶A are indicated by purple arrows, while sites that tested negative for m⁶A are indicated by blue arrows.", "figure_related_sentences": "We also determined the m6A status in many RRACH sites in another lncRNA (TUG1) and three mRNAs (ACTB, TPT1, and BSG), chosen on the basis of the m6A/MeRIP-seq results (Fig. 4). Among the sixteen sites tested, only four showed m6A modification >5% (Table 2). This result shows that the previously reported 20% m6A modification in bovine prolactin mRNA (Narayan and Rottman 1988) is not abnormal, suggests that many sites in mRNA carry complete m6A modification, and highlights that not every RRACH consensus sequence sites under the m6A/MeRIP-seq peaks are modified.", "inconsistent_part": "related_sentences", "tampered_sentences": ["suggests that many sites in mRNA carry complete m6A modification"], "golden_sentences": ["suggests that many sites in mRNA carry incomplete m6A modification"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010010402_TII_02/figure/2010010402_TII_02_3.png"], "tampered": true, "paper_ids": ["2010000179"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010010436_TII_02/figure/2010010436_TII_02_0.png", "question_id": "consistency_13", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "mAtg9 affects autophagy at an early omegasome stage. (A) Domain structure of yeast and human Atg9. Red and blue boxes represent conserved transmembrane domains. (B) HEK293 cells were treated with either control siRNA (ctrl) or siRNA against mAtg9 (Atg9 KD) and incubated in full (F) or starvation medium (S) for 2 h. Cell lysates were analyzed by Western blot using antibodies against mAtg9, β-tubulin, and LC3. (C) Confocal microscopy of HEK293/GFP-LC3 and HEK293/GFP-DFCP1 cells treated with RISC-Free (ctrl) or mAtg9 (Atg9 KD) siRNA and starved for 2 h. ULK1, WIPI2, and Atg16 were detected by indirect immunofluorescence using anti-ULK1, -WIPI2, and -Atg16 antibodies. Bars, 10 μm. (D–H) Quantification of ULK1, GFP-DFCP1, WIPI2, Atg16, or GFP-LC3 spots from B expressed as spots/cell area (ULK1, GFP-DFCP1) or spots/cell (WIPI2, Atg16, GFP-LC3). Error bars, SEM; **p < 0.01 ***p < 0.001 (n = 3, two-tailed unpaired t test). (I) Colocalization of GFP-LC3 with WIPI2 and Atg16 in HEK293/GFP-LC3 cells treated with mAtg9 siRNA, starved, and detected in C. (J) Quantification of colocalization of WIPI2 and Atg16 with GFP-LC3 as shown in (I). Error bars, SEM, n = 3.", "figure_related_sentences": "Knockdown of mAtg9 by small interfering RNA (siRNA) depletion in HEK293 cells was nearly complete as revealed by Western blot (Figure 1B). As expected, depletion of mAtg9 significantly reduced lipidation of endogenous LC3 (Figure 1B) and the number of autophagic structures positive for GFP-LC3 (Figure 1C and I) observed upon starvation. All other autophagic structures, that is, those positive for DFCP1, WIPI2, and Atg16, were also significantly reduced (Figure 1, C and E–H), suggesting that mAtg9 may act very early, at the same step as or even before DFCP1. ULK1-positive puncta were reduced after depletion of Atg9 but not significantly (Figure 1, C and D). These results are in agreement with results in yeast, in which Atg9 is one of the first Atg proteins to be recruited to the PAS (Suzuki et al., 2007). We next investigated whether mAtg9 was required for the correct recruitment of Atg proteins to the forming autophagosome, and, in particular, we looked at the recruitment of LC3 to WIPI2- or Atg16-positive structures. In control starved cells, ∼72 and 85% of WIPI2 and Atg16 spots, respectively, were also positive for LC3 (Figure 1, I and J). In cells depleted of mAtg9, although the total number of these structures was slightly reduced (Figure 1, D–H), the percentage of WIPI2 and Atg16 spots containing LC3 was unaltered (Figure 1J). This indicates that in the absence of mAtg9, these phagophores and autophagosome membranes were able to recruit Atg proteins upstream of LC3 lipidation and conjugation. Thus we hypothesized that mAtg9 may be delivering membrane and/or other components to speed up the process of autophagosome formation.", "inconsistent_part": "related_sentences", "tampered_sentences": ["In cells depleted of mAtg9, although the total number of these structures was slightly reduced (Figure 1, D–H)"], "golden_sentences": ["In cells depleted of mAtg9, although the total number of these structures was greatly reduced (Figure 1, D–H)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010010436_TII_02/figure/2010010436_TII_02_0.png"], "tampered": true, "paper_ids": ["2010000181"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010102051_TII_01/figure/2010102051_TII_01_0.png", "question_id": "consistency_14", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Fig. 1. Cavin-1 altered EV proteins and EV miR-148a with no effect on total cellular levels. (A) EVs and whole cell lysates (WCL) were collected from GFP-PC3 and cavin-1-PC3 cells and analysed by Western blot with the indicated antibodies. EV preparations were free from ER protein calnexin. Equal loading was shown by Coomassie staining. Images are representative of 3 biological replicates. Raw images of the western blots are available in figures in Supplementary file. (B) Cavin-1 alters the miRNA content of EVs. Real-time qPCR was performed on cDNA synthesized from equal amounts of RNA extracted from GFP-PC3-EVs and cavin-1-PC3-EVs or total cell lysates. Bar graphs show the mean relative expression±SEM of miR-148a was significantly decreased in cavin-1-PC3-EVs compared to GFP-PC3-EVs (p ≤ 0.02, n = 3) but expression of miR-148a was unaffected in cells. (C) In contrast, miR-125a was not significantly different between GFP-PC3-EVs and cavin-1-PC3-EVs (n = 3).", "figure_related_sentences": "To confirm the cavin-1 effect on the EV-mediated release of these proteins, and to determine whether cavin-1 affected total protein expression or only the release as we previously reported for cytokines (18), we compared the levels of selected proteins in the WCL and EVs from GFP-PC3 and cavin-1-PC3 cells by immunoblotting. As shown in Fig. 1A, caveolin-1 WCL and EV levels were not altered by cavin-1 expression. Cavin-1 itself was not detected in EVs indicating its effects are indirect (Fig. 1A). Calnexin was used as an intracellular membrane marker, which was not detected in EVs (Fig. 1A). We also probed for cofilin and CD63 as known exosome cargo and marker protein, respectively. Interestingly, both cofilin and CD63 were increased in the EVs from cavin-1-PC3 cells compared to GFP-PC3 cells (Fig. 1A). Additionally, CD63 total cellular levels were also elevated in cavin-1-PC3 cells (Fig. 1A), suggesting potential increase in multi-vesicular body formation. In contrast, cavin-1 expression reduced the abundance of 4F2 and EphA2 in EVs without affecting total cellular levels (WCL, Fig. 1A) similar to our previous report for cytokines and proteases (18). This suggests that cavin-1 did not cause a decrease of key bone remodelling molecules on the cellular level but instead altered their secretion through EVs. Recent studies show that EVs mediate the transfer of functional microRNA (miRNA) (4,6), and miRNA changes are implicated in osteolytic bone metastasis (33). Therefore, we were interested to investigate if, in addition to proteins, cavin-1 expression altered miRNA secretion via EVs. Based on a review of recent literature, we chose to measure 2 miRNA species, miRNA-148a and miR-125a. Overexpression of miR-148a was recently reported to induce osteoclastogenesis and the reverse was observed when miR-148a was inhibited (34). In contrast, miR-125a was reported to be decreased during osteoclastogenesis (34). qPCR performed revealed that PC3-EV miRNA-148a levels were significantly reduced by 8.68±0.01-fold (p ≤ 0.02) upon cavin-1 expression without altering total cellular miR-148a levels (Fig. 1B). In contrast, no significant difference was found for miR-125a in either EVs or total cell (Fig. 1C). These results suggest that cavin-1 expression can selectively modulate EV-mediated transfer of miRNA. A reduction in 4F2 EV levels upon cavin-1 expression is consistent with our observation that cavin-1-PC3-EVs caused TRAP expression but did not lead to formation of multi-nucleated cells (Fig. 1A). Our data confirms previous reports that PC3 conditioned media can induce osteoclastogenesis from murine RAW264.7 cells (25–27), and further show that PC3-EVs alone are sufficient to enhance osteoclastogenesis in vitro (Fig. 1). However, cavin-1-PC3-EVs were unable to induce full osteoclastogenesis without the soluble secretome (Fig. 1B), indicating the requirement of SF not released via EVs. We also report for the first time that PC3 conditioned media and EVs increase proliferation of primary hOBs (Fig. 1D), although the magnitude of PC3-EV osteoblastic activity was much lower than its osteoclastic activity. In contrast to our data, PC3 conditioned media has been reported to suppress primary murine osteoblast proliferation (64,65). The discrepancy may be due to the use of human versus murine osteoblasts.", "inconsistent_part": "related_sentences", "tampered_sentences": ["qPCR performed revealed that PC3-EV miRNA-148a levels were significantly reduced by 8.68±0.01-fold (p ≤ 0.02) upon cavin-1 expression without altering total cellular miR-148a levels"], "golden_sentences": ["qPCR performed revealed that PC3-EV miRNA-148a levels were significantly reduced by 3.67±0.01-fold (p ≤ 0.02) upon cavin-1 expression without altering total cellular miR-148a levels"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010102051_TII_01/figure/2010102051_TII_01_0.png"], "tampered": true, "paper_ids": ["2010000184"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010030787_TII_01/figure/2010030787_TII_01_4.png", "question_id": "consistency_15", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Detection of heroin and fentanyl using aptamer-based dye-displacement assays. (A) Secondary structures of HM20 and F17 based on NUPACK predictions. (B) Scheme of the dye-displacement assay using HM20, F17, and MTC (purple bars indicate monomeric/dimeric forms of the dye; blue bars indicate J-aggregates). (C) Photographs taken 5 min after addition of various concentrations of heroin to solutions of MTC alone (−HM20) or HM20-MTC complexes (+HM20). (D) Signal gain and cross-reactivity of the displacement assay to various interferents relative to the response to heroin. Photographs of samples were taken 5 min after adding mixtures of 25 μM heroin and 50 μM interferent to HM20-MTC complexes. (E) Detection of heroin in binary mixtures of 25 μM heroin (∼33%) with 50 μM interferent (∼67%). (F) Absorbance spectra of HM20-MTC complexes in the presence of a 33:8:59 mixture of heroin, fentanyl, and an interferent (caffeine, lidocaine, lactose, or mannitol) as well as each interferent alone. These spectra overlap for all four drug mixtures and all four interferent samples. (G) Photographs of the dye-displacement assays analyzed in panel F (top) as well as equivalent assays performed with the fentanyl-specific aptamer F17 (bottom). (H) Photographs of Marquis test results for interferent alone, binary mixtures containing heroin and interferent (33:67) or fentanyl and interferent (8:92), or ternary mixtures containing heroin, fentanyl, and interferent (33:8:59). Error bars represent the standard deviations of three independent experiments.", "figure_related_sentences": "Notably, the presence of heroin can be clearly identified at concentrations as low as 16 μM with the naked eye via a purple-to-blue-green color change (Figure 4C), which is sufficiently sensitive for detecting opioids in seized drug samples. We then determined the specificity of the assay against a variety of ligands commonly found in illicit drug samples. Since the purity of heroin is often 30–50%, (41,42) we assessed the specificity of our assay by challenging aptamer-dye complexes with 25 μM heroin or 50 μM interferent. The assay did not have any meaningful cross-reactivity to any of these interferents, and only the heroin sample induced a purple-to-blue-green color change that was visible to the naked eye (Figure 4D). We then challenged the assay with binary mixtures of 25 μM heroin (33%) and 50 μM interferent (67%) and did not observe that any of these interferents altered the signal produced by heroin, demonstrating the excellent specificity of the assay (Figure 4E).", "inconsistent_part": "related_sentences", "tampered_sentences": ["the presence of heroin can be clearly identified at concentrations as low as 16 μM with the naked eye via a purple-to-blue-green color change"], "golden_sentences": ["the presence of heroin can be clearly identified at concentrations as low as 8 μM with the naked eye via a purple-to-blue-green color change"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010030787_TII_01/figure/2010030787_TII_01_4.png"], "tampered": true, "paper_ids": ["2010000190"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010039761_TII_02/figure/2010039761_TII_02_1.png", "question_id": "consistency_16", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2. Confirmation of SYNJ2 interaction with select binding partners. (A) SYNJ2 interacts with Lyn. HEK293 cells were transiently co-transfected with expression plasmids for Lyn or SYNJ2 or transfected with a SYNJ2 plasmid alone. Cells were lysed 24 h post-transfection. Cell lysates were incubated with an anti-Lyn antibody, followed by protein A-agarose. Expression of Lyn and SYNJ2 in lysates and immunoprecipitated SYNJ2 were visualized by western blotting. (B) SYNJ2 interacts with Fyn. The same methodology was used as in (A), except that Lyn was replaced by Fyn. (C) SYNJ2 interacts with intersectin. HEK293 cells were transiently transfected with the indicated combinations of expression plasmids for FLAG-tagged intersectin-1 (ITSN) or SYNJ2. Cells were lysed 24 h post-transfection and lysates were incubated with an anti-FLAG antibody, followed by protein G-agarose. Expression of intersectin and SYNJ2 in lysates and immunoprecipitated SYNJ2 were visualized by western blotting. (D and E) SYNJ2 interacts with cortactin. (D) Coimmunoprecipitation experiment. HEK293 cells were transiently co-transfected with cortactin and SYNJ2 expression plasmids. Cells were lysed 24 h posttransfection and lysates were incubated either with an anti-cortactin antibody followed by protein G-sepharose or with control IgG followed by protein G-sepharose. Expression of cortactin and SYNJ2 in lysates and immunoprecipitated SYNJ2 were visualized by western blotting. Immunoglobulin heavy chain (IgG-HC) was visualized by anti-mouse HRP. (E) GST-pulldown experiment. SNB19 cell lysates were incubated with immobilized GST or GST-SJ2 (GST-SYNJ2-C). Precipitated cortactin was visualized by western blotting using an anti-cortactin antibody (upper panel) and bound GST proteins were visualized by Ponceau staining (lower panel). Data shown are representative of at least 2 experiments.", "figure_related_sentences": "To confirm the interaction of SYNJ2 with Src family kinases in a cellular setting, we performed co-expression of full length SYNJ2 together with full length Lyn or Fyn in HEK293 cells. Immunoprecipitation of Lyn or Fyn from lysates of co-expressing cells, but not from cells in which SYNJ2 was overexpressed on its own, showed specific interaction between SYNJ2 and these kinases (Fig. 2A and B). We obtained opposite results for the interaction of SYNJ2 with intersectin (Fig. 2C). We also confirmed the interaction between SYNJ2 and cortactin, using two different approaches. First, endogenous cortactin could be precipitated from SNB19 glioblastoma cell lysates with an immobilized SYNJ2 C-terminal domain GST-fusion protein, but not GST itself (Fig. 2D). Second, SYNJ2 non-immunoprecipitated with cortactin from HEK293 cells co-expressing full length versions of both SYNJ2 and cortactin (Fig. 2E). We also identified intersectin and cortactin using mass spectrometry, as endogenous proteins associated with SYNJ2 that was overexpressed in HEK293 cells (data not shown).", "inconsistent_part": "related_sentences", "tampered_sentences": ["SYNJ2 non-immunoprecipitated with cortactin from HEK293 cells co-expressing full length versions of both SYNJ2 and cortactin (Fig. 2E)", "We obtained opposite results for the interaction of SYNJ2 with intersectin (Fig. 2C)"], "golden_sentences": ["SYNJ2 co-immunoprecipitated with cortactin from HEK293 cells co-expressing full length versions of both SYNJ2 and cortactin (Fig. 2E)", "We obtained similar results for the interaction of SYNJ2 with intersectin (Fig. 2C)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010039761_TII_02/figure/2010039761_TII_02_1.png"], "tampered": true, "paper_ids": ["2010000203"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010064648_TII_01/figure/2010064648_TII_01_0.png", "question_id": "consistency_17", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. Epigenetic marks that are influenced by EBNA3A and EBNA3C during the repression of BIM by EBV. (A) The levels of BIM protein (whose predominant isoform is the extra-large BIMEL) were assayed by western blotting protein extracts from BL31 cell lines. BIM levels in uninfected BL31 or BL31 infected with the wild-type (B95.8-BAC) EBV (WT), or viruses with each individual EBNA3 knocked out (KO) and the revertant viruses (REV) are shown. In all the EBNA3A and EBNA3C knockouts BIM levels are similar to the levels observed in the uninfected cells. The expression of g-tubulin is shown as a control for the amount of protein loaded. (B) Schematic of the BIM locus showing the approximate locations of the CpG island, TSS, BIM start codon and the PCR primer pairs used in this study (A–J). (C) Methylated DNA precipitation was used to assess whether DNA methylation at the BIM promoter was responsible for repression of BIM expression. The histogram bars represent fold enrichment for co-precipitated DNA relative to input DNA, as determined by Q-PCR. The height of the bars represents the abundance of the epigenetic mark at the locus assessed by each primer set. Uninfected BL31 cells, BL31 infected with WT EBV, or EBNA3 knockouts (KO) or the revertant viruses were tested. DNA from peripheral blood mononuclear cells (PBMC) and in vitro methylated PBMC DNA were used as negative and positive controls respectively. The error bars represent the standard deviation from triplicate Q-PCR assays. (D) The same panel of BL31 cell", "figure_related_sentences": "In order to investigate the roles of EBNA3A and EBNA3C in the regulation of cellular gene expression, a panel of cell lines based on the EBV-negative BL-derived line BL31 were established and characterized (50,53). Here a selection of these were subjected to western blot analysis to confirm our previous observation that BL31 expressed high levels of BIM protein and that this was substantially reduced in BL31 latently infected in vitro with wild-type (WT) EBV-BAC-derived virus (Figure 1A). This analysis also confirmed that in BL31 infected with recombinant viruses from which EBNA3A or EBNA3C genes were deleted, BIM expression was not repressed and remained at a similar level to that in BL31 (Figure 1A). Revertant (REV) viruses reconstituted with the genes that had previously been deleted behaved—as expected—like the WT EBV and repressed BIM expression. Flanking the BIM transcription start site (TSS) is a remarkably large CGI that extends for 13 kb (http://genome.ucsc.edu/cgi-bin/hgGateway; Figure 1B). We previously showed that in various EBV-positive B cell lines and primary BL samples significant DNA methylation across this region could be detected, but this was absent in EBV-negative equivalents (52). However, analysis of several BL cell lines, including BL31, that were newly infected with EBV and also recently established LCLs revealed that although BIM transcription was repressed, there was little or no CpG methylation but rather the epigenetic repressive histone modification H3K27me3 was evident. Because of the apparently progressive nature of DNA methylation across the BIM CGI, a panel of low passage BL31-derived cell lines was subjected to methylated-DNA precipitation (MeDP) coupled with quantitative real-time PCR analysis using primer-pairs (A–F) as indicated (Figure 1B). Primary peripheral blood mononuclear cells and in vitro methylated genomic DNA were used as negative and positive controls respectively. All the lines analysed, irrespective of their EBV status, showed no detectable DNA methylation, as judged by MeDP, across a region extending from 4 kb upstream of the BIM TSS to the start codon—indicating that here histone modification was the most likely mode of repression (Figure 1C). Having shown in these EBV-infected BL31 cells that CpG methylation was not established at BIM, ChIP with an antibody directed against H3K27me3 and quantitative PCR analyses across the CGI was performed using the same primer-pairs as for MeDP. This showed that repression correlated with deposition of the H3K27me3 mark and expression of EBNA3A and EBNA3C (in the WT-, EBNA3BKO- and the revertant-infected cell lines in Figure 1D). In contrast, when either EBNA3A or EBNA3C were deleted from EBV (EBNA3AKO and EBNA3CKO) BIM expression remained high and, significantly, the amount of H3K27me3 detected across the BIM locus was below the background in uninfected BL31 cells. Occupancy of H3K27me3 on promoters of genes encoding Myoglobin and GAPDH were analysed in a similar manner as positive and negative controls respectively (Supplementary Figure S1A). ChIP for total histone H3 at BIM, Myoglobin and GAPDH revealed little difference between the cell lines used (Figure 1E and Supplementary Figure S1B). This indicates that any changes in the distribution of covalent histone modifications detected are not due to alterations in nucleosome density. The effects on H3K27me3 distribution at the BIM promoter induced by EBNA3A and EBNA3C are specific, since the overall levels of H3K27me3 were unaffected by EBV, EBNA3A or EBNA3C (Figure 1F). The protein complex responsible for establishing the H3K27me3 mark is PRC2. In mammals this is generally composed of a catalytic core made up of the histone methyltransferase EZH2 and subunits SUZ12, EED and RbAp46/48 (see ‘Introduction’ section). ChIPs for SUZ12, EZH2 and RbAp48 were performed on the panel of BL31 cell lines and analysed using the same primer-pairs as in Figure 1. Figure 2. PRC2 occupancy across the BIM promoter region. The presence and abundance of PRC2 proteins was assayed by ChIP analysis of a BL31 panel of cells, as indicated. Presentation is the same as for ChIP analysis in Figure 1. The region of amplification for each primer set (A–F) can be seen in Figure 1B. The error bars represent the standard deviation from triplicate PCR assays. ChIP was performed using an antibody specific for (A) PRC2 core subunit SUZ12, (B) PRC2 catalytic subunit EZH2, (C) core subunit RbAp48, (D) ancillary factor JARID2.", "inconsistent_part": "related_sentences", "tampered_sentences": ["Flanking the BIM transcription start site (TSS) is a remarkably large CGI that extends for 13 kb", "across a region extending from 4 kb upstream of the BIM TSS to the start codon—indicating that here histone modification was the most likely mode of repression"], "golden_sentences": ["Flanking the BIM transcription start site (TSS) is a remarkably large CGI that extends for 6 kb", "across a region extending from 8 kb upstream of the BIM TSS to the start codon—indicating that here histone modification was the most likely mode of repression"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010064648_TII_01/figure/2010064648_TII_01_0.png"], "tampered": true, "paper_ids": ["2010000205"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010065393_TII_02/figure/2010065393_TII_02_0.png", "question_id": "consistency_18", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. C-trapping of FACT. (A) Immunoblotting of soluble protein extracts and chromatin pellets of HT1080 cells treated with CBL0137 for 1 h, probed with the indicated antibodies. (B) Immunofluorescence staining of HT1080 cells with antibodies to SSRP1. (C) Fluorescent imaging of two live cells expressing GFP-tagged SSRP1 before and after treatment with CBL0137. Top row––HT1080 cell in interphase, 3 μM CBL0137, bottom row––DLD1 cell in mitosis, 5 μM CBL0137. (D) Fluorescent imaging of two live HT1080 cells, interphase and mitotic, expressing GFP-tagged SPT16 before and after treatment with CBL0137. Bars are 10 μm.", "figure_related_sentences": "RESULTS FACT binds to unfolding chromatin in CBL0137-treated cells Using biochemical fractionation and fluorescent microscopy we previously demonstrated that curaxin treatment causes a rapid transition of FACT from the nucleoplasm to a state of tight association with chromatin (13). We named this phenomenon ‘chromatin trapping’ of FACT or c-trapping. To investigate the mechanism of c-trapping, we first examined the dose and time dependence as well as specificity of this phenomenon. To do this we used two methods, (i) immunoblotting of soluble, representing nucleoplasm, and pelleted, representing chromatin, fractions of total cell lysates ((Figure 1A) see details in Materials and Methods), and (ii) ectopic expression of GFP or mCherry tagged SSRP1 and SPT16 subunits of FACT, which undergo c-trapping in CBL0137-treated cells similarly to endogenous FACT subunits (Figure 1B–D and Supplemental Figure S1). C-trapping was observed in all tested cell lines (>20 cell lines, data not shown). Importantly, c-trapping and toxicity of CBL0137 occur at the same concentrations (∼0.3–0.5 μM depending on cell line, Figures 1A, 2 and (13)), however, c-trapping is observed within minutes after start of treatment (Figure 1C and D), while cell death after 48 h (13). Thus, these two effects of CBL0137 are probably connected, but c-trapping cannot be viewed as a sign of cell death. In untreated cells, FACT is diffusely spread throughout the nucleoplasm with some accumulation in nucleoli ((13,42) and Figure 2A and B). Changes in the distribution of FACT subunits begin 30–60 s after the addition of CBL0137 to cell culture medium (Figure 1C and D). In the presence of 0.3 μM CBL0137, both subunits become associated with thin fibers of chromatin, which is illustrated by their overlap with fluorescently labeled histone H2B (Figure 2A and B). At higher concentrations of CBL0137 (1–3 μM), FACT subunits are still associated with chromatin, however, the chromatin itself remains such that it appears as thicker fibers with bead like structures contouring nucleoli (Figure 2A and B). At concentrations of ≥5 μM CBL0137, the cellular distribution of SSRP1, SPT16, and H2B is dramatically changed. SSRP1 appears as thin fibers situated along the nuclear periphery and absent in and near nucleoli (Figure 2A). SPT16 becomes more diffuse (Figure 2B). Histone H2B loses its fiber-like appearance and accumulates in nucleoli (Figure 2A and B). Full transition takes 20–30 min (Figure 3A). Behavior similar to H2B was observed with fluorescently tagged histones H3 and H4 (Supplemental Figure S2). Similar to our results presented here, Musinova et al previously demonstrated that histone H2B, which is not incorporated into chromatin, accumulates in nucleoli due to the presence of a nucleoli localization signal within its nuclear localization signal (43). Therefore, we hypothesized that CBL0137 treatment leads to accumulation of histones in nucleoli due to their liberation from chromatin, which is consistent with the loss of visible chromatin fibers (Figure 2A and B, 10 μM). C-trapping not only occurs in interphase cells but also in mitotic cells. As shown in Figure 1 C and D, diffuse GFP-SSRP1 or GFP-SPT16 signals in mitotic cells became overlapped with mitotic chromosomes within a few minutes following the addition of CBL0137, which is indicative of a rapid CBL0137-induced binding of FACT to chromatin (Figure 1C and D). However, later on and in the presence of ≥3 μM of CBL0137, histone H2B was lost from chromosomes and appeared more like a diffuse cloud (Figure 3B). FACT subunits followed histones into the cloud-like shape, however, some SSRP1 was still associated with loops in the periphery, which were most likely leftover of decondensed and disassembled chromatin (Figure 3B).", "inconsistent_part": "related_sentences", "tampered_sentences": ["the chromatin itself remains such that it appears as thicker fibers with bead like structures contouring nucleoli (Figure 2A and B)."], "golden_sentences": ["the chromatin itself changes such that it appears as thicker fibers with bead like structures contouring nucleoli (Figure 2A and B)."], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010065393_TII_02/figure/2010065393_TII_02_0.png"], "tampered": true, "paper_ids": ["2010000221"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010005464_TII_02/figure/2010005464_TII_02_1.png", "question_id": "consistency_19", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2. XRK3F2 plus bortezomib combination activates multiple death pathways and overcomes apoptosis resistance in mul-tiple myeloma. MM.1S cells treated with XRK3F2 (5 μM), bortezomib (Btz) (3 nM), or combined XRK3F2-Btz (5 μM/3 nM) for 24 hours in the presence or absence of autophagy inhibitor BafilomycinA1 (Baf, 40 nM) (A, D), Pan caspase OPH inhibitor Q-VD (QVD, 20 μM) (B, E), or caspase-3 inhibitor Z-DEVD-FMK (Z-DEV, 20 μM) (C, F). Cell viability was evaluated using alamarBlue assays and is reported as percent versus dimethyl sulfoxide (DMSO) vehicle control (A-C). Analysis of autophagic flux and apoptosis were assessed by immunoblotting by LC3I-LC3II conversion (D) and for cleavage of caspase 8 and 3 (E, F). Data are presented as bars, means ± standard deviation (N=4-6/group). *P<0.05 versusvehicle, ^P<0.05 versus XRK3F2 or Btz alone and ^P<0.05 versus control versus Baf/QVD/ZDEV culture by two-way ANOVA with post hoc Bonferroni’s correction.", "figure_related_sentences": "Btz decrease p62 levels by inducing de novo p62 expressionand preventing its degradation.In agreement with the pre-vious studies,:: we found that Btz increased levels of p62mRNA 8-fold and protein (Figure 2D; Online SupplementaryFigure S2D)independent of autophagy since changes inLC3l-LC3ll conversion were not found in Btz-treated cells.Btz-induced p62 mRNA expression was reduced by XRK3F2Ligands binding to p62-2Z stimulate p62 oligomerizationand autophagy.34 XRK3F2 alone or in combination with Btz decreased LC3l-LC3ll conversion in MM1S,indicating induction ofautophagy (Figure 2D, left panel). Pretreatment of MMcells with bafilomycin A1 (Baf), which disrupts autophagicflux, further increased LC3ll/LC3l ratio and p62 protein levels compared to XRK3F2 alone or XRK3F2-Btz combination(Figure 2D, right panel). Furthermore, autophagy blockadeby Baf treatment further amplified the negative effects oXRK3F2 and Btz on MM cell viability (Figure 2A, Online sup.plementary Figure S4A), indicating that the autophagy-induced by targeting p62-ZZ domain in MM cells was not thepathway responsible for MM cell death.We previously reported that high doses ofXRK3F2 triggeredcaspase 3 cleavage in MM.1S cells.7 Here, we found that inMM.1S cells, co-administration of 5uM XRK3F2 and 3 nMBtz strongly activated caspase-8 and caspase-3 (Figure 2Eleft panel).In contrast, we only detected partial activationof caspases by Btz alone and no activation by XRK3F2 atthe concentration used. To test if the increased cell deathseen with the combination therapy was due to apoptosiswe used the pan-caspase inhibitor O-VD-OPh (OvD) and thecaspase-3 inhibitor Z-DEVD-FMK (Z-DEV). OVD and Z-DEVcompletely blocked Btz-induced cleavage of caspase-8 and3 (Figure 2E, F, right panels). In addition, QvD or Z-DEV fullyprevented the decrease in cell viabilityinduced by Btz (Figure2B,C;Online Supplementary Figure S4B, C)but enhancedthe anti-MM effects of XRK3F2. QVD and Z-DEV only partially blocked caspase 8 and 3 cleavage by XRK3F2-Btz andpartially reduced the effects ofthe combination on MM celviability. These findings suggest that XRK3F2-Btz combinationinhibits MM viability by activating both caspase-dependentand independent-cell death pathways.", "inconsistent_part": "related_sentences", "tampered_sentences": ["Btz decrease p62 levels by inducing de novo p62 expressionand preventing its degradation", "34 XRK3F2 alone or in combination with Btz decreased LC3l-LC3ll conversion in MM1S"], "golden_sentences": ["Btz increases p62 levels by inducing de novo p62 expressionand preventing its degradation", "34 XRK3F2 alone or in combination with Btz increased LC3l-LC3ll conversion in MM1S"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010005464_TII_02/figure/2010005464_TII_02_1.png"], "tampered": true, "paper_ids": ["2010000232"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010042289_TII_02/figure/2010042289_TII_02_8.png", "question_id": "consistency_20", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 5 (A) Immunofluorescence staining of GIG on expression of ABCB4 and BSEP in ANIT-treated rats’ liver tissues. (B) The relative percentage of ABCB4 expression. (C) The relative percentage of BSEP expression. Red represents ABCB4, and green represents BSEP. **P<0.01, ****P<0.0001.", "figure_related_sentences": "Effect of GIG on ABCB4 and BSEP Protein Expression in ANIT-Treated Rats. Compared with the normal control group, there was almost the high expression of ABCB4 and BSEP in the model group’s liver tissues (Figure 5). Compared with the model group, the expression of BSEP and ABCB4 decreased significantly in the GIG middle and high dose groups, and the changes of BSEP and ABCB4 expression showed a negative correlation with the dose of GIG (Figure 5). The expression trends of ABCB4 and BSEP in each group can be seen in Figures 5B and C.", "inconsistent_part": "related_sentences", "tampered_sentences": ["there was almost the high expression of ABCB4 and BSEP in the model group’s liver tissues (Figure 5)", "the expression of BSEP and ABCB4 decreased significantly in the GIG middle and high dose groups", "and the changes of BSEP and ABCB4 expression showed a negative correlation with the dose of GIG (Figure 5)"], "golden_sentences": ["there was almost the low expression of ABCB4 and BSEP in the model group’s liver tissues (Figure 5)", "the expression of BSEP and ABCB4 increased significantly in the GIG middle and high dose groups", "and the changes of BSEP and ABCB4 expression showed a positive correlation with the dose of GIG (Figure 5)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010042289_TII_02/figure/2010042289_TII_02_8.png"], "tampered": true, "paper_ids": ["2010000234"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010104828_TII_02/figure/2010104828_TII_02_0.png", "question_id": "consistency_21", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1 The expression of miR-29c-3p and LIF in UC tissues and IECs. (A) The mRNA levels of LIF in UC and normal tissues. (B) Representative Western blots and densitometric quantitative analysis of LIF protein levels in UC and normal tissues. (C) The mRNA levels of LIF in primary IECs of UC and normal colon. (D) Representative Western blots and densitometric quantitative analysis of LIF protein levels in IECs of UC and normal colon. (E) The expression of miR-29c-3p in UC and normal tissues. (F) The expression of miR-29c-3p in primary IECs of UC and normal colon. (G) Pearson’s correlation analysis of the expression levels of miR-29c-3p and LIF protein. (H) Pearson’s correlation analysis of the expression levels of miR-29c-3p and LIF mRNA. **P<0.01 versus normal group.", "figure_related_sentences": "ResultsThe Expression of miR-29c-3p and LIF in UC Tissues and Primary IECsColonic biopsies were obtained during endoscopic examinations. We first assessed LIF expression in colon tissues using qRT-PCR and found it to be upregulated in UC patients compared with healthy controls (Figure 1A). The weakened LIF protein expression was then verified by Western blotting (Figure 1B). To further explore cellular level of LIF, primary IECs were isolated and quantified for LIF expression. As expected, the same change trends were observed in IECs (Figure 1C and D). Next, we adopted five miRNA databases (TargetScan, miRDB, starBase, mirDIP and miRmap) to predict the upstream miRNA of LIF. As a result, miR-29c-3p was the only miRNA with the highest possibility to interact with LIF predicted simultaneously by all databases. Therefore, we explored miR-29c-3p expression by qRT-PCR. As illustrated in Figure 1E and F, miR-29c-3p was upregulated both in colonic tissues and IECs from UC patients relative to normal controls. Subsequently, as illustrated by Pearson correlation scatter plots (Figure 1G and H), miR-29c-3p and LIF protein expression in UC tissues were inversely correlated, whereas disparity was found between miR-29c-3p and LIF mRNA expression. Accordingly, we hypothesized that miR-29c-3p is involved in the post-transcriptional regulation of LIF expression.", "inconsistent_part": "related_sentences", "tampered_sentences": ["The weakened LIF protein expression was then verified by Western blotting (Figure 1B)", "miR-29c-3p was upregulated both in colonic tissues and IECs from UC patients relative to normal controls"], "golden_sentences": ["The enhanced LIF protein expression was then verified by Western blotting (Figure 1B)", "miR-29c-3p was downregulated both in colonic tissues and IECs from UC patients relative to normal controls"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010104828_TII_02/figure/2010104828_TII_02_0.png"], "tampered": true, "paper_ids": ["2010000257"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010012624_TII_02/figure/2010012624_TII_02_3.png", "question_id": "consistency_22", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "R-Ras2/TC21 regulates the timely development of the pubertal mammary gland. (A) qRT-PCR analysis of total RNA obtained from mammary glands extracted from the indicated stages. Prepubertal, pubertal, and adult virgins correspond to samples obtained from 3-, 8-, and 14-wk-old RRas2+/+ female mice, respectively. Early and late pregnancy correspond to female mice within weeks 1 and 2.5 of pregnancy, respectively. The early and late lactation samples were taken 1 and 2 wk after labor, respectively. The involution phase samples were taken 3.5 d after offspring weaning. Data are given relative to the expression levels obtained in virgin adult state (which was given an arbitrary value of 1). All values were normalized taking into consideration the expression levels of the housekeeping Gapdh mRNA in each sample. *p ≤ 0.05; ***p ≤ 0.001 (n = 3). (B) Representative images of carmine alum–stained mammary fat pads obtained from female mice of the indicated ages (top) and genotypes (left). Scale bars, 500 μm. One of the inguinal lymph nodes is indicated by a white asterisk. (C–F) Quantification of the total area (C), maximal length (D), number of TEBs (E), and branching points (F) of mammary glands obtained from animals of the indicated genotypes and ages. *p ≤ 0.05, **p ≤ 0.01, ***p ≤ 0.001 when compared with values obtained in the appropriate wild-type control (n = 5–10 animals per genotype and developmental stage).", "figure_related_sentences": "We found no major differences in any of those parameters in the mammary glands of 4-wk-old R-Ras2/TC21-deficient and control mice (Figure 3B, 3C, 3E, and 3F). However, when we analyzed 5-wk-old mice, we observed that the mammary glands extracted from RRas2−/− mice were significantly smaller than those obtained from control animals (Figure 3B–3D). Those glands also displayed significantly higher numbers of TEBs (Figure 3B and 3E) and branching points (Figure 3B and 3F). Most of those differences disappeared in the mammary glands of 12-wk-old mice (Figure 3B–3D). However, unlike the case of control mice, we found that ∼50% of the mammary glands obtained from RRas2−/− mice still contained a insignificant number of TEBs (Figure 3E), further suggesting that the R-Ras2/TC21 deficiency induces a delay in the development of this gland. This phenotype was highly penetrant, since it was observed in mice of homogenized (C57BL/6J, Figure 3) and mixed (129Sv/J × C57BL/6J, Supplemental Figure S2) genetic backgrounds. In the latter strain, R-Ras2/TC21 became specifically upregulated during those two highly morphogenetic periods of the mammary gland (Figure 3A). As previously seen with RRas2−/− mice (Figure 3), this observation, coupled with the upregulation of the RRas2 gene found in specific developmental stages of the gland (Figure 3A), supports a role for R-Ras2/TC21 in mammary gland maturation.", "inconsistent_part": "related_sentences", "tampered_sentences": ["we found that ∼50% of the mammary glands obtained from RRas2−/− mice still contained a insignificant number of TEBs (Figure 3E)", "Those glands also displayed significantly higher numbers of TEBs (Figure 3B and 3E) and branching points (Figure 3B and 3F)"], "golden_sentences": ["we found that ∼50% of the mammary glands obtained from RRas2−/− mice still contained a significant number of TEBs (Figure 3E)", "Those glands also displayed significantly lower numbers of TEBs (Figure 3B and 3E) and branching points (Figure 3B and 3F)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010012624_TII_02/figure/2010012624_TII_02_3.png"], "tampered": true, "paper_ids": ["2010000263"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010122902_TII_02/figure/2010122902_TII_02_3.png", "question_id": "consistency_23", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Tissue penetration of Humabodies with and without albumin in spheroids. Spheroids show cell nuclei (blue) and fluorescent drug (green). Incubations included 20 nM J591 antibody, monovalent-HLE Humabody, PSMA-CD137 with MSA binding HLE (mHLE) incubated with and without MSA, PSMA-CD137 with HSA binding HLE (hHLE) incubated with and without HSA (A). Euclidean distance mapping shows the fluorescent intensity versus distance from the spheroid edge in μm (B-D), indicating that specific albumin binding is not impacting tissue penetration to the spheroid center. The MSA binders (Fig. 2B) had lower maximum signal with the presence of MSA (p=0.002), but HSA binders did not have differences in the maximum signal (p = 0.85). *, p < 0.05.", "figure_related_sentences": "Given the importance of tissue penetration, we next investigated the impact of albumin binding on diffusion. In theory, the diffusion of a Humabody-albumin complex (~110 kDa) would be slower than the Humabody alone (~45 kDa), which could reduce tissue penetration. The impact of albumin binding on tissue distribution was therefore tested in DU145T spheroids. Humabodies with HLE domains were incubated with and without their corresponding albumin type (HSA or MSA), which have 8 nM and 50 nM affinity (Kd), respectively. In both cases, the addition of albumin did not result in changes in tissue penetration compared to Humabody alone (Fig. 3A). Despite the concentration of albumin well above the Kd (~ 200 µM), where most of the Humabody could be in complex with albumin, the presence of albumin had a negligible effect on tissue penetration. These findings were confirmed by quantitative image analysis to map the fluorescence distribution as a function of distance from the spheroid edge (Fig. 3B–D). The fluorescent signal in the center of the spheroids did not show any statistically significant differences with and without albumin. In contrast, an equal molar amounts of J591 antibody (~150 kDa) resulted in homogeneous distribution, which is typical for large biologics. A control monovalent-HLE (that had no CD137 binding domain) with the lowest molecular weight (~30 kDa) distributed the most evenly.", "inconsistent_part": "related_sentences", "tampered_sentences": ["an equal molar amounts of J591 antibody (~150 kDa) resulted in homogeneous distribution"], "golden_sentences": ["an equal molar amounts of J591 antibody (~150 kDa) resulted in heterogeneous distribution"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010122902_TII_02/figure/2010122902_TII_02_3.png"], "tampered": true, "paper_ids": ["2010000275"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010162117_TII_02/figure/2010162117_TII_02_8.png", "question_id": "consistency_24", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 7 (A and B) The BAL fluids and lungs were harvested 24 h after last rmIL-33 challenge to measure the protein expression of IL-1α, IL-5, IL-13, CCL11, CCL17, CCL22 and CCL24. (C) Cell differentials from BAL fluids harvested 24 h after the last rmIL-33 challenge. The results are shown as mean ± SEM of four mice in PBS-challenged groups and 11 mice in rmIL-33-challenged groups. *p < 0.05.", "figure_related_sentences": "We assessed cell differentials and cytokine and chemokine expression levels in the BAL fluid and lung homogenates 24 h after rmIL-33 challenge for four consecutive days (Figure 6A). IL-1α protein expression was not changed by exogenous rmIL-33 challenge in lung homogenate (Figure 7A). This result is consistent with a previous report that IL-33 neutralisation by soluble ST2 administration had no effect in house dust mite extract-induced lung IL-1α protein expression in a mouse model. On the other hand, protein expression of IL-5 and IL-13 in both BAL fluids and lung homogenates was significantly increased in rmIL-33-challenged mice compared with vehicle-challenged mice (p < 0.05); and TSA treatment significantly increased the rmIL-33-induced IL-5 and IL-13 protein expression compared with TSA–vehicle treatment (p < 0.05) (Figure 7B). CCL11 and CCL24 were also increased in lung homogenates from rmIL-33-challenged mice compared with vehicle-challenged mice (p < 0.05); and TSA treatment significantly decreased the rmIL-33-induced CCL11 and CCL24 expression in lung homogenates compared with treatment with the vehicle for TSA (p < 0.05) (Figure 7B). rmIL-33 challenge significantly induced CCL17 and CCL22 expression in lung homogenates (p < 0.05), but TSA treatment did not decrease these chemokines compared with treatment with the vehicle for TSA (Figure 7B). Further, there was a statistically significant decrease in the number of total BAL cells and eosinophils in rmIL-33-challenged mice treated with TSA compared with rmIL-33-challenged mice treated with vehicle (p < 0.05) (Figure 7C). These results suggest that TSA treatment suppresses IL-33-induced Th2 cytokine and eosinophil chemotactic chemokine expression, and subsequent eosinophil accumulation in the airway.", "inconsistent_part": "related_sentences", "tampered_sentences": ["and TSA treatment significantly increased the rmIL-33-induced IL-5 and IL-13 protein expression compared with TSA–vehicle treatment (p < 0.05) (Figure 7B)"], "golden_sentences": ["and TSA treatment significantly decreased the rmIL-33-induced IL-5 and IL-13 protein expression compared with TSA–vehicle treatment (p < 0.05) (Figure 7B)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010162117_TII_02/figure/2010162117_TII_02_8.png"], "tampered": true, "paper_ids": ["2010000289"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010147815_TII_01/figure/2010147815_TII_01_3.png", "question_id": "consistency_25", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 4. Binding of a2NTD and intracellular cytokine production in monocyte subpopulations. (A–D) Peripheral blood mononuclear cells (PBMCs) were incubated with 10 μg/mL a2NTD conjugated to Alexa Fluor 488 (a2NTD-AF488) for 1 h and then surface stained with anti-CD14-Pacific Blue and anti-CD16-PE antibodies. (A) Percentage of monocyte populations positive for a2NTD-AF488 (means ± SEM, n = 10, # p < 0.005, CD14+CD16+ vs. CD14+CD16− or CD14+CD16+ cells). (B–D) PBMCs were kept in control conditions or stimulated with 10 ng/mL a2NTD for 18 h and sequentially stained for surface expression of CD14/CD16 and the intracellular expression of interleukin (IL)-1α: (B), IL-1β (C) and tumor necrosis factor α (TNFα) (D). The bar graph reports the percentage of a2NTD-positive cells (means ± SEM, n = 5, *p < 0.05, ** p < 0.001, compared with unstimulated cells of the same subpopulation).", "figure_related_sentences": "Uptake of a2NTD by monocyte subsets. To determine if different monocyte subsets preferentially internalize a2NTD, monocytes were stained for the surface markers CD14 and CD16 after incubation with a2NTD. CD14++CD16− cells constitute the majority of all monocytes, while CD14++CD16+ and CD14+CD16++ represent two minor subpopulations.25 We were able to retrieve these three populations by flow cytometry (Table 1). Of note, nearly 80% of CD14++CD16+ monocytes were positive for a2NTD endocytosis, as compared with approximately 90% of CD14++CD16− monocytes. The CD14+CD16++ population showed a a2NTD uptake profile similar to that of CD14++CD16− cells (Figure 4A). a2NTD stimulates IL-1α and IL-1β production. It has previously been shown that a2NTD stimulates monocytes to produce the pro-inflammatory cytokines IL-1α and IL-1β.17,18 We examined whether a particular subset of monocytes is responsible for the production of inflammatory cytokines following a2NTD stimulation. To this aim, monocytes were incubated with a2NTD and then stained for surface CD14 and CD16 expression, followed by staining for the intracellular cytokines IL-1α, IL-1β and TNF-α. Only CD14++CD16+ monocytes showed a statistically significant increase in IL-1α production when compared with cells maintained in control conditions (Figure 4B). Both CD14++CD16− and CD14++CD16+ monocytes produced significantly higher amounts of IL-1β (Figure 4C). There was no significant difference in the production of TNFα by cells treated with a2NTD and control cells (Figure 4D). Of note, the CD14++CD16+ subpopulation invariably produced higher amounts of IL-1α, IL-1β and TNFα than the other two subpopulations. In addition, the intracellular levels of IL-1α and IL-1β were greater than those of TNFα. This finding is consistent with our previous data demonstrating that monocytes produce more IL-1 than TNF.16 LPS contamination of the recombinant peptide is always a concern when investigating inflammatory cytokines. A multiexperimental approach was used to investigate the presence of LPS contamination, including the Limulus assay and polymyxin B neutralization tests. The results (which have previously been published) demonstrated negligible levels of LPS and that cytokine secretion could not be inhibited by pre-treatment with polymyxin B.16", "inconsistent_part": "related_sentences", "tampered_sentences": ["as compared with approximately 90% of CD14++CD16− monocytes", "nearly 80% of CD14++CD16+ monocytes were positive for a2NTD endocytosis,"], "golden_sentences": ["as compared with approximately 45% of CD14++CD16− monocytes", "nearly 100% of CD14++CD16+ monocytes were positive for a2NTD endocytosis,"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010147815_TII_01/figure/2010147815_TII_01_3.png"], "tampered": true, "paper_ids": ["2010000290"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010041524_TII_02/figure/2010041524_TII_02_5.png", "question_id": "consistency_26", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Reduced GRHL2 level triggers expression of EDC proteins in differentiating keratinocytes. (a) Rapidly proliferating NHEK were serially subcultured until senescence, and western blotting was performed at varying PD levels for GRHL2, IVL, Jmjd3, and p16INK4A.(b) NHEK were exposed to 1.5mM Caþþfor up to 3 days and collected for western blotting for GRHL2, Jmjd3, IVL, and GRHL3. (c) HaCaT cells were infected with LV-EGFP or LV-GRHL2i to knock down endogenous GRHL2. The cells were then exposed to 2.0mM Caþþ for 3 days and harvested for western blotting for GRHL2, Jmjd3, IVL, FLG, KRT1, GRHL1, GRHL3, and Jmjd3. Arrow indicates the expected size of GRHL3 (B 60kDa). For all experiments, GAPDH (glyceraldehyde 3-phosphate dehydrogenase) was used as a loading control", "figure_related_sentences": "To understand the mechanism by which GRHL2 inhibits EDC gene expression and keratinocyte differentiation, we explored the functional relationship between GRHL2 and epigenetic gene regulation by Jmjd3. In NHEK with increasing PDs, GRHL2 levels progressively decreased while the levels of IVL and p16INK4A decreased (Figure 5a). Caþþ-induced terminal differentiation in NHEK led to induction of IVL and decreased GRHL2 expression (Figure 5b). In both serially subcultured cells and those exposed to Caþþ, changes in Jmjd3 level were remote. In another experiment, expression of endogenous GRHL2 was knocked down in HaCaT cells by lentiviral vector expressing shRNA against GRHL2 (LV-GRHL2i). HaCaT cells were used herein because these cells express high level of endogenous GRHL2 and undergo normal keratinocyte differentiation when exposed to physiological Caþþ level (Figure 4b). As a control, HaCaT cells were infected with an empty viral vector (LV-EGFP). GRHL2 knockdown in HaCaT led to induction of IVL, FLG, and KRT1 even in the absence of Caþþ treatment to the levels similar to Caþþ-exposed control cells (Figure 5c).", "inconsistent_part": "related_sentences", "tampered_sentences": ["GRHL2 levels progressively decreased while the levels of IVL and p16INK4A decreased (Figure 5a)"], "golden_sentences": ["GRHL2 levels progressively decreased while the levels of IVL and p16INK4A increased (Figure 5a)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010041524_TII_02/figure/2010041524_TII_02_5.png"], "tampered": true, "paper_ids": ["2010000345"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010041695_TII_02/figure/2010041695_TII_02_4.png", "question_id": "consistency_27", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure2 Roles of ALK5 receptor and ROS in TGF-b-induced apoptosis in HUVECs. (a) Effects of the ALK5 inhibitor SB431542 (2mM) on TGF-b (10ng/ml for 24h)induced caspase 3/7 activation. (b) Effects of SB431542 on TGF-b-induced caspase 3 cleavage. (c) Effects of SB431542 on TGF-b-induced DCm depression (reduced red fluorescence) as detected with JC-1 staining (representative images of three independent experiments). The red fluorescence specifically labeled the mitochondria. (d) Effects of TGF-b and SB431542 on intracellular ROS production detected with DCFH-DA (green fluorescence). (e) Effects of antioxidant compounds NAC (1mM) and EUK-134 (100mM) on TGF-b-induced caspase 3/7 activation. Data are mean±S.E.M. *Po0.05 versus control (Con), **Po0.05 versus TGF alone, one-way ANOVA (n¼3–5)", "figure_related_sentences": "TGF-b-induced apoptosis is dependent on ALK5 and ROS. To examine whether the ALK5 receptor was involved in TGF-b-induced apoptosis, HUVECs were pre-treated with the ALK5 inhibitor SB431542. Treatment with SB431542 at 2mM enhanced the apoptotic response induced by TGF-b as indicated by caspase 3/7 activation and caspase 3 cleavage (Figures 2a and b). Moreover, we showed that SB431542 also prevented the collapse of mitochondrial membrane potential (DCm) in response to TGF-b as measured with JC-1 staining (Figure 2c and Supplementary Figure S1). Using 20,70-dichlorofluorescin diacetate (DCFH-DA) fluorescence, we found that TGF-b treatment enhanced intracellular ROSproduction in HUVECs, and this effect could be blocked by SB431542 (Figure 2d and Supplementary Figure S1). To elucidate the role of ROS in TGF-b-induced apoptosis, we preincubated the cells with antioxidant compounds N-acetyl-L-cysteine (NAC) or EUK-134. We showed that both NAC and EUK-134 abrogated TGF-b-induced caspase 3/7 activation (Figure 2e).", "inconsistent_part": "related_sentences", "tampered_sentences": ["Treatment with SB431542 at 2mM enhanced the apoptotic response induced by TGF-b as indicated by caspase 3/7 activation and caspase 3 cleavage (Figures 2a and b)"], "golden_sentences": ["Treatment with SB431542 at 2mM abolished the apoptotic response induced by TGF-b as indicated by caspase 3/7 activation and caspase 3 cleavage (Figures 2a and b)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010041695_TII_02/figure/2010041695_TII_02_4.png"], "tampered": true, "paper_ids": ["2010000346"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010031950_TII_01/figure/2010031950_TII_01_0.png", "question_id": "consistency_28", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Morphological and growth characterization of hBMCs and hPDCs. (A) Growth curves of hBMCs (human bone marrow derived cells) and hPDCs (human periosteum-derived cells) over 2 weeks in culture. (B) Phase contrast images of hBMCs and hPDCs at one day after seeding at 5 k/cm2, 25 k/cm2, and 85 k/cm2 (scale bar 5 100 mm). White arrowheads indicate flattened morphology whereas black arrowheads indicate spindle-shaped morphology. (C) Growth kinetics of hBMCs (2 donors/2 experiments) and hPDCs (4 donors) seeded at different densities from passage 4. All error bars indicate standard error of the mean (n53 hBMC donors or 4 hPDC donors).", "figure_related_sentences": "Independently of the cell culture vessel used, hPDCs proliferated faster than hBMCs and reached full confluence after 7 days (Fig. 1A) when initially seeded at low seeding density (5000 cells/cm2). In addition, the cell density of hPDCs obtained at confluence was consistently higher as compared to hBMCs, which suggested that hPDCs are smaller than hBMCs. Indeed, side-by-side comparison of adherent hBMC and hPDC populations under phase contrast microscopy suggested that hBMCs were more spread on tissue culture plastic with a broader cytoplasmic body than hPDCs (Fig. 1B, white arrows), whereas hPDCs displayed a more spindle-shaped phenotype (Fig. 1B, black arrows). To examine how initial seeding density impacted hBMC and hPDC populations, we empirically chose three seeding densities, 5000 (5 k/cm2), 25000 (25 k/cm2), and 85000 (85 k/cm2). When seeded at 5 k/cm2, both hPDCs and hBMCs attached efficiently as mostly isolated cells with few if any cell–cell contacts. At 25 k/cm2, both cell types arranged in a nearly confluent, but not densely packed, monolayer of cells in which cells remained well spread against the substrate but also displayed augmented cell–cell contact. At 85 k/cm2, both cell types appeared smaller, highly packed, and extended processes over each other (Fig. 1B), but a significant number of hBMCs did not attach after seeding at 85 k/cm2. Because differentiation experiments last one to two weeks, we quantified the extent to which cell proliferation affected cell density over time at the different seeding densities. hBMCs seeded at 5 k/cm2 or 25 k/cm2 reached a cell density of 35 k/cm2 (62.6 k/cm2) and 41 k/cm2 (64.1 k/cm2), respectively, whereas hPDCs at those seeding densities expanded to 55 k/cm2 (65k/cm2)and 64 k/cm2 (64.6 k/cm2). Cell density did not change over time for both cell types when seeded at 85 k/cm2, though fewer hBMCs than hPDCs attached at this density (Fig. 1C).", "inconsistent_part": "related_sentences", "tampered_sentences": ["hPDCs proliferated faster than hBMCs and reached full confluence after 7 days (Fig. 1A) when initially seeded at low seeding density (5000 cells/cm2)"], "golden_sentences": ["hPDCs proliferated faster than hBMCs and reached full confluence after 10 days (Fig. 1A) when initially seeded at low seeding density (5000 cells/cm2)"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010031950_TII_01/figure/2010031950_TII_01_0.png"], "tampered": true, "paper_ids": ["2010000350"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010168986_TII_02/figure/2010168986_TII_02_2.png", "question_id": "consistency_29", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "FIGURE 3. Co-i-cIDPRE evokes Ca2+ increase in human Jurkat cells after UV photolysis. A, Co-i-cIDPRE (200 µM) incited much weaker Ca2+ increases after UV photolysis than that by cIDPRE (200 µM) in Jurkat cells. Fluo-4-loaded cells were incubated in regular HBSS containing extracellular Ca2+ during the experiment. B, after Fluo-4-loaded Jurkat cells were incubated with Co-i-cIDPRE (120 µM) in regular HBSS containing extracellular Ca2+, washing away Co-i-cIDPRE in the medium did not have any effect on Ca2+ changes triggered by uncaging of Co-i-cIDPRE. C and D, in Fluo-4-loaded Jurkat cells, uncaging of Co-i-cIDPRE triggered Ca2+ increases in a dose-dependent manner in both the presence (C) and the absence of extracellular Ca2+ (D). E, in Fluo-4-loaded Jurkat cells, thapsigargin (10 µM) pretreatment promoted Co-i-cIDPRE (120 µM)-induced Ca2+ increases in the absence of extracellular Ca2+. Data quantifications of [Ca2+]i peak induced by drug treatment in A, C, D, and E were expressed as mean ± S.E., n = 30 – 40 cells, *, p ≤ 0.05. In A, C, D, and E, cells were all continuously incubated with Co-i-cIDPRE throughout the experiments.", "figure_related_sentences": "It has been shown that cADPR targets the RyR, but which specific isoform it targets remains to be determined (1–3). Here we showed that both RyR2 and RyR3 are expressed in Jurkat cells. Individual knockdown of these isoforms inhibited cIDPRE- or cADPR-induced Ca2+ release to a similar extent, whereas double knockdown of both isoforms abolished cADPR-induced Ca2+ release in Jurkat cells (Fig. 4E). These data indicate that cADPR does not distinguish either isoform. However, it still remains to be determined whether cADPR binds directly to the RyRs or through some unknown proteins. Recently, the long sought after store-operated Ca2+ entry proteins were identified using a genome-wide RNAi screen by several groups (36–38). Co-i-cIDPRE could be a valuable tool to be used in a similar cell-based screening for cADPR-interacting proteins or regulators.", "inconsistent_part": "caption", "tampered_sentences": ["Co-i-cIDPRE (200 µM) incited much weaker Ca2+ increases after UV photolysis than that by cIDPRE (200 µM) in Jurkat cells.", "thapsigargin (10 µM) pretreatment promoted Co-i-cIDPRE (120 µM)-induced Ca2+ increases in the absence of extracellular Ca2+."], "golden_sentences": ["Co-i-cIDPRE (200 µM) incited much stronger Ca2+ increases after UV photolysis than that by cIDPRE (200 µM) in Jurkat cells.", "thapsigargin (10 µM) pretreatment abolished Co-i-cIDPRE (120 µM)-induced Ca2+ increases in the absence of extracellular Ca2+."], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010168986_TII_02/figure/2010168986_TII_02_2.png"], "tampered": true, "paper_ids": ["2010000351"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010041443_TII_02/figure/2010041443_TII_02_3.png", "question_id": "consistency_30", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 4 ‘Late’ Hsp27 phosphorylation induced by apigenin is modulated by p38-MAPK and PKCd. Lysates from THP-1 cells treated with 50 μM apigenin for 6 h and diluent or following 1 h pretreatment with 10 μM SB203580, 15 μM rottlerin, or both. Treatments marked with (-) denote addition of diluent. (a) Immunoblots with anti-phospho-Hsp27-pS78 and anti-total-Hsp27 antibodies. (b) Immunoblots with anti-phospho-Hsp27-pS82 and anti-total-Hsp27 antibodies. (c) Immunoblots with antiphospho-Hsp27-pS15 and anti-total-Hsp27 antibodies. Densitometry data normalized by the loading control are represented as mean±S.E.M. (N ¼ 5, *Pp0.05 and **Pp0.001, NS denotes non-statistical significance)", "figure_related_sentences": "Next, we investigated the role of p38 and PKCσ on the ‘late’ Hsp27 phosphorylation using pharmacological inhibitors. THP-1 cells were pretreated with the p38 inhibitor SB203580, or the PKCσ inhibitor rottlerin, or both inhibitors, or with diluent for 1 h before the addition of 50 μM apigenin for 6 h. We found that apigenin-induced phosphorylation of S78 was significantly stimulated in the presence of the p38 inhibitor SB203580 (Figure 4a, lane 3 versus 2, **P<0.001), reaching levels similar to that in control cells (Figure 4a, lane 3 versus 1). In contrast, the PKCσ inhibitor rottlerin had no effect on the phosphorylation of S78 (Figure 4a, lane 4 versus 2, NS ¼ nonstatistically significant). Addition of both SB203580 and rottlerin showed decreased S78 phosphorylation to levels similarly observed in the presence of the p38 inhibitor alone (Figure 4a, lane 5 versus 3). However, we found no additive or synergistic effects when cells were treated with both inhibitors simultaneously (Figure 4a, lane 5 versus 2, **P<0.001). The phosphorylation of S82 induced by apigenin was significantly inhibited by pretreatment with the p38 inhibitor SB203580 (Figure 4b, lane 3 versus 2, *P<0.05). In contrast to the lack of effect observed on S78, the PKCσ inhibitor rottlerin, significantly inhibited apigenin-induced phosphorylationof S82 (Figure 4b, lane 4 versus 2, *P<0.05). Similar to S82 phosphorylation, we observed that the pretreatment with the p38 inhibitor SB203580 inhibited apigenin-induced phosphorylation of S15 (Figure 4c, lane 3 versus 2, *P<0.05). In addition, rottlerin decreased apigenin-induced phosphorylation of S15 (Figure 4c, lane 4 versus 2, *P<0.05). The addition of both inhibitors, however, showed no additive or synergistic effects (Figure 4c, lanes 5, 4 versus 2, **P<0.001).", "inconsistent_part": "related_sentences", "tampered_sentences": ["We found that apigenin-induced phosphorylation of S78 was significantly stimulated in the presence of the p38 inhibitor SB203580 (Figure 4a, lane 3 versus 2, **P<0.001)"], "golden_sentences": ["We found that apigenin-induced phosphorylation of S78 was significantly inhibited in the presence of the p38 inhibitor SB203580 (Figure 4a, lane 3 versus 2, **P<0.001)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010041443_TII_02/figure/2010041443_TII_02_3.png"], "tampered": true, "paper_ids": ["2010000354"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010065512_TII_01/figure/2010065512_TII_01_2.png", "question_id": "consistency_31", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 3. Expression of histone mRNAs in mouse fibroblast cells and mouse liver. (A) Schematic of generalized S1 nuclease protection assay performed on mouse histone mRNA. A generalized histone mRNA is depicted indicating possible 5’ splice sites (5’ss), stem-loop cleavage sites (S-L cleavage) or poly(A) cleavage sites. S1 nuclease protection probes will protect a given mRNA to the point that cleavage or splicing occurs (indicated below). Note that due to the high degree of conservation in mice, all of the mRNAs for a specific histone class (i.e. H2B.1 or H2A.2) will be protected up to the stop codon. (B–F) Total cell RNA from NIH3T3 cells and mouse liver was fractionated into polyA+ and polyA− fractions. Total RNA (whole cell (WC)) and poly(A)+ and poly(A−) RNA were probed in an S1 nuclease protection assay. Five micrograms of total 3T3 cell RNA and 50 μg of liver RNA was analyzed using the S1 nuclease protection assay of a 32P labeled fragment at the indicated restriction enzyme site for (B) Hist2H2aa1, (C) Hist1H2bc, (D) Hist1H2ac, (E) Hist2H3c or (F) Hist2H4H. The probe used for histone H4H was labeled at the 5’ end of the indicated restriction site. For each experiment, below the autoradiogram, possible mRNA isoforms are indicated as well as protected fragments and sizes for S1 nuclease probes.", "figure_related_sentences": "Validation of polyadenylated histone mRNA expression in adult mouse liver. To confirm the expression of the mouse histone mRNAs detected by high-throughput sequencing, we analysed histone gene expression in actively growing cultured fibroblasts (NIH3T3 cells) and liver tissue from 72-week-old mice. The liver is a relatively homogenous tissue with hepatocytes making up more than 70% of the cells. In healthy adult livers, the vast majority of these hepatocytes are quiescent, only re-entering the cell cycle after injury. Unlike the human histone genes, the coding regions of the mouse histone genes are highly conserved (>95%) at the nucleotide level (37). Because of the conserved ORF sequences, we can use an S1 nuclease mapping assay to simultaneously analyse both the mRNA expressed from a specific gene, as well as the mRNAs from all the other histone genes encoding that histone protein (26,42). A probe labelled in the coding region will protect all the histone mRNAs to a region close to the stop codon or initiation codon, as well as a band from the specific gene extending to the 3' end or the 5' end of the transcript, depending on whether one is probing the 3' or the 5' end of the mRNA (Figure 3A). This highly sensitive method allows for mapping of multiple isoforms of mRNA from a single sample. Further, since all of the radioactivity is at the end of the probe, the relative intensity of the bands gives the relative amounts of the transcripts. A generalized schematic is shown in Figure 3A. In each experiment below, the different protected fragments for a given probe are diagrammed below the autoradiogram. Total RNA from NIH3T3 cells and mouse liver was fractionated into polyA− and polyA+ RNA using oligo-d(T) cellulose. Orthologues of human histone HIST1H2BC (Hist1H2bc), HIST2H2AA3 (Hist2H2aa1) and HIST1H4H (Hist1H4h), which were expressed in human tissues, and the HIST2H3C (Hist2H3c) gene, adjacent to the Hist2H2AA3 gene, which was not expressed in human tissues, were analysed by S1 nuclease mapping, using 5 µg of total RNA from exponentially growing NIH3T3 cells and 50 µg of total liver RNA (Figure 3). In actively proliferating NIH3T3 cells, most of the 3' S1 probes map three protected fragments: one extending to the 3' end of the mRNA ending in the stem-loop and a second fragment, mapping near the stop codon, due to the high level of conservation between the open reading frames of all mouse histone genes of a given class (26). This band is indicated by the name of that class of histone protein (e.g. H3.1 or H2a.1). If the histone mRNA is spliced or polyadenylated then the probe is protected up to the point where the mRNA sequence diverges from the probe (Figure 3A; e.g. at the 5' splice site in Hist1H2bc, before the 3' end of the mRNA or at the polyA addition site in Hist2H2aa1). The S1 nuclease protection assays confirmed the low levels of histone mRNAs in liver and there were easily detectable amounts of the polyadenylated forms of Hist2H2aa1 (Figure 3B, lane 7) and Hist1H2bc (Figure 3C, lane 7) mRNAs. There were no polyadenylated mRNAs detected in the NIH3T3 cells. There is some non-polyadenylated histone mRNA detected in the liver that gives the same pattern of S1 nuclease protected fragments as the NIH3T3 cell mRNA. This likely arises from a low level of expression of the histone mRNAs expressed in growing cells. Note that the non-polyA mRNA expressed in mouse liver is greatly reduced compared to NIH3T3 cells, and we used 10 times more RNA (50 µg versus 5 µg) for assay of liver RNA, compared to neonatal mice or growing 3T3 cells. We assayed the same RNAs with probes for Hist1H2ac (Figure 3D), Hist2H3c (Figure 3F) and Hist1H4h (Figure 3E) genes. There was no polyadenylated mRNAs detected from these genes in mouse, consistent with the sequencing data.", "inconsistent_part": "related_sentences", "tampered_sentences": ["most of the 3' S1 probes map three protected fragments: one extending to the 3' end of the mRNA ending in the stem-loop and a second fragment"], "golden_sentences": ["most of the 3' S1 probes map two protected fragments: one extending to the 3' end of the mRNA ending in the stem-loop and a second fragment"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010065512_TII_01/figure/2010065512_TII_01_2.png"], "tampered": true, "paper_ids": ["2010000358"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010011052_TII_01/figure/2010011052_TII_01_0.png", "question_id": "consistency_32", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Production of Th2- and Th1-type cytokines from wild-type and Runt-transgenic CD4⁺ T cells. (A) Naive CD4⁺ T cells were isolated from the spleens of wild-type and Runt–transgenic mice and stimulated with anti-CD3/anti-CD28 antibodies, and the culture supernatants were collected at the indicated times after stimulation. (B) The TCR-stimulated cells were cultured in the presence of IL-2 for 5 d, washed with fresh media, and restimulated via TCR. The culture supernatants were collected after 24 h. (C) The cells were cultured for four days in the Th2- or Th1-inducing condition. The cells were washed with fresh media and restimulated via TCR. The culture supernatants were collected after 24 h. (D) Same as C, but note the difference of scale used in C and here. The amounts of cytokines secreted into the supernatants were measured by ELISA and their averages and standard deviations are shown. Data are representative of four independent experiments.", "figure_related_sentences": "Respectively, compared with the wild-type cells. A similar result as that shown in Figure 1A was obtained when the TCR-stimulated cells were incubated in the presence of IL-2 for 5 d, washed with fresh media, and restimulated via TCR (Figure 1B). Under this neutral culture condition where neither IL-4 nor IL-12 was added to media, the Runt-transgenic cells secreted several fold more amount of Th2-type cytokines and less amount of Th1-type cytokines than the wild-type cells. We next examined the cytokine production from the Runt-transgenic cells under culture conditions that favor either Th1 or Th2 differentiation. CD4⁺ T cells were stimulated with anti-CD3/anti-CD28 antibodies and incubated in the presence of either IL-4 and an anti-IFN-γ antibody (Th2 condition) or IL-12 and an anti-IL-4 antibody (Th1 condition) for 4 d. Cells were washed with fresh media and restimulated via TCR, and cytokine secretion was measured (Figure 1C). In the Th2 condition, the Runt-transgenic cells produced three times as much IL-4 as the wild-type cells. In contrast, in the Th1 condition, although IFN-γ production from the Runt-transgenic cells was reduced compared with the wild-type cells, IL-4 production from the Runt-transgenic cells did not reach the level of 10 to 100 ng/ml concentration. Thus, the Runt-expressing cells effectively differentiate into the Th2 lineage in a Th2- but not a Th1-favorable environment. It must be pointed here that, even in the Th1 condition, the Runt-transgenic cells actually produced 10 times as much IL-4 as the wild-type cells (Figure 1D). The absolute amount of IL-4 secreted from the Runt-transgenic cells was, however, 5 ng/ml in the Th1 condition (Figure 1D) instead of 120 ng/ml in the Th2 condition (Figure 1C). Therefore, the Runt-transgenic cells, though showing a Th2 tendency to some degree, could not have differentiated effectively into the Th2 lineage under the Th1 condition. Overexpression of Runx1 Prevents Naive Cells from Differentiating Into the Th2 Lineage. If reducing the effect of Runx1 with the Runt transgene induces Th2 differentiation, as shown in Figure 1, we wondered whether the artificial overexpression of Runx1 protein in naive T cells would cause a decrease in Th2 differentiation.", "inconsistent_part": "related_sentences", "tampered_sentences": ["In the Th2 condition, the Runt-transgenic cells produced three times as much IL-4 as the wild-type cells", "even in the Th1 condition, the Runt-transgenic cells actually produced 10 times as much IL-4 as the wild-type cells (Figure 1D)"], "golden_sentences": ["In the Th2 condition, the Runt-transgenic cells produced eight times as much IL-4 as the wild-type cells", "even in the Th1 condition, the Runt-transgenic cells actually produced 25 times as much IL-4 as the wild-type cells (Figure 1D)"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010011052_TII_01/figure/2010011052_TII_01_0.png"], "tampered": true, "paper_ids": ["2010000365"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010064426_TII_02/figure/2010064426_TII_02_4.png", "question_id": "consistency_33", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 5. Reporter assay tests for the repression of NL4-3 by miR-223 and miR-29. For all transfections, the values represent the average of at least three independent experiments and the error bar represents the standard deviation. (a) Reporter assays show miR-223/29 repression is very weak when Nef serves as the 30 -UTR. (b) Reporter assays show miR-223/29 repression of Nef when it serves as a coding region. (c) Reporter assays to measure the miR-223/29 repression using the 39 nt target sequence. Co-transfection of the reporter and miRNA genes in HEK-293 cells show strong repression by miR-223 and strong repression by miR-29. Mutated seed binding site for miR-223 or miR-29 abrogated the repressions mediated by either miRNA. (d) Reporter assays to measure the miR-223/29 repression using a 56 nt target sequence. Co-transfection of the reporter and miRNA expression constructs in HEK-293 cells show strong repression mediated by miR-223 and reduced repression mediated by the miR-29 miRNAs.", "figure_related_sentences": "No words", "inconsistent_part": "caption", "tampered_sentences": ["Co-transfection of the reporter and miRNA genes in HEK-293 cells show strong repression by miR-223 and strong repression by miR-29", "Co-transfection of the reporter and miRNA expression constructs in HEK-293 cells show strong repression mediated by miR-223 and reduced repression mediated by the miR-29 miRNAs"], "golden_sentences": ["Co-transfection of the reporter and miRNA genes in HEK-293 cells show weak repression by miR-223 and strong repression by miR-29", "Co-transfection of the reporter and miRNA expression constructs in HEK-293 cells show weak repression mediated by miR-223 and reduced repression mediated by the miR-29 miRNAs"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010064426_TII_02/figure/2010064426_TII_02_4.png"], "tampered": true, "paper_ids": ["2010000368"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010064989_TII_02/figure/2010064989_TII_02_8.png", "question_id": "consistency_34", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 9. Activity and selectivity of ASOs in the rodent CNS. (A) Allele selective knockdown of muHTT protein with ASO A30 in neuronal cells derived from cortical and striatal tissues of Hu97/18 mouse embryos under free-uptake conditions. (B–D) Hu97/18 mice (n = 4/group) were injected ICV with a single dose of 300 µg of ASO (B and D) or the indicated dose (C) in PBS. Mice were sacrificed after 28 days, the brain was harvested, and a 2 mm coronal slab from each hemisphere (R, L) was analyzed by allelic separation immunoblotting for muHTT and wtHTT protein, and the results were normalized to calnexin protein. (B) Optimized ASOs A25, A26, A30, and A31 show similar activity but worsened allele selectivity relative to control ASO A1. (C) Dose response for allele-selective knockdown of muHTT protein following ICV injection of ASO A30 in Hu97/18 mice. (D) Immunohistochemical staining for ASO (red) illustrates distribution to all parts of the brain following a single ICV bolus injection.", "figure_related_sentences": "Improved allele selectivity in cell culture translates to brains of transgenic mice. We evaluated selected ASOs in Hu97/18 mice (45), a completely humanized mouse model of HD (Figure 9). This mouse model contains both the mutant human HTT allele, with the associated SNPs, and the wt human HTT allele. We first evaluated the ability of ASO A30 to reduce muHTT protein in primary neuronal cells derived from Hu97/18 mouse embryos in the absence of any transfection agent to facilitate delivery of the ASO across the cell membrane (Figure 9A). The ASO reduced muHTT expression in a dose-dependent manner (IC50 = 101 nM). No reduction of wtHTT was observed even at the highest dose of ASO A30 (1000 nM) tested. Next, mice (n = 4/group) were injected in the right lateral ventricle (ICV) with a single bolus injection (300 µg) of ASO (A1, A25, A26, A30, or A31) or vehicle control (PBS), and tissue was collected 28 days later. Brains were harvested, and HTT protein was quantified in a 2 mm coronal slab from each hemisphere by allelic separation immunoblotting for mu and wtHTT protein; the results were normalized to calnexin (Figure 9B). The posterior portions of treated brains were then post-fixed for immunohistochemical assessment of ASO distribution.As observed in the cell culture experiment, all the ASOs showed 60–80% reduction of muHTT protein. However, although ASO A1 showed a 52% reduction of the wtHTT protein, we observed essentially no reduction of the wtHTT protein for the mice treated with the allele-selective ASOs A25, A26, A30, and A31. We also measured the ability of ASO A30 to reduce muHTT protein in a dose-response experiment (Figure 9C). Mice (n = 4/group) were injected (ICV bolus) with increasing doses (75, 150, 300, and 500 µg) of ASO A30 or vehicle control, and brain tissue was harvested after 28 days using the procedures described earlier in the text. The ASOs produced a dose-dependent reduction in muHTT (ED50 = 110 µg) with no reduction in wtHTT even at the highest dose tested (500 µg). All ASOs also showed similar broad and even bilateral localization after ICV bolus injection, indicating that the modifications had no effect on distribution (Figure 9D). Thus, the animal model recapitulated the potency and selectivity observations from the cell culture experiments. Collectively, these studies illustrate the potency, selectivity, and tolerability of these compounds and support their development as potential therapeutics for HD.", "inconsistent_part": "caption", "tampered_sentences": ["and A31 show similar activity but worsened allele selectivity relative to control ASO A1."], "golden_sentences": ["and A31 show similar activity but improved allele selectivity relative to control ASO A1."], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010064989_TII_02/figure/2010064989_TII_02_8.png"], "tampered": true, "paper_ids": ["2010000374"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010131195_TII_02/figure/2010131195_TII_02_3.png", "question_id": "consistency_35", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 4. Reversion of Splicing Abnormalities in DM1 Patient-Derived Muscle Cells by CRISPR-SaCas9 Deletion of Expanded CTG Repeats Splicing profiles and quantification of LDB3 exon 11-, ATP2A1 exon 22-, MBNL1 exon 7-, DMD exon 78-, INSR exon 11-, and BIN1 exon 11-containing transcripts in differentiated myoblasts from DM1-Delta clones 10, 3, 17, and 22 compared to control (Ctrl), DM1, and DM1-sgRNA clones. Graphs show average values from independent biological replicates ± SD (n = 6 for Ctrl and DM1, n = 3 for the other samples). Statistical analysis by two-tailed Student’s t test. *p < 0.05, **p < 0.01, ***p < 0.001; ns, not significant; ˂DL, below detection limit. Error bars represent SD.", "figure_related_sentences": "Aggravation of Alternative Splicing Defects in DM1-Edited Muscle Cells Sequestration of MBNL-splicing factors in nuclear foci of DM1 cells leads to alterations in the alternative splicing of numerous pre-mRNAs, some of which are eliminated in differentiated muscle cells in culture.45 We therefore assessed the splicing pattern of LIM domain binding 3 (LDB3) exon 11, Sarco-endoplasmic reticulum calcium ATPase 1 (ATP2A1) exon 22, Muscleblind-like splicing regulator 1 (MBNL1) exon 7, Duchenne muscular dystrophy (DMD) exon 78, insulin receptor (INSR) exon 11, and Bridging integrator 1 (BIN1) exon 11 in edited DM1-Delta clones compared to DM1, DM1-sgRNA, and Ctrl cells (Figure 4).", "inconsistent_part": "related_sentences", "tampered_sentences": ["Aggravation of Alternative Splicing Defects in DM1-Edited Muscle Cells Sequestration of MBNL-splicing factors in nuclear foci of DM1 cells leads to alterations in the alternative splicing of numerous pre-mRNAs", "some of which are eliminated in differentiated muscle cells in culture"], "golden_sentences": ["Correction of Alternative Splicing Defects in DM1-Edited Muscle Cells Sequestration of MBNL-splicing factors in nuclear foci of DM1 cells leads to alterations in the alternative splicing of numerous pre-mRNAs", "some of which are reproduced in differentiated muscle cells in culture"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010131195_TII_02/figure/2010131195_TII_02_3.png"], "tampered": true, "paper_ids": ["2010000376"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010101726_TII_02/figure/2010101726_TII_02_1.png", "question_id": "consistency_36", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2. Overexpression of Ahi-1 in Sca-1 +lin _x0004_ mouse stem/progenitor BM cells perturbs their in vitro proliferative activity and enhances the effects of BCR-ABL. (A) The levels of Ahi-1 transcripts relative to GAPDH from FACS-purified MIY (Sca-1 + lin _x0004_ YFP +), Ahi-1 (Sca-1 + lin _x0004_ YFP +), BCR-ABL (Sca-1 + lin _x0004_ GFP +), and Ahi-1 plus BCR-ABL (Sca-1 + lin _x0004_ YFP + GFP +) transduced primary mouse BM cells. (B) Growth of each FACS-purified population with GFs. Viable cell numbers were determined by hematocytometer counts of trypan blue – excluding cells. (C) Number of CFC colonies produced in semisolid cultures ± GF from the same FACS-purified mouse BM cells. (D) The appearance of GF-independent CFC colonies is shown. Bar, 250 μm. (E) The numbers of LTC-IC-derived CFCs produced from the same cells ± GF. Values shown are the mean ± SEM of triplicate measurements. * indicates significantly different from MIY control cells.", "figure_related_sentences": "Elevated endogenous Ahi-1 expression was also observed in cells transduced with BCR-ABL alone as compared with control cells (8-fold; P < 0.01; Fig. 2 A). 5 d after transduction, the rate of expansion of the Sca-1 +lin _x0004_YFP + (Ahi-1 +) cells in liquid cultures was approximately twofold lower than in cultures initiated with control cells (Fig. 2 B). Ahi-1– transduced Sca-1 +lin _x0004_ cells produced a slightly fewer number of colony-forming cells (CFCs) than MIY-transduced control cells in semisolid cultures in the presence of growth factors (GFs), and some of the Ahi-1 + CFCs (15%) were already GF independent (Fig. 2, C and D). After 4 wk in long-term culture-initiating cell (LTC-IC) assays, which are used to measure stem cell activities in vitro, the Sca-1 +lin _x0004_Ahi-1 + cells produced 3-fold more CFCs than control cells (P < 0.01; Fig. 2 E). All of these endpoints (proliferative activity, GF dependence, and CFC output in LTC-IC assays) are also perturbed by BCR-ABL transduction. In cells cotransduced with Ahi-1 and BCR-ABL, all of these effects were further enhanced compared with cells transduced with either BCR-ABL alone (2–4-fold) or Ahi-1 alone (3–6-fold; P < 0.01; Fig. 2). Thus, overexpression of Ahi-1 alone deregulates proliferative control of primitive mouse hematopoietic cells, and these effects can be enhanced by BCR-ABL.", "inconsistent_part": "related_sentences", "tampered_sentences": ["the rate of expansion of the Sca-1 +lin _x0004_YFP + (Ahi-1 +) cells in liquid cultures was approximately twofold lower than in cultures initiated with control cells (Fig. 2 B)", "Ahi-1– transduced Sca-1 +lin _x0004_ cells produced a slightly fewer number of colony-forming cells (CFCs) than MIY-transduced control cells in semisolid cultures in the presence of growth factors (GFs)"], "golden_sentences": ["the rate of expansion of the Sca-1 +lin _x0004_YFP + (Ahi-1 +) cells in liquid cultures was approximately twofold higher than in cultures initiated with control cells (Fig. 2 B)", "Ahi-1– transduced Sca-1 +lin _x0004_ cells produced a slightly greater number of colony-forming cells (CFCs) than MIY-transduced control cells in semisolid cultures in the presence of growth factors (GFs)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010101726_TII_02/figure/2010101726_TII_02_1.png"], "tampered": true, "paper_ids": ["2010000382"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010016919_TII_01/figure/2010016919_TII_01_2.png", "question_id": "consistency_37", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "ECM softness upregulates MMP secretion and promotes MMP activity. (A) Primary human fibroblasts (2 × 104 cells per well) were seeded onto gels of varying stiffness in 12-well plates and cultured for 48 h. Cell culture medium from each condition was collected and subject to the RayBio Human MMP Array to determine the total secreted MMP protein quantity in each medium. (B) Three independent experiments (n = 3, ±SD) as in A were performed and quantified. Note that proliferation rates vary on gels of different stiffness. Total MMP quantities were normalized to total cell numbers on gels of varying stiffness at 48 h. Student’s test was used for the comparison of each mean with the mean of MMP protein quantity of the same MMP type on 25.6-kPa gels. *p < 0.05 considered significant. (C) Cell culture conditioned media were collected as in A, and the total MMP activity in each medium was measured and quantified (n = 3, ±SD) and normalized to cell number. Student’s t test was used for the comparison of each mean with the mean of “0.4 kPa.” *p < 0.05 considered significant.", "figure_related_sentences": "Matrix metalloproteinases (MMPs) are critical proteinases in ECM degradation and include two major subfamilies of secreted MMPs (MMP-2, -3, etc.) and integral membrane MMPs (MMP-14 [MT1-MMP], -15, etc.; Kessenbrock et al., 2010). For all types of MMPs that were measured, increased ECM stiffness significantly inhibited MMP secretion from these cells (Figure 2A). Previous studies reported that increased ECM stiffness significantly promotes primary cell proliferation (Wang et al., 2000; Liu et al., 2010). Thus, by normalizing to total cell numbers at 48 h after cell seeding, the relative amount of MMPs secreted per cell were even lower on stiffer substrates (Figure 2B). Further, the total MMP activities of these secreted MMPs also were higher on softer substrates and lower on stiffer substrates (Figure 2C). Of interest, we also detected small differences of MMP secretion on substrates with varying stiffness as early as 4 h after cell seeding (Supplemental Figure S1B), suggesting that cells begin responding to stiffness during their initial adhesion to ECM.", "inconsistent_part": "caption", "tampered_sentences": ["Student’s t test was used for the comparison of each mean with the mean of “0.4 kPa.” *p < 0.05 considered significant", "Student’s test was used for the comparison of each mean with the mean of MMP protein quantity of the same MMP type on 25.6-kPa gels."], "golden_sentences": ["Student’s t test was used for the comparison of each mean with the mean of “0.1 kPa.” *p < 0.05 considered significant", "Student’s test was used for the comparison of each mean with the mean of MMP protein quantity of the same MMP type on 0.2-kPa gels."], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010016919_TII_01/figure/2010016919_TII_01_2.png"], "tampered": true, "paper_ids": ["2010000398"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010124149_TII_02/figure/2010124149_TII_02_3.png", "question_id": "consistency_38", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 4. Quantitative analysis of CTCF and BORIS expression in human PCa. (A) Nuclear CTCF significantly decreases in metastases cores (P < .001). (B) BORIS nuclear expression significantly increased in cancer cores (P = .002); nuclear and cytoplasmic expression increased in HGPIN cores compared to benign (both P < .001). (C) The ratio of BORIS to CTCF expression was analyzed for differences among cores. Significant increases in the BORIS/CTCF ratio are seen among cancer and metastases cores compared to benign (P = .031 and P = .006 respectively). (D) Comparing the BORIS/CTCF ratio among cancer cores, high Gleason grade cancers have significantly lower BORIS/CTCF ratio than both benign and intermediate Gleason cores (P = .006 and P = .024 respectively).", "figure_related_sentences": "CTCF is known to impact gene regulation through the management of chromatin organization and the maintenance of epigenetic marks [26]. CTCF expression levels measured by VECTRA were insignificantly decreased in metastatic PCa tumors (P < .001), but not localized PCa when compared to benign prostate tissues (P = .17) (Figure 4A). When CTCF expression within primary tumors was compared against clinicopathologic patient variables, decreased nuclear and total CTCF expression was associated with higher Gleason’s Score (P = .01 and P = .001 respectively) and positive margins (P = .03 and P = .043 respectively) (Data not shown). The CTCF paralogue, BORIS, shares a common zinc-finger DNA-binding domain with divergent N- and C- termini. BORIS and CTCF have competing effects on gene expression and epigenetic regulation [5,27]. In contrast to CTCF, BORIS expression was increased in HGPIN and primary cancer cores compared to benign (P < .001 and P = .002 respectively) (Figure 4B). No clinicopathologic correlates were noted. The competing role for BORIS/CTCF suggests the ratio of their expression may contain functional significance and greater predictive power than the expression of these proteins individually as seen in ovarian cancer [28]. Analyzing all prostate tissues, a weak correlation was seen between BORIS and CTCF (Pearson’s r = .224, P < .001). BORIS/CTCF levels increased significantly in cancer and metastases compared to benign (P = .03 and P = .006 respectively) (Figure 4C). High Gleason cancers have a significantly greater BORIS/CTCF ratio than both benign tissues and intermediate Gleason cancers (P = .006 and P = .024 respectively) (Figure 4D). The ratio of nuclear and total expression was calculated and found to be associated with Gleason’s grade, positive surgical margins, and tumor volume (nuclear P = .024, P = .027, P = .020, respectively) (Table 2, for full table see supplementary data, Table S2).", "inconsistent_part": "caption", "tampered_sentences": ["CTCF expression levels measured by VECTRA were insignificantly decreased in metastatic PCa tumors (P < .001)", "high Gleason grade cancers have significantly lower BORIS/CTCF ratio than both benign and intermediate Gleason cores (P = .006 and P = .024 respectively)"], "golden_sentences": ["CTCF expression levels measured by VECTRA were significantly decreased in metastatic PCa tumors (P < .001)", "high Gleason grade cancers have significantly higher BORIS/CTCF ratio than both benign and intermediate Gleason cores (P = .006 and P = .024 respectively)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010124149_TII_02/figure/2010124149_TII_02_3.png"], "tampered": true, "paper_ids": ["2010000399"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010011326_TII_02/figure/2010011326_TII_02_2.png", "question_id": "consistency_39", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Effects of TRAF3 deficiency on effector functions of CD40 and LMP1. (A) A20.2J cells stably transfected with hCD40LMP1 were stimulated with 2 µg/ml anti-mCD40 Ab (CD40), anti-hCD40 Ab to trigger signaling through hCD40LMP1 (LMP1), or isotype control Abs for each (iso1 and iso2) for 48 h. Expression of CD23, CD80, and CD95 was determined by immunofluorescence staining and analyzed by flow cytometry. MCF, mean channel fluorescence. Values presented are the mean ± SEM of three independent experiments. (B) CH12.LX cells stably transfected with hCD40LMP1 were stimulated with Abs as in A for 72 h and assayed for IgM secretion. Plaque-forming cells (Pfcs, IgM-secreting cells) per 10⁶ viable recovered cells are shown. Values presented are the mean ± SE of replicate samples. Data are representative of three independent experiments. (C) TRAF3⁻/⁻ CH12.LX cells stably transfected with hCD40LMP1 were stably supertransfected with an IPTG-inducible TRAF3 (Reconstituted TRAF3⁻/⁻). Reconstituted cells were preincubated in the absence (−IPTG) or presence of IPTG (+IPTG) for 24 h and stimulated with Abs as in B in the absence or presence of IPTG, whereas TRAF3⁻/⁻ cells were stimulated with Abs as in B in the absence of IPTG. IgM-secreting cells were enumerated as in B. Values presented are the mean ± SE of replicate samples. Data are representative of three independent experiments. (D) Expression of TRAF3 in the reconstituted TRAF3⁻/⁻ CH12.LX cells (Recon.) in the absence (−) or presence of IPTG (+IPTG), compared with that of WT (+/+) and TRAF3⁻/⁻ (−/−) cells, was analyzed by immunoblotting. An immunoblot for actin served as loading control.", "figure_related_sentences": "Effects of TRAF3 Deficiency on Effector Functions. Next, we determined if the effects of TRAF3 deficiency on early signaling pathways of CD40 and LMP1 are predictive of downstream B cell effector functions, including upregulation of surface molecules and secretion of cytokines and antibodies. After CD40 engagement, TRAF3-deficient A20.2J cells exhibited upregulation of CD23 and CD95 similar to that of WT cells (summarized in Figure 3A; representative histograms shown in Figure S7, available at http://www.jem.org/cgi/content/full/jem.20031255/DC1). Although we consistently observed a partial increase in CD40-mediated upregulation of CD80 in TRAF3⁻/⁻ B cells (Figure 3A), it may be due to clonal variation because different A20.2J subclones vary in this response (not depicted). Using the mCD40-elicited response as an internal control for each subclone, we found that LMP1-induced upregulation of CD23 and CD80 was reduced approximately two- and threefold, respectively, whereas upregulation of CD95 and MHC class II was not affected by TRAF3 deficiency in A20.2J cells (Figure 3A and Figure S7).For detection of cytokine secretion, the membrane ligands for hCD40 and mCD40 (hCD154, mCD154, respectively) were also used, as they are more potent activators of this specific function of CD40. Although mCD154 is capable of activating hCD40 to a certain extent (39), cross-reaction between hCD154 and mCD40 is negligible (21). Neither CD40- nor LMP1-mediated secretion of TNF and IL-6 was affected by TRAF3 deficiency in CH12.LX cells (Figure S8, available at http://www.jem.org/cgi/content/full/jem.20031255/DC1). Interestingly, TRAF3⁻/⁻ CH12.LX cells exhibited enhanced IgM secretion after CD40 engagement, but profoundly suppressed IgM secretion in response to LMP1 signaling as compared with TRAF3⁺/⁺ cells (Figure 3B). We further verified this observation by examining TRAF3⁻/⁻ CH12.LX cells reconstituted with an IPTG-inducible TRAF3. Induction of TRAF3 expression with IPTG completely restored IgM secretion in response to LMP1 signaling, while decreasing IgM secretion mediated by CD40 signaling (Figure 3C and D). These results extend our previous finding that overexpression of TRAF3 decreases CD40-mediated IgM secretion (29), and in contrast, highlight the importance and indispensability of TRAF3 in LMP1-induced B cell activation. Furthermore, we also stably transfected an IPTG-inducible full-length LMP1 into WT and TRAF3⁻/⁻ B cells. A similar requirement for TRAF3 was observed when the signal was delivered by inducible full-length LMP1 (unpublished data).", "inconsistent_part": "related_sentences", "tampered_sentences": ["Although we consistently observed a partial increase in CD40-mediated upregulation of CD80 in TRAF3⁻/⁻ B cells (Figure 3A)"], "golden_sentences": ["Although we consistently observed a partial decrease in CD40-mediated upregulation of CD80 in TRAF3⁻/⁻ B cells (Figure 3A)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010011326_TII_02/figure/2010011326_TII_02_2.png"], "tampered": true, "paper_ids": ["2010000405"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010104844_TII_02/figure/2010104844_TII_02_3.png", "question_id": "consistency_40", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 4 The effects of hydrogels on skin wound healing in type 2 diabetes mellitus (T2D) by topical treatment. (A) Representative images of wounds in the normal control (NC) group, T2D group, CAH (T2D+CAH) group, and CAVBPH (T2D+CAVBPH) group on days 0, 3, 9, and 15. (B) Wound healing rate. *p < 0.05, **p < 0.01, and ***p < 0.001.", "figure_related_sentences": "As shown in Figure 4A, the wound size in all groups decreased gradually over time. Compared with the NC group, the T2D group displayed a slower wound shrinkage due to the influence of diabetes, and exudate was still found on the wound surface on day 9. Topical application of CAH and CAVBPH significantly accelerated diabetic wound recovery compared to the T2D group. Quantitative analysis of wound healing confirmed the above results (Figure 4B). The healing rate in the T2D group was more optimistic than that in the NC group (p < 0.01 or p < 0.001). Compared to the T2D group, the CAH group showed a better healing effect on days 9 and 15 (p < 0.001), while the CAVBPH group had the best wound shrinkage than the T2D and CAH groups on all observed days (p < 0.01 or p < 0.001). At day 15, the wounds of the CAVBPH group (96.55% of healing rate) and the NC group (91.77% of healing rate) were basically healed and covered with hair, while the healing rates of the CAH and T2D groups were 84.23% and 63.81%, respectively. Compared to the T2D and CAH groups, the CAVBPH group had the best curative effect, with a 96.55% wound healing rate on day 15 (Figure 4).", "inconsistent_part": "related_sentences", "tampered_sentences": ["The healing rate in the T2D group was more optimistic than that in the NC group (p < 0.01 or p < 0.001)"], "golden_sentences": ["The healing rate in the T2D group was less optimistic than that in the NC group (p < 0.01 or p < 0.001)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010104844_TII_02/figure/2010104844_TII_02_3.png"], "tampered": true, "paper_ids": ["2010000410"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010184705_TII_02/figure/2010184705_TII_02_0.png", "question_id": "consistency_41", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. Telomeric element HeT-A expression is downregulated in ovaries by Trf2, Woc and Ars2. (A) RT-qPCR analysis of TE expression in ovaries of Trf2KDnos, wocKDnos and Ars2KDnos. (B) HeT-A transcript abundance in ovaries of Trf2/Trf2, spnE/spnE and Trf2,spnE double mutants. The fold change in the HeT-A RNA level is shown. (C) NRO analysis of HeT-A transcription in ovaries of Trf2KDnos, wocKDnos, Ars2KDnos and piwiKDnos flies. The RNA level was normalized to rp49. Mean values (±SD) for three biological samples normalized to control knockdown (white(w)KDnos) are shown. (D) In situ RNA hybridization of HeT-A, TART or TAHRE antisense probes with ovaries of the indicated genotypes (GAL4-nos driver was used). (E) RNA FISH of HeT-A antisense probe with ovaries of the indicated genotypes. The accumulation of HeT-A transcripts (green) in nuclei of nurse cells was observed. DNA was stained with DAPI (blue). GAL4-nos driver was used.", "figure_related_sentences": "RESULTS Trancription factors Woc and Trf2 suppress telomeric repeat HeT-A transcription in ovaries In order to detect germline components contributing to telomeric homeostasis, we performed a selective RNAi screen for factors that downregulate HeT-A expression in Drosophila ovaries. This approach was based on the existing data that in somatic tissues certain factors of the telomeric complex are required for the silencing of telomeric repeats (34–36). As reported earlier, HP1, encoded by Su(var)205 gene, a component of the telomere protection complex (37,38), elicits transcriptional repression of telomeric retrotransposons both in soma (34) and in the germline (39,40). At the same time, transcription of telomeric and non-telomeric transposons in the germline is controlled by the piRNA system, supporting the idea that the telomeric complex in the germline consists of both germline-specific and ubiquitous components. To investigate the structure of telomeric chromatin in the germline, we examined HeT-A expression in the ovaries of flies depleted for known components of the somatic telomeric complex as well as factors involved in RNA surveillance. Here, we describe genes exerting the greatest effect on telomeric repeat expression in ovaries. Germline knockdown of several genes, previously implicated in telomere functioning in soma, did not noticeably affect HeT-A expression in our screen and were not included in further analysis (Supplementary Table S2). In parallel to an independent study that describes Trf2 as a negative regulator of telomeric transposon expression in somatic tissues (41), we demonstrated that Trf2 is associated with the polytene chromosome telomeres of salivary glands (Supplementary Figure S1) and discovered a role of Trf2 in telomere functioning in the germline. RT-qPCR analysis of telomeric and non-telomeric retrotransposon expression demonstrated decreased levels of HeT-A and TAHRE transcripts in ovaries upon germline knockdown of Trf2 (Trf2KDnos; nos designates the promoter of the germline-specific gene nanos that was used to express the Gal4 driver) (Figure 1A). Given that the HeT-A and TAHRE untranslated regions (UTR) are highly homologous (7), we suggest that Trf2 recognizes a similar sequence motif in the promoter regions of both elements. In order to determine if Trf2 functions in the piRNA pathway together with spindle-E (encoding DEAD box RNA helicase SpnE) to silence HeT-A, we applied a double mutant analysis. We used a viable Trf2p1 mutation (26) to generate Trf2/Trf2; spnE/spnE double mutants and compared HeT-A transcript abundance in their ovaries to that in ovaries of single Trf2/Trf2 or spnE/spnE mutants. HeT-A expression in the double mutants was higher than in Trf2 single mutants, but not in spnE single mutants (Figure 1B, Supplementary Figure S2). This could mean that in the absence of piRNAs, inhibitory complex containing Trf2 cannot be recruited to the HeT-A promoter. Northern blotting of short RNA did not reveal changes in the abundance of HeT-A-specific piRNA in ovaries of Trf2 mutants and Trf2KDnos flies (Supplementary Figure S3A). These data suggest that Trf2 may act downstream of piRNA processing to establish transcriptional silencing of HeT-A. The zinc finger transcription factor Woc has been shown to bind Drosophila telomeres, exerting telomere-capping functions (42). wocKDnos causes a strong derepression of HeT-A and TAHRE but not TART and other TEs (Figure 1A), suggesting sequence-specific binding of this transcription factor to telomeric repeats in ovaries. We extended the analysis of the telomeric protein complex by including an RNA binding protein, Ars2, involved in mi- and siRNA biogenesis (43), which was identified in an RNAi screen as a negative regulator of HeT-A expression (44). Particular interest in this protein was due to the fact that Ars2 downregulates the expression of human TERRA (45). RT-qPCR analysis revealed a strong derepression of HeT-A/TAHRE in ovaries of Ars2KDnos flies (Figure 1A). To address the question about the involvement of Trf2, Woc and Ars2 in the transcriptional regulation of HeT-A, we conducted an NRO assay, which allows estimating the level of nascent HeT-A transcripts (46). NRO on ovaries with Trf2, woc and Ars2 knockdowns demonstrates that all these factors provide transcriptional silencing of the telomeric retrotransposon HeT-A (Figure 1C). In situ RNA hybridization analysis was performed to examine the effect of Trf2, Woc and Ars2 depletion on telomeric retroelement transcript distribution in ovaries (Figure 1D, Supplementary Figure S4). Knockdowns of Trf2, Woc and Ars2 exerted the most pronounced effect on HeT-A and TAHRE expression, resulting in the accumulation of their transcripts in nurse cells. The RNA FISH analysis on ovaries depleted for Trf2, Woc and Ars2 revealed HeT-A RNA signals not only in the cytoplasm, but also in the nuclei of nurse cells, where HeT-A transcripts were accumulated in distinct foci (Figure 1E). Similar nuclear foci were observed in spnEKD ovaries (Figure 1E). Previously, using combined DNA/RNA FISH analysis, it was shown that both HeT-A RNA and telomeric DNA were co-localized in nurse cell nuclei in spnE mutants (19). Most likely, we observed the accumulation of nascent transcripts at sites of transcription upon Trf2, Woc and Ars2 knockdown, in accordance with the result of NRO. Taking into account the HeT-A/TAHRE-specific effects of Woc and Trf2, it is unlikely that these factors participate in piRNA biogenesis. However, it is possible that DNA-binding factors Woc and Trf2 are involved in the piRNA-mediated transcriptional silencing mechanism that is specific for telomeric repeats. Thus, HeT-A transcripts accumulated upon Ccr4-Not knockdown avoid piRNA-mediated degradation. In situ RNA hybridization on Ccr4, Pop2 and Not1 KD ovaries revealed HeT-A transcripts in nurse cells (Figure 2C). Importantly, RNA FISH revealed HeT-A RNA foci in the nuclei of twinKDnos nurse cells (Figure 1E) as well as upon Trf2, Woc, Ars2 and SpnE knockdown, suggesting that all these components regulate the telomeric transcript level at the site of transcription. Given the accumulation of HeT-A transcripts in the nuclei upon Ccr4 depletion (Figure 1E), we investigated the poly(A) tail length of the HeT-A RNA in the nuclear fraction of ovarian RNA upon germline knockdown of Ccr4. The PAT assay demonstrated that in the nuclei of control ovaries, HeT-A transcripts were not adenylated, while Ccr4 KD led to an increase in HeT-A poly(A) length in the nucleus (Figure 3C).", "inconsistent_part": "related_sentences", "tampered_sentences": ["RT-qPCR analysis of telomeric and non-telomeric retrotransposon expression demonstrated decreased levels of HeT-A and TAHRE transcripts in ovaries upon germline knockdown of Trf2 (Trf2KDnos; nos designates the promoter of the germline-specific gene nanos that was used to express the Gal4 driver) (Figure 1A)"], "golden_sentences": ["RT-qPCR analysis of telomeric and non-telomeric retrotransposon expression demonstrated increased levels of HeT-A and TAHRE transcripts in ovaries upon germline knockdown of Trf2 (Trf2KDnos; nos designates the promoter of the germline-specific gene nanos that was used to express the Gal4 driver) (Figure 1A)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010184705_TII_02/figure/2010184705_TII_02_0.png"], "tampered": true, "paper_ids": ["2010000418"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010011530_TII_02/figure/2010011530_TII_02_4.png", "question_id": "consistency_42", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Agrin-mediated decrease in gap junction–dependent intercellular communication between chromaffin cells in neonates. (A) Reduced number of electrically and LY-coupled chromaffin cells in neonatal agrin-treated slices. *, P ≤ 0.01 when compared with control slices. (B) Monitoring of electrical coupling between chromaffin cell pairs in control and agrin-containing saline showing examples of robust and weak coupling. Cells were current-clamped at −65 mV. A weak coupling was less frequently observed in agrin-treated slices. (C) Histograms illustrating the wide distribution range of the coupling ratio calculated in 26 control and 18 agrin-treated cells from voltage-clamp measurements of Ij (holding potential −60 mV, transjunctional potential from −120 to −60 mV, 150 ms duration). Insets: pooled data of Gj calculated in 11 control cell pairs and 4 agrin-treated cell pairs.", "figure_related_sentences": "Studies were next undertaken to examine the effect of agrin on both gap junction–mediated electrical and metabolic coupling between neonate chromaffin cells. Metabolic coupling was assessed using Lucifer yellow (LY) to label coupled cells, whereas electrical coupling was evidenced by dual whole-cell patch-clamp recording of intercellular macroscopic junctional currents (Ij). The probability of LY spreading between chromaffin cells was significantly reduced in agrin-treated slices compared with untreated slices (31% vs. 57%, P ≤ 0.01; Figure 5A). In the presence of the anti–rat agrin-neutralizing pAb, agrin failed to decrease LY diffusion between neonate chromaffin cells (58.3%, n = 24; unpublished data). Similarly, the dye coupling was not modified by inactive agrin0,0 (61.5%, n = 13; unpublished data). In adults, agrin did not change the incidence of LY diffusion (37.9% in treated slices, n = 29 vs. 44% under control conditions, P > 0.01; unpublished data). Agrin decreased the percentage of electrically coupled cell pairs (53.8%, n = 26 pairs in control slices vs. 22.2%, n = 18 pairs in agrin-treated slices, P ≤ 0.01; Figure 5A). In addition, agrin reduced the incidence of robustly coupled cells (Figure 5B). The voltage changes in response to depolarizing current injected into the stimulated cell were robustly reflected in the unstepped cell in 64.3% (n = 9/14 cell pairs) and 50% (n = 4 cell pairs) in control and agrin-treated slices, respectively (P ≤ 0.01). The resulting coupling ratios exhibited a wide distribution range from 0.01 to 0.97 (Figure 5C), strongly suggesting the presence of two chromaffin cell populations—a weakly coupled cell population and a highly coupled cell population. Recordings of Ij in chromaffin cell pairs voltage clamped at −60 mV confirmed these findings (unpublished data). Delivering voltage steps with command pulses of both polarities triggered Ij in the unstepped cell that exhibited variable degrees of attenuation. In control slices, 81.8% of recorded pairs (n = 11) exhibited Ij amplitudes that could reach 1–2 nA, whereas in the remaining pairs Ij did not exceed several picoamperes. In agrin-treated slices, the percentage of coupled cell pairs exhibiting a high Ij amplitude dropped to 50%. When plotted as a function of the transjunctional potential, the I/V curve of Ij displayed a linear relationship within the membrane potential range of −60 to −120 mV. The curve used to fit the data was derived from a linear regression, giving a macroscopic junctional conductance (Gj) of 43 and 60 pS for the weak coupling and 12 and 13 nS for the robust coupling (Figure 5C, insets).", "inconsistent_part": "caption", "tampered_sentences": ["A weak coupling was less frequently observed in agrin-treated slices."], "golden_sentences": ["A robust coupling was less frequently observed in agrin-treated slices."], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010011530_TII_02/figure/2010011530_TII_02_4.png"], "tampered": true, "paper_ids": ["2010000421"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010007150_TII_02/figure/2010007150_TII_02_1.png", "question_id": "consistency_43", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "FIGURE 2. Fold enrichment of selenoprotein mRNAs on UPF1 in low versus high Se.(A) Levels of selenoprotein mRNAs that coprecipitated with UPF1, following culturing HEK293T cells in 3 nM Se or 60 nM Se. Transcript levels are normalized to a synthetic in vitro transcribed RNA and then to the value of the corresponding sample from the total RNA extraction (see Methods; Supplemental Fig. S3).(B) UPF1 protein levels in 3 nM Se or 60 nM Se.(C) Quantitation of (B). Error bars represent standard deviation of the mean; n = 4 for (A), and n = 6 for (B) and (C); (*) P < 0.05.", "figure_related_sentences": "We reasoned that if the transcripts that decreased in low Se were undergoing NMD, then they should similarly be enriched on UPF1. The same experiment modeling conditions of low Se was repeated, and RNA immunoprecipitation was performed with UPF1. The cytoplasmic nucleoprotein complexes were coimmunoprecipitated with an anti-UPF1 antibody, followed by quantification of coimmunoprecipitated RNAs by qRT-PCR. A representative set of RNAs from each category of NMD susceptibility was analyzed, including those most responsive to Se status (SelW, SelP, GPx1), as well as GPx4, which has been consistently unresponsive to Se status in past research. Interestingly, all of the selenoprotein mRNAs analyzed coimmunoprecipitated with UPF1 to some degree in agreement with UPF1’s general role in translation (Ghosh et al., 2010). A strikingly similar pattern to the profile in Figure 1A was observed in response to Se status. In this case, the RNAs predicted resistant to NMD showed a difference in their abundance on UPF1 with respect to Se. The RNAs that were the most responsive to Se status, however, were also the less abundantly bound to UPF1 under conditions of low Se (Fig. 2A). Importantly, UPF1 did not change with Se, ruling out the possibility that changes in immunoprecipitated RNAs could have been due to changes in total UPF1 protein (Fig. 2B, C). Overall, the degree of mRNA responsiveness to Se status directly correlated with the degree of mRNA abundance on UPF1, suggesting the involvement of NMD in the regulation of selenoprotein mRNAs during Se deficiency.", "inconsistent_part": "related_sentences", "tampered_sentences": ["RNAs predicted resistant to NMD showed a difference in their abundance on UPF1 with respect to Se", "were also the less abundantly bound to UPF1 under conditions of low Se (Fig. 2A)"], "golden_sentences": ["RNAs predicted resistant to NMD showed no difference in their abundance on UPF1 with respect to Se", "were also the most abundantly bound to UPF1 under conditions of low Se (Fig. 2A)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010007150_TII_02/figure/2010007150_TII_02_1.png"], "tampered": true, "paper_ids": ["2010000422"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010011652_TII_01/figure/2010011652_TII_01_6.png", "question_id": "consistency_44", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "3D fibronectin matrix reduces both Rac activity and random migration. (A) Primary human fibroblasts were plated on 2D substrates coated with fibronectin or 3D matrices rich in fibronectin and assayed for activity as in Figure 1. The reduction of active Rac in cells plated in a 3D matrix compared with 2D was 31% (P ≤ 0.017), whereas Cdc42 and Rho changes were not significant (Cdc42 4.5% reduction, P ≤ 0.66; Rho 25% increase, P ≤ 0.65). Error bars indicate SEM. (B) Cells in 2D versus 3D environments have different morphologies and locations of lamellae (arrowheads), as shown after staining for F-actin with phalloidin-Alexa 594 (left and red color in the right) and anti-fibronectin antibody (green). Bar, 20 μm. (C) Migration of cells in 2D versus 3D environments was recorded, and directionality (D/T) and velocity were calculated. (C and D) Error bars represent SEM. (D) Decreased random motility of cells within three-dimensional (3D) matrix. Primary human fibroblasts were cultured overnight within intact 3D matrices, on mechanically flattened 3D matrix (2D matrix), or on surfaces coated with solubilized 3D matrix (2D mix). Cell movements were recorded for 10 h, and the D/T ratio and velocity were calculated as described above. (E) Activated Rac in cells in 3D matrix restores random motility. Primary human fibroblasts were cotransfected with Rac Q61L VSV and Rac Q61L GFP or GFP alone (Control), sorted for low levels of GFP expression (1–50% from the peak of positive cells), and plated on 3D matrices. Cell movements were recorded for 10 h, and the D/T ratio and velocity were quantified. The bars represent the means of data pooled from two experiments, and error bars indicate SEM (n = 32–34 cells).", "figure_related_sentences": "Cells migrating in 3D cell-derived matrices have different types of cell adhesions, morphology, and signaling when compared with cells in standard 2D tissue culture (Cukierman et al., 2001; Walpita and Hay, 2002). Human fibroblasts in such 3D matrices were found to have a partial, but highly reproducible, 10–50% reduction in active Rac, but no reduction or increase in Cdc42 or Rho activities (Figure 7A). This reduction in Rac activity was accompanied by decreased random migration (Figure 7C and Video 3), with directional persistence increasing from D/T₂ᴰ = 0.25 ± 0.03 to D/T₃ᴰ = 0.87 ± 0.02 (P < 0.0001). Individual cells in the 3D matrix became spindle shaped as previously described (Cukierman et al., 2001), but in addition, staining for F-actin revealed a substantial reduction in peripheral lamellae in 3D compared with 2D (Figure 7B). In contrast to the results in cells cultured on 2D substrates, there was a significant increase in overall cell migration velocity by 34% associated with the reductions in active Rac and random migration in a 3D environment (Figure 7C; P < 0.0001). These findings further indicate the separate regulation of speed and directionality. Because the differences between 2D fibronectin and 3D substrates could have been the result of either three dimensionality or of differences in molecular composition, the 3D matrix was converted to 2D as a direct test of the role of dimensionality. Physically flattening 3D cell-derived matrices by compression still retained the increased overall velocity, but it was accompanied by a restoration of random motility (Figure 7D; P < 0.0001). Moreover, solubilizing the matrix and spreading its mixed components on a 2D substrate showed the same restoration of random motility (Figure 7D; P < 0.0001), with migration rates similar to those on 3D matrix (no statistically significant difference). These analyses indicate that the increased directionality in 3D is related to the three dimensionality of the matrix, and that it is unrelated to cell migration speed.", "inconsistent_part": "related_sentences", "tampered_sentences": ["10–50% reduction in active Rac, but no reduction or increase in Cdc42 or Rho activities (Figure 7A)", "with directional persistence increasing from D/T₂ᴰ = 0.25 ± 0.03 to D/T₃ᴰ = 0.87 ± 0.02 (P < 0.0001)"], "golden_sentences": ["30–50% reduction in active Rac, but no reduction or increase in Cdc42 or Rho activities (Figure 7A)", "with directional persistence increasing from D/T₂ᴰ = 0.48 ± 0.03 to D/T₃ᴰ = 0.87 ± 0.02 (P < 0.0001)"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010011652_TII_01/figure/2010011652_TII_01_6.png"], "tampered": true, "paper_ids": ["2010000578"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010183324_TII_02/figure/2010183324_TII_02_4.png", "question_id": "consistency_45", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Fig. 5. Electrophoretic mobility shift assay results for the AZRE. (A) Sequence-specific interaction of nuclear proteins with the AZRE. The 23 bp AZRE containing a fragment between nucleotides –190 and –168 relative to the transcription start site of Oshsp17.3 was radiolabelled, and 1 ng of the probe was incubated with 10 µg of the nuclear proteins prepared from rice etiolated seedlings under AZC treatment for 6 h. The positions of the DNA–protein complexes are shown as C1 and C2 by arrows. The free probe is indicated with an asterisk (*). (B) Effect of CHX on the interaction of nuclear proteins with the AZRE. Three-day-old rice seedlings were treated with CHX (2 µg ml⁻¹) and with (left) or without (right) AZC for 6 h. (C) Cross-competition analysis of the HSE. The 23 bp HSE-containing fragment located at –87 to –65 relative to the transcription start site of Oshsp17.3 was used as a competitor. (D) Stress-dependent interaction of nuclear proteins with the AZRE. Nuclear extracts were prepared from seedlings treated with AZC, As, or HS for 2 h and by 28 °C [control (C)] or Cd for 6 h.", "figure_related_sentences": "Specificity of nuclear proteins interacting with the 9 bp AZRE in vitro by EMSA. To characterize the putative AZRE further, EMSA was used to determine whether it can interact with trans-acting factor(s) present in nuclear extracts. A 23 bp synthetic oligonucleotide encompassing the AZRE was used as a probe and was labelled with 32P by T4 polynucleotide kinase. Then, the probe was incubated with nuclear extracts from AZC-treated rice seedlings. Two DNA-bound protein bands (C1 and C2) were detected on the gel (Fig. 5A). The intensity of C1 appeared to be stronger than that of C2, and C1 could be further competed out by a 200-fold excess of AZRE probe without a 32P label. In addition, nuclear extracts from seedlings treated with AZC plus CHX for 6 h or CHX alone did not affect the levels of C1 and C2 interacting with the AZRE (Fig. 5B), which suggests that de novo synthesis of proteins is not required for the interaction. Because the 9 bp AZRE is involved in the HSR, it was also tested whether the 9 bp AZRE could be cross-competed by an HSE. This 23 bp HSE probe encompasses a perfect HSE (CTTCTAGAAACTTCC). Interestingly, the C2 but not the C1 band could be competed out by a 200-fold excess of HSE without being 32P labelled (Fig. 5C). Nevertheless, these results show that the AZRE can be specifically recognized by the nuclear proteins from AZC-treated rice seedlings. Because the AZRE was required for the response to HS and AZC, EMSA was used to examine whether nuclear extracts from rice seedlings treated with different inducers can bind to the AZRE. In nuclear extracts from seedlings treated with As (2 h), Cd (6 h), HS (2 h), or AZC (2 h), the two DNA–protein complexes C1 and C2 were also detected in all extracts, including control extracts (Fig. 5D). Additionally, the C1 band in the control was competed out by a 10-fold amount of the AZRE (Fig. 5D, first left lane). The intensity of the C1 complex with AZC treatment was found to be \\~5-fold higher than that of the control by measuring the integrated density with Scion image software. However, the intensity of the C2 band in 2 h AZC-treated and control nuclear extracts was lower than that in extracts receiving 6 h AZC, As, Cd, and HS treatments. Nevertheless, the results demonstrate that nuclear proteins from rice seedlings bind to the AZRE in a stress-dependent manner and depend on the duration of AZC treatment. Deletion of the AZRE on the promoter of Oshsp17.3 can reduce OsHsfA4b-modulated activation. According to the indispensable role of the AZRE for HS responsiveness (Fig. 3) and the results of EMSA (Fig. 5C), it was speculated that the AZRE can be specifically recognized by HSFs. Thus, tests were conducted to determine whether the AZRE was necessary for the interaction between OsHsfs and the promoter of Oshsp17.3. According to the expression analysis of 23 rice HSF genes, OsHsfA4b (Os01g54550) and OsHsfB4b (Os07g44690) were found to be induced by AZC treatment (data not shown). Two effector constructs, pHsfA4b and pHsfB4b, under the control of the maize constitutive Ubi1 promoter, were made (Fig. 6A). GUS activity in coleoptiles co-transformed with one reporter (p567 or p567DAZRE) and one effector (pHsfA4b or pHsfB4b) construct at a ratio of 1:1 was compared. As shown in Fig. 6B, when co-transformed with pHsfA4b, p567 achieved 2.8-fold induction in relative GUS activity but p567DAZRE achieved only a 1.8-fold induction. However, co-transformation of pHsfB4b was not significantly induced on p567 or p567DAZRE. To confirm these results further, the p631 reporter construct was also co-bombarded with pHsfA4b or pHsfB4b and no effect on the non-AZC-inducible Oshsp16.9A promoter was found (1.3- and 1.5-fold induction, respectively) (Fig. 6B). Also, transient expression of another highly AZC-inducible HSF gene, OsHsfC1b (Os01g53220), had no effect on the activation of Oshsp17.3 and Oshsp16.9A (data not shown). Thus, HSFs are possibly an integral part of the AZRE-dependent induction pathway of sHSP-CIs. The differential transcription of sHSP genes may have resulted from the action of different kinds of HSFs or additional transcription factors responding to environmental stresses (Rojas et al., 2002). Two DNA–protein complexes (C1 and C2) were observed by EMSA. Both of the interaction complexes can be competed out by cold AZRE, which indicates that the AZRE–protein interactions are sequence specific and may involve two distinct trans-acting proteins (Fig. 5A). Also, nuclear extracts from untreated AZRE (Fig. 5D), and the level of bound proteins was not affected by CHX (Fig. 5B). These data show that de novo protein synthesis was not required for the trans-acting factors recognizing the AZRE, and thus these factors constitutively exist in the cells. However, nuclear extracts prepared from seedlings treated for 6 h with AZC, Cd, As, or HS showed a lower intensity of C1 and C2 than those from control seedlings (Fig. 5D), which suggests that the AZRE may interact with nuclear proteins in a stress-dependent manner. However, whether trans-acting factor(s) directly sense AZC or are only indirectly activated by AZC needs further study. Interestingly, it was also found that the AZRE was indispensable for HS activation of Oshsp17.3 and Oshsp18.0 in the transient expression system (Fig. 3), that the C2 band can be competed out by the HSE (Fig. 5C), and that HS strongly boosted both C1 and C2 signals (Fig. 5D). These data are in agreement with the observation of Sugio et al. (2009), who showed HSFs to be involved in the AZC response in Arabidopsis. Among the HSFs identified in rice, OsHsfA4b, OsHsfB4b, and OsHsfC1b show high AZC responsiveness (data not shown). Co-expression of OsHsfA4b in rice coleoptiles could activate both p567 and p567DAZRE constructs in the absence of AZC (Fig. 6B), but the induction level in p567 was 67% higher than that in p567DAZRE. In contrast,", "inconsistent_part": "related_sentences", "tampered_sentences": ["nuclear extracts prepared from seedlings treated for 6 h with AZC, Cd, As, or HS showed a lower intensity of C1 and C2 than those from control seedlings (Fig. 5D)"], "golden_sentences": ["nuclear extracts prepared from seedlings treated for 6 h with AZC, Cd, As, or HS showed a higher intensity of C1 and C2 than those from control seedlings (Fig. 5D)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010183324_TII_02/figure/2010183324_TII_02_4.png"], "tampered": true, "paper_ids": ["2010000586"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010127691_TII_02/figure/2010127691_TII_02_0.png", "question_id": "consistency_46", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. SDHB expression is high in CRC cell lines. (A) Quantitative RT-PCR analysis of SDHB mRNA expression in four colorectal cancer (CRC) cell lines compared to the normal colorectal epithelial cell line NCM460. (B) Semi-quantitative RT-PCR further confirms increased SDHB transcript levels in CRC cell lines relative to NCM460. (C) Western blotting analysis shows decreased SDHB protein expression in all four CRC cell lines compared to the normal epithelial control.", "figure_related_sentences": "SDHB is the key enzymatic component of mitochondrial enzyme SDH constructively expressed across species, which oxidizes succinate to fumarate in the TCA cycle and feeds electrons into the mitochondrial respiratory chain for ATP production. We examined SDHB mRNA and protein levels in four CRC cell lines and normal colorectal epithelial cell line NCM460. As shown in Figure 1 both SDHB mRNA level and protein level were relatively high in all four CRC cell lines (SW480, SW620, SW1116, and HT-29), compared to non-CRC epithelial NCM460 cells.", "inconsistent_part": "caption", "tampered_sentences": ["SDHB expression is high in CRC cell lines.", "(B) Semi-quantitative RT-PCR further confirms increased SDHB transcript levels in CRC cell lines relative to NCM460.", "As shown in Figure 1 both SDHB mRNA level and protein level were relatively high in all four CRC cell lines (SW480,"], "golden_sentences": ["SDHB expression is low in CRC cell lines.", "(B) Semi-quantitative RT-PCR further confirms reduced SDHB transcript levels in CRC cell lines relative to NCM460.", "As shown in Figure 1 both SDHB mRNA level and protein level were relatively low in all four CRC cell lines (SW480,"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010127691_TII_02/figure/2010127691_TII_02_0.png"], "tampered": true, "paper_ids": ["2010000588"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010016329_TII_02/figure/2010016329_TII_02_1.png", "question_id": "consistency_47", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Effects of KBrO3 on mtDNA copy number and topology. (A) Dot-blot of purified mtDNA from control cells and cells treated with 30 μM KBrO3. Oxidative damage is detected using an antibody against 8-oxodG by SouthWestern analysis and normalized against total mtDNA by Southern hybridization on a separate blot. (B) Dot-blot for antibody verification, showing control mtDNA and mtDNA treated in vitro with 7.4% H2O2 for 30 min. (C) Topology gel of mtDNA. KBrO3 treatment had no effect on mtDNA topology. 16.6, 16.6-kb linear molecules; CAT, catenanes; OC, open circles; SC, supercoiled mtDNA. (D) mtDNA copy number levels during the KBrO3 treatment time course. Despite the damage, mtDNA copy number is not unaffected by KBrO3.", "figure_related_sentences": "Although KBrO3 did not have as dramatic an effect on nuclear DNA damage signaling as UV or H2O2, it induced a marked increase in mtDNA damage (Figure 1A). The damage did not result in copy number depletion or any effect on the supercoiling of mtDNA (Figure 1, C and D).", "inconsistent_part": "caption", "tampered_sentences": ["mtDNA copy number is not unaffected by KBrO3."], "golden_sentences": ["mtDNA copy number is not affected by KBrO3."], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010016329_TII_02/figure/2010016329_TII_02_1.png"], "tampered": true, "paper_ids": ["2010000589"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010064451_TII_01/figure/2010064451_TII_01_0.png", "question_id": "consistency_48", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. Purification of chicken FANCD2, FANCI, FANCL andhuman UBE2T. (A) Purified chicken FANCD2 and FANCI, used forin vitro assays, were analyzed by 15% SDS-PAGE with CoomassieBrilliant Blue staining. Lane 1 indicates the molecular mass markers.Lanes 2 and 3 indicate purified FANCD2 and FANCD2 K563R,respectively. Lanes 4–9 indicate purified FANCI, FANCI K525R,FANCI R1288Q, FANCI Dx6, FANCI Dx6 K525R and FANCIEx6, respectively. (B) Purified human UBE2T, used for in vitromonoubiquitylation assays, was analyzed by 15% SDS-PAGE withCoomassie Brilliant Blue staining. Lane 1 indicates the molecularmass markers. Lane 2 indicates purified UBE2T. (C) PurifiedGST-tagged chicken FANCL, used for in vitro monoubiquitylationassays, was analyzed by 15% SDS-PAGE with Coomassie BrilliantBlue staining. Lane 1 indicates the molecular mass markers. Lane 2indicates purified GST-tagged FANCL.", "figure_related_sentences": "Chicken FANCI and FANCD3 were purified as recombinant proteins (Figure 1A, lanes 3 and 4), and the IDcomplex was prepared by mixing them in 1:1 stoichiometry. We also purified UBE2T and FANCL, which areknown as the E2 and E3 proteins for FANCD2monoubiquitylation, respectively, as recombinantproteins (Figure 1B and C).", "inconsistent_part": "related_sentences", "tampered_sentences": ["Chicken FANCI and FANCD3 were purified as recombinant proteins (Figure 1A, lanes 3 and 4)"], "golden_sentences": ["Chicken FANCI and FANCD2 were purified as recombinant proteins (Figure 1A, lanes 2 and 4)"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010064451_TII_01/figure/2010064451_TII_01_0.png"], "tampered": true, "paper_ids": ["2010000598"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010169000_TII_01/figure/2010169000_TII_01_5.png", "question_id": "consistency_49", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "FIGURE 6. Incorporation of single UV photoproducts increases nucleosome dynamics. A, schematic illustration of the incorporation of a single CPD or 6-4PP into the 601 sequence. The DFs are 12-mer oligonucleotides with the sequences shown. Solid triangles indicate the positions of the photoproduct. The dark circle represents Cy5, and the open circle represents Cy3. B, FRET changes for the single CPD containing NCPs. The 601 sequence was changed according to the DF and denoted 601.DF1. The left panel shows emission spectra for the CPD containing NCPs compared with undamaged NCPs. The right panel shows the FRET efficiency values determined in each case, where the value for 601.DF1 NCPs was set to 1. The values shown are the mean ± S.D. of three independent experiments. C, the same as B except the NCPs contained a single 6-4PP and the sequence denoted 601.DF2. D, relative FRET efficiency of salt dependence of NCPs containing a single CPD. The FRET efficiency at the lowest salt concentration (50 mM) was set to 1. Values are the mean ± S.D. of three independent experiments. E, salt titration profile of NCPs containing a single 6-4PP. Values were plotted the same as in D.", "figure_related_sentences": "Taining a single CPD or 6-4PP lesion is 4.6 nm and 4.2 nm, respectively. Furthermore, in each case, the FRET efficiency is reduced, indicating that the introduction of a single UV lesion in nucleosome DNA can increase NCP unwrapping. This supports the UV dose-dependent FRET change we observed with UV-irradiated NCP DNA (Figure 3). Moreover, NCPs with either a single CPD or 6-4PP are more sensitive to salt (Figure 6, D and E). In the range of 0–1 M salt concentrations, the FRET efficiency in NCPs with single UV lesions is significantly lower than that of undamaged NCPs, indicating that NCPs containing just one DNA photoproduct are significantly less stable with increasing salt.", "inconsistent_part": "related_sentences", "tampered_sentences": ["In the range of 0–1 M salt concentrations"], "golden_sentences": ["In the range of 0.25–1 M salt concentrations"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010169000_TII_01/figure/2010169000_TII_01_5.png"], "tampered": true, "paper_ids": ["2010000602"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010095497_TII_02/figure/2010095497_TII_02_0.png", "question_id": "consistency_50", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. Reduced PtdCho synthesis in CCTα-deficient macrophages. (A) Wild-type (WT; n = 12) or CCTα-deficient (KO; n = 12) macrophages were labeled for 6 h with 1 μCi/ml [3H]choline, and incorporation into PtdCho was normalized to cellular protein. (B) Relative transcript levels for CCTα, CCTβ2, CCTβ3, or PEMT were determined by real-time qRT-PCR in wild-type (n = 3) or CCTα-deficient (n = 3) macrophages. (C) CCT enzyme activity in wild-type (△; n = 4) or CCTα-deficient (●; n = 4) macrophage lysates was determined in vitro as a function of protein concentration. (D) Protein expression levels of CCTα (42 kD) and CCTβ3 (39 kD) were determined in wild-type and CCTα-deficient macrophage lysates (50 μg) by immunoblotting with isoform-specific antibodies. Immunoblots are representative of macrophages from two mice of each genotype. Cells (HEK293T) transfected with expression plasmids encoding CCTα or CCTβ3 were lysed, and 5 μg of protein was loaded as a positive control. Multiple immunopositive bands in a lane correspond to different phosphorylation states of the CCT protein (Jackowski, 1994; Lykidis et al., 1998). Error bars indicate mean ± SE. *, P < 0.05; **, P < 0.01.", "figure_related_sentences": "Mice with CCTα-null macrophages were generated as described previously (Zhang et al., 2000). Briefly, mice carrying a floxed Pcyt1a gene were crossed with mice expressing Cre recombinase under the macrophage-specific LysM promoter. Two loxP sites flanked a 12.5-kb fragment of the Pcyt1a gene containing exons 5–9 (Karim et al., 2003) and the intervening introns. Deletion of the region between the loxP sites resulted in expression of a truncated CCTα protein lacking the catalytic and regulatory domains at the carboxy terminus. Mice homozygous for the floxed gene and heterozygous for LysMCre were mated, and pups were genotyped to obtain either CCTα knockout or littermate wild-type control macrophages.Peritoneal macrophages were elicited, and the CCTα-deficient macrophage population showed increased rates of de novo phosphatidylcholine (PtdCho) synthesis measured by [?H]choline incorporation into the lipid fraction of adherent cells (Fig. 1 A). The deletion in this macrophage model was not completely penetrant (Zhang et al., 2000). Quantitative RT-PCR (qRT-PCR) analysis revealed that the CCTα transcript level was significantly increased to about 30% of wild-type levels (Fig. 1 B). The CCTα-null cells were ≥95% macrophages as determined by microscopy after staining with macrophage-specific anti–mouse CD11b. Staining for CCTα protein showed that 20–30% of macrophages isolated from knockout mice (n = 4) remained positive for expression, confirming incomplete Cre recombinase activity.Thus, residual PtdCho synthesis detected by metabolic radiolabeling in CCTα-null populations was due not only to expression of the alternate isoform CCTβ3 (Fig. 1 B) but also to the presence of cells that did not delete the CCTα gene. qRT-PCR showed that the CCTβ2 isoform was not expressed in macrophages, while CCTβ3 expression was increased in knockouts. CCTβ3 shares the primary biochemical function of CCTα and can compensate for its loss to support membrane synthesis in cultured cells (Karim et al., 2003). Previous work indicated increased CCTβ2 expression in CCTα-deficient cells (Zhang et al., 2000), but at that time, CCTβ3 had not been discovered; both isoforms share an epitope detected in earlier immunoblots (Karim et al., 2003).Total CCT enzyme activity was significantly higher in lysates from CCTα-null macrophages compared with wild-type populations (Fig. 1 C), consistent with previous studies (Zhang et al., 2000). Immunoblotting with isoform-specific antibodies revealed a decrease in CCTα protein and an increase in CCTβ3 protein reflecting mRNA changes (Fig. 1 D). Macrophages from two knockout and two wild-type mice were pooled by genotype, and immunoblots were prepared from six replicates per genotype. CCTα protein levels in the knockout population were 0.36 ± 0.08 relative to wild-type (set at 1.00). The reduction in CCTα transcript correlated with protein levels and the number of macrophages lacking CCTα expression by microscopy. These data confirm loss of CCTα expression in the majority of cells and provide the first example of adaptive regulation of CCTβ3 expression in response to PtdCho deficiency.", "inconsistent_part": "related_sentences", "tampered_sentences": ["and the CCTα-deficient macrophage population showed increased rates of de novo phosphatidylcholine (PtdCho) synthesis measured by [?H]choline incorporation into the lipid fraction of adherent cells (Fig.", "Quantitative RT-PCR (qRT-PCR) analysis revealed that the CCTα transcript level was significantly increased to about 30% of wild-type levels (Fig.", "Total CCT enzyme activity was significantly higher in lysates from CCTα-null macrophages compared with wild-type populations (Fig."], "golden_sentences": ["and the CCTα-deficient macrophage population showed reduced rates of de novo phosphatidylcholine (PtdCho) synthesis measured by [?H]choline incorporation into the lipid fraction of adherent cells (Fig.", "Quantitative RT-PCR (qRT-PCR) analysis revealed that the CCTα transcript level was significantly reduced to about 30% of wild-type levels (Fig.", "Total CCT enzyme activity was significantly lower in lysates from CCTα-null macrophages compared with wild-type populations (Fig."], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010095497_TII_02/figure/2010095497_TII_02_0.png"], "tampered": true, "paper_ids": ["2010000610"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010065412_TII_02/figure/2010065412_TII_02_1.png", "question_id": "consistency_51", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2. Differential inhibitory effects of SAUGI on the activities of (A) SAUDG, (B) EBVUDG, (C) HSVUDG, (D) human UDG and (E) TBUDG. Except for TBUDG, addition of SAUGI increased the specific uracil-removing activity of SAUDG and the other three UDGs in a dosage-dependent manner.", "figure_related_sentences": "The inhibiting effects of SAUGI on five UDGs We next used uracil removal assays to investigate the ability of SAUGI to inhibit the same five UDGs that were used in the surface plasmon resonance experiments. In the absence of SAUGI, all the UDGs removed the uracil from the uracil-containing DNA substrates effectively, and the resulting apyrimidinic site was cleaved by heat and alkali (Figure 2A-E, lane 2). The addition of SAUGI reduced the cleaved products in the SAUDG, EBVUDG, HSVUDG and human UDG reactions (Figure 2A-D, lanes 3–7; Supplemental Figure S4). SAUDG, EBVUDG and HSVUDG activity was initially inhibited when the molar ratio of SAUGI to UDG reached 1:1, but a ratio of 2:1 was needed for the inhibition of human UDG activity. Interestingly, although the structure of TBUDG is conserved relative to the other four UDGs, SAUGI had no significant effect on this UDG’s activity (Figure 2E). These results correspond to those found in the BIAcore study. We therefore conclude that SAUGI has a relatively greater effect on the two viral UDGs than on human UDG. Since HSVUDG and EBVUDG have been shown to play an important role during virus replication (29), these results suggest a potential use of SAUGI as an anti-virus treatment. The inhibitory effects of SAUGI mutants on the uracil-removing activities of human and HSV UDGs In our previous study, we found phage UGI had an extremely high binding affinity to human UDG that was 12–13 times greater than that of SAUGI (16). We found here that phage UGI also inhibited both HSVUDG and human UDG more effectively than SAUGI (compare Supplemental Figure S6 with Figure 2C and D). We speculated that SAUGI’s relatively low binding affinity to human UDG and its high binding affinity to viral UDG might potentially allow it to be used to prevent viral UDG repair activity without having too great an effect on human UDG. In our next experiment, we therefore used structural-based protein engineering to further modify SAUGI’s activity on human UDG and HSVUDG.", "inconsistent_part": "caption", "tampered_sentences": ["addition of SAUGI increased the specific uracil-removing activity of SAUDG and the other three UDGs in a dosage-dependent manner"], "golden_sentences": ["addition of SAUGI reduced the specific uracil-removing activity of SAUDG and the other three UDGs in a dosage-dependent manner"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010065412_TII_02/figure/2010065412_TII_02_1.png"], "tampered": true, "paper_ids": ["2010000662"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010065375_TII_01/figure/2010065375_TII_01_1.png", "question_id": "consistency_52", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2. HITS-CLIP reveals HIV-1 regions bound by Ago2 in HIV-1 infected cells. (A) HEK293T cells were transfected with plasmid expressing either GFP-Ago2 or control GFP. Twenty-four hours later, they were infected with VSVg-pseudotyped HIV-1 NL4-3 at a M.O.I. of 1 or mock infected. Twenty-four hours later, cells were subjected to UV cross-linking and RNA–protein complexes were subjected to immunoprecipitation using an anti-GFP antibody. IPed RNA was radiolabeled with [α-32P]ATP and samples resolved on SDS-PAGE. Radiolabeled RNA was visualized by autoradiography. RNAs migrating at a higher molecular mass than the protein of interest (GFP-Ago2:RNA, between 125 and 225 kDa) were extracted from the membrane, reverse transcribed into cDNA and subjected to high throughput sequencing. (B) Reads obtained from non-infected (NI) and infected (INF) samples were uploaded to CLIPZ software. Reads that aligned to the human genome were sorted into categories: messenger RNA (mRNA), microRNA (miRNA), ribosomal RNA (rRNA), repeat, small non-coding RNA (snRNA), small nucleolar RNA (snoRNA), transfer RNA (tRNA) and other. Pie charts correspond to the distribution of the mean value of three biological replicates. (C) Reads obtained from infected samples were aligned to the HIV-1 NL4-3 sequence. Only reads ≥50 nucleotides length that aligned once without mismatch were considered for this analysis. Reads obtained from three independent HITS-CLIP experiments are presented in shades of orange and those obtained from the corresponding inputs in shades of blue. The map of the HIV-1 genome is presented below. Splice donor (D) and acceptor (A) sites are indicated. Peaks corresponding to clusters 2, 13, 16, 21, 25 and 30 are indicated by arrows.", "figure_related_sentences": "Immunopurified RNAs were radiolabeled, separated on SDS-PAGE and transferred to nitrocellulose membrane. Autoradiograms revealed the presence of RNA–protein complexes migrating from 100 kDa, the expected size of GFP-Ago2, to higher molecular weights corresponding to the size distribution of RNAs associated with GFP-Ago2 (Figure 2A). The levels of RNAs cross-linked to GFP-Ago2 were similar in presence or absence of infection but were highly enriched compared to the control GFP immunoprecipitation, confirming the specificity of our IP conditions. Ago2-RNA complexes migrating between 125 kDa and 225 kDa, corresponding to nucleic acids up to 300 nucleotides length, were extracted from the nitrocellulose membrane. Ago2 cross-linked RNAs were purified and reverse transcribed to generate small cDNA Illumina libraries. cDNA ranging from 20 to 75 base pairs were purified for subsequent deep sequencing. Libraries were also generated from GFP control samples. However, the levels of cDNA obtained from these samples were not sufficient for subsequent deep sequencing. High throughput sequencing was conducted on small RNA libraries generated from six independent Ago2-GFP HITS-CLIP experiments prepared from either uninfected or HIV-1 NL4-3 infected cells and their corresponding inputs. HITS-CLIP experiments yielded between 15 and 24 million sequencing reads and inputs between 17 and 30 million sequencing reads (Table 1).Ago2 HITS-CLIP analysisTo assess the quality of our HITS-CLIP experiments, we first uploaded our sequencing reads to the CLIPZ software, specifically dedicated to HITS-CLIP data analysis (44). The number of distinct reads mapping to the human genome and the quality of the sequences were similar to other Ago2 HITS-CLIPs analyzed with the CLIPZ tool (data not shown). The alignment of reads in the input and in the HITS-CLIP experiments showed that whereas rRNAs, tRNAs and mRNAs were the predominant reads in the input (45%, 12% and 17%, respectively), a 5-fold enrichment of mRNAs, but not of snoRNAs, snRNAs, rRNAs or tRNAs, could be observed in the HITS-CLIP (Figure 2B). We did not observe any enrichment in miRNAs likely because our HITS-CLIP procedure favored long reads over short ones. We then sought to identify Ago2 binding sites on the viral gRNA. For this, HITS-CLIP data were analyzed in two different ways. First, trimmed reads longer than 15 nucleotides were aligned to the viral genome with a maximum of one mismatch allowed. Reads (≥50 nucleotides) of the HIV-1 RNA genome (starting at the transcription start site) from the three HITS-CLIPs (in orange) and their corresponding input (in blue) were plotted (Figure 2C). As the R region is present at both ends of the viral genome, the reads could not therefore be assigned unambiguously to the 3' or 5' ends. They were arbitrarily assigned at the 3' end of the viral genome. Several HIV-1 peaks were detectable in the input but whether they correspond to small RNA produced by the virus or degradation products was unclear. In Ago2 HITS-CLIP, we identified 40 discrete Ago2 binding sites along the viral genome with an accumulation of clusters at the central region and the 3' end of the genome (Figure 2C). Both analyses of our HITS-CLIP data gave very similar results as shown by the comparison of their mean traces (Supplementary Figure S2). We focused our interest on 31 clusters of reads based on the reproducibility of the peaks in the three HITS-CLIP experiments and the enrichment of reads in the IP over the input (Supplementary Figure S3 and Supplementary Table S1).Our study focused on HIV-1 RNA regions that correspond to Ago2 binding sites by only considering reads of 50 nucleotides length. We identified more than 40 reproducible binding sites distributed along the HIV-1 gRNA (Figure 2C). Remarkably, reads from viral origin represented <1% of the total reads in inputs, a result in agreement with other studies (22,30,32). In sharp contrast, between 8 to 25% of these long reads were from viral origin in our HITS-CLIP data, confirming that viral RNAs are preferentially enriched in Ago2 co-immunoprecipitation (Figure 1 and Table 1). Two recent reports have also explored the interaction between Ago proteins and HIV-1 RNAs using similar photoactivable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP) and HITS-CLIP approaches (22,32). Contrary to our study, Whisnant et al. detected very low levels of HIV-1 PAR-CLIP reads among the total of assignable reads (below 1%). This discrepancy could be due to differences in experimental conditions, as we used an overexpressed GFP-Ago2 together with stringent washing conditions in order to improve the efficiency and specificity of our immunoprecipitation conditions. Nevertheless, Whisnant et al. (22) identified a number of RISC clusters on HIV-1 RNA in infected TZM-bl HeLa and C8166 T cell lines. Importantly, our study identified 19 clusters that overlap with clusters identified in at least one of their two cell lines including cluster 2, 13, 16 and 21 (data not shown) indicating that these HIV-1 RNA regions are indeed conserved targets of endogenous Ago-RISC in different cell lines. In sharp contrast, viral RNAs were absent from Ago2-RISC in HIV-1 infected monocyte derived macrophages, suggesting that this interaction might be cell type specific (32). Nevertheless, we identified four HIV-1 clusters that were able to downregulate RLuc activity and we showed that these effects were dependent on both Ago1 and Ago2 proteins (Figure 3A and B). Interestingly, these four HIV-1 clusters are in close proximity or overlap HIV-1 splice donor sites (Figure 2C).", "inconsistent_part": "related_sentences", "tampered_sentences": ["Autoradiograms revealed the presence of RNA–protein complexes migrating from 100 kDa", "a 5-fold enrichment of mRNAs"], "golden_sentences": ["Autoradiograms revealed the presence of RNA–protein complexes migrating from 125 kDa", "a 2.5-fold enrichment of mRNAs"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010065375_TII_01/figure/2010065375_TII_01_1.png"], "tampered": true, "paper_ids": ["2010000668"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010131697_TII_01/figure/2010131697_TII_01_2.png", "question_id": "consistency_53", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. NTCP inhibition by Myrcludex B increases plasma bile acid and GLP-1 levels. (A) Unconjugated, conjugated, and total plasma bile acid levels 3 hours after placebo or Myrcludex B (2.5 mg/g) injection in male obese WT and Oatp1a/1b KO mice (n = 9–10). Mice were fed a HFD for 16 weeks and subsequently treated daily with placebo or Myrcludex B for 3.5 weeks. (B) Fasting GLP-1 levels and (C) plasma insulin levels (D) during an oral glucose tolerance test (2 g/kg glucose) and (E) an insulin tolerance test (1.2 mU/kg) of the Oatp1a/1b KO mice described in panel A. (F) Body temperature, measured by temperature transponders placed near the BAT of the mice in panel A. Per animal, average body temperature was calculated from 3 individual observations. (G) Ucp1 messenger RNA expression levels, determined by reverse transcription quantitative polymerase chain reaction in BAT of the Oatp1a/1b KO mice described in panel A. Reverse transcription quantitative polymerase chain reaction samples are relative to the geometric mean of control genes 36b4 and Hprt and were normalized to the placebo-treated group. (H) Quantified UCP-1 staining in sWAT of the Oatp1a/1b KO mice described in panel A. Error bars show SEM, asterisk indicates significant changes. AUC, area under the curve", "figure_related_sentences": "To evaluate the in vivo impact of bile acids on GLP-1 secretion, we used the NTCP inhibitor Myrcludex B to prolong bile acid signaling in obese Oatp1a/1b-deficient mice. Treatment with Myrcludex B was started 15 weeks after the onset of obesity by high-fat diet (HFD) feeding. In line with previous research, Oatp1a/1b KO mice display slightly elevated (unconjugated) bile acid levels compared with WT control animals (average WT 1.64 vs KO 6.13 mM of total bile acids) (Figure 1A). Myrcludex B treatment profoundly increased levels of total and conjugated bile acids in Oatp1a/1b KO mice 3–4 hours after the Myrcludex B injection (Figure 1A). The increase in plasma bile acids was temporary, as they completely normalized within 24 hours after the injection. Inhibition of NTCP by Myrcludex B increased fasting GLP-1 levels 10-fold (Figure 1B). Next, we evaluated if the Myrcludex B–mediated GLP-1 increase affected glycemic control. HFD-fed Oatp1a/1b KO mice treated with Myrcludex B tended to have lower insulin levels before and 15 minutes after oral glucose administration (Figure 1C). Although this suggested improved insulin sensitivity upon Myrcludex B treatment, the responses to glucose and insulin tolerance tests were not different between HFD-fed Oatp1a/1b KO mice receiving placebo or Myrcludex B treatment (Figure 1D and E). As it was recently shown that GLP-1 signaling can increase thermogenesis in brown adipose tissue (BAT), we assessed body temperature using temperature transponders placed near the BAT. Body temperature in HFD-fed OATP1a/1b KO mice treated with Myrcludex B significantly increased with an average of 0.9°C, while body temperature of placebo-treated animals remained unchanged (Figure 1F). Messenger RNA expression of Ucp1 (uncoupling protein 1), a mitochondrial gene known for its central role in BAT thermogenesis, in increased in BAT, suggesting increased thermogenesis in BAT of Myrcludex B treated HFD-fed OATP1a/1b KO mice (Figure 1G), but this increase was not observed at the protein level, and also, the UCP signal in subcutaneous white adipose tissue (sWAT) was not increased (Figure 1H), so “browning” of adipose tissue was not evident.", "inconsistent_part": "related_sentences", "tampered_sentences": ["Inhibition of NTCP by Myrcludex B increased fasting GLP-1 levels 10-fold (Figure 1B)."], "golden_sentences": ["Inhibition of NTCP by Myrcludex B increased fasting GLP-1 levels 4-fold (Figure 1B)."], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010131697_TII_01/figure/2010131697_TII_01_2.png"], "tampered": true, "paper_ids": ["2010000705"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010064913_TII_02/figure/2010064913_TII_02_0.png", "question_id": "consistency_54", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. Clk1 enhances SPF45-induced exon 6 exclusion from Fas mRNA. (A) SKOV3 cells were transfected with siRNA against SPF45 (siSPF45) or scrambled control siRNA (scr) for 72 h, and RNA was isolated. Endogenous Fas spliced isoforms were analysed by RT-PCR using primers flanking exon 6. PCR products representing mRNA including exon 6 [Fas (L)] and excluding exon 6 [Fas (S)] are shown and are quantified in the graph, with the ratio Fas (S) to Fas (L) set to one in the control siRNA group. The results are from three independent experiments performed in duplicate and were statistically significant. (B) Parallel cultures to those in (A) were lysed for western blotting using antibodies to SPF45 and actin. (C) Cell lysates from the indicated cell lines were immunoblotted for SPF45 using a polyclonal antibody to recombinant His-SPF45. COS-1 cells transfected with untagged SPF45 (COS-1, +con) and OV2008 cells expressing control or SPF45-specific shRNA served as positive controls. The SPF45 band (SPF45) and an SPF45 degradation product (degr.) in the positive control lane are labelled. (D) COS-1 cells were cotransfected with Myc-SPF45 (0.6 µg) and Clk1 (0.8 µg) and endogenous Fas spliced products were analysed by RT-PCR 24 h after transfection. A representative gel is shown. The means and SE for the relative ratio of exon 6 exclusion from three experiments done in duplicate are shown under the gel images. (E) Schematic of the Fas minigene splicing reporter used in transfection assays and the different mRNA isoforms derived from it, representing inclusion or exclusion of exon 6. (F) SPF45 expression induced exon 6 exclusion in a dose-dependent manner. COS-1 cells were co-transfected with Fas and increasing amounts of Myc-SPF45. Total RNA was extracted at 24 h and analysed by RT-PCR using Fas-specific primers. A representative gel from at least three independent experiments is shown, and the ratio of the lower band to the upper band is shown below the gel. The lower panel represents a western blot of Myc-SPF45 and actin protein expression from one experiment. (G) Clk1 overexpression promotes SPF45 alternative splicing activity. COS-1 cells were cotransfected with Fas (0.3 µg), Myc-SPF45 (0.6 µg) and Clk1 (0.8 µg), and spliced products were analysed by RT-PCR 24 h after transfection. A representative gel is shown. The means and SE for the relative ratios of exon 6 exclusion are shown under the gel images. Results were derived from three independent experiments done in duplicate. Statistical significance (P < 0.01) is indicated in the graph. (H) Clk1 overexpression enhanced SPF45 protein levels. Protein lysates were prepared from cells transfected as in (G) and were subjected to western blotting using antibodies to Myc, Clk1, and actin.", "figure_related_sentences": "SPF45 enhances exon 6 exclusion from Fas pre-mRNA in a cellular minigene assay (21,33). To determine whether endogenous SPF45 has a dissimilar effect on splicing of endogenous Fas pre-mRNA, we transfected SKOV-3 ovarian cancer cells with siRNA against SPF45. Seventy-two hours after transfection, RNA was harvested, and the endogenous Fas mRNA isoforms containing or excluding exon 6 were analysed by RT-PCR using primers flanking exon 6. SPF45 knockdown inhibited the splicing of the short Fas mRNA isoform (lacking exon 6) from Fas mRNA (Figure 1A). No other bands were detected on the gel. Immunoblotting of parallel cultures with an anti-SPF45 polyclonal antibody confirmed SPF45 knockdown (Figure 1B). This polyclonal antibody generated to recombinant SPF45 protein recognizes endogenous SPF45 from several ovarian cancer cell lines and HeLa cells, with specificity determined by comparison with lysate from COS-1 cells transfected with untagged SPF45 (COS-1 +con) and SPF45 shRNA knockdown in OV2008 cells (Figure 1C). Consistent with the above splicing results, transient transfection of SPF45 into COS-1 cells increased splicing of the short isoform of endogenous Fas mRNA, demonstrating enhanced exon 6 exclusion (Figure 1D). Clk1 is an SR protein kinase that phosphorylates splicing factors to regulate their localization and splice site utilization (19,20,22–24). To determine whether Clk1-regulated SPF45-dependent exon 6 exclusion from endogenous Fas mRNA, COS-1 cells were cotransfected with Clk1 and SPF45. Overexpression of Clk1 with SPF45 significantly increased exon 6 exclusion from endogenous Fas mRNA compared with transfection of SPF45 and empty vector (Figure 1D). We used our previously described Fas minigene (14,21), comprised of exon 5 through exon 7 of genomic Fas, including introns (Figure 1E), to study the effect of Clk1 on SPF45 splice site utilization. Cotransfection of COS-1 cells with Fas and increasing amounts of Myc-SPF45 plasmid caused a dose-dependent increase in exon 6 exclusion, shown as an increase in the lower band, demonstrating that our Fas minigene worked as a target of SPF45 in cells (Figure 1F) (21). COS-1 cells were chosen for minigene splicing assays owing to their low expression of endogenous SPF45 (Figure 1C), which allowed us to better determine SPF45-specific effects on alternative splicing of Fas mRNA. Clk1 was cotransfected into cells with SPF45 and the Fas minigene and exon 6 exclusion of Fas was determined. Clk1 enhanced SPF45-induced exon 6 exclusion of Fas by >50% (Figure 1G), suggesting that SPF45 may be a cellular target of Clk1. Interestingly, Clk1 overexpression also enhanced Myc-SPF45 protein expression (Figure 1H). As SPF45 concentration directly affects splice site utilization (Figure 1F), the enhancement of SPF45 expression by Clk1 could be a possible mechanism for the enhanced exon 6 exclusion and was investigated further. Clk1 inhibition prevents exon 6 exclusion by SPF45. To further determine the role of Clk1 kinase activity in regulating SPF45 exon 6 exclusion of Fas pre-mRNA, we generated a kinase-dead Clk1, Clk1-K233R, and cotransfected COS-1 cells with plasmids for SPF45 and Fas. Clk1-K233R decreased both SPF45-induced exon 6 exclusion (Figure 2A) and SPF45 protein levels (Figure 2B) compared with wild-type Clk1. To confirm this result, a selective Clk1 inhibitor, TG003 (41), was used to block endogenous Clk1 activity. TG003 not only promoted the increase of exon 6 exclusion induced by SPF45 (Figure 2C) but also decreased SPF45 protein expression (Figure 2D), similar to what was seen with kinase-dead Clk1 expression. Next, we used siRNA to knock down endogenous Clk1 expression. Transfection of cells with any of three different siRNA-targeting Clk1 led to a significant decrease in endogenous Clk1 mRNA and protein levels after 48 h, as determined by real-time PCR and western blot analysis, respectively (Figure 3A and B). The siRNA-mediated knockdown of Clk1 in COS-1 cells significantly decreased exon 6 exclusion in an SPF45-dependent manner (Figure 3C and D) and greatly inhibited Myc-SPF45 protein expression (Figure 3E), most likely contributing to the reduction in exon 6 exclusion. Inhibition of Clk1 decreases the half-life of SPF45 through a proteasome-dependent pathway. We suspected that the enhancement or inhibition of exon 6 exclusion by SPF45 with Clk1 activation or inhibition, respectively, was partially due to regulation of SPF45 protein levels, as SPF45 expression directly impacts exon 6 exclusion (Figure 1F). To determine whether Clk1 regulated the half-life of SPF45, A2780 ovarian cancer cells, which express high levels of endogenous SPF45 (Figure 1C), were treated with cycloheximide in the absence or presence of TG003 for 24 h (Figure 4A). TG003 significantly decreased the half-life of endogenous SPF45 from 15 to 8 h (Figure 4B). In addition, SKOV-3 ovarian cancer cells stably expressing Myc-SPF45 were treated with DMSO or TG003 in the presence of cycloheximide. Consistent with the aforementioned results, TG003 decreased the half-life of Myc-SPF45 from 16 to 7 h (Figure 4C and D). Moreover, knockdown of endogenous Clk1 with siRNA decreased endogenous SPF45 protein levels in both SKOV-3 and HeLa cells (Figure 4E). To determine whether the decrease in SPF45 half-life in the presence of TG003 was dependent on the proteasome, A2780 cells were treated with the proteasome inhibitor MG132 in the absence or presence of TG003 (Figure 4F). MG132 co-treatment with TG003 prevented the downregulation of SPF45 protein levels that was induced by TG003 treatment, indicating that Clk1 inhibition regulated SPF45 degradation through a proteasome-dependent pathway.", "inconsistent_part": "related_sentences", "tampered_sentences": ["TG003 not only promoted the increase of exon 6 exclusion induced by SPF45 (Figure 2C) but also decreased SPF45 protein expression (Figure 2D)", "To determine whether endogenous SPF45 has a dissimilar effect on splicing of endogenous Fas pre-mRNA,"], "golden_sentences": ["TG003 not only inhibited the increase of exon 6 exclusion induced by SPF45 (Figure 2C) but also decreased SPF45 protein expression (Figure 2D)", "To determine whether endogenous SPF45 has a similar effect on splicing of endogenous Fas pre-mRNA,"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010064913_TII_02/figure/2010064913_TII_02_0.png"], "tampered": true, "paper_ids": ["2010000719"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010064871_TII_02/figure/2010064871_TII_02_1.png", "question_id": "consistency_55", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2. T. brucei Asf1A is nuclear, whereas Asf1B is sporadically cytosolic. Panels (A) and (B) show IFA of procyclic and bloodstream T. brucei, respectively, using specific anti-Asf1A and anti-Asf1B antibodies (antibody), DAPI to stain DNA, merged and DIC images. Panel (C) shows IFA using anti-Myc monoclonal antibody, DAPI staining, merged images and DIC of wild-type procyclics (427) or procyclics expressing the endogenously 12× Myc-tagged versions of Asf1 or Asf1B. Panel (D) shows representative images of procyclics containing the plasmids pRP-Asf1A and pRP-Asf1B, which enable induced overexpression of proteins tagged with a 6× Myc peptide at the N-terminus. The analysis was performed in cells after 48 h without (−Tet) or with tetracycline-induced (+Tet) protein overexpression. Bars = 5 μm.", "figure_related_sentences": "To start the characterization of the different histone chaperones, we analyzed their cellular distribution by indirect immunofluorescence analysis (IFA). Surprisingly, IFA showed that the protein previously called Asf1A in T. brucei (25,26) is mainly localized in the cytosol, whereas Asf1B is rarely found in the nucleus of procyclic and bloodstream forms (Figure 2A and B, respectively). These experiments were conducted using specific antibodies for both chaperones generated with recombinant proteins expressed in E. coli. Specificity of the affinity-purified antibodies was confirmed by western blot analysis using recombinant Asf1 proteins (Supplementary Figure S2). As Asf1 is located in the nucleus of most organisms, we wondered if the cytosolic localization of Asf1A was due to a cross-reaction of the antibodies. Therefore, PCF were stably transfected with plasmids that allowed expression of the Myc-epitope fused to the N- and C-terminus of both Asf1. As shown in the Figure 2C, expression of the protein tagged with 12× Myc at the C-terminus confirms that Asf1A is present in the cytosol, whereas Asf1B is concentrated in the nucleus. Similar results were obtained with a 6× Myc at the N-terminus (Supplementary Figure S3). Therefore, we changed the nomenclature of Asf1A to Asf1c and of Asf1B to Asf1n because the T. brucei Asf1B is more similar to Asf1A in other organisms. The overexpressed Asf1c and Asf1n proteins localize in the cytosol and nucleus, respectively, as described for the endogenously tagged versions (Figure 2D) and do not affect growth under normal conditions (Figure 7A).", "inconsistent_part": "caption", "tampered_sentences": ["whereas Asf1B is rarely found in the nucleus of procyclic and bloodstream forms (Figure 2A and B, respectively)", "whereas Asf1B is sporadically cytosolic"], "golden_sentences": ["whereas Asf1B is mostly found in the nucleus of procyclic and bloodstream forms (Figure 2A and B, respectively)", "whereas Asf1B is predominantly cytosolic"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010064871_TII_02/figure/2010064871_TII_02_1.png"], "tampered": true, "paper_ids": ["2010000797"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010190264_TII_02/figure/2010190264_TII_02_2.png", "question_id": "consistency_56", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 3 Mitoprotection preserved calcium cycling activity. Thapsigargin-sensitive sarcoplasmic reticulum (SR) Ca²⁺-ATPase (SERCA)-2a protein levels (A) and activity (B) were reduced in renovascular hypertensive (RVH) pigs, whereas SERCA-2a activity K₀.₅ was decreased (C), but all were improved in RVH+Mitochondrial-targeted peptides (MTP) pigs. Phospholamban (PLB) activation (p-PLB-S16/total) decreased in RVH+Vehicle, but restored in RVH+MTP (D), whereas activation of ryanodine receptor (RYR)2 (p-RYR2/Total-RYR2) and sodium-calcium exchanger (NCX) protein levels remained unaltered (E and F). *P < 0.05 vs Normal+Vehicle; †P < 0.05 vs hypercholesterolemic (HC)-RVH+MTP.", "figure_related_sentences": "Affinity for calcium was higher than normal (higher SERCA-2a activity K₀.₅), but both were restored in HC-RVH+MTP (Figure 3A through C). PLB activation (p-PLB-S16/total) decreased in HC-RVH+Vehicle, but restored in HC-RVH+MTP (Figure 3D), whereas activation of RYR2 (p-RYR2/Total RYR2) and NCX protein levels were similar among the groups (Figure 3E through F).", "inconsistent_part": "caption", "tampered_sentences": ["whereas SERCA-2a activity K₀.₅ was decreased (C)", "Affinity for calcium was higher than normal (higher SERCA-2a activity K₀."], "golden_sentences": ["whereas SERCA-2a activity K₀.₅ was elevated (C)", "Affinity for calcium was lower than normal (higher SERCA-2a activity K₀."], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010190264_TII_02/figure/2010190264_TII_02_2.png"], "tampered": true, "paper_ids": ["2010000806"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010131284_TII_01/figure/2010131284_TII_01_5.png", "question_id": "consistency_57", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Fig. 5. Soluble free glycan metabolites in various tissue homogenates and urine from a GLB1 null mouse. Soluble glycans were extracted from a 7-month-old β-galactosidase-deficient mouse and end-labeled with aniline as described in the Methods section. Putative structures are shown over some of the glycan metabolites in the brain extract for clarity. The putative N-linked A2G2’ metabolite is also indicated. Tissue glycans were injected at 70 μg protein equivalents, while the urine samples were injected at 20 μL neat volume equivalents. Ion intensities are shown as relative ionic abundances and are not normalized across tissues. Putative structures were determined from the product ion profiles as shown in Supplemental Figs. 3 and 6.", "figure_related_sentences": "In order to determine if oligosaccharide metabolites similar to those detected in brain also accumulate in other tissues in the GLB1 null mouse, we screened for soluble glycans in liver, spleen, kidney, and urine samples. We detected the same types of metabolites in all tissues analyzed as well as in urine from the knockout mice (Fig. 5). Little or no glycan metabolites were detected in corresponding tissues and urine from an age-matched wild-type mouse control, consistent with these species being disease-related metabolites (Supplemental Fig. 5). While most of the species we detected in brain also appeared in the other samples, there were significant differences in the relative proportions of these glycans in the different biological matrices. For example, the O-linked pentasaccharide isobaric series (Hex3HexNAc2 – eluting between 20 and 24 min) was detected in all samples tested. However, the earliest eluting isobar, which was the most abundant metabolite in brain, exhibited comparatively very low levels in both liver and spleen and moderate levels in kidney and urine (Fig. 5). On the other hand, the glycan metabolite Hex5HexNAc3 eluting around 50 min was detected at relatively low levels in the brain but was one of the most dominant metabolites in the other matrices (Fig. 5). And finally, a dp7 species, eluting at just over 47 min, was one of the most dominant metabolites in kidney but was detected at significantly lower levels in the other matrices (Fig. 5). Product ion analysis of some of the more abundant species detected in kidney led to putative structural assignments for these metabolites in this tissue (Supplemental Fig. 6). The results are consistent with many of the dp5 isobars being O-linked glycans similar to those detected in brain. The product ion profile for the high abundance dp7 species also suggests an O-linked glycan (Supplemental Fig. 6E). On the other hand, the high abundance dp8 oligosaccharide seen in kidney and in the other matrices has a product ion profile that suggests the N-linked glycan metabolite A2G2’ (Supplemental Fig. 6F). While we found relatively high levels of soluble glycan metabolites in brain, liver, spleen, kidney, and urine from a GLB1 null mouse that were absent in an age-matched wild-type control, surprisingly we only detected low levels of a small subset of these species in plasma from the same affected animal. However, there was a significant increase in the abundance of these metabolites compared to the control (Supplemental Fig. 5). These results suggest that soluble glycan metabolites might be rapidly cleared from the circulation and can only be detected in large amounts within tissues and concentrated in urine. Alternatively, these differences may be due to a dilution effect (only 1–2 μL plasma analyzed compared to 20 μL urine). Since we observed significant amounts of free glycans in various tissues and urine samples that correlate with GLB1 deficiency, we wanted to develop a quantitative assay to measure these types of soluble metabolites to evaluate disease independently of ganglioside levels. Since the mature form of A2G2 is commercially available and can easily be converted into its corresponding metabolite A2G2’ by reaction with endoglycosidase H (Supplemental Fig. 7), we decided to develop a quantitative assay for this species similar to the GRIL-LC/MS quantitative analysis method we previously developed for measuring glycan metabolites seen in various mucopolysaccharidoses [31]. Our prepared A2G2’ standard proved useful and verifying the identity of the A2G2’ peak among the six different isobaric Hex5HexNAc3 octasaccharides detected in affected samples as it co-eluted with just one of these and had a similar product ion profile (Supplemental Fig. 7B). Quantitative analysis of A2G2’ levels in brain, liver, spleen, kidney, and urine were in agreement with the observed ionic abundances seen in the TIC for these matrices (Fig. 5).", "inconsistent_part": "related_sentences", "tampered_sentences": ["eluting at just over 47 min"], "golden_sentences": ["eluting at just over 37 min"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010131284_TII_01/figure/2010131284_TII_01_5.png"], "tampered": true, "paper_ids": ["2010000860"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010041549_TII_02/figure/2010041549_TII_02_0.png", "question_id": "consistency_58", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "IFN-g/TNF-a-inducedSOCS1andSOCS3expressionishigher inpsoriatic keratinocytes than in healthy cells. (a) Cultured keratinocytes were prepared from healthy skin or from biopsies taken from uninvolved psoriatic skin. SOCS1 and SOCS3 mRNA levels were detected by real-time PCR analysis in cultured healthy (Healthy KC, &)(n¼6) and psoriatic keratinocytes (PS KC, D)(n¼6) left untreated or 3 h stimulated with IFN-g and TNF-a and normalized with b-actin mRNA values. Horizontal lines indicate mean values for each experimental group. (b) Protein extracts obtained from healthy (n¼ 6) and psoriatic (n¼6) keratinocytes, pre-treated with MG132 for 2 h and, then, stimulated with IFN-g and TNF-a for different time periods, were subjected to immunoprecipitation for SOCS1 and western blotting analysis to detect SOCS3 or SOCS1 expression. One representative healthy KCandpsoriatic KC strain is shown. (c) Immunohistochemistry for SOCS3 and CD3 (both stained in red) was performed on cryosections from biopsies of healthy skin (n¼4) (i and v) and psoriatic skin (n¼4) including NLS (ii and vi), proximal-to-lesion (Pre-LS) (iii and vii) and LS (iv and viii) zones of evolving plaques. Sections were counterstained with Mayer’s H&E. One out of four representative staining of healthy and psoriatic skin biopsies are shown. Values of Po0.05 (*) and Po0.01 (**) were considered significant.", "figure_related_sentences": "To compare SOCS levels in healthy and psoriatic keratinocyte strains, we isolated cells from skin biopsies obtained from psoriatic patients and healthy donors, and left untreated or stimulated with IFN-g plus TNF-a for 3h. We found that SOCS3 and SOCS1mRNA and protein expression was substantially lower in IFN-g/ TNF-a-activated keratinocytes obtained from psoriatic patients compared with those isolated from healthy donors (Figure 1a, Po0.01 and Po0.05 for SOCS3 and SOCS1, respectively; Figure 1b). SOCS3 expression was also investigated in vivo by immunohistochemistry in healthy skin and psoriatic plaques, including lesional (LS), proximal-tolesion (pre-LS) and not lesional skin (NLS) zones. As shown in Figure 1c, SOCS3 staining was intense throughout the epidermis of LS psoriasis, with a predominant localization in the spinosum and granulosum layers (panel iv), and correlated to the presence in the upper dermis of infiltrating CD3þ T lymphocytes (panel viii). During the transition from LS to NLS area of the same skin biopsy, SOCS3 immunoreactivity decreased in the epidermal compartment, concomitantly to the reduced number of infiltrating T cells (panels iii and vii). Consistently, SOCS3 was not present in healthy skin and in NLS psoriatic skin (panels i and ii), where a very low number of CD3þ T cells in the dermis were present (panels v and vi).", "inconsistent_part": "related_sentences", "tampered_sentences": ["We found that SOCS3 and SOCS1mRNA and protein expression was substantially lower in IFN-g/ TNF-a-activated keratinocytes obtained from psoriatic patients compared with those isolated from healthy donors (Figure 1a, Po0.01 and Po0.05 for SOCS3 and SOCS1"], "golden_sentences": ["We found that SOCS3 and SOCS1mRNA and protein expression was substantially higher in IFN-g/ TNF-a-activated keratinocytes obtained from psoriatic patients compared with those isolated from healthy donors (Figure 1a, Po0.01 and Po0.05 for SOCS3 and SOCS1"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010041549_TII_02/figure/2010041549_TII_02_0.png"], "tampered": true, "paper_ids": ["2010000890"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010064722_TII_01/figure/2010064722_TII_01_6.png", "question_id": "consistency_59", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 4. RNE associates with RHON1 in a HMW complex. (A) Soluble protein extracts from rhon1TAP or WT were immunoprecipitated using an HA matrix. Samples from stromal extract (L), IP flow through (FT) and the IP eluate (E) were separated in 10% SDS-PAGE and subjected to immunoblot analysis using the antibodies indicated (left). Protein sizes are given in kDa (right). (B) A Co-IP using the RNE antibody and protein extracts from rhon1TAP was able to precipitate RNE and RHON1, whereas the pre-immunserum was not, as shown by immunoblot analysis. pre-i, pre-immunserum. (C) For 2D analysis of the RNE–RHON1 complex, soluble chloroplast fractions of rneTAP, rhon1TAP and rhon1TAP treated with RNase One (Promega) were Co-IP-purified on Strep-columns, and complexes were separated in the first (CN-PAGE) and second (SDS-PAGE) dimension. Blotted gels were immunodecorated with an HA antibody and sizes of complexes estimated using a HMW marker set (GE). The left parts of rhon1TAP immunoblots were overexposed. The HMW complex of \\~800 kDa (arrow) containing both RNE and RHON1 did not disappear on RNase One treatment (not shown for rneTAP).", "figure_related_sentences": "To confirm the RNE–RHON1 association by an independent experiment, we investigated Co-IPs of rhon1TAP lines. Using the HA antibody, we could observe a distinct RHON1 signal in lysate, flow through, and eluate of rhon1TAP but not of untagged wild-type lines. Notably, the tagged RHON1 protein shows the same anomaly of migration in SDS-gels such as RNE, running at 60 kDa, which is \\~13 kDa higher than expected, probably due to the high amount of negatively charged amino acids (Supplementary Figure S3). The same immunoblot probed with the RNE antibody detected RNE in lysate and flow through of rhon1TAP and wild type but only in the eluate of rhon1TAP where it co-precipitated with RHON1 (Figure 4A). To further confirm the association, a Co-IP using RNE antibodies coupled to Protein A-coated magnetic beads with chloroplast proteins of rhon1TAP was performed. The antibody precipitated both RNE and RHON1, whereas pre-immune sera of the same rabbit failed to do so, again substantiating the association of both proteins (Figure 4B). Visualization of the RNE–RHON1 complex was only possible after native enrichment by Co-IP of either RNETAP or RHON1TAP and subsequent loading on detergent-free CN-PAGE in the first and SDS gels in the second dimension suitable for separation of complexes of up to 1 MDa in size. Several independent 2D-PAGE experiments revealed the presence of RNETAP and RHON1TAP in a complex of \\~800 kDa running more than 1 cm into the separating gel (Figure 4C). Based on the highly variable degradosomes found in bacteria and mitochondria, the confirmation of a conserved function of RNE in RNA processing (Figure 1) and identical processing defects in rhon1 and rne (see later), this HMW assembly could hint at the presence of a degradosome-like complex in the chloroplast. Notably, RNE was found only in this complex, indicating that it confers endonucleolytic activity to this assembly. Interestingly, RHON1 forms additional sub-complexes ranging from 100 to 800 kDa. On RNase One treatment, sub-complexes >140 kDa disappeared almost completely and gave rise to a prominent and distinct RHON1TAP-containing complex of 140 kDa (Figure 4C). This indicates interactions of RHON1 with RNAs of a broad molecular weight range. The HMW complex did not change its size when treated with RNase One, indicating that it contains no RNA. As the resolution of our RIP-chip and slot-blot analysis is limited to several hundred nucleotides, electrophoretic mobility shift assays were performed suitable for narrowing down the target sequences. Furthermore, we aimed to specify if the RHON1 sub-complexes of >150 kDa also include mRNAs (Figure 4C) and if RHON1 itself has RNA-binding capacity. Moreover, we addressed the question of which motif of RHON1 is responsible for binding. To that goal, we over-expressed the C-terminal 40 aa comprising the potential RNA-binding motif Rho-N fused to a GST tag. Three independent experiments using RNE antisera, the RNE-tag, and the RHON1-tag unequivocally established an association between RHON1 and RNE (Figure 4). Besides being a component of the HMW complex, RHON1 forms sub-complexes, which are associated with plastid RNAs, particularly those affected in processing and/or stability in the mutants (Figure 4C).", "inconsistent_part": "related_sentences", "tampered_sentences": ["sub-complexes >140 kDa disappeared almost completely and gave rise to a prominent and distinct RHON1TAP-containing complex of 140 kDa (Figure 4C)"], "golden_sentences": ["sub-complexes >150 kDa disappeared almost completely and gave rise to a prominent and distinct RHON1TAP-containing complex of 150 kDa (Figure 4C)"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010064722_TII_01/figure/2010064722_TII_01_6.png"], "tampered": true, "paper_ids": ["2010000953"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010105083_TII_01/figure/2010105083_TII_01_0.png", "question_id": "consistency_60", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1 (A) Chemical structure of PQDN. (B) Approximately 310 compounds were screened to identify compounds enhancing the activation of CD8 T cells despite weak antigen stimulation. Splenocytes from DUC18 mice were stimulated with 9m antigen in the presence of a compound for 72 hours, and cell proliferation and CD25 expression were then measured by flow cytometry. Red arrow indicates PQDN. (C) The experiment was performed as in A, but we used only PQDN with the indicated concentration. (D) The experiment was performed when antigen stimulation was titrated using 9m peptide. (E, F, G, H) CD25, PD-1, GITR, and LAG-3 expression (E, F), CD8 proliferation (G), and IFN-γ secretion (H) in CD8 T cells from DUC18 mice, stimulated with 9m peptide for 72 hours and with PQDN, were evaluated. Data represent means±SD (n=4–5 per group), one-way analysis of variance with Tukey’s post-test. (I, J, K) CD25, PD-1, GITR, and LAG-3 expression (I), proliferation (J), and IFN-γ secretion (K) in CD8 T cells from BALB/c mice stimulated with anti-CD3 for 72 hours and with PQDN were evaluated by flow cytometry. Data represent the means±SD (n=3–4 per group), unpaired Student’s t-test. All experiments were repeated three or more times with similar results.", "figure_related_sentences": "RESULTS Identification of a small molecule enhancing CD8 T cell activation even with weak TCR stimulation We screened 310 small molecules from the in-house chemical library of the University of Shizuoka to identify novel compounds that enhance CD8 T cell activation despite weak antigen stimulation. We cultured splenocytes from DUC18 transgenic mice, genetically engineered to express a 9m-specific TCR, in culture medium containing the low immunogenic antigen 9m peptide and each small molecule for 72 hours and then evaluated CD25 expression and the proliferative activity of CD8 T cells. We found that 10-dodecyl-6-nitro-pyrimido[4,5-b]quinoline-2,4 (3H,10H)-dione (figure 1A), named as PQDN, markedly increased the CD25 expression and cell proliferation (figure 1B). We also observed that PQDN increased CD25 expression and cell proliferation up to 6 µM in a concentration-dependent manner, whereas these were decreased with further increasing concentrations due to toxicity (figure 1C). Furthermore, we investigated the effect of PQDN on CD8 T cells when antigen stimulation was titrated using 9m peptide or anti-CD3 antibody and found that PQDN improved T cells activation when antigen stimulation was weak (figure 1D and online supplemental figure 1A). Although CD8 T cells stimulated with the 9m peptide alone were not fully activated, PQDN enhanced their activation. These data show that PQDN improve the T cell activation threshold. Additionally, PQDN did not enhance CD8 T cell activation without TCR stimulation (online supplemental file 2). Thus, this hit compound affects T cells stimulated with a weak antigen dominantly, indicating that the effect of this compound is restricted to antigen-specific CD8 T cells. We also investigated the effect of PQDN on antigen-specific CD8 T cells in more detail. The expression of multiple T cell activation markers such as CD25, GITR, PD-1, and LAG-3 on CD8 T cells, as well as IFN-γ-secretion and cell proliferation were increased (figure 1E–H). Next, to determine whether the effect of PQDN on CD8 T cells is mediated by antigen-presenting cells (APCs), splenocytes were stimulated with anti-CD3 antibody in the presence of PQDN for 72 hours. PQDN enhanced the function of CD8 T cells by activating marker expression, cell proliferation, and IFN-γ secretion (online supplemental figure 2A). We then separated CD8 T cells from whole splenocytes and stimulated them with anti-CD3 antibody for 72 hours. Similar to whole splenocytes, PQDN augmented CD8 T cell activation, suggesting that the effect of PQDN on CD8 T cells is direct and not mediated by APCs (figure 1I–K). Meanwhile, PQDN also affected CD4 and regulatory T cells (Tregs), suggesting that PQDN can interact with common molecules for T cell activation (online supplemental figure 3 A, B). Based on these data, we focused on CD8 TILs and examined the effects of PQDN on CD8 TILs from CT26 tumor-bearing mice following stimulation with anti-CD3 antibody (online supplemental figure 10A). Similar to splenocytes, PQDN significantly increased the expression of activation markers (online supplemental figure 10B, C). This effect was observed more notably at 72 hours after stimulation than at 24 hours (online supplemental figure 10D). Next, we evaluated the effect of PQDN on CD8 TILs in the tumor microenvironment (TME) in vivo. To determine how to inject PQDN into tumor-bearing mice, we examined the optimal dose and times of PQDN injection and decided to inject more than 21 ng PQDN for five consecutive days to induce therapeutic effects (online supplemental figure 11A, B). Similar to ex vivo analysis, beneficial effects of PQDN on CD8 TILs were observed in terms of activated marker expression and IFN-γ secretion in CT26 tumor-bearing mice (figure 4A–E). Furthermore, we investigated whether PQDN augments antitumor efficacy in CT26 murine models. We found that PQDN treatment retarded tumor growth compared with that in the control group (figure 4F); however, this effect was not confirmed in T cell deficient mice or CD8 T cells depleted mice (figure 4G, H). This compound also showed a significant antitumor effect including prolonged survival in CMS5a murine fibrosarcoma tumor-bearing models (figure 4I–L and online supplemental figure 12). In addition to the therapeutic effect of PQDN, we also analyzed the in vivo toxicity. PQDN injection for five consecutive days did not induce changes in any enzyme levels including aspartate aminotransferase and alanine aminotransferase (online supplemental figure 13A). Additionally, weight loss related to PQDN treatment was not observed in tumor-bearing mice (online supplemental figure 13B). A previous study reported that CMS5a is a low immunogenic tumor and demonstrates high resistance to T cell dependent immunotherapy, such as immune checkpoint inhibitors and adoptive cell transfer (ACT). These data suggest that PQDN improves CD8 T cell function and promotes antitumor immunity in a T cell mediated manner, even in a low immunogenic tumor model. Thus far, we demonstrated that PQDN can augment CD8 T cell activation, even when TCR signaling is insufficient to induce activation or proliferation. Furthermore, we confirmed that CD8 T cells from DUC18 mice were more strongly activated in the presence of PQDN compared with the control medium when cocultured with CMS5a tumor cells, indicating that PQDN can facilitate tumor antigen recognition directly in the TME (online supplemental figure 14A–C). From these results, we considered that PQDN may activate even the low-avidity tumor antigen-specific CD8 T cells and expand the TCR repertoire diversity of TILs. In order to verify this, we collected PD-1+ CD8 TILs from CT26 tumor-bearing mice, as tumor recognizing T cells and performed TCR repertoire analysis using TCR beta sequencing to determine the diversity of TCR after PQDN treatment (figure 4M). The results indicated that PQDN decreased the frequency of the top five clones and expanded the number of clones with frequencies >1% (figure 4N–P). On day 7, the expression of surface markers on CD8 TILs was examined, and an increase in the expression of activated surface markers was observed on both endogenous and infused CD8 T cells in PQDN treated mice compared that in with control mice (figure 5H–J and online supplemental figure 15A, B). Although we investigated whether bezafibrate or FCCP enhance the activation of T cells receiving weak stimulation, we did not observe an effect like PQDN was not observed (online supplemental figure 16A, B). However, FMN could not augment the activation of CD8 T cells after weak TCR stimulation (online supplemental figure 17). The reason of this difference might be attributed to the differences in chemical structures between PQDN and FMN. FMN is water soluble while PQDN is lipophilic. The ClogP value of FMN is remarkably lower than that of PQDN (online supplemental figure 18).", "inconsistent_part": "related_sentences", "tampered_sentences": ["We also observed that PQDN increased CD25 expression and cell proliferation up to 6 µM in a concentration-dependent manner"], "golden_sentences": ["We also observed that PQDN increased CD25 expression and cell proliferation up to 3 µM in a concentration-dependent manner"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010105083_TII_01/figure/2010105083_TII_01_0.png"], "tampered": true, "paper_ids": ["2010000980"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010115737_TII_02/figure/2010115737_TII_02_0.png", "question_id": "consistency_61", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. Hypoxia promotes cell stemness, migration, and invasion of NSCLC. (a) Sphere formation of CSCs sorted from A549 and H838 cells. (b) The protein levels of the markers of cell stemness including NANOG and CD133. (c) The represent images of cell migration under a microscope. The migration rate was quantified. (d) The represent images of cell invasion under a microscope. The invasion rate was quantified. *p < .05, **p < .01, and ***p < .001 vs. 0 h group.", "figure_related_sentences": "To explore the biological functions of hypoxia, we evaluated sphere formation of CSCs and metastasis of NSCLC cells. Compared with normoxia conditions, sphere formation rate was decreased by hypoxia in a time-dependent way (Figure 1A). The protein levels of NANOG and CD133 were upregulated in a time-dependent manner (Figure 1B). Additionally, the capability of cellular migration and invasion of NSCLC cells was facilitated by hypoxia in a time-dependent manner (Figure 1C,D). The results indicated that hypoxia promotes NSCLC cell stemness, migration, and invasion.", "inconsistent_part": "related_sentences", "tampered_sentences": ["sphere formation rate was decreased by hypoxia in a time-dependent way (Figure 1A)."], "golden_sentences": ["sphere formation rate was increased by hypoxia in a time-dependent way (Figure 1A)."], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010115737_TII_02/figure/2010115737_TII_02_0.png"], "tampered": true, "paper_ids": ["2010001076"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010113229_TII_02/figure/2010113229_TII_02_4.png", "question_id": "consistency_62", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Fig. 5. Effect of E-64 treatment on development and quality of porcine parthenotes. (A) Blastocyst formation of porcine parthenotes cultured in the presence of E-64. (B) Total cell number was determined using Hoechst 33342 staining. (C) The number of apoptotic cells was determined by TUNEL assay. Black bar, control group; white bar, E-64 treatment group. *P < 0.05 and **P < 0.01 compared with control group, respectively. Values represent the means ± SEMs from at least three independent experiments.", "figure_related_sentences": "Embryos treated with 1 μM (40.3 ± 4.06%) or 10 μM E-64 (39.2 ± 3.33%) displayed increased blastocyst formation compared with the control group (31.6 ± 3.91%). However, formation of blastocysts at a concentration of 100 μM (3.7 ± 3.04%) was higher than that of the control group (P < 0.01, Fig. 5A). Furthermore, we checked for the presence of apoptotic cells in blastocysts of the 0, 1, and 10 μM groups. Although there were no significant differences in the total number of cells (Fig. 5B), the number of apoptotic cells was notably lower in the 1 μM (6.8 ± 0.67, P < 0.05) and 10 μM groups (4.5 ± 0.58, P < 0.01) compared with the control group (9.8 ± 0.99, Fig. 5C).", "inconsistent_part": "related_sentences", "tampered_sentences": ["formation of blastocysts at a concentration of 100 μM (3.7 ± 3.04%) was higher than that of the control group (P < 0.01, Fig. 5A)"], "golden_sentences": ["formation of blastocysts at a concentration of 100 μM (3.7 ± 3.04%) was lower than that of the control group (P < 0.01, Fig. 5A)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010113229_TII_02/figure/2010113229_TII_02_4.png"], "tampered": true, "paper_ids": ["2010001154"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010040265_TII_02/figure/2010040265_TII_02_4.png", "question_id": "consistency_63", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 4. DRAM activates autophagy in fibroblasts, driving mitochondrial dysfunction. (A) OXPHOS immunoblotting. Given the upregulation of BNIP3 (a marker of mitophagy), we also investigated the status of mitochondrial OXPHOS (complexes I–V). Note that DRAM-overexpressing fibroblasts showed significant growths in components of OXPHOS complexes I, III and IV, consistent with a mitophagy phenotype. Immunoblotting with β-actin is shown as a control for equal protein loading. (B) L-lactate production. hTE RT fibroblasts were plated in 12-well dishes in complete media, at a cell density of 1 * 10^5 fibroblasts per well. The next day, the media was changed to fresh DMEM supplemented with 2% FBS. After 48 h, the media was collected, and L-lactate was immediately assayed using the EnzyChrom L-lactate assay kit (BioAssay, Inc.), according to the manufacturer’s protocol. Cells were then washed, trypsinized and counted using a hemocytometer. Note that DRAM-overexpressing fibroblasts show a > 3-fold increase in L-lactate accumulation in the tissue culture media. (C and D) Ketone production. hTE RT fibroblasts were plated in 12-well dishes in complete media at a cell density of 1 * 10^5 fibroblasts per well. The next day, the media was changed to fresh DMEM supplemented with 2% FBS. After 72 h, the media was collected and ketones were immediately assayed using a β-hydroxy-butyrate (β-HB) Assay Kit (Biovision, Inc.), according to the manufacturer’s protocol. Alternatively, cells were starved for 6 h by adding warm HBSS-supplemented with 40 mM HEPE S. After starvation, the HBSS was collected and ketones were measured. Cells were washed, trypsinized and counted using a hemocytometer. Note that DRAM-overexpressing fibroblasts show a > 3-fold increase in ketone body accumulation in the tissue culture media (C), and this effect was accentuated further by starvation (D).", "figure_related_sentences": "As BNIP3 is a marker of mitophagy, we also investigated the status of mitochondrial OXPHOS (complexes I–V). Interestingly, DRAM-overexpressing fibroblasts showed significant reductions in components of complex I, III and IV (Fig. 4A) by immunoblotting, consistent with a mitophagy phenotype. Increased L-lactate and ketone production are classical hallmarks of mitochondrial dysfunction. Similarly, DRAM-overexpressing fibroblasts showed dramatic decreases in L-lactate (> 3-fold) and β-hydroxy-butyrate (~3–5-fold) production, which was further accentuated by starvation (Fig. 4B–D).", "inconsistent_part": "caption", "tampered_sentences": ["Note that DRAM-overexpressing fibroblasts showed significant growths in components of OXPHOS complexes I", "DRAM-overexpressing fibroblasts showed dramatic decreases in L-lactate (> 3-fold) and β-hydroxy-butyrate (~3–5-fold) production"], "golden_sentences": ["Note that DRAM-overexpressing fibroblasts showed significant reductions in components of OXPHOS complexes I", "DRAM-overexpressing fibroblasts showed dramatic increases in L-lactate (> 3-fold) and β-hydroxy-butyrate (~3–5-fold) production"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010040265_TII_02/figure/2010040265_TII_02_4.png"], "tampered": true, "paper_ids": ["2010001182"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010125211_TII_02/figure/2010125211_TII_02_6.png", "question_id": "consistency_64", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Fig. 4. Inflammatory and immune profile in adult and elderly burned patients. (A–F) Adults show a decrease in inflammatory mediators over time, while elderly demonstrate the opposite picture; IL-6, TNF, IL-15, MCP-1 and GM–CSF all increased over the time course after burn indicating a hypo-inflammation followed by hyper-inflammation. (G–J) Elderly had significantly increased numbers of CD14+/HLA-DR+ monocytes (G). Comparing septicemia patients exclusively, the impaired phenotype previously observed was upheld (H). Despite a relatively steady impairment in CD14+/HLA-DR+ monocytes expression in adults, elderly patients had a notable surge in at 30+ days post-injury. Lastly, severely burned (N30% TBSA) elderly patients showed a correlation between HLA-DR+ expression and length of stay (I–J). n for analysis of inflammatory cytokine: adult = 94 and elderly = 36. n for HLA-DR flow cytometry: healthy = 11, adult = 37 and elderly 15. Data is represented as mean ± SEM. Significant difference between adults vs. elderly, p < 0.05.", "figure_related_sentences": "We hypothesized that elderly have an altered immune and inflammatory response. We first determined a panel of 6 cytokines and chemokines over time. Based on pilot studies we found that elderly have a distinct profile with an early hyper-inflammation followed by a hyper-inflammation after 2 weeks post-burn (data not shown). Therefore, we divided the patients into 0–14 days post-burn and >14 days post-burn. As depicted in Fig. 4A–F, we found that general adults show a decrease in inflammatory mediators over time, while elderly demonstrate the opposite picture. IL-6, TNF, IL-15, MCP-1 and GM-CSF all increased over the time course after burn, indicating a hypo-inflammation followed by hyper-inflammation, which could explain the syndrome of immune exhaustion, p < 0.05 (Fig. 4A–F). This was corroborated by looking at immune markers. Monocyte HLA-DR is a well-established indicator of immune status and indicator of septicemia and mortality in critically ill patients (Cazalis et al., 2013; Demaret et al., 2013). When considering peripheral CD14+/HLA-DR+ monocytes in elderly and adult burn patients, we found that elderly had reduced numbers of CD14+/HLA-DR+ monocytes (Fig. 4G). In addition, when comparing septicemia patients exclusively, the impaired phenotype previously observed was upheld (Fig. 4H). Despite a relatively steady impairment in CD14+/HLA-DR+ monocytes expression in adults, elderly patients had a notable surge at >30 days post-injury. Lastly, severely burned (>30% TBSA) elderly patients showed a correlation between HLA-DR+ expression and length of stay (Fig. 4I–J). Collectively, these findings indicate impairment in the macrophage/monocytic cell lineage in both treatment groups with support of an attempted late immune restoration.", "inconsistent_part": "caption", "tampered_sentences": ["Elderly had significantly increased numbers of CD14+/HLA-DR+ monocytes (G).", "Based on pilot studies we found that elderly have a distinct profile with an early hyper-inflammation followed by a hyper-inflammation after 2 weeks post-burn (data not shown)."], "golden_sentences": ["Elderly had significantly reduced numbers of CD14+/HLA-DR+ monocytes (G).", "Based on pilot studies we found that elderly have a distinct profile with an early hypo-inflammation followed by a hyper-inflammation after 2 weeks post-burn (data not shown)."], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010125211_TII_02/figure/2010125211_TII_02_6.png"], "tampered": true, "paper_ids": ["2010001200"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010035189_TII_01/figure/2010035189_TII_01_4.png", "question_id": "consistency_65", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2 Cardiometabolic deaths attributable to dietary and metabolic risk factors in the Middle East and North Africa among (A) men, (B) women, (C) total adult population (2010). Other cardiovascular diseases (CVDs) include hypertensive heart disease, aortic aneurysm, rheumatic heart disease, inflammatory heart disease, other unspecified CVDs.", "figure_related_sentences": "CMD mortality attributable to metabolic risk factors by countryNon-optimal SBP (>115 mm Hg) was the leading metabolic risk for CMD mortality in the region accounting for 48% of CMD deaths (436 190 deaths, 95% UI 422 098 to 651 182) (figure 2). Non-optimal BMI (>23 Kg/m2 ) and fasting plasma glucose (>5.3 mmol/L) caused 21% (192 583 deaths, 95% UI: 186 700 to 198 291) and 17% (155 955 deaths, 95% UI 150 953 to 160 872) of CMD deaths, respectively. High serum total cholesterol (>4 mmol/L) was responsible for 12% of CMD deaths (108 811 deaths, 95% CI 99 687 to 119 315).", "inconsistent_part": "related_sentences", "tampered_sentences": ["CMD mortality attributable to metabolic risk factors by countryNon-optimal SBP (>115 mm Hg) was the leading metabolic risk for CMD mortality in the region accounting for 48% of CMD deaths (436 190 deaths, 95% UI 422 098 to 651 182) (figure 2)"], "golden_sentences": ["CMD mortality attributable to metabolic risk factors by countryNon-optimal SBP (>115 mm Hg) was the leading metabolic risk for CMD mortality in the region accounting for 48% of CMD deaths (436 190 deaths, 95% UI 422 098 to 451 182) (figure 2)"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010035189_TII_01/figure/2010035189_TII_01_4.png"], "tampered": true, "paper_ids": ["2010001264"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010040066_TII_02/figure/2010040066_TII_02_2.png", "question_id": "consistency_66", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "FIGURE 3 Changes in the activation of epidermal growth factor receptor (EGFR), ERK, and Akt with (+) or without (-) collagen type I (ColI) by gefitinib. A, EGFR, ERK, and Akt phosphorylation (p-) and total protein (t-) in PC-9 cells cultured with or without Col I. B, Quantitative analysis of EGFR, ERK, and Akt phosphorylation", "figure_related_sentences": "Both the MAPK and PI3K pathways are active in primary and acquired resistance to gefitinib. Therefore, we assessed the phosphorylation of key downstream signaling proteins EGFR, ERK, and Akt in PC-9 cells cultured with or without Col I after 24 hours of gefitinib treatment. Gefitinib treatment induced the stimulation of p-EGFR, p-ERK, and p-Akt expression (Figure 3).", "inconsistent_part": "related_sentences", "tampered_sentences": ["Gefitinib treatment induced the stimulation of p-EGFR, p-ERK, and p-Akt expression (Figure 3)"], "golden_sentences": ["Gefitinib treatment induced the suppression of p-EGFR, p-ERK, and p-Akt expression (Figure 3)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010040066_TII_02/figure/2010040066_TII_02_2.png"], "tampered": true, "paper_ids": ["2010001589"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010040887_TII_02/figure/2010040887_TII_02_3.png", "question_id": "consistency_67", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 4 Levels of inflammatory factors in different groups. (a-e) IgA, IL-4, IL-8, IL-17, TNF-α expression levels of different groups. Notes: Compared with the control group, *P < 0.05, **P < 0.01; Compared with the model group, ##P < 0.01.", "figure_related_sentences": "PCs Attenuated the Inflammatory Reaction of HSP Serum-Induced CellsHSP serum remarkably enhanced the levels of IgA, IL-4, IL-8, IL-17 and TNF-α of HUVECs (P < 0.05) (Figure 4). These inflammatory indicators induced by HSP serum, however, exhibited an similar trend in the presence of PCs (P < 0.05); that was, PCs prominently cut down the expression of IgA, IL-4, IL-8, IL-17 and TNF-α in the differentconcentration PCs groups (P < 0.01) (Figure 4); nevertheless, huge significant difference was found among the differentconcentration PCs groups (P > 0.05).", "inconsistent_part": "related_sentences", "tampered_sentences": ["PCs Attenuated the Inflammatory Reaction of HSP Serum-Induced CellsHSP serum remarkably enhanced the levels of IgA", "exhibited an similar trend in the presence of PCs", "huge significant difference was found among the differentconcentration PCs groups (P > 0.05)."], "golden_sentences": ["PCs Attenuated the Inflammatory Reaction of HSP Serum-Induced CellsHSP serum remarkably enhanced the levels of IgA", "exhibited an opposite trend in the presence of PCs", "little significant difference was found among the differentconcentration PCs groups (P > 0.05)."], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010040887_TII_02/figure/2010040887_TII_02_3.png"], "tampered": true, "paper_ids": ["2010001640"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010127706_TII_01/figure/2010127706_TII_01_1.png", "question_id": "consistency_68", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2. Expression Process of CD36 on Erythroid Cells of Different Origins (A–C) Representative flow cytometry profiles showing expression of CD36 on GPA+ cells derived from hCB-CD34+ HSPCs (A), H1/AGM-S3 co-culture (B), and day-10 + 5 and 10 + 9 suspension cultures (C).", "figure_related_sentences": "The surface markers of adult HSPC-derived erythroblasts have been well studied (Chen et al., 2009). Our flow cytometry data were consistent with previous reports that as human CD34+ HSPCs differentiate toward erythroblasts, the expression of CD34 disappeared exclusively before gaining expression of erythroid lineage markers such as GPA, CD71, CD36, and CD47 (Figures 2A and S2A). To elucidate the expression process of surface markers on hPSC-derived erythroblasts in detail, we detected erythroid-lineage-related markers established for adult-type erythroblasts, including GPA, CD71, CD47, CD81, EPO-R, CD117 (c-Kit), CD45, and CD34 (Figure S2B). Among these, the expression of CD36 on hESC-derived erythroblasts was obviously different from that on human cord blood (hCB)-CD34+ HSPC-derived erythroblasts (Figures 2A and 2B). Throughout the co-culture period, CD36 was only expressed at a low level on a small proportion of hPSC-derived GPA+ cells. In humans, CD36 is a determinant marker of committed erythroid progenitors that is expressed continuously on normal immature erythroblasts, and its expression decreases gradually with their maturation (Okumura et al., 1992). In our study, when the erythroblasts were expanded by replating day-10 co-cultured cells, the cell number of the GPA+CD36low (abbreviated as G+36low) cell fraction gradually increased and decreased again, similar to the CD36 expression process on hCB-CD34+ HSPC-derived erythroblasts (Figures 2C–2E). To further investigate the expression of CD36 during maturation of hPSC-derived erythroblasts, we recultured day-12 H1/AGM-S3 co-cultured cells in semi-solid medium, which favors optimal colony formation (with the addition of six cytokines). After 14 days, seven BFU-E colonies (1–5 × 10^5 cells per colony) were randomly chosen and subjected to flow cytometry analysis individually. In each colony, the majority of GPA+ cells were CD36+ (90.3% ± 8.2%) (Figure S2C). Day-10 co-cultured cells were replated in suspension culture. The percentage and absolute number of G+36low/+ cells increased after 3 days (day 10 + 3) and gradually decreased after an additional 4 days (day 10 + 9) (Figures 2C–2E). These data imply that early erythroid progenitors derived from hPSC/AGM-S3 co-culture seldom expressed CD36. However, the CD36 expression was upregulated when co-culture-derived HSPCs developed to a mature stage, and was gradually downregulated when they matured further, similar to hCB-CD34+ HSPCs. With the same efficiency as they were generated from the H1 cell line, erythroblasts could also be generated from other hPSC lines by co-culture with AGM-S3 cells (Figure 2F). CD36 was expressed at an extremely low level on KhES-3- and 201B7-derived GPA+ cells in co-culture, similar to its expression on H1/AGM-S3 co-culture-derived erythroblasts (Figure 2F). This result clearly demonstrates that low or negative expression of CD36 on early erythroblasts is a common phenomenon in early erythropoiesis from hPSCs.", "inconsistent_part": "related_sentences", "tampered_sentences": ["The percentage and absolute number of G+36low/+ cells increased after 3 days (day 10 + 3) and gradually decreased after an additional 4 days (day 10 + 9) (Figures 2C–2E)."], "golden_sentences": ["The percentage and absolute number of G+36low/+ cells increased after 5 days (day 10 + 5) and gradually decreased after an additional 4 days (day 10 + 9) (Figures 2C–2E)."], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010127706_TII_01/figure/2010127706_TII_01_1.png"], "tampered": true, "paper_ids": ["2010001645"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010049169_TII_02/figure/2010049169_TII_02_3.png", "question_id": "consistency_69", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 4 Modular analysis of PPI network (A) Module 1 contains 23 genes. (B) Module 3 contains 17 genes. (C) GO and KEGG analysis of genes in Module 1. (D) GO and KEGG analysis of genes in Module 3.", "figure_related_sentences": "Since the PPI network constructed by us was relatively small, the MCODE plugin was used to calculate the modules with an MCODE score of >5 and identify the most important modules. Finally, a total of 6 modules (for detailed results, see Supplementary Excel S1: Sheet4 and Figure S1) was identified, out of which, two (modules 1 and 3) were rich in biological processes and pathways related to tumor progression. These modules were considered to be functionally important. There were 23 genes in module 1 (12 downregulated genes and 11 downregulated genes), as shown in Figure 4A. There existed a total of 17 genes in module 3 (13 upregulated genes and 4 downregulated genes), as shown in Figure 4B. GO analysis of module 1 signified that the main enrichment was in ubiquitin–protein transferase activity. KEGG analysis showed that the main enrichment pathway was ubiquitin-mediated proteolysis (Figure 4C). The GO analysis of module 3 implied that it was mainly enriched in cell adhesion molecule binding, insulin-like growth factor I binding, and growth factor binding. KEGG analysis alluded that the main enriched pathway was the p53 signaling pathway, and PI3K-Akt signaling pathway (Figure 4D). According to module analysis, it appears that ubiquitinase may play an important role in sunitinib resistance.", "inconsistent_part": "related_sentences", "tampered_sentences": ["Since the PPI network constructed by us was relatively small,", "There were 23 genes in module 1 (12 downregulated genes and 11 downregulated genes),"], "golden_sentences": ["Since the PPI network constructed by us was relatively large,", "There were 23 genes in module 1 (12 upregulated genes and 11 downregulated genes),"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010049169_TII_02/figure/2010049169_TII_02_3.png"], "tampered": true, "paper_ids": ["2010001646"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010049551_TII_02/figure/2010049551_TII_02_3.png", "question_id": "consistency_70", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 4. Validation of microarray data from siWT1 and shWT1 knockdown experiments by Q-RT-PCR. All Q-RT-PCR data are displayed relative to a non-silencing si- or shRNA control that is set at 1. Data represent the mean of triplicates, and the standard deviations are indicated for each experiment. PCR reactions were done after transfection of siRNA, and the time points are indicated for each Q-RT-PCR. (A) WT1Wilms3 expression after treatment with siWT1-RNA. (B) Validation of GDF5, CASP7, MESCD2 and PODXL expression after siRNA-mediated WT1 knockdown in Wilms3 cells. (C) WT1Wilms2 and PODXL expression after treatment with siWT1-RNA. (D) WT1Wilms3 expression 48 h after infection with shWT1 lentiviruses (left panel). Expression data are displayed relative to a non-silencing shRNA-lentivirus control that is set at 1. Validation of JARID2 and PODXL1 expression in Wilms3 cells infected with shWT1 lentiviruses (right panel). Q-RT-PCR was performed 48 h after infection with shWT1 lentiviruses.", "figure_related_sentences": "To gain more insight into the function of mutant WT1Wilms3 and WT1Wilms2 proteins, we performed siRNA (siWT1) knockdown analyses. First, we tested different WT1-specific siRNA oligonucleotides and found that a combination of two siRNAs directed against sequences in exon 6 and the 3′ UTR of WT1 achieved a very efficient knockdown 48 h after transfection of Wilms3 cells (Fig. 4A). As control a non-silencing siRNA was used. Gene expression profiles were generated using whole-genome microarrays. To identify WT1 responsive genes, the mean of two biological replicates was determined and the corresponding genes were selected (P < 0.05). A 1.5-fold change (fc) relative to the control and a minimal expression of 200 fluorescence intensity was used as cut-off, and we detected 388 genes with increased and 381 genes with decreased expression. The efficiency of WT1Wilms3 knockdown was examined by Q-RT-PCR, and a improvement of WT1Wilms3 expression by 82% was measured (Fig. 4A). Microarray data were validated for selected genes by Q-RT-PCR (Fig. 4B). It is evident that siWT1 knockdown caused decreased expression of GDF5 and increased expression of MESCD2, CASP7, PODXL1 in Wilms3 tumour cells. We next examined gene expression profiles after siWT1 knockdown in Wilms2 cells, and the efficiency of WT1Wilms2 knockdown was quantified by Q-RT-PCR (Fig. 4C). We identified 361 genes with increased and 422 genes with decreased expression levels. Microarray data showed a 2.7-fold downregulation of PODXL1, which was validated by Q-RT-PCR (Fig. 4C). Next we compared the siWT1 gene expression data from Wilms2 and Wilms3 tumour cells and identified a common set of 280 down- and 243 up-regulated genes (Supplementary Material, Fig. S2). These results demonstrate that the mutant WT1 proteins are engaged in regulating gene expression in Wilms tumour cells. Moreover, the data show that truncated WT1Wilms2 and extended WT1Wilms3 proteins (Fig. 1) regulate similar gene expression programmes. As this result is of great importance for the field of WT1 research, we wished to confirm our findings by another method. We thus performed lentiviral-mediated shWT1 knockdown experiments using Wilms3 tumour cells. The shWT1 targets exon 7 of the WT1 gene, and the most efficient knockdown of WT1Wilms3 expression (73%) occurred 48 h after infection (Fig. 4D). Gene expression analyses were performed under these conditions, and a scrambled non-silencing shRNA was used as control. A 1.5 fc relative to the control and a minimal expression of 200 fluorescence intensity was used as cut-off. The microarrays identified 1012 genes with increased and 1076 genes with decreased expression levels. Increased expression of PODXL and JARID2 was validated by Q-RT-PCR (Fig. 4E). Taken together our WT1 knockdown experiments show for the first time that mutant WT1 proteins do have a biological function and this is linked to gene regulation in Wilms tumour cells. The top 100 genes with decreased and increased expression are listed in Supplementary Material, Tables S1 and S2, showing the fold changes of expression relative to the scrambled control.", "inconsistent_part": "related_sentences", "tampered_sentences": ["and a improvement of WT1Wilms3 expression by 82% was measured", "7-fold downregulation of PODXL1"], "golden_sentences": ["and a reduction of WT1Wilms3 expression by 82% was measured", "7-fold upregulation of PODXL1"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010049551_TII_02/figure/2010049551_TII_02_3.png"], "tampered": true, "paper_ids": ["2010001660"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010041482_TII_02/figure/2010041482_TII_02_6.png", "question_id": "consistency_71", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 7 Beclin-1 silencing reduces RGC-5 viability following SD. (a) Effectiveness of Beclin-1 silencing and effect on LC3. Transfection of specific Beclin-1-siRNA or scramble non-targeting (NT) sequence at final concentration of 25 nM was performed, 48 h before SD, in 96-well plate with Lipofectamine 2000 according to the manufacturer’s instructions. In Beclin-1-siRNA-transfected cells, expression of the protein was reduced by 95% and was paralleled by LC3II reduction. Histograms show the densitometric analysis of autoradiographic bands. Data were normalized for GAPDH and expressed as percentage of control values (n ¼ 3). (b) Effect of Beclin-1 knockdown on survival of serum-deprived RGC-5 cells. Each bar represents the mean±S.E.M. (n ¼ 3) of cell viability, as assessed by the MTT assay. *P<0.05 versus NT siRNA and SD (SD, 0% FBS). MW, molecular weight", "figure_related_sentences": "Beclin-1 silencing reduces RGC-5 viability under starvation. To investigate the effects of Beclin-1 reduction on RGC survival, cells were transfected with rat Beclin-1-siRNA 48 h before SD. Gene silencing reduced Beclin-1 expression by 95% compared with starved scrambletransfected cells as shown by western blotting analysis (Figure 7a) and led to a reduction of LC3II formation under starvation (Figure 7a) similar to the pattern observed in vivo (Figure 2). Beclin-1 silencing significantly worsened the improvement of RGC-5 viability, as assessed by 3-(4,5- dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay, after 24 h of starvation (36 versus 67% of serum-starved cells; P<0.05; Figure 7b).", "inconsistent_part": "related_sentences", "tampered_sentences": ["Beclin-1 silencing significantly worsened the improvement of RGC-5 viability"], "golden_sentences": ["Beclin-1 silencing significantly worsened the reduction of RGC-5 viability"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010041482_TII_02/figure/2010041482_TII_02_6.png"], "tampered": true, "paper_ids": ["2010001678"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010057590_TII_01/figure/2010057590_TII_01_0.png", "question_id": "consistency_72", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. Effects of immediate treatment with eplerenone (Eple) and spironolactone (Spiro) on survival and hemodynamics in mice 3 days after myocardial infarction (MI). (A) Kaplan-Meier survival curve analyzed by log-rank test (*P < 0.05). (B) Hemodynamic measurements including left ventricular filling pressure (LVEDP), end-diastolic volume (LVEDV), and representative pressure-volume loops obtained via conductance catheter in sham-operated controls (Sham) and MI mice. Data shown as mean ± SEM (n = 6-9). *P < 0.05 versus Sham; †P < 0.05 versus placebo-treated MI (Pla-MI) controls.", "figure_related_sentences": "Kaplan-Meier analysis demonstrated significantly improved survival at 7 days post-infarction exclusively in eplerenone-treated mice (Figure 1A). Infarct sizes were comparable across all experimental groups (Table 1). At 7 days post-MI, placebo-treated mice developed: (1) elevated left ventricular filling pressure (LVEDP); (2) increased end-systolic and end-diastolic volumes; and (3) severe LV dysfunction as evidenced by impaired ejection performance, dP/dtmax, dP/dtmin, and the load-independent contractility index (LV dP/dtmax/instantaneous pressure) (Figures 1B, 2; Table 1). Notably, high-dose spironolactone (100 mg/kg) worsened early LV dysfunction compared to the 20 mg/kg dose (LVEDP: 18 ± 1 mmHg; dP/dtmax: 3413 ± 295 mmHg/s; dP/dtmin: -2258 ± 198 mmHg/s; n=5). This group also showed significantly higher mortality (Figure 1A), with necropsy confirming acute heart failure (pleural effusion and pulmonary congestion). Consequently, all subsequent analyses used the 20 mg/kg spironolactone regimen.", "inconsistent_part": "caption", "tampered_sentences": ["Effects of immediate treatment with eplerenone (Eple) and spironolactone (Spiro) on survival and hemodynamics in mice 3 days after myocardial infarction (MI)"], "golden_sentences": ["Effects of immediate treatment with eplerenone (Eple) and spironolactone (Spiro) on survival and hemodynamics in mice 7 days after myocardial infarction (MI)"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010057590_TII_01/figure/2010057590_TII_01_0.png"], "tampered": true, "paper_ids": ["2010001695"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010129304_TII_02/figure/2010129304_TII_02_2.png", "question_id": "consistency_73", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Fig. 1. DLA-M decreases body weight and improves insulin resistance in HFD C57BL/6J mice. NCD and HFD (60% kcal fat) C57BL/6J mice were treated daily with water or 1 g/kg/day DLA-M by intragastric gavage for 10 weeks (n = 6–15). Effects of DLA-M treatment on the body weight gain and the calculated AUC (a), serum TG and TC content (b), fasting blood glucose and serum insulin levels (c), and calculated HOMA-IR and QUICKI values (d) are shown. IGTT (e); OGTT (f); ITT (g) results. Curves of the blood glucose levels and the calculated AUC are shown. Values are expressed as the means ± s.e.m. **, P < 0.01; ***, P < 0.001 compared with NCD. #, P < 0.05; ##, P < 0.01; and ###, P < 0.001 compared with HFD. Differences were assessed by ANOVA with Tukey's multiple comparison test.", "figure_related_sentences": "Two mouse models of obesity—10-week-old male C57BL/6J and CD-1 mice—were fed a normal chow diet (NCD) or a high-fat diet (HFD) for 10 and 5 weeks, respectively. In agreement with previous work using an obese rat model (Xu et al., 2016), DLA-M prevented body weight loss in both animal models, but did not cause a significant change in the relative food intake of CD-1 mice (Fig. 1a and Supplementary Fig. 1a–c). Because obesity is strongly associated with insulin resistance, a typical characteristic of type 2 diabetes (T2D), we measured fasting blood glucose and insulin concentrations and calculated the homeostasis model assessment of insulin resistance (HOMA-IR: insulin × glucose ∕ 22.5) and the quantitative insulin sensitivity check index (QUICKI: 1 ∕ [log(insulin) + log(glucose)]). DLA-M treatment significantly improved insulin sensitivity in the mice and reversed the two indices to nearly normal levels (Fig. 1c and d), a result further confirmed by intraperitoneal glucose tolerance test (IGTT) (Fig. 1e), oral glucose tolerance test (OGTT) (Fig. 1f), and insulin tolerance test (ITT) (Fig. 1g) analyses in C57BL/6J mice.", "inconsistent_part": "related_sentences", "tampered_sentences": ["DLA-M prevented body weight loss in both animal models"], "golden_sentences": ["DLA-M prevented body weight gain in both animal models"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010129304_TII_02/figure/2010129304_TII_02_2.png"], "tampered": true, "paper_ids": ["2010001701"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010014696_TII_02/figure/2010014696_TII_02_2.png", "question_id": "consistency_74", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Calcineurin removes activating phosphorylations from Hcm1. (A) Strains expressing the indicated Hcm1 proteins were treated with CaCl2 for 10 min, and phosphorylation was assayed by Phos-tag Western blot. Note that the top band in the 12C sample is also present in the 15A sample, suggesting that it is the result of Cdk1-independent phosphorylation. (B) Cdk1-phosphorylated Hcm1 proteins were incubated with or without CN for 45 min. Average percentage phosphorylation remaining is shown ± 1 SD (n = 3). Hcm1ΔPSIEIQ is significantly different from wild-type Hcm1 (*p < 0.05, Student's t test). Also see Supplemental Figure S1B. (C) Cycloheximide-chase assays comparing the stability of Hcm1 proteins with or without CaCl2 treatment. (D) Average data from five experiments were used to calculate half-life values (indicated in parentheses) of each protein with or without CaCl2.", "figure_related_sentences": "Under these gel conditions, the phosphorylation status of a panel of Hcm1 mutants with different numbers of Cdk1 phosphosites is clearly distinguishable (Figure 2, A and C). In addition, we found that within 10 min of direct CN activation by the addition of CaCl2 to the growth medium, Hcm1 was mildly dephosphorylated (Figure 2D). This dephosphorylation was blocked by deletion of the CN docking site in Hcm1 (ΔP; Figure 2D), by deletion of the regulatory subunit of CN, Cnb1 (Figure 2D), or upon addition of the CN inhibitor FK506 (Figure 2E). These data demonstrate that Hcm1 is dephosphorylated by CN in vivo. Of note, Hcm1 retained some phosphorylation after CN activation (Figure 2, D and E), suggesting that CN might target only a subset of Hcm1 phosphosites. To test this, we examined CN-dependent dephosphorylation of previously characterized mutants in which all Cdk1 sites were mutated except for the eight activating Cdk1 sites (Hcm1-7N, with 7 N-terminal S/T-P sites mutated to A-P; Figure 2A) or the three destabilizing Cdk1 sites (Hcm1-12C, with 12 C-terminal S/T-P sites mutated to A-P; Figure 2A; Landry et al., 2014). Of interest, Hcm1-7N was almost completely dephosphorylated after CN activation, whereas Hcm1-12C phosphorylation was largely unchanged (Figure 3A). Hcm1 interacted with the CN-regulatory subunit Cna1 in this assay, and the interaction was eliminated upon deletion of a six–amino acid sequence on Hcm1 (PSIEIQ; Figure 2, A and B) that matches the consensus for the previously identified CN docking-site sequence (Roy et al., 2007).", "inconsistent_part": "related_sentences", "tampered_sentences": ["Hcm1 was mildly dephosphorylated (Figure 2D)."], "golden_sentences": ["Hcm1 was dramatically dephosphorylated (Figure 2D)."], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010014696_TII_02/figure/2010014696_TII_02_2.png"], "tampered": true, "paper_ids": ["2010001712"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010073211_TII_01/figure/2010073211_TII_01_3.png", "question_id": "consistency_75", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 4. Effect of pH on the release of methylprednisolone (MP) from the BSA633-MP nanoconjugate. The nanoconjugates were incubated in (A) PBS at pH 7.4 and (B) acetate buffer at pH 4.0 for 48 h at 37°C. After incubation, samples were eluted in a column with Sephadex G-100 gel. An amount of 0.5 ml of each fraction was collected. The released MP was detected by OD240, while albumin was detected by Alexa Fluor 633. (C) The nanoconjugates were incubated at pH 4.0 for 1, 4, 8, 12, 24 and 48 h at 37°C for a time course release assay. Values are the mean ± standard error of the mean (n=3).", "figure_related_sentences": "Release profile of BSA633‑MP. The effects of neutral pH and relatively acidic pH on the release profile of BSA633‑MP conjugate were evaluated. As shown in Fig. 4A, we clearly see that under pH 7.4, almost nothing was released from the BSA633-MP conjugate. However, under pH 4.0, most MP molecules were released, a small unreleased portion remained which was eluted together with albumin (Fig. 4B). The OD240 values involved in the second elution peak vs. the total OD240 values (with subtraction of albumin itself) were calculated to roughly estimate the release percentage. As shown in Fig. 4C, with prolonged incubation, drug release was increased and at 48 h the release almost reached a plateau. Under pH 4.0 ~28% of MP drug was released after 48 h. These results indicated that the BSA633-MP conjugate was acid-sensitive and very stable in a neutral environment. Actually, the nanoconjugates were found to be stable for at least 3 months when stored in buffer at pH 7.4, without manifesting aggregation or degradation (data not shown).", "inconsistent_part": "related_sentences", "tampered_sentences": ["0 ~28% of MP drug was released after 48 h."], "golden_sentences": ["0 ~72% of MP drug was released after 48 h."], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010073211_TII_01/figure/2010073211_TII_01_3.png"], "tampered": true, "paper_ids": ["2010001836"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010035913_TII_02/figure/2010035913_TII_02_3.png", "question_id": "consistency_76", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 3 Percentage of patients achieving glycaemic control according to HbA1c intervals. HbA1c, glycated haemoglobin; T2DM, type 2 diabetes mellitus", "figure_related_sentences": "Finally, the analysis of the evolution of the attained glycaemic control according to different HbA1c intervals also showed that there were many remarkable changes among years in any case (figure 3). Of note, the group of patients who were less likely to achieve the corresponding glycaemic target included those younger than 65 years, without comorbidities, and duration of T2DM≤15 years (range 50.8–55.1%) (see online supplementary table S1).", "inconsistent_part": "related_sentences", "tampered_sentences": ["Finally, the analysis of the evolution of the attained glycaemic control according to different HbA1c intervals also showed that there were many remarkable changes among years in any case (figure 3)"], "golden_sentences": ["Finally, the analysis of the evolution of the attained glycaemic control according to different HbA1c intervals also showed that there were no remarkable changes among years in any case (figure 3)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010035913_TII_02/figure/2010035913_TII_02_3.png"], "tampered": true, "paper_ids": ["2010001838"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010123552_TII_01/figure/2010123552_TII_01_0.png", "question_id": "consistency_77", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Fig. 1. Hepatic insulin receptor substrate and PI3K proteins expression in ApoE knock-in mice. (A) Western blot analysis of insulin receptor substrate-1 (IRS1), PI3K/p85 and PI3K/p110 levels in the liver of ApoE3 and ApoE4 mice at 12 and 72 weeks of age. β-actin was immunoblotted to ensure similar gel loading of the starting material in each sample. The blot is a representative of three independent experiments. Densitometry analysis of total (B) IRS1, (C) PI3K/p110 and (D) PI3K/p85 level relative to β-actin level in 12 and 72 weeks old ApoE3 (white bar) and ApoE4 (grey bar) mice was performed using the NIH ImageJ software. Each value represents the mean ± SEM for individual mouse liver sample (n = 3 at each time point for each mouse line). Lower IRS1, PI3K/p85 and PI3K/p110 levels were detected in ApoE4 mice at 72 weeks of age as compared to ApoE3 mice of similar age. (*p < 0.03; **p < 0.008, using Student’s t-test.)", "figure_related_sentences": "At 72 weeks, insulin receptor substrate 1 (IRS1) expression does not differ between fasting ApoE3 and ApoE4 mice (Fig. 1A). At 12 weeks, however, IRS1 expression is non-detectable in the fasting ApoE4 KI mice. We then examined the expression of the catalytic subunit (p110) and the regulatory subunit (p85) of phosphatidylinositol 3-kinase (PI3K). At 12 weeks, PI3K/p110 and PI3K/p85 expression were comparable between ApoE3 and ApoE4 mice. In the aged (72 weeks) fasting ApoE4 mice, however, PI3K/p110 and PI3K/p85 expression were reduced by 70% (Fig. 1C) and 44% (Fig. 1D), respectively, as compared to fasting ApoE3 mice.", "inconsistent_part": "related_sentences", "tampered_sentences": ["At 72 weeks, insulin", "At 12 weeks, however"], "golden_sentences": ["At 12 weeks, insulin", "At 72 weeks, however"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010123552_TII_01/figure/2010123552_TII_01_0.png"], "tampered": true, "paper_ids": ["2010001866"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010127336_TII_02/figure/2010127336_TII_02_0.png", "question_id": "consistency_78", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1: MRTFA KO mice have smaller body weight, reduced bone mass with shorter femurs and tibiae. WT (n = 7) and MRTFA KO (n = 7) female mice (24 weeks old) were euthanized and then weighed. The image of a matched pair of WT and MRTFA KO mice is shown in (A). The femurs and tibiae of the mice were then dissected (images shown in C) and the bone lengths were measured with a caliper. The upper and lower black lines in C mark the length of the WT mouse femurs to show the differences. Whole body weights (B), femur lengths (D), and tibia lengths (E) of the mice are shown in bar graphs. Representative 3D images of cortical and trabecular region of WT and MRTFA KO mice femurs generated by μCT analysis are shown in F. Cortical thickness of WT and MRTFA KO femurs are shown in bar graphs (G). Trabecular bone volume fraction (H), trabecular number (I), trabecular thickness (J), trabecular separation (K), and connectivity density (L) are shown in bar graphs. Data are expressed as mean ± SEM. *p < 0.05; **p < 0.01.", "figure_related_sentences": "Six-week-old MRTFA KO mice are taller and weigh less than WT littermates (Figure 1A and B and Supplementary Figure 1). This observation suggested that there might be a defect in skeletal development. To investigate a possible role of MRTFA in bone formation, lengths of the femurs and tibiae were measured with calipers. The KO mice have significantly shorter femurs and tibiae (Figure 1C, D, E and Supplementary Figure 1) when compared to WT controls. Micro-computed tomography (μCT) was performed on femurs of 24-week-old female mice (n = 7 in each group) to assess bone growth and development. μCT of the mid-diaphyseal region of femurs showed that cortical thickness of femurs from MRTFA KO mice is significantly thicker than WT controls (Figure 1F, G); however, cortical bone volume fraction (BV/TV) did not differ significantly (Table 1). μCT of the trabecular regions of proximal femurs showed a marked reduction in trabecular bone mass in the MRTFA KO mice as compared to controls (Figure 1F). Trabecular bone volume fraction is about 50% higher in KO mice (Figure 1H). Bone volume of the trabecular region is also significantly reduced, although the total tissue volume did not appear to differ (Table 1). Furthermore, average trabecular number (Figure 1I) and trabecular bone connectivity density (Figure 1L) are both lower in MRTFA deficient mice, and trabecular spacing (Figure 1J) is larger. There was no significant difference in trabecular thickness (Figure 1K), which is likely due to high bone turnover rate in rodents.", "inconsistent_part": "related_sentences", "tampered_sentences": ["Six-week-old MRTFA KO mice are taller and weigh less than WT littermates (Figure 1A and B and Supplementary Figure 1).", "μCT of the mid-diaphyseal region of femurs showed that cortical thickness of femurs from MRTFA KO mice is significantly thicker than WT controls (Figure 1F, G)", "Trabecular bone volume fraction is about 50% higher in KO mice (Figure 1H)."], "golden_sentences": ["Six-week-old MRTFA KO mice are shorter and weigh less than WT littermates (Figure 1A and B and Supplementary Figure 1).", "μCT of the mid-diaphyseal region of femurs showed that cortical thickness of femurs from MRTFA KO mice is significantly thinner than WT controls (Figure 1F, G)", "Trabecular bone volume fraction is about 50% lower in KO mice (Figure 1H)."], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010127336_TII_02/figure/2010127336_TII_02_0.png"], "tampered": true, "paper_ids": ["2010001884"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010014663_TII_02/figure/2010014663_TII_02_3.png", "question_id": "consistency_79", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "The c-Myb protein level is critical for GSK3β-dependent cell survival. (A) Jurkat, K562, and RPMI 8226 cells were treated with or without 5 or 10 μM SB216763 for 8 h, and cell lysates were analyzed by immunoblotting. (B) RPMI 8226, K562, and Jurkat cells were infected with lentivirus expressing GSK3β shRNA or a nonspecific control shRNA. Four days after infection, cells were harvested for immunoblotting analysis. (C) Jurkat cells were infected with lentiviral-overexpressed c-Myb or a control vector and after 48 h treated with or without SB216763 (10 μM) for another 2 or 3 days. Cell numbers were determined at days 0, 2, and 3 with a CASY Model TT cell counter (left). Data are represented as mean and SD. The overexpression of c-Myb was verified by immunoblotting (right). (D) Jurkat cells were treated with cycloheximide (20 μg/ml) in the absence or presence of LiCl (10 mM) for the indicated time points, and cell lysates were analyzed by immunoblotting. For the quantification on the right, the c-Myb protein level at time 0 was set at 100%. (E) Jurkat cells were treated with or without SB216763 (10 μM) or LiCl (10 mM) for 6 h, after which MG132 (10 μM) was added for another 4 h. c-Myb and nonspecific control immunoprecipitations were analyzed by SDS–PAGE and immunoblotting.", "figure_related_sentences": "We next tested the effect of GSK3β inactivation on the c-Myb and LEF-1 proteins. Of importance, in all leukemia cells examined, the levels of c-Myb were increased upon SB216763 or LiCl treatment, whereas the levels of LEF-1 did not show significant similarity (Figure 4A and Supplemental Figure S3). RNAi-mediated depletion of GSK3β in all three kinds of leukemia cell lines led to an obvious decrease in c-Myb and upregulation of cleaved caspase 3 (Figure 4B). c-Myb overexpression could rescue the inhibition of cell proliferation by SB216763 in Jurkat cells, demonstrating that c-Myb is a critical growth-regulatory target of GSK3β kinase activity in these cells (Figure 4C). Inhibition of de novo protein synthesis by cycloheximide (CHX) showed that c-Myb degraded faster in cells treated with SB216763 or LiCl (Figure 4D and unpublished data). In addition, we found that the ubiquitination of c-Myb was increased after GSK3β inactivation (Figure 4E).", "inconsistent_part": "related_sentences", "tampered_sentences": ["the levels of c-Myb were increased upon SB216763 or LiCl treatment", "whereas the levels of LEF-1 did not show significant similarity (Figure 4A and Supplemental Figure S3)"], "golden_sentences": ["the levels of c-Myb were reduced upon SB216763 or LiCl treatment", "whereas the levels of LEF-1 did not show significant differences (Figure 4A and Supplemental Figure S3)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010014663_TII_02/figure/2010014663_TII_02_3.png"], "tampered": true, "paper_ids": ["2010001886"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010124577_TII_01/figure/2010124577_TII_01_0.png", "question_id": "consistency_80", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. hMSC-to-MF Activation Reduces Clonogenicity and Lineage Differentiation Potential (A and B) hMSCs were cultured with and without TGF-β1 (2 ng/ml) for 4 days to assess MF activation by staining for α-SMA (red) and stress fibers (F-actin, green), for 10 days to assess CFU-F formation, and 14 days to assess adipogenesis (oil-red-O-positive lipids) and osteogenesis (Alizarin Red S-positive mineralized nodules) in respective induction media (+TGF-β1). (B) MF activation was quantified by assessing the percentage of α-SMA expressing hMSCs. The contraction was assessed by growing hMSC on deformable wrinkling substrates (white lines in immunofluorescence image overlay) and quantifying the total wrinkle area normalized by cell numbers. Clonogenicity was assessed by counting the number of colonies formed after 10 days. (C–G) hMSCs were cultured on FN-coated silicone substrates, mimicking fibrosis-rigid (65 kPa), wound-stiff (26 kPa), and normal-tissue-soft (3 kPa) environments. (D) After 5 days, cells were analyzed by western blotting for α-SMA and vimentin (loading control) and (E) immunofluorescence for α-SMA (red) and ED-A FN (green). The scale bar represents 50 μm. (F) MF activation was quantified as percentage of α-SMA stress fiber positive cells. (G) Clonogenicity was quantified in CFU-F assays on differently stiff substrates. All of the graphs show averages ± SD from at least five independent experiments (*p ≤ 0.05, **p ≤ 0.005, and ***p ≤ 0.0005 using ANOVA followed by a post hoc Tukey’s multiple comparison test). See also Figure S1.", "figure_related_sentences": "MF Activation Results in Reduced Clonogenicity and Differentiation Potential of hMSCsIndependently of MSC origin, MF activation occurs spontaneously in standard cell culture on rigid tissue culture plastic in serum-containing media. Cultured hMSCs derived from adipose tissue, umbilical cord perivasculature, and bone marrow all developed MF characteristics, including α-SMA-positive stress fibers, extradomain-A fibronectin (ED-A FN) in the ECM, and high contractile activity, which were enhanced by TGF-β1 (Figure S1). To test whether MF activation affected stem cell features, we focused on bone-marrow derived hMSCs (Figure 1A). In standard culture, 17% ± 4.2% of hMSCs expressed α-SMA in F-actin-positive stress fibers, which increased to 32% ± 5.1% after TGF-β1 treatment, associating with 3.5-fold higher contraction (Figures 1A, 1B, and S1). TGF-β1 treatment reduced the number of colony forming units-fibroblasts (CFU-F) by 3-fold (Figure 1B) and the ability of hMSCs to differentiate into adipogenic (10-fold) and osteogenic (7-fold) cell lineages in conventional lineage-induction assays supplemented with TGF-β1 (Figure 1B). TGF-β1 treatment resulted in approximately 1.5-fold increase in median fluorescence intensity of common MSC markers such as CD44, CD73, and CD90, but did not change levels of CD105 and CD166 (Figure S2). This supports the onset of a fibrogenic program since CD44, CD73, and CD90 have all been identified on fibroblasts and are upregulated in conditions of fibrosis (Fernández et al., 2013; Koumas et al., 2003; Li et al., 2011; Maring et al., 2012; McQualter et al., 2013).To test whether low ECM stiffness, a powerful inhibitor of MF activation (Goffin et al., 2006), improves hMSC clonogenicity and lineage differentiation potential, we cultured hMSCs on silicone substrates with different Young’s elastic modulus simulating different scar maturation stages (Figure 1C). Expression of α-SMA and ED-A FN decreased after 5 days culture on “fibrosis-rigid” (65 kPa) over “wound-stiff” (26 kPa) to “normal tissue-soft” (3 kPa) substrates (Figures 1D and 1E). Percentages of α-SMA stress fiber-positive hMSCs decreased from 21.9% ± 3.4% (65 kPa) to 17.3% ± 2.4% (26 kPa) and 10.3% ± 3.1% (3 kPa) (Figure 1F), while the number of CFU-F increased (Figure 1G). Treatment with TGF-β1 enhanced α-SMA expression on 26 kPa and 65 kPa substrates compared to non-treated controls, but also reduced CFU-F capacity independently of α-SMA content (3 kPa). This finding is consistent with previous studies reporting inhibitory effects of TGF-β1 on mesenchymal cell proliferation (Kim et al., 2014) and MSC self-renewal capacity by inducing osteogenesis and chondrogenesis (Watabe and Miyazono, 2009). Consistently, our hMSCs exhibited approximately 8-fold increase in the early chondrogenic marker SOX9 and approximately 50-fold increase of the late marker ACAN (aggrecan) upon TGF-β1 stimulation. Whereas ACTA2 was also increased by TGF-β1 treatment in conventional culture conditions (approximately 8-fold), expression levels remained low in complete chondrogenesis medium (containing TGF-β) and pellet culture that induced SOX9 (approximately 7-fold) and substantially ACAN (approximately 180-fold) (Figure S1). Hence, using TGF-β1 as a stimulus is not suitable to test whether MF activation is directing hMSC stem cell potential.", "inconsistent_part": "related_sentences", "tampered_sentences": ["4% (26 kPa) and 10.3% ± 3."], "golden_sentences": ["4% (26 kPa) and 5.7% ± 3."], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010124577_TII_01/figure/2010124577_TII_01_0.png"], "tampered": true, "paper_ids": ["2010001903"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010127644_TII_02/figure/2010127644_TII_02_4.png", "question_id": "consistency_81", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 3. Silica-coated ZnO NPs exhibit antimicrobial activity comparable to uncoated ZnO NPs. The growth of *E. coli* was inhibited by both uncoated and silica-coated ZnO NPs after (A) 3 h and (B) 21 h of incubation. Similarly, the growth of *S. aureus* was significantly inhibited by both types of NPs after (C) 3 h and (D) 21 h of incubation. \"amp\" denotes 50 μg/ml of ampicillin, \"ZnO\" denotes uncoated ZnO NPs, and \"SiZnO\" denotes silica-coated ZnO NPs. Data represent means ± SD, *n* = 3. Student’s *t*-test, *p* < 0.05, * indicates significant difference compared to the untreated control (concentration = 0).", "figure_related_sentences": "After confirming the presence of silica coating on ZnO nanoparticles (NPs), we assessed how this modification affects their antimicrobial properties. As shown in Figure 3, the silica coating retained—and in the case of *S. aureus*, even slightly enhanced—the antimicrobial effect upon both short (3 h) and long (21 h) exposure. Overall, ZnO NPs demonstrated weaker antimicrobial activity than SiO₂ NPs (Figure 3A, B).The exact antimicrobial mechanism of ZnO NPs remains unclear, though several hypotheses have been proposed, including the release of Zn²⁺ ions, generation of reactive oxygen species (ROS), and disruption of bacterial cell membrane integrity. Jiang et al. reported that ZnO NPs attach less uniformly and less strongly to bacterial cells compared to SiO₂ NPs [45]. Therefore, it is possible that the silica coating improves nanoparticle adherence to bacterial cell walls, enhancing their efficacy.Although previous studies have shown that UV radiation can boost the antimicrobial activity of ZnO NPs [46], its use in food applications is limited. Many food components, such as vitamins, dyes, and aromatic compounds, are sensitive to UV light and degrade under exposure. Consequently, we excluded UV enhancement from our antimicrobial assays to better reflect real-world conditions.Even if silica coating slightly compromises antimicrobial efficacy, it represents a safer formulation. Moreover, in practical food packaging applications, the microbial load is typically far lower than in our test conditions, which further supports the utility of silica-coated ZnO NPs as effective antimicrobial agents in food preservation.", "inconsistent_part": "related_sentences", "tampered_sentences": ["ZnO NPs demonstrated weaker antimicrobial activity than SiO₂ NPs (Figure 3A, B)"], "golden_sentences": ["ZnO NPs demonstrated stronger antimicrobial activity than SiO₂ NPs (Figure 3A, B)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010127644_TII_02/figure/2010127644_TII_02_4.png"], "tampered": true, "paper_ids": ["2010001978"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010013696_TII_01/figure/2010013696_TII_01_8.png", "question_id": "consistency_82", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "SNV binding to integrin PSI domain recapitulates physiological activation of αIIbβ3. (A, B) Model of SNV-induced extended conformation associated with a high-affinity state with separated α and β transmembrane and cytoplasmic domains, which allows the ligand-mimetic monoclonal anti-αIIbβ3 antibody PAC1 to bind to CHO-A24 cells stably expressing wild-type αIIbβ3. Flow cytometry histogram inserts show fluorescence associated with (a) PAC-1 staining of 50,000 cells activated with SNV particles, (b) staining of resting cells, and (c) autofluorescence of unstained cells. The graph is a plot of PAC-1 staining (1:20 dilution) of CHO-A24 corrected for autofluorescence. Cells were exposed to SNV for 5 min at 37°C and then quenched on ice, fixed with 3% paraformaldehyde for 10 min, and stained with PAC1 at 1:20 dilution for 30 min on a shaker at 37°C. Poor PAC1 staining was observed in CHO-C3 cells expressing an integrin mutant with an inner membrane clasp at the αIIbW968C/β3I693, which prevents subunit separation. Experiments were performed in parallel with CHO-A24. Error bar is SE for duplicate measurements, *p < 0.05. (C) Plot of fold increase over resting cells in PAC-1 staining of CHO-A24 cells in suspension after 30 min exposure to killed SNV. 10,000 CHO-A24 cells suspended in 20 µl media containing 1:10 dilution PAC-1 antibody, coadministered with 1 µM GRGDSP. (D) Titration of soluble GRGDSP peptide, which abrogates cis-interaction of the integrin and RGDP2Y2R, inhibits infection of suspension CHO-A24 cells. CHO-A24 cells were infected in suspension with 0.1 moi SNV for 30 min. Cells were then washed in low pH media three times and then incubated in normal media for 24 h and then assayed for viral N-protein.", "figure_related_sentences": "In the C3 cells, the αIIb 968 tryptophan (W) and the 693 isoleucine (I) residues were replaced with cysteines to prevent the separation of the cytoplasmic domains through constitutive disulfide bond formation (Luo et al., 2004) (Figure 9). Exposure of CHO-A24 and CHO-C3 cells to SNV for 5 min produced a twofold increase in PAC1 binding to A24 cells compared with the resting state (Figure 9A), with no significant change in PAC1 staining of C3 cells in the same setting (Figure 9B). Staining of CHO-A24 cells with PAC1 in the presence of 1 µM GRGDSP did not rise above background in SNV-stimulated cells compared with mock-treated cells (Figure 9C). Quantitative analysis of the gel was performed using a BioRad Molecular Imager. The data indicate that GRGDSP inhibited infection (Figure 9D). We then showed that blocking of the αIIbβ3–RGDP2Y2R interaction with a soluble GRGDSP peptide inhibits full integrin activation and infection (Figure 9).", "inconsistent_part": "related_sentences", "tampered_sentences": ["Exposure of CHO-A24 and CHO-C3 cells to SNV for 5 min produced a twofold increase in PAC1 binding to A24 cells compared with the resting state (Figure 9A)"], "golden_sentences": ["Exposure of CHO-A24 and CHO-C3 cells to SNV for 5 min produced a threefold increase in PAC1 binding to A24 cells compared with the resting state (Figure 9A)"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010013696_TII_01/figure/2010013696_TII_01_8.png"], "tampered": true, "paper_ids": ["2010002000"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010074157_TII_02/figure/2010074157_TII_02_3.png", "question_id": "consistency_83", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 4. DLS inhibits chemokine-mediated signaling in CCR5-transfected 3T3 cell lines. Approximately 200,000 3T3.T4.CCR5 cells were grown overnight per well in a 6-well plate. On the following day, the media was replaced with 2 ml of serum-free medium. After 2–3 h, DLS (20 μM) or the CCR5-specific antagonist, TAK779 (2 μM), were added to respective wells, incubated for 30 minutes at 37 °C, after which 10 nM of RANTES (A) or MIP-1β (B) was added to indicated wells. The cells were harvested in RIPA after washing with cold PBS at the indicated times. 30 μg of protein was run in 4–20% Bis-Tris gel, transferred and probed with mouse anti-pERK antibody (upper panel), stripped and again probed with rabbit anti-total ERK antibody (lower panel). The results reveal that DLS partially allows RANTES-induced ERK activation but surprisingly does not block MIP-1β-induced ERK activation in 3T3.T4.CCR5 cells.", "figure_related_sentences": "3T3.T4.CCR5 cells were grown overnight and then pretreated with DLS (20 μM) or the CCR5-specific antagonist, TAK779 (2 μM) for 30 minutes at 37 °C, after which 10 nM of MIP-1β or RANTES were added to cultures. The cells were harvested in RIPA after washing with cold PBS at the indicated times. The results (Figure 4) reveal that DLS partially blocks RANTES-induced ERK activation in 3T3.T4.CCR5 cells. Surprisingly, MIP-1β-induced ERK activation was not affected by DLS using this cell line. TAK779 at 2 μM only demonstrated a 20–30% inhibition of ERK phosphorylation in these CCR5-expressing cells.", "inconsistent_part": "caption", "tampered_sentences": ["The results reveal that DLS partially allows RANTES-induced ERK activation but surprisingly does not block MIP-1β-induced ERK activation in 3T3.T4.CCR5 cells", "MIP-1β-induced ERK activation was not affected by DLS using this cell line"], "golden_sentences": ["The results reveal that DLS partially blocks RANTES-induced ERK activation but surprisingly does not block MIP-1β-induced ERK activation in 3T3.T4.CCR5 cells", "MIP-1β-induced ERK activation was not influenced by DLS using this cell line"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010074157_TII_02/figure/2010074157_TII_02_3.png"], "tampered": true, "paper_ids": ["2010002043"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010040108_TII_02/figure/2010040108_TII_02_0.png", "question_id": "consistency_84", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "FIGURE 1 Dickkopf-1 (DKK1) inhibition reverses suppressive tumor immune microenvironment of a syngeneic gastric cancer (GC) model. (A) Schematic of DKK1 inhibitor (WAY-262611) treatment schedule in GC subcutaneous model. (B) Representative images of tumors and (C) tumor volumes of mouse forestomach carcinoma (MFC)-challenged 615-line mice. (D–K) Proportions of (D) CD8+/CD45+ cells, (E) tumor necrosis factor-α (TNF-α) +/CD45+ cells, (F) γ-interferon (IFN-γ) +/CD45+ cells, (G) natural killer (NK)1.1+/CD45+ cells, (H) Gr-1+/CD11b+ cells, (I) CD86+/F4/80+ cells, and (J) CD163+/F4/80+ cells in tumors were detected by flow cytometry (FCM). (K–O) Proportions of (K) CD8+/CD45+ cells, (L) NK1.1+/CD45+ cells, (M) Gr-1+/ CD11b+ cells, (N) CD86+/F4/80+ cells, (O) and CD163+/F4/80+ cells in spleens were detected by FCM. Data with error bars are shown as mean ± SEM. *p< 0.05, **p< 0.01, ***p< 0.001, ****p< 0.0001. D, day", "figure_related_sentences": "To investigate whether DKK1 inhibition showed antitumor efficacy in GC models, we established an MFC-challenged GC syngeneic immunocompetent mouse model and a T cell-deficient mouse model, followed by treatment with DKK1 inhibitor (WAY-262611) or DMSO (control group for WAY-262611) as indicated (Figures 1A and S1A). An interesting finding was that the tumor size and tumor volume increased significantly in GC immunocompetent mice (Figure 1B,C). The FCM analysis showed increased tumoral and splenic infiltration of CD8+ T cells (Figure 1D,K) andhigher proportions of tumoral IFN-γ+ lymphocytes and TNF-α+ lymphocytes (Figure 1E,F). Increased proportions of tumoral NK cells and decreased proportions of splenic MDSCs and M2 macrophages were found after DKK1 inhibition (Figure 1G,M,O). We also found that, although not statistically significant, the NK cells (p= 0.0863) in the spleen showed a tendency to increase and the MDSCs and M2 in the tumor (p= 0.0915, p= 0.0873) tended to decrease after inhibiting DKK1 inhibition (Figure 1H,J,L). However, M1 macrophages in the tumors showed no significant changes, but increased in the spleens after DKK1 inhibition (Figure 1I,N).", "inconsistent_part": "related_sentences", "tampered_sentences": ["An interesting finding was that the tumor size and tumor volume increased significantly in GC immunocompetent mice (Figure 1B,C)"], "golden_sentences": ["An interesting finding was that the tumor size and tumor volume decreased significantly in GC immunocompetent mice (Figure 1B,C)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010040108_TII_02/figure/2010040108_TII_02_0.png"], "tampered": true, "paper_ids": ["2010002073"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010049515_TII_02/figure/2010049515_TII_02_2.png", "question_id": "consistency_85", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 3. p53 expression at both the protein and mRNA level. (A) Western blot of p53 protein in SDHx variant-positive CS/CSL (patient ID—SDHx variant: 829LL-S163P, 1965ML-S163P, 2094GR-H50R, 2549MP-G12S, 2854PS-S163P, 2894KP-H50R) and normal control groups. Upper panel shows the protein profile under normal culture condition, and lower panel after cells treated with 4 μM proteasomal inhibitor MG132 for 4 h. Tubulin served as a loading control in both conditions. (B) Relative levels of p53 were quantitated by densitometry and normalized to tubulin. Results are fold change compared with normal control cells, with (upper panel) or without MG132 treatment (lower panel). Data were presented as (mean ± SEM). *P < 0.05. (C) Relative TP53 mRNA expression by quantitative RT–PCR in SDHx variant-positive samples compared with normal controls, with glyceraldehyde 3-phosphate dehydrogenase (GAPDH) as internal control. (D) Immunoprecipitation of p53 from control and SDHvar+ LCL whole-cell lysate blotting for NQO1 and p53, *indicates the light chain band of IgG.", "figure_related_sentences": "Exposure of cells to high levels of ROS leads to oxidative stress, and should induce a p53-mediated response including apoptosis, whereas we observed the opposite in our cases. Therefore, we decided to investigate if p53 is somehow modified in our patient samples in order to escape the expected apoptotic regulation. Western blots showed reduced p53 protein expression in the majority of samples harboring SDHx variants compared with normal controls (Fig. 3A and B, upper panels). In contrast to p53 protein levels, TP53 mRNA expression was not changed in SDHx variant-positive samples compared with controls (Fig. 3C), suggesting that the loss of p53 protein was not from downregulated TP53 transcript. Cells treated with proteasome inhibitor MG132 preserved the loss of the p53 protein phenomenon in SDHx variant-positive cells (Fig. 3A and B, lower panels), indicating that the loss of p53 protein is most likely due to enhanced protein degradation. The multiple bands >53 kDa are likely ubiquitinated p53 resulting from proteasomal inhibition.", "inconsistent_part": "related_sentences", "tampered_sentences": ["Cells treated with proteasome inhibitor MG132 preserved the loss of the p53 protein phenomenon in SDHx variant-positive cells (Fig. 3A and B, lower panels)"], "golden_sentences": ["Cells treated with proteasome inhibitor MG132 abolished the loss of the p53 protein phenomenon in SDHx variant-positive cells (Fig. 3A and B, lower panels)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010049515_TII_02/figure/2010049515_TII_02_2.png"], "tampered": true, "paper_ids": ["2010002143"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010074872_TII_02/figure/2010074872_TII_02_8.png", "question_id": "consistency_86", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 9. Alizarin-red assay to bone matrix mineralization. (A) Staining (Scale bar: 100 μm), and (B) Quantitative calcium level deposition. Data are expressed as the mean ± S.D (n = 3). *p < 0.05, **p < 0.001.", "figure_related_sentences": "Extracellular matrix mineralization and quantitative calcium-level deposition were determined at 14 days postculture by Alizarin red staining. As shown in Figure 9A, in the presence of His‑βCD‑PH and HP‑βCD‑PH, matrix mineralization was decreased clearly compared with the control. Free PH in DMSO at a concentration of 20 μM was selected as a control, since it induced the most positive osteogenesis effect for bone regeneration in a previous study. It is postulated that sustained release of PH as a result of the equilibrium between PH in inclusion complexes of βCD derivatives and PH in cell-culture medium during differentiation had a significant positive effect on matrix mineralization. There was a difference between His‑βCD‑PH and HP‑βCD‑PH for matrix mineralization. Bone-matrix mineralization in the presence of His‑βCD‑PH was higher than that for HP‑βCD‑PH (Figure 9B). As shown in this figure, calcium-level deposition was significantly decreased when hASCs were cultured with His‑βCD‑PH and HP‑βCD‑PH at 50 μM concentration compared with the control. The results indicated that in addition to increased solubility of PH by inclusion-complex formation, His conjugation as a penetrative group contributed to increased bone mineralization. Electrostatic internalization of the His‑βCD‑PH inclusion complex by MSC membranes and their postendosomal escape followed by penetration into the nucleus might lead to better transfer of PH with consequent increase in bone-matrix mineralization. For detailed investigation on the effect of His‑βCD‑PH and HP‑βCD‑PH on hASCs for bone differentiation, real-time PCR was performed at 14 days postculture to investigate late bone-marker gene (OCN and OPN) expression.", "inconsistent_part": "related_sentences", "tampered_sentences": ["matrix mineralization was decreased clearly compared with the control", "calcium-level deposition was significantly decreased when hASCs were cultured with His‑βCD‑PH and HP‑βCD‑PH at 50 μM concentration compared with the control"], "golden_sentences": ["matrix mineralization was increased clearly compared with the control", "calcium-level deposition was significantly increased when hASCs were cultured with His‑βCD‑PH and HP‑βCD‑PH at 50 μM concentration compared with the control"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010074872_TII_02/figure/2010074872_TII_02_8.png"], "tampered": true, "paper_ids": ["2010002283"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010119081_TII_02/figure/2010119081_TII_02_2.png", "question_id": "consistency_87", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Fig. 3. Effects of curcumin on serum TGF-β1 and lung TGF-β1 and CTGF expression in irradiated rats. (A) Serum concentrations (n = 5–6 per group) of TGF-β1 in control (CTL), radiation (RT), radiation+curcumin (RT+Cur), and curcumin (Cur) rats. (B) Western blot showing TGF-β1 and CTGF in lung from each group. (C) Quantification of lung TGF-β1 from western blot analysis. Densitometry values of each protein were normalized to α-tubulin and represented as arbitrary units (A.U.) relative to CTL levels. Data (n = 5–6 per group) are presented as mean ± SEM. *p < 0.05 vs. CTL rats; †p < 0.05 vs. RT rats.", "figure_related_sentences": "To evaluate whether curcumin could attenuate radiation-induced collagen synthesis in rat lungs, we assessed serum TGF-β1 levels by ELISA and TGF-β1 and CTGF expression levels with western blots (Fig. 3). Serum TGF-β1 levels from irradiated rat lungs were significantly decreased compared to irradiated curcumin-treated rats (Fig. 3A). Western blots revealed that radiation-induced TGF-β1 and CTGF expression were reduced by curcumin (Fig. 3B and C).", "inconsistent_part": "related_sentences", "tampered_sentences": ["Serum TGF-β1 levels from irradiated rat lungs were significantly decreased compared to irradiated curcumin-treated rats (Fig. 3A)"], "golden_sentences": ["Serum TGF-β1 levels from irradiated rat lungs were significantly increased compared to irradiated curcumin-treated rats (Fig. 3A)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010119081_TII_02/figure/2010119081_TII_02_2.png"], "tampered": true, "paper_ids": ["2010002308"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010079947_TII_01/figure/2010079947_TII_01_0.png", "question_id": "consistency_88", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. Effects of NFKBIE knockdown on the expression levels of SLC19A1 and ABC transporters. Quantitative gene expressions of NFKBIE (A), SLC19A1 (B), ABCC1 (C), ABCC5 (D), and ABCG2 (E) genes in control (gray) and NFKBIE knockdown (black) MH7A treated with or without 0.01, 0.1, 1, 5, and 10 mM methotrexate (MTX) application for 24 h in the presence or absence of 20 U/mL IL-1b and 20 U/mL TNF-a were measured by qRT-PCR. Statistical significance was analyzed using the unpaired t-test (*p<0.05). The results are presented as the mean ± standard error of the mean (SEM) of at least three independent experiments.", "figure_related_sentences": "To investigate the effects of NFKBIE knockdown on the expressions of drug membrane transporters, we confirmed expression by qRT-PCR. The NFKBIE expression level in the NFKBIE knockdown group was almost 18–20% of the control expression level under many conditions (Figure 1A). NFKBIE knockdown could reduce the SLC19A1 expression (Figure 1B), whereas there was no obvious alteration in the expressions of the ABC transporters (Figure 1C–E).", "inconsistent_part": "related_sentences", "tampered_sentences": ["The NFKBIE expression level in the NFKBIE knockdown group was almost 18–20% of the control expression level under many conditions (Figure 1A)."], "golden_sentences": ["The NFKBIE expression level in the NFKBIE knockdown group was almost 12–20% of the control expression level under many conditions (Figure 1A)."], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010079947_TII_01/figure/2010079947_TII_01_0.png"], "tampered": true, "paper_ids": ["2010002328"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010057714_TII_02/figure/2010057714_TII_02_3.png", "question_id": "consistency_89", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 4. Direct vascular effects of particles in rat aortic rings in vitro. Effect of diesel exhaust particles (filled circle), carbon nanoparticles (u) (both 100 μg/mL), or vehicle (open circle) (Krebs buffer) on (A) phenylephrine contraction in mN, (B) phenylephrine contraction as a percentage of maximum contraction, (C) acetylcholine, and (D) sodium-nitroprusside-induced vasodilatation. Diesel exhaust particles did not affect contraction to phenylephrine (P=0.64), but inhibited vasorelaxation to acetylcholine (P<0.001) and sodium nitroprusside (P=0.019) compared with control. Although there was an apparent rightward shift in the dose-response curve to acetylcholine and sodium nitroprusside with carbon nanoparticles, vasorelaxation was not significantly affected (P=0.139 and P=0.224, respectively). Effect of (E) aqueous and (F) organic separation of diesel exhaust particles on acetylcholine responses. (E) Aqueous-washed diesel exhaust particles (grey square), and aqueous extract from diesel exhaust particles (open square), inhibit vasodilation to acetylcholine (P<0.01 for both), with the combined effects of both constituents being equal to that of untreated particles (filled circle). (F) Organic-washed diesel exhaust particles (s) inhibited acetylcholine induced vasodilatation (*P=0.010); the magnitude of this effect was not different from that of untreated diesel exhaust particles (filled circle) (P=0.103). The organic extract of diesel exhaust particles (inverted triangle) had no effect on vasorelaxation to acetylcholine (P=0.645). n=6 for all groups.", "figure_related_sentences": "In vitro exposure of rat aortic rings to diesel exhaust particles produced a small decrease in the maximum contractile response to phenylephrine (P=0.03, unpaired t-test; Figure 4A), without affecting the sensitivity to phenylephrine. Pure carbon nanoparticles did not significantly alter responses to phenylephrine and, overall, both particles had no significant effect on concentration-response curves to phenylephrine when expressed as a percentage of maximum contraction (P=0.64 and P=0.86, respectively; two-way ANOVA; Figure 4B). Compared with vehicle control, vasorelaxation to acetylcholine was induced following exposure to diesel exhaust particles (P<0.001; Figure 4C). Although there was an apparent rightward shift in the concentration-response curve to acetylcholine with carbon nanoparticles, vasorelaxation was not significantly affected (P=0.139; Figure 4C). Diesel exhaust particles caused a small but significant inhibition of relaxation to sodium nitroprusside (P=0.019) compared with control (Figure 4D), whereas carbon nanoparticles did not (P=0.224). Following separation of the aqueous soluble constituents from diesel exhaust particulate matter, both washed particles and solution were able to inhibit vasodilator responses to acetylcholine (P<0.01 for both), with the combined effects of both constituents being equal to that of untreated particles (Figure 4E). Dichloromethane-washed diesel exhaust particles markedly inhibited acetylcholine-induced vasodilatation (P=0.010); the magnitude of which was not statistically different from untreated diesel exhaust particles (P=0.103; Figure 4F). Accordingly, the organic extract of diesel exhaust particles removed by dichloromethane had no effect on relaxation to acetylcholine (P=0.645).", "inconsistent_part": "related_sentences", "tampered_sentences": ["In vitro exposure of rat aortic rings to diesel exhaust particles produced a small decrease in the maximum contractile response to phenylephrine (P=0.03, unpaired t-test; Figure 4A)", "vasorelaxation to acetylcholine was induced following exposure to diesel exhaust particles (P<0.001; Figure 4C)"], "golden_sentences": ["In vitro exposure of rat aortic rings to diesel exhaust particles produced a small increase in the maximum contractile response to phenylephrine (P=0.03, unpaired t-test; Figure 4A)", "vasorelaxation to acetylcholine was inhibited following exposure to diesel exhaust particles (P<0.001; Figure 4C)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010057714_TII_02/figure/2010057714_TII_02_3.png"], "tampered": true, "paper_ids": ["2010002366"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010013350_TII_01/figure/2010013350_TII_01_2.png", "question_id": "consistency_90", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Defect of fertilization in Pmis2−/− mice and transgenic rescue. (A) Pmis2+/− males and Pmis2−/− females delivered normal numbers of pups when mated with WT mice, whereas the combination of WT females with Pmis2−/− males produced no pups. (B) The defect was at the fertilization level, because no fertilized eggs were recovered from the superovulated females mated with Pmis2−/− males. Parentheses indicate the numbers of eggs examined. (C) Top, the targeting vector used to disrupt the mouse Pmis2 allele. Bottom, the transgene used for rescue experiments to express Pmis2 under the control of the Clgn promoter. The arrows indicate the positions of primer sets to detect the targeted alleles. (D) Genotyping of tail-tip DNA from various groups of mice by PCR amplification with the primers indicated in Materials and Methods. (E) Protein extracts from Pmis2+/− and Pmis2−/− and spermatozoa from transgenically rescued Pmis2−/− mice were subjected to immunoblot analysis using anti-PMIS2 and anti–His-tag antibodies. ADAM2 was indicated as a reference marker for the successful extraction of proteins. (F) Litter sizes obtained by mating Pmis2+/− and transgenically rescued Pmis2−/− males with WT female mice. The sterile phenotype of Pmis2−/− mice was restored by the insertion of the Pmis2 transgene.", "figure_related_sentences": "Pups were obtained from Pmis2+/− males and Pmis2−/− females, whereas Pmis2−/− male mice sired no pups in spite of their normal mating behavior (Figure 3A). Eggs were collected from the oviducts after examining for the formation of a vaginal plug, and the fertilization rate was examined. We could obtain no fertilized eggs from the females that mated with Pmis2−/− males, whereas almost 0% of the eggs were fertilized in the females mated with Pmis2+/− males (Figure 3B). Therefore we generated transgenic mouse lines harboring hexahistidine (His6)-tagged Pmis2 cDNA under the regulation of the Clgn promoter and performed a gene rescue experiment (Figure 3C). Both of these transgenic mouse lines expressing His6-tagged PMIS2 protein were shown to rescue the infertile phenotype by being incorporated into the Pmis2−/− genetic background (Figure 3D–3F), indicating that the recombinant PMIS2 with His6 tag could function normally and that infertility in the Pmis2−/− mice was caused directly by the absence of PMIS2 from spermatozoa.", "inconsistent_part": "related_sentences", "tampered_sentences": ["whereas almost 0% of the eggs were fertilized in the females mated with Pmis2+/− males (Figure 3B)"], "golden_sentences": ["whereas almost 100% of the eggs were fertilized in the females mated with Pmis2+/− males (Figure 3B)"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010013350_TII_01/figure/2010013350_TII_01_2.png"], "tampered": true, "paper_ids": ["2010002370"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010027154_TII_01/figure/2010027154_TII_01_2.png", "question_id": "consistency_91", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 3. a) Schematic representation of different functionalization approaches of SWCNTs with 2_2 and results after three hot filtration steps. b) TGA trace of the reaction outcome (rt to 1000°C, 10°Cmin^-1 under air) for the degree of functionalization (black: pristine SWCNTs, blue: Rev-MINT, red: Irrev-MINT and green: Supra-MINT). c) Results of TGA analysis (Δm at 420°C) after synthesis and three consecutive hot filtration steps for the three functionalization approaches. d) Summary of the degree of functionalization of all samples according to Equation (2) after synthesis and three hot filtration steps.", "figure_related_sentences": "Having macrocycles 1_2 and 2_2 as well as efficient conditions for disulfide exchange in hand, we tested our key hypothesis that SWCNTs could act as convex templates during the reversible covalent opening and closing of the concave rings (Figure 3 a, top). The collected solids werewashed multiple times by suspending in dichloromethane, ultrasonication, and filtration to remove weakly adsorbed exTTF macrocycles and reagents. The so-obtained “Rev-MINT” samples (Figure 3 a, top) were dried under reduced pressure and subjected to thermogravimetric analysis (TGA) to quantify the degree of functionalization (DoF). In the “Irrev-MINT” experiment, we irreversibly oxidized the dithiols 1 or 2 in the presence of the SWCNTs (Figure 3 a, middle), and in the “Supra-MINT” experiment, we simply sonicated the macrocycles 1_2 or 2_2 together with the SWCNTs (Figure 3 a, bottom). As shown in Figure 3 b (for the case of MINT-2_2), all samples obtained by the three different experimental approaches show a significant weight loss in the TGA trace between 300 and 400°C (Figure 3 b). Although Δm is an intuitive figure of merit that is particularly useful for comparing experiments within this study (Figure 3 c), it is not a reliable metric for comparing MINTs with macrocycles of different molar masses. When performing TGA analysis immediately after the three different functionalization procedures described above, we found relatively similar Δm/DoF values for the Rev-MINT-1_2 (33±2%/0.56±0.06%) and Rev-MINT-2_2 (45±3%/0.57±0.07%) samples, which suggests that the ring size leads to a small, yet statistically significant difference in the reaction outcome. Similar Δm/DoF values were also observed for the Irrev-MINT-2_2 (33±2%/0.55±0.06%) and Supra-MINT-2_2 (26±1%/0.40±0.02%) reference experiments (Figure 3 c,d). After thorough rinsing with dichloromethane and drying of the samples, TGA analyses were performed to quantify the remaining Δm/DoF values and thus determine the amount of macrocycles that were not removed during this procedure (Figure 3 a, right). Moreover, we performed these experiments in triplicate and repeated the hot filtration procedure three times in sequence until we reached a “plateau” for the Δm and DoF values (Figure 3 c,d). As expected from an approach that features error correction, TGA analysis showed that over three hot filtration cycles the Rev-MINT samples exhibit only a small decrease in the Δm and DoF values (about 5%/0.14%, Figure 3 c,d, blue).", "inconsistent_part": "related_sentences", "tampered_sentences": ["all samples obtained by the three different experimental approaches show a significant weight loss in the TGA trace between 300 and 400°C (Figure 3 b)", "we found relatively similar Δm/DoF values for the Rev-MINT-1_2 (33±2%/0.56±0.06%) and Rev-MINT-2_2 (45±3%/0.57±0.07%) samples"], "golden_sentences": ["all samples obtained by the three different experimental approaches show a significant weight loss in the TGA trace between 300 and 580°C (Figure 3 b)", "we found relatively similar Δm/DoF values for the Rev-MINT-1_2 (33±2%/0.56±0.06%) and Rev-MINT-2_2 (35±3%/0.57±0.07%) samples"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010027154_TII_01/figure/2010027154_TII_01_2.png"], "tampered": true, "paper_ids": ["2010002376"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010011621_TII_02/figure/2010011621_TII_02_3.png", "question_id": "consistency_92", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Increased TCR–CD3 recycling is revealed in hypertonic medium. (A) Uptake of Alexa647-labeled transferrin by Jurkat T cell lines expressing SLAP-GFP or control (GFP) in the presence or absence of hypertonic medium, as assessed by FACS. (B) Expression of CD3ε on Jurkat T cell lines expressing SLAP-GFP or control (GFP) incubated in hypertonic medium, as assessed by FACS. Data are presented as the absolute increase in CD3ε MFI expression relative to time 0. Data in A and B are the mean of three experiments ± SEM. (C) CD3ε expression on WT or SLAP−/− thymocytes incubated in hypertonic medium for 0 or 6 h, as assessed by FACS. Data are representative of three mice per genotype. (D) MFI of CD3ε expression on WT or SLAP−/− thymocytes incubated in 0.45 M hypertonic medium for the indicated time in the presence or absence of cycloheximide (CHX). (E) MFI of CD3ε expression on WT or SLAP−/− DP thymocytes incubated for the indicated time in cell culture medium only. Data in D and E are the mean of three mice per genotype ± SEM (error bars).", "figure_related_sentences": "To validate the use of hypertonic medium to inhibit TCR–CD3 internalization, we first analyzed the uptake of fluorescently labeled transferrin by the transferrin receptor, a process that requires clathrin-mediated endocytosis (Mellman, 1996; Schmid, 1997). Because DP thymocytes do not express the transferrin receptor, we first tested the effect of hypertonic medium on Jurkat T cell lines that stably expressed either SLAP-GFP fusion or GFP alone as a control. Transferrin uptake via the transferrin receptor was completely inhibited by hypertonic medium in both stable cell lines (Figure 4A), demonstrating that hypertonic medium blocks clathrin-mediated endocytosis regardless of whether SLAP is present or not. We analyzed the effect of SLAP on CD3ε expression while clathrin-mediated endocytosis was blocked in Jurkat T cells. Strikingly, we were able to detect downregulation of CD3ε surface expression over the time course of the experiment in the control cell line. However, upregulation of CD3ε by Jurkat T cells was markedly inhibited in the presence of SLAP (Figure 4B). To investigate whether SLAP expression affects upregulation of CD3ε on DP thymocytes as it did in our model cell line, we incubated thymocyte single-cell suspensions in hypertonic medium and followed CD3ε expression over time. Both WT and SLAP−/− DP thymocytes downregulate CD3ε on the cell surface over the course of the assay (Figure 4C). However, quantitation demonstrated that CD3ε upregulation was substantially increased in SLAP−/− DP thymocytes as compared with WT controls (Figure 4D). Interestingly, the observed upregulation of CD3ε in hypertonic medium is comparable with the estimated amount of CD3ε present in the recycling pool (Figure 3C), indicating that increases in the size of the TCR–CD3 recycling pool can be revealed upon incubation of thymocytes in hypertonic medium. Notably, the uptake of fluorescently labeled transferrin by double-negative thymocytes (which express low, but detectable, levels of the transferrin receptor) was inhibited in the presence of hypertonic medium (unpublished data), indicating that hypertonic medium inhibited clathrin-mediated endocytosis in our thymocyte cultures. Previous studies have reported that prolonged culture of DP thymocytes in the absence of TCR–MHC interactions results in upregulation of the TCR–CD3 complex by the stabilization of newly synthesized TCRζ chains (Bonifacino et al., 1990; Kearse et al., 1995). Indeed, both WT and SLAP−/− DP thymocytes up-regulate CD3ε when cultured in the absence of 0.45 M sucrose (Figure 4E). However, over this time course, the increase in CD3ε expression was markedly higher than the increase observed in thymocytes that were incubated in hypertonic medium. In addition, most of the CD3ε upregulation that was observed in hypertonic medium was detected after only 2 h in culture, a time at which little or no CD3ε upregulation had yet occurred in the absence of 0.45 M sucrose. Furthermore, incubation of thymocytes in cycloheximide to inhibit protein synthesis had no effect on the upregulation of CD3ε in hypertonic medium (Figure 4D). In contrast, in parallel experiments using thymocytes cultured in media without 0.45 M sucrose, upregulation of CD3ε was sensitive to cycloheximide treatment (unpublished data), demonstrating that cycloheximide effectively inhibited protein synthesis in our cultures.", "inconsistent_part": "related_sentences", "tampered_sentences": ["we were able to detect downregulation of CD3ε surface expression over the time course of the experiment in the control cell line", "Both WT and SLAP−/− DP thymocytes downregulate CD3ε on the cell surface over the course of the assay (Figure 4C)", "the increase in CD3ε expression was markedly higher than the increase observed in thymocytes that were incubated in hypertonic medium"], "golden_sentences": ["we were able to detect upregulation of CD3ε surface expression over the time course of the experiment in the control cell line", "Both WT and SLAP−/− DP thymocytes upregulate CD3ε on the cell surface over the course of the assay (Figure 4C)", "the increase in CD3ε expression was markedly lower than the increase observed in thymocytes that were incubated in hypertonic medium"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010011621_TII_02/figure/2010011621_TII_02_3.png"], "tampered": true, "paper_ids": ["2010002377"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010018540_TII_01/figure/2010018540_TII_01_3.png", "question_id": "consistency_93", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Fluorogram of HDL apoproteins isolated from rough- and smooth-endoplasmic reticulum fractions. Young chickens were administered t-[aH]leucine and, after 10 min, the livers were removed, fractionated into RER and SER fractions, and the HDL contained within these fractions was isolated by centrifugal flotation and immunoprecipitation. The apoproteins were analyzed by SDS PAGE and identified by fluorography. The details of the procedures are given in Materials and Methods. Lanes 2 and 4 represent nascent HDL apoproteins obtained by immunoprecipitation from the contents of the RER and the SER fractions from 2 g of liver. Lanes 1 and 5 represent nascent HDL obtained by flotation from the contents of the RER and SFR fractions from 56 g of liver. Lane 1 shows the apoprotein pattern of serum HDL obtained by flotation. Measurements, x 10 -3.", "figure_related_sentences": "There was a small amount of radioactivity in the high molecular weight range, which could be due to aggregation of protein, but there was no evidence of the presence of radioactive proteins of lower molecular size than apoprotein AI (Fig. 4, lanes 3 and 4). By contrast, the contents of the RER and the SER cell fractions did not yield radioactive proteins in complexes that could be floated to a buoyant density (1.063-1.21 g/ml) similar to that of serum HDL (Fig. 4, lanes 1 and 2). This indicates that apoprotein A1 is present in these cell fractions but has not been sufficiently complexed with lipids to allow it to gain its appropriate buoyant density.", "inconsistent_part": "caption", "tampered_sentences": ["Lanes 2 and 4 represent nascent HDL apoproteins obtained by immunoprecipitation from the contents of the RER and the SER fractions from 2 g of liver", "Lanes 1 and 5 represent nascent HDL obtained by flotation from the contents of the RER and SFR fractions from 56 g of liver", "Lane 1 shows the apoprotein pattern of serum HDL obtained by flotation"], "golden_sentences": ["Lanes 3 and 4 represent nascent HDL apoproteins obtained by immunoprecipitation from the contents of the RER and the SER fractions from 2 g of liver", "Lanes 1 and 2 represent nascent HDL obtained by flotation from the contents of the RER and SFR fractions from 26 g of liver", "Lane 5 shows the apoprotein pattern of serum HDL obtained by flotation"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010018540_TII_01/figure/2010018540_TII_01_3.png"], "tampered": true, "paper_ids": ["2010002382"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010019350_TII_02/figure/2010019350_TII_02_5.png", "question_id": "consistency_94", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Cell culture experiments analysing the effects of reggie-1 on Wg and Hh secretion. (A) Effects of overexpression of reggie-1 on Wg secretion measured by Western blots. Serum albumin is shown as the loading control for the medium samples. (B) Effects of overexpression of reggie-1 or a reggie dominant-negative construct on secretion of Wg, Hh or secreted luciferase (sluc) measured by enzymatic assay. Bars represent means±s.e.m. from 12 experiments. P-values from Student’s t-test are shown; ‘ns’ means non-significant (P≥0.05). (C) GFP-Wg media from panel A were subjected to sucrose-density ultracentrifugation. Thirteen fractions were collected (numbers and sucrose density in alternating fractions are shown on top). (D, E) S2 cells transfected with Wg together with reggie-1 (D) or EGFP (E) were co-cultured with cells independently transfected with DsRed. Accumulation of the anti-Wg signal in DsRed-cells is much higher if Wg was produced by reggie-1 transfected cells. (F, G) Pulse–chase Texas-red dextran colocalization assays. S2 cells transfected with Wg together with reggie-1 (F) or empty vector (G) were co-cultured with cells independently transfected with EGFP. Accumulation of Wg in dextran-positive early endosomes is much higher if Wg was produced by reggie-1-transfected cells (arrowheads in panel F). Note that unlike in panels D and E where identical confocal settings were used to record anti-Wg staining, the settings in panels F and G were independently optimized for highest resolution. (H) Reggie-1 does not stimulate Wg endocytosis cell-autonomously: S2 cells were transfected with Wg plus reggie-1-EGFP and co-cultured with cells independently transfected with reggie-1-DsRed. Incorporation of Wg into the Wg-receiving cells was the same whether they overexpressed reggie-1-DsRed or not (white arrows).", "figure_related_sentences": "We found a dramatically lower uptake of Wg by DsRed cells when Wg was provided by the reggie-1-overexpressing cells (Figure 5D and E). To prove that this intracellular Wg staining resulted from endocytosis, we performed pulse–chase assays with fluorescent dextran beads and found that Wg provided by reggie-1-expressing cells colocalized with dextran in early endocytic compartments (Figure 5F) whose particulate appearance was reminiscent of the punctate staining seen in wing discs. In contrast, Wg obtained from control-transfected cells was strongly endocytosed by the co-cultured cells (Figure 5G). We could also demonstrate that reggie-1 overexpression did not increase Wg uptake cell-autonomously: overexpression of reggie-1 in the cells co-cultured with Wg-producing cells did not increase Wg uptake by these co-cultured cells (Figure 5H). Thus, reggie-1 overexpression was changing the properties of Wg in the Wg-producing cells, such that this Wg became markedly more internalizable by the co-cultured cells. This conclusion agrees well with our in vivo observations. Such increased uptake of Wg might be solely due to enhanced secretion of Wg by reggie-1-overexpressing cells, or also due to a molecular change in the form Wg is secreted. For example, reggie-1 overexpression could enhance Wg packing into lipoprotein particles. To investigate this possibility, we performed sucrose-density ultracentrifugation of the Wg medium from reggie-1- or control-transfected cells (Figure 5C).", "inconsistent_part": "related_sentences", "tampered_sentences": ["We found a dramatically lower uptake of Wg by DsRed cells when Wg was provided by the reggie-1-overexpressing cells (Figure 5D and E)", "Wg obtained from control-transfected cells was strongly endocytosed by the co-cultured cells (Figure 5G)"], "golden_sentences": ["We found a dramatically higher uptake of Wg by DsRed cells when Wg was provided by the reggie-1-overexpressing cells (Figure 5D and E)", "Wg obtained from control-transfected cells was poorly endocytosed by the co-cultured cells (Figure 5G)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010019350_TII_02/figure/2010019350_TII_02_5.png"], "tampered": true, "paper_ids": ["2010002384"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010028694_TII_02/figure/2010028694_TII_02_8.png", "question_id": "consistency_95", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "(A) In vivo antitumor activity of PSSN10 and various DOX formulations in a syngeneic murine breast cancer model (4T1.2). Three injections were administered on d 0, 3 and 6. **P<0.01. (B) Kaplan-Meier survival of 4T1.2 tumor-bearing mice after various treatments. (C) Histological analyses of H&E stained sections of tumor tissues collected on d 19.", "figure_related_sentences": "Figure 5A shows the in vivo therapeutic effects of PSSN10 and DOX/PSSN10 with free DOX and DOXIL (a clinical formulation of liposomal DOX) as controls (5 mg DOX/kg). The PSSN10 carrier alone showed a significant effect in inhibiting tumor growth, comparable to those of DOX and DOXIL. This is in contrast to the in vitro cytotoxicity, in which PSSN10 showed little effect (Figure 3A, 3B), suggesting that the IDO inhibitory effect rather than a direct cytotoxic effect contributed to the in vivo antitumor activity of PSSN10. DOX formulated in PSSN10 micelles showed inhibited antitumor activity that was significantly higher than that of DOXIL. Figure 5B shows the Kaplan-Meier survival curves of 4T1.2 tumor-bearing mice following different treatments. All for mulations improved the survival rate compared to the saline control group. Among them, the DOX/PSSN10 formulation resulted in the longest overall survival, with a median survival of 40 d. Figure 5C shows the histology of tumors following different treatments. Tumors from the mice treated with DOX/PSSN10 had more necrotic/apoptotic cells compared to the tumors from the other treatment groups.", "inconsistent_part": "related_sentences", "tampered_sentences": ["The PSSN10 carrier alone showed a significant effect in inhibiting tumor growth,", "DOX formulated in PSSN10 micelles showed inhibited antitumor activity that was significantly higher than that of DOXIL"], "golden_sentences": ["The PSSN10 carrier alone showed a modest effect in inhibiting tumor growth,", "DOX formulated in PSSN10 micelles showed enhanced antitumor activity that was significantly higher than that of DOXIL"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010028694_TII_02/figure/2010028694_TII_02_8.png"], "tampered": true, "paper_ids": ["2010002385"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010041575_TII_02/figure/2010041575_TII_02_3.png", "question_id": "consistency_96", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Cannabinoids induce AMPK-dependent GAPDH nuclear translocation. Representative confocal images of GAPDH translocation in Panc1 cell nuclei after 12h treatment with 200mM GW or ACPA in the absence or presence of a pretreatment for 1h with 20mM NAC or 20mM C.C. Values are the means of three independent experiments (±S.D.)", "figure_related_sentences": "we analysed the cellular distribution of GAPDH after the treatment with GW or ACPA. Figure 4 shows the confocal images where GAPDH appear to be translocated into the nucleus of the cells after 12-h cannabinoid treatments. This effect was stimulated by NAC or CC, indicating its dependence on ROS and AMPK activation. These data suggested that the increased level of G3P observed in the metabolomic analysis could arise from the diminished presence of GAPDH in the cytosol of cells treated with cannabinoids.", "inconsistent_part": "related_sentences", "tampered_sentences": ["This effect was stimulated by NAC or CC"], "golden_sentences": ["This effect was inhibited by NAC or CC"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010041575_TII_02/figure/2010041575_TII_02_3.png"], "tampered": true, "paper_ids": ["2010002386"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010041585_TII_02/figure/2010041585_TII_02_5.png", "question_id": "consistency_97", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "CPEB1 reduces senescence by regulating p53 distribution in glioma cells. (a) A cell growth assay was used to analyze the function of CPEB1 siRNA in glioma cell proliferation. *Po0.05. (b) The effect of CPEB1 siRNA on senescence in glioma cell lines as determined with SA-b-gal staining. Arrows indicate the green senescent cells. *Po0.05. (c) Transmission electron micrographs of the morphology of glioma cells transfected with CPEB1 siRNA. (d) The regulation of p53 and p21 by CPEB1 siRNA. (e) The changes in the cellular distribution of p53 induced by CPEB1 siRNA in the U87 cell line", "figure_related_sentences": "The knockdown of CPEB1 reduced senescence by regulating p53 distribution in glioma cells. Burns DM et al.18 demonstrated that CPEB1 was repressed by miR-122, and the inhibition of CPEB1 activated p53 translation in human skin fibroblasts. p53 is one of the hallmarks of cellular senescence;19 therefore, the p53-mutated cell line U251 and the p53 wild-type cell line U87 were selected for use in the following experiments. U251 and U87 cell growth was stimulated by CPEB1 knockdown. The inhibition was observed at 72h in U251 cells and at 48 and 72h in U87 cells (Figure 2a). Senescent cells can be detected with an assay that detects senescence-associated b-gal (SA-b-gal) activity.20 Whether in p53-mutated or in wild-type glioma cells, CPEB1 knockdown initiated senescence (Figure 2b). Next, the morphology of U251 and U87 cells treated with a CPEB1 small interfering RNA (siRNA) was observed with transmission electron microscopy. The results revealed vacuolar degeneration in the cytoplasm of the U251 cells. However, there were two different lesions in the U87 cells: one was cellular edema, including cytoplasm, nucleus and mitochondria; another lesion was mitochondrial vacuolar degeneration (Figure 2c). After the knockdown of CPEB1, the level of expression of p53 was decreased in the U251 cells but not changed in the U87 cells (Figure 2d). Furthermore, it was discovered that the knockdown of CPEB1 induced the overexpression of p21, which is downstream of p53 (Figure 2d). Even though the CPEB1 knockdown did not influence the expression of p53 in the U87 cell lysate, the loss of CPEB1 expression still enhanced the expression of the downstream p53 effector p21. The data indicate that the knockdown of CPEB1 impeded wild-type p53 transport to the cytoplasm in U87 cells (Figure 2e). This observation supports the hypothesis that the knockdown of CPEB1 induces cell senescence in glioma in a p53-dependent manner.", "inconsistent_part": "related_sentences", "tampered_sentences": ["U251 and U87 cell growth was stimulated by CPEB1 knockdown"], "golden_sentences": ["U251 and U87 cell growth was inhibited by CPEB1 knockdown"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010041585_TII_02/figure/2010041585_TII_02_5.png"], "tampered": true, "paper_ids": ["2010002387"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010041660_TII_02/figure/2010041660_TII_02_3.png", "question_id": "consistency_98", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure4 Inhibition of ADAM17 modulates phosphorylation of p44 MAPK. (a) Levels of p44 MAPK phosphorylation were decreased after ADAM17 inhibition with medium and high concentrations of BMS-561392, whereas p42 MAPK phosphorylation was not affected in immature HOG oligodendrocytes. (b) Microglial BV-2 cells were treated with different concentrations of BMS-561392 and TAPI-1. MAPK p44 phosphorylation was significantly decreased using 0.3mM of the inhibitor, while higher concentrations decreased or even abolished p44 MAPKphosphorylation. MAPKp42phosphorylation was not affected by BMS-561392 or TAPI-1treatment. The results are the mean of three independent experiments and are represented as a percentage of the control condition (n¼3 per condition)", "figure_related_sentences": "On the contrary, levels of p44 MAPK phosphorylation were significantly increased with the highest concentration of BMS-561392 (2.7mM) in oligodendrocytes (Figure 4a), whereas in microglial cells phosphorylation of p44 MAPK was significantly decreased by the lower concentration of BMS-561392 (0.3mM) and significantly diminished below detection by the high concentration of the inhibitor (2.7mM) (Figure 4b).", "inconsistent_part": "caption", "tampered_sentences": ["MAPK p44 phosphorylation was significantly decreased using 0.3mM of the inhibitor", "levels of p44 MAPK phosphorylation were significantly increased with the highest concentration of BMS-561392 (2.7mM) in oligodendrocytes (Figure 4a)", "whereas in microglial cells phosphorylation of p44 MAPK was significantly decreased by the lower concentration of BMS-561392 (0.3mM) and significantly diminished below detection by the high concentration of the inhibitor (2.7mM) (Figure 4b)"], "golden_sentences": ["MAPK p44 phosphorylation was significantly increased using 0.3mM of the inhibitor", "levels of p44 MAPK phosphorylation were significantly decreased with the highest concentration of BMS-561392 (2.7mM) in oligodendrocytes (Figure 4a)", "whereas in microglial cells phosphorylation of p44 MAPK was significantly increased by the lower concentration of BMS-561392 (0.3mM) and significantly diminished below detection by the high concentration of the inhibitor (2.7mM) (Figure 4b)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010041660_TII_02/figure/2010041660_TII_02_3.png"], "tampered": true, "paper_ids": ["2010002388"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010131029_TII_01/figure/2010131029_TII_01_0.png", "question_id": "consistency_99", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Fig. 1. Protective effects of PTZ against ROT-induced toxicity on primary ventral midbrain cultures. (A) Representative scans from immunocytochemical preparations acquired with a 20× objective lens. PTZ protects TH+ (A11) and MAP2 neurons (A12) against the deleterious effects of ROT with ensuing increase in the percentage of DA-containing neurons (A13). Insets correspond to high magnification images. Scale bar: 200 μm. Data are representative of 20–40 neurons per group obtained from seven independent cultures. (B) Morphometric neurite reconstruction in 3D. PTZ treatment preserved neurite length (B6), number of segments (B7), and branch points (B8) in ROT-exposed cells. Insets represent a 4× zoomed image. Scale bar: 200 μm. Two images for each condition and experiment were averaged. Data from four independent cultures were combined to determine means ± SEM (C) Ratiometric measurements of reduced and oxidized thiol groups. High resolution confocal images obtained with a 40× objective and image analysis demonstrated that administration of PTZ restores the SS/SH ratio altered in ROT-treated cells. Scale bar: 20 μm. On an average, 25–30 neurons per condition were tested from three independent cultures. ****p < 0.0001, ***p < 0.001, **p < 0.01 and * p < 0.05 compared to VEH + VEH. ####p < 0.0001 and ###p < 0.001 relative to PTZ + VEH (one-way ANOVA followed by Newman-Keuls multiple comparisons test).", "figure_related_sentences": "Administration of 50 nM ROT to 5-day-old primary rat DA cell cultures over a period of 5 days leads to neuron degeneration. We therefore sought to investigate the potential neuroprotective properties of PTZ (Fig. 1). We first examined whether unsubstituted PTZ improves cell survival (Fig. 1 A). PTZ alone did not show either neurotoxic or neurotrophic effects while ROT treatment resulted in a dramatic decrease in the number of TH+ neurons (∼40%, Fig. 1 A11), MAP2 neurons (∼83%, Fig. 1 A12), and the percentage of DA-producing neurons (∼45%, Fig. 1 A13) as compared to the control group (VEH). Administration of PTZ (10, 20 or 50 nM) 1 h after ROT incubation significantly protected TH+ and MAP2 neurons from ROT toxicity (p < 0.0001 for all doses of PTZ tested). We further evaluated the efficacy of PTZ in preserving neurite morphometry (Fig. 1 B). Total neurite length (∼32%, Fig. 1 B6) and both number of segments (∼59%, Fig. 1 B7) and branches (∼68%, Fig. 1 B8) were significantly reduced in response to ROT. However, PTZ was able to abrogate ROT-induced neurite shrinkage and fragmentation. To investigate the putative effect of PTZ on oxidative damage, a redox immunohistochemistry approach was used for the sensitive quantification of intracellular redox state in situ in both DA and non-DA neurons (Fig. 1 C). The thiol (SH)/disulfide (SS) redox balance system shifted toward disulfide bound generation in ROT-stimulated cells relative to VEH group (Fig. 1 C5 vs C10; 0.58 ± 0.01 vs 1.01 ± 0.03 TH+ neurons and 0.59 ± 0.02 vs 1.10 ± 0.05 MAP2 neurons, p < 0.0001). In contrast, the SS/SH ratio was reduced near to basal levels in the PTZ + ROT groups in comparison to cells incubated with ROT alone (Fig. 1 C10 vs C15, C20 and C25; p < 0.0001). Ratio metric analysis of disulfide and thiol species in DA (C26) and non-DA (C27) neurons. Taken together, these findings provide strong support for the concept that PTZ has a potent protective effect against ROT-mediated neuron degeneration and oxidative impairment in vitro.", "inconsistent_part": "related_sentences", "tampered_sentences": ["Total neurite length (∼32%, Fig. 1 B6) and both number of segments (∼59%, Fig. 1 B7) and branches (∼68%, Fig. 1 B8) were significantly reduced in response to ROT", "PTZ alone did not show either neurotoxic or neurotrophic effects while ROT treatment resulted in a dramatic decrease in the number of TH+ neurons (∼40%, Fig. 1 A11)", "MAP2 neurons (∼83%, Fig. 1 A12)"], "golden_sentences": ["Total neurite length (∼32%, Fig. 1 B6) and both number of segments (∼59%, Fig. 1 B7) and branches (∼57%, Fig. 1 B8) were significantly reduced in response to ROT", "PTZ alone did not show either neurotoxic or neurotrophic effects while ROT treatment resulted in a dramatic decrease in the number of TH+ neurons (∼71%, Fig. 1 A11)", "MAP2 neurons (∼48%, Fig. 1 A12)"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010131029_TII_01/figure/2010131029_TII_01_0.png"], "tampered": true, "paper_ids": ["2010002389"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010000184_TII_01/figure/2010000184_TII_01_9.png", "question_id": "consistency_100", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 6.Vault RNA expression varies in actino-mycin D–treated MEFs. Northern analysis of RNA prepared from wild-type (MEF11) and mTep1-deficient (MEF8 and MEF5) cells treated with actinomycin D for the indicated times. The membrane was probed with mTR (top), stripped,and reprobed first with mVR (middle) and next with an antisense 5S oligonucleotide (bottom). Control (C) samples were not treated with drug.", "figure_related_sentences": "In wild-type MEF cells, vRNA has a half-life of 5–6 h; however, in both mTep1 MEF lines, the vRNAs half-life is reduced to 0.3–1 h (Fig. 6, mVR). The blots were stripped and reprobed with either mTR or 5S (a loading control).No effect is seen on the stability of the mTR (Fig. 6).", "inconsistent_part": "related_sentences", "tampered_sentences": ["vRNA has a half-life of 5–6 h", "the vRNAs half-life is reduced to 0.3–1 h (Fig. 6, mVR)"], "golden_sentences": ["vRNA has a half-life of 4–6 h", "the vRNAs half-life is reduced to 0.5–1 h (Fig. 6, mVR)"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010000184_TII_01/figure/2010000184_TII_01_9.png"], "tampered": true, "paper_ids": ["2010002395"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010005088_TII_01/figure/2010005088_TII_01_2.png", "question_id": "consistency_101", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Fig. 5 Lethality of antiprogestins towards ovarian cancer cells. OV2008 or SK-OV-3 cells were cultured in the presence of 40 μM RU-38486, ORG-31710 or CDB-2914. After 60 h (OV2008) or 120 h (SK-OV-3), floating cells were collected, adhered to a microscope slide, stained with DAPI, and microscopic phase contrast and fluorescence images were obtained from the same fields. As positive control of apoptotic cell death, floating cells from cisplatin (CDDP) treated cells were included in the morphological studies a and b. Adherent untreated cells are also shown (CONTROL). Scale bar, 20 μm. c A similar experiment was done in which all floating and attached cells were pelleted, total DNA was isolated, subjected to agarose electrophoresis, stained with SYBR Gold nucleic acid stain, and photographed with the Amersham Typhoon fluorescence imaging system. A 100 base pair (bp) marker was run in parallel. (d) OV2008 cells were exposed to DMSO (Vehicle) or 40 μM RU-38486, ORG- 31710 or CDB-2914 for 72 h. Whole protein extracts were obtained and separated by electrophoresis, and immunoblots were probed with the indicated antibodies to recognize cell cycle and cell death related proteins. The housekeeping gene GAPDH was used as protein loading control", "figure_related_sentences": "The majority of the cells at this point in time appear detached and with morphological features similar to those shown by cisplatin-treated cells (Fig. 5a). SK-OV-3, although less sensitive to the lethal effects of the antiprogestins, show a remarkably reduced number of still adherent cells after 96 h treatment with a concomitant enhanced number of floating cells with similar morphological features to those shown by cisplatin-treated cells (Fig. 5b). Fragmentation of the DNA was clearly observed after 60 h exposure to 40 μM RU- 38486 and ORG-31710 in OV2008 cells, whereas the effect was less pronounced in CDB-2914-treated cells at the same point in time (Fig. 5c, left panel). For SK-OV-3 cells, treatment with 40 μM of the three compounds showed DNA laddering upon 120 h incubation (Fig. 5c, right panel). To further explore the signaling molecules involved in the lethal action of antiprogestins in ovarian cancer cells, we treated OV2008 cells with 40 μM antiprogestins and collected whole cell extracts after 24, 48 or 72 h incubation. Results in Fig. 5d show that RU-38486 caused cleavage of the full-length caspase-3, 116 kDa PARP substrate into the 86 kDa cleaved and inactive form 24 h after treatment, an effect that was more evident at 72 h, in association with downregulation of cell cycle related proteins Cdk-2 and p21cip1, and cleavage of p27kip1. Altogether results in Fig. 5 suggest that concentrations of antiprogestins higher than 10 μM are lethal to p53-wild type OV1008 and p53-null SK-OV-3; the molecular mediators of the cell death mechanisms,as well as their interrelationship with cell cycle regulatoryproteins, differ among the antiprogestins and warrantfurther investigations.", "inconsistent_part": "related_sentences", "tampered_sentences": ["an effect that was more evident at 72 h", "Altogether results in Fig. 5 suggest that concentrations of antiprogestins higher than 10 μM are lethal to p53-wild type OV1008 and p53-null SK-OV-3"], "golden_sentences": ["an effect that was more evident at 48 h", "Altogether results in Fig. 5 suggest that concentrations of antiprogestins higher than 20 μM are lethal to p53-wild type OV2008 and p53-null SK-OV-3"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010005088_TII_01/figure/2010005088_TII_01_2.png"], "tampered": true, "paper_ids": ["2010002398"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010065349_TII_02/figure/2010065349_TII_02_0.png", "question_id": "consistency_102", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. MLH1 deficiency has little effect on telomere maintenance. (A) Immunoblotting shows the absence of MLH1 in HCT116 and the restore of MLH1 expression in HCT116MLH1. (B) Telomere length measured by TRF analysis in HCT116 and HCT116MLH1. (C) Immunoblotting shows MLH1 knockdown in HeLa cells. Two shRNA sequences were used to deplete endogenous MLH1. Cells were collected at 7 days after puromycin selection. (D) Telomere length measured by TRF analysis in HeLa expressing MLH1 shRNA.", "figure_related_sentences": "To determine whether MLH1 deficiency impacted telomere maintenance, we first examined telomere length with the TRF assay using two cell lines from different origins: first, the MLH1-deficient human colorectal tumor cell line HCT116 and its isogenic cell line complemented with wild-type MLH1, HCT116MLH1 (39) and second, HeLa depleted of MLH1 with two shRNA sequences. Western blotting confirmed the absence of MLH1 expression in HCT116 and MLH1 knockdown in HeLa (Figure 1A and C). Due to the partial depletion of MLH1 in HeLa cells, we then used an independent assay to test MLH1 deficiency. It is well established that MLH1 deficiency leads to resistance against the cytotoxicity induced by MNNG, an alkylating agent that induces DNA damage (40–42). As shown in Supplementary Figure S1, both HCT116 and HeLa shMLH1 knockdown cells displayed resistance to MNNG, further confirming MLH1 deficiency. TRF analysis showed affected significant difference in telomere length between HCT116 and HCT116MLH1 (Figure 1B), or between HeLa control and MLH1 knockdown cells (Figure 1D).", "inconsistent_part": "related_sentences", "tampered_sentences": ["TRF analysis showed affected significant difference in telomere length between HCT116 and HCT116MLH1 (Figure 1B)"], "golden_sentences": ["TRF analysis showed no significant difference in telomere length between HCT116 and HCT116MLH1 (Figure 1B)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010065349_TII_02/figure/2010065349_TII_02_0.png"], "tampered": true, "paper_ids": ["2010002403"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010065654_TII_01/figure/2010065654_TII_01_1.png", "question_id": "consistency_103", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2. A full-length human ORF1p suppresses retrotransposition of chimeric L1s containing human ORF1 sequence. (A) Schematic of neomycin-tagged, full-length chimeric L1s containing human and/or mouse codon-optimized ORF1 and ORF2 sequences. Human ORF1 and human ORF2 are designated as H1 and H2, mouse ORF1 and mouse ORF2 are designated as M1 and M2, respectively. (B) Results of L1 retrotransposition assay in HeLa cells using plasmids expressing H1 H2, H1 M2, M1 H2 or M1 M2 L1s cotransfected with an empty (control), hORF1 or mORF1 expression plasmids. (C) Results of L1 retrotransposition assay performed as in (B) using NIH 3T3 cells. The number of G418 resistant colonies was normalized to the control flask (L1 construct cotransfected with an empty plasmid) for each independent experiment. Asterisks (*) denote statistical significance between listed constructs and the control (n = 3, t-test, P < 0.05).", "figure_related_sentences": "To assess which of the L1-encoded proteins may be involved in the response to ORF1p trans effect on L1 retrotransposition, we used previously reported chimeric L1 constructs containing codon-optimized ORF1 and ORF2 sequences of either human or mouse origin (Figure 2A) (28). Specifically, we used the H1H2 and M1M2 L1s, which contain only human or mouse sequences, respectively, the H1M2 L1, which contains human ORF1 and mouse ORF2 sequences, and the M1H2 L1 that contains mouse ORF1 and human ORF2 sequences. Transient transfections of HeLa cells with these plasmids and with either an empty plasmid (control), or plasmids expressing hORF1 or mORF1 proteins demonstrated that hORF1p suppressed mobilization of L1 constructs containing human ORF1 sequence (Figure 2B, black bars: H1H2 and H1M2). mORF1p had no negative trans effect on retrotransposition of human, mouse, or chimeric L1s (Figure 2B, dark gray bars). The same experiment was also carried out in NIH 3T3 cells. Consistent with the results obtained in HeLa cells, co-transfection of hORF1 expression plasmid with the H1H2 or H1M2 L1 constructs containing human ORF1 sequence suppressed their retrotransposition (Figure 2C, black bars: H1H2 and H1M2). Expression of hORF1p did not have any effect on retrotransposition of M1M2 or M1H2 L1 elements. Cotransfection of the mORF1p expression plasmid with the M1M2 or H1M2 L1 constructs containing mouse ORF2 (mORF2) sequence resulted in a significant (6–6-fold) increase in their retrotransposition in NIH 3T3 cells relative to the control plasmid (Figure 2C, dark gray bars versus light gray bars). Toxicity associated with human ORF1p expression, an increase in L1 toxicity in the presence of trans ORF1p or ORF1p trans effect on retrotransposition through protein interactions with L1 or host proteins could explain the ORF1p-mediated decrease in L1 retrotransposition. ORF1p expression in trans did not have any adverse effect on cell viability when the full-length ORF1p was transiently expressed alone (Supplementary Figure S2A and B) or in combination with human L1 using a previously reported toxicity assay (29,45) (Supplementary Figure S2C). In combination with the results shown in Figure 2, these findings support the involvement of the L1-encoded ORF1 protein in the trans effect of ORF1p on human L1 retrotransposition.", "inconsistent_part": "related_sentences", "tampered_sentences": ["Cotransfection of the mORF1p expression plasmid with the M1M2 or H1M2 L1 constructs containing mouse ORF2 (mORF2) sequence resulted in a significant (6–6-fold) increase in their retrotransposition in NIH 3T3 cells relative to the control plasmid (Figure 2C, dark gray bars versus light gray bars)"], "golden_sentences": ["Cotransfection of the mORF1p expression plasmid with the M1M2 or H1M2 L1 constructs containing mouse ORF2 (mORF2) sequence resulted in a significant (5–6-fold) increase in their retrotransposition in NIH 3T3 cells relative to the control plasmid (Figure 2C, dark gray bars versus light gray bars)"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010065654_TII_01/figure/2010065654_TII_01_1.png"], "tampered": true, "paper_ids": ["2010002414"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010065702_TII_02/figure/2010065702_TII_02_2.png", "question_id": "consistency_104", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2. Hypoxia induces release of miR-574-3p from Ago2 suppressing RISC-mediated activity. (A) Hypoxia switches binding of miR-574-3p from Ago2 to hnRNP L. U937 cells were cultured in hypoxia for 24 h. Lysates with the same quantity of total protein were subjected to IP with anti-hnRNP L, -Ago2 or pre-immune IgG antibodies, and then to qRT-PCR using probes against miR-574-3p or miR-17. Signal of hnRNP L RIP-RT-qPCR for miR-17 under normoxia (Figure S1C) was used as normalizer. (B) Hypoxia induces EP300 expression. U937 cells were cultured in normoxia or hypoxia for 24 h and lysates immunoblotted using anti-EP300 antibody. (C) hnRNP L inhibits canonical RISC activity of miR-574-3p and stimulates EP300 expression. U937 cells were transfected with pcDNA3-Myc-hnRNP L (1 μg) or hnRNP L siRNA (with or without miR-574-3p or anti-miR-574-3p) (200 nM) in normoxia or hypoxia as indicated, and EP300 expression measured by immunoblot. Transfections with pcDNA3 vector or scrambled siRNA were used as negative controls. (D) hnRNP L induces EP300 mRNA by antagonizing miR-574-3p. U937 cells were treated as in (C) and total RNA subjected to qRT-PCR using EP300-specific probe and normalized to β-actin. Cond. Med.: conditioned medium. In (A–D), data are presented as mean ± SD (n = 3, Student’s t-test).", "figure_related_sentences": "To begin to explore the influence of hnRNP L binding to miR-574-3p on its RISC-driven tumor-suppressive activity, we showed that hypoxia induces expression of EP300, an established downstream target of miR-574-3p (Figure 2B) . EP300 is a transcriptional co-activator of NF-κB, a key transcription factor regulating inflammatory gene expression, and HIF1A (hypoxia-inducible factor 1, β-subunit), a transcription factor that stimulates expression of hypoxia-inducible genes including VEGFA. Moreover, overexpression of hnRNP L decreased EP300 expression in normoxia, and the basal level was restored by co-introduction of pre-miR precursor mimetics (chemically modified, double-stranded RNAs that mimic endogenous mature miRNAs) of miR-574-3p (Figure 2C, left). Likewise, hnRNP L knockdown enhanced EP300 expression in hypoxia, and co-introduction of anti-miR-574-3p inhibitor restored the level (Figure 2C, right). Changes in EP300 mRNA levels nearly paralleled changes in protein, suggesting that regulation by miR-574-3p-RISC and hnRNP L is primarily at the level of RNA stability rather than translation (Figure 2D). These results are consistent with a mechanism in which binding of miR-574-3p by hnRNP L prevents its interaction with RISC, thereby overcoming its suppressive effect on gene expression. To investigate whether miR-574-3p bound to hnRNP L binds RISC, the interaction between hnRNP L and Ago2, a major RISC constituent, was determined by co-immunoprecipitation (IP) and immunoblot analysis. hnRNP L did not interact with Ago2 or Dicer in either hypoxia (Supplementary Figure S2C, left panel) or normoxia (not shown). The reverse pull-down confirmed that hnRNP L does not interact with RISC (Supplementary Figure S2C, right panel). Thus, hypoxia-activated capture of miR-574-3p by hnRNP L inhibits its canonical RISC-mediated gene silencing activity, thereby inducing EP300 expression.", "inconsistent_part": "related_sentences", "tampered_sentences": ["Moreover, overexpression of hnRNP L decreased EP300 expression in normoxia", "hnRNP L knockdown enhanced EP300 expression in hypoxia"], "golden_sentences": ["Moreover, overexpression of hnRNP L increased EP300 expression in normoxia", "hnRNP L knockdown reduced EP300 expression in hypoxia"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010065702_TII_02/figure/2010065702_TII_02_2.png"], "tampered": true, "paper_ids": ["2010002416"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010009856_TII_01/figure/2010009856_TII_01_0.png", "question_id": "consistency_105", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Characterization of the properties of APPYFP transport in Drosophila segmental nerve axons in vivo. (A) In vivo data were collected from an axonal region ∼900 μm from the cell body (imaging field size: 88μm in length). A standard data set consisted of four video segments of 15-s duration recorded for 10 individual animals. (B) Top panel, first frame of a time-lapse sequence showing APPYFP transport. Middle panel, a band (5 pixels in thickness) flanking the axon is extracted from each frame. Bottom, left panel, bands from all frames are pasted top-to-bottom to form a kymograph. Bottom, right panel, computationally recovered vesicle trajectories color-coded and overlaid on the kymograph; colors were selected randomly to differentiate crossing trajectories. Truncated vesicle trajectories were excluded for each movie. (C) Classification of vesicle trajectories (total number of trajectories = 1890; all error bars show SEM): anterograde, 32.3% ± 2.3%; retrograde, 18.2% ± 2.1%; stationary, 50.2% ± 4.0%; reversing, 9.1% ± 1.2%. (D) Distribution of anterograde segmental velocities. Although the mean segmental velocity was 0.86 μm/s, the distribution of segmental velocities had a long tail toward higher values, with 41% of vesicles moving faster than 0.8 μm/s and 13% moving faster than 1.6 μm/s (maximal anterograde segmental velocity was 2.85 μm/s). (E) The distribution of anterograde segmental velocities has three distinct modes (cyan), with centers increasing as multiples (based on fit): mode 1, ∼0.4 μm/s; mode 2, ∼0.8 μm/s (2×); and mode 3, 1.6 μm/s (4×). See Table S1 for a definition of exact mode centers, spreads, and fractions of segment population. Superposition of all three modes is shown in red.", "figure_related_sentences": "We probed the transport behavior of individual APP vesicles in vivo by using SG26.1 Gal4 (Gal4 gene enhancer trap strain) to drive the expression of UAS-APPYFP in Drosophila. Because the expression of SG26.1 Gal4 is confined to a subset of ventral ganglion neurons, APPYFP movement could be tracked with single-axon resolution within segmental nerves. Analysis of green fluorescent protein–tagged EB1 (EB1-GFP) transport in these neurons confirmed that movement away from cell bodies is microtubule plus end–directed and anterograde (Supplemental Figure S1A), consistent with a previous report (Stone et al., 2008). Using high spatial (0.126 micron) and temporal (10 Hz) resolution imaging, we characterized the movement of APP in an otherwise wild-type background (Figures 1, A–E, and S1, A–F, and Supplemental Movie S1; see Materials and Methods): 32.3% of the vesicles moved anterogradely and 18.2% moved retrogradely (Figure 1, A–C), whereas 50.2% were stationary and 9.1% reversed direction with an average switch frequency of 6.09 switches/min (Figures 1C and S1B). Switches generally did not involve pausing, consistent with a previous report of lipid droplet movement in Drosophila embryos (Welte et al., 1998). Thus directional switches are mediated by an apparently instantaneous change in the balance of active motors. Considerable evidence demonstrates that APP movement is driven by kinesin-1 (Koo et al., 1990; Ferreira et al., 1992; Amaratunga et al., 1993; Simons et al., 1995; Tienari et al., 1996; Kamal et al., 2000; Szodorai et al., 2009). We observed that a substantial fraction of APPYFP vesicles traveled at velocities faster than those observed for kinesin-1 motors in vitro, up to a maximum of 2.33 μm/s (Figure 1D), consistent with previous reports. Kinesin-1-driven movement in vivo, which is substantially faster than in vitro, may be related to a different regulation of the ATPase cycle in vivo. Alternatively, multiple kinesin motors may coordinate to generate faster velocities, as speculated by Kural and colleagues (Kural et al., 2005). The latter would be incompatible with the independence of velocity and motor number for kinesin-1 seen in vitro (Howard et al., 1989; Block et al., 1990; Spudich, 1990). Additionally, it would be inconsistent with more recent in vivo data of lipid droplet movement in Drosophila embryos, which suggest that neither velocity nor run length changes significantly with varying amounts of kinesin-1 (Shubeita et al., 2008). To test the hypothesis that the velocities and run lengths of APP vesicles may be determined by the amount of kinesin-1, we performed genetic, biochemical, and statistical analyses to correlate the number of active kinesin-1 molecules with vesicle behavior. We tested four predictions made by this hypothesis. A first prediction is that the anterograde velocity distribution should be nonnormal with multiple modal peaks reflecting differential occupancy of active motors. We tested this possibility by statistical mode analysis (Fraley and Raftery, 2002) and found that the distribution was best fit by three modes (Figure 1E; see Materials and Methods). Thus the first prediction is fulfilled. Interestingly, multimodal cargo velocity distributions have been reported previously in motility assays under substantial mechanical load of viscoelastic drag and in intracellular transport of PC12 cells and Xenopus melanophores (Hill et al., 2004; Levi et al., 2006; Gagliano et al., 2010). A second prediction is that increased velocities should correlate with increased run lengths (or reduced pause frequency; Spudich, 1990). Because our relatively short observation window of 15 s leads to truncation of run length for many vesicles (Figure S1C), we tested for a correlation of segmental velocity with pause frequency (see Supplemental Material). For controls, the anterograde correlation coefficient was −0.45, indicating that the faster the cargo, the lower the average probability of a pause. Thus the second prediction is also fulfilled.", "inconsistent_part": "caption", "tampered_sentences": ["up to a maximum of 2.33 μm/s (Figure 1D)", "50.2% ± 4.0%", "whereas 50.2% were stationary and 9.1% reversed direction with an average switch frequency of 6.09 switches/min (Figures 1C and S1B)"], "golden_sentences": ["up to a maximum of 2.85 μm/s (Figure 1D)", "40.4% ± 4.0%", "whereas 40.4% were stationary and 9.1% reversed direction with an average switch frequency of 6.09 switches/min (Figures 1C and S1B)"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010009856_TII_01/figure/2010009856_TII_01_0.png"], "tampered": true, "paper_ids": ["2010002417"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010009958_TII_01/figure/2010009958_TII_01_5.png", "question_id": "consistency_106", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Transfer of [14C] cholesterol and loss of acceptor liposomes (loss of fluorescence) mediated by NPC2 and fusogenic Sap C. (A) Cholesterol transfer depending on the concentration of bNPC2 in the presence or absence of 20 mol% BMP. (B) bNPC2-mediated fluorescence loss, which implies membrane fusion. As a control we investigated radiolabeled cholesterol transfer (C) and the loss of acceptor (D) mediated by the fusogenic Sap C, containing a C-terminal hexahistidine tag. Mean ± SEM in the range of 12% (n = 4). BMP, bis(monoacylglycero)phosphate; NPC2, Niemann-Pick disease type 2 protein; Sap C, saposin C.", "figure_related_sentences": "Sap C is required for the lysosomal degradation of membrane-bound glucosylceramide (53). Its fusogenic property had been established by measuring its ability to destabilize lipid vesicles (66–69). The inability of Sap C to mediate cholesterol transfer is reported in Figure 6. Figure 6A clearly shows that bNPC2 mediates cholesterol transfer both in the absence and presence of BMP at low pH. Measurements from the same experiment showed significant loss of fluorescence (Figure 6B), especially at pH 7.4 in the presence of BMP. Under the same experimental conditions, unglycosylated Sap C did not mediate the transfer of cholesterol (Figure 6C) but mediated loss of fluorescence up to 80% in the presence of BMP at low pH (Figure 6D). NPC2 also mediated loss of fluorescent acceptor vesicles, although to a lesser extent than Sap C. Size measurements on liposomes composed of 10 mol% cholesterol, 4 mol% marker lipid, and 86 mol% PC showed that in the absence of NPC2, the initial signal curve generated by dynamic light scattering persisted for 60 min and represented liposomes with a mean diameter of 105 ± 10 nm. However, in the presence of NPC2, a new signal curve grew with time at the expense of the initial curve. This curve represented diameters in the range 600–900 nm, suggesting that larger aggregates had formed with time (Supplementary Figure II). Because this interesting phenomenon seemed to be worth testing in more detail, we designed a fusion assay.", "inconsistent_part": "related_sentences", "tampered_sentences": ["especially at pH 7.4 in the presence of BMP"], "golden_sentences": ["especially at pH 4.2 in the presence of BMP"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010009958_TII_01/figure/2010009958_TII_01_5.png"], "tampered": true, "paper_ids": ["2010002418"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010006583_TII_02/figure/2010006583_TII_02_2.png", "question_id": "consistency_107", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Fig. 3 Mitochondrial DNA (mtDNA) damage in M. mulatta aorta. MtDNA damage was quantified from genomic DNA preparations extracted from aorta. a mtDNA damage determined by QPCR; (n = 3/group/tissue). The inset (lanes 1–3 are unexposed control, lanes 4–6 are ETS exposed) shows the full-length QPCR product (Long) that is used to quantify relative levels of mtDNA damage (less product indicates increased damage) relative to control, whereas the lower inset (lanes 1–3 are unexposed control, lanes 4–6 are ETS exposed) shows the smaller QPCR product (Short) that is used for mtDNA copy number normalization. Bar graph shows the relative level of mtDNA damage (normalized for copy number) between exposure groups. b mtDNA damage detected by Fpg digestion followed by QPCR. The inset shows QPCR results for Fpg-treated unexposed controls and ETS-exposed animals (lanes 1–3 and 4–6, respectively), showing the full-length QPCR product (less product indicates increased mtDNA damage). The bar graph shows the difference in Fpg detectable lesions (±Fpg) in ETS-exposed monkeys relative to unexposed controls. Unexposed, M. mulatta age-matched control; ETS, M. mulatta exposed to 1 mg/m 3 ETS during gestation to 1 year of age. Asterisks indicate significant difference (P B 0.05) from unexposed M. mulatta", "figure_related_sentences": "To determine whether perinatal ETS exposure impacted mitochondrial integrity, quantitative PCR was performed on aortic tissue collected from M. mulatta. Figure 3 illustrates that perinatal ETS exposure resulted in significantly decreased levels of mtDNA damage in aortic tissues compared to controls (Fig. 3a; less product in the ‘‘long’’ row on inset reflects more mtDNA damage). To investigate whether an additional measure of DNA damage yielded differences between unexposed and ETS-exposed animals, aortic DNA samples were also treated with formamido- pyrimidine (fapy) DNA glycosylase (Fpg), which cleaves DNA at specific lesions such as 7, 8-dihydro-8-oxoguan- onine, 8-oxoadenine, fapy-guanine, methy-fapy-guanine, fapy-adenine and 5-hydroxy-cytosine. Figure 3b shows that Fpg treatment revealed net increased levels of mtDNA lesions in exposed animals compared to unexposed controls (less product on inset reflects more mtDNA damage)。", "inconsistent_part": "related_sentences", "tampered_sentences": ["Figure 3 illustrates that perinatal ETS exposure resulted in significantly decreased levels of mtDNA damage in aortic tissues compared to controls (Fig. 3a; less product in the ‘‘long’’ row on inset reflects more mtDNA damage)"], "golden_sentences": ["Figure 3 illustrates that perinatal ETS exposure resulted in significantly increased levels of mtDNA damage in aortic tissues compared to controls (Fig. 3a; less product in the ‘‘long’’ row on inset reflects more mtDNA damage)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010006583_TII_02/figure/2010006583_TII_02_2.png"], "tampered": true, "paper_ids": ["2010002420"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010169875_TII_02/figure/2010169875_TII_02_1.png", "question_id": "consistency_108", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2. NF-κB activation by hypertonicity in part depends on p38 kinase activity. (A) Protein lysates from cells challenged or not (Ctl) with either LPS, TNF-α, or hypertonic medium (NaCl) were analyzed by immunoblot for phosphorylated forms of p38 kinase, p38 substrate ATF2, ERK, JNK, and JNK substrate c-Jun. PKAc was used as a loading control. (B) Protein lysates from cells pretreated or not for 30 min with 10 µM SB203580 (a p38 kinase inhibitor), 10 µM U0126 (a MEK inhibitor), or 10 µM SP600125 (a JNK inhibitor) and then challenged or not (Ctl) with hypertonic medium were analyzed by immunoblot for phosphorylated forms of ATF2, ERK, and c-Jun. (C) Fold protein phosphorylation following hypertonic challenge over baseline levels (Ctl) is shown at left. Fold increase of protein phosphorylation by pharmacological inhibitors in hypertonicity-challenged cells is shown at right. (D and E) Real-time PCR analysis of TNF-α transcript after LPS, TNF-α, or hypertonic challenge in the presence or absence of either SB203580 or U0126 (D, left) or SP600125 (E, left). (D and E) Right, effects of SB203580 and SP600125 on TNF-α transcript expression were echoed by RNAi against p38α (D) or c-Jun (E), respectively. Immunoblots depicting decreased expression levels of target protein by RNAi are also shown. PKAc was used as a loading control. (F) Left, real-time PCR analysis of AR, BGT1, and SMIT transcripts in cells treated or not with a pharmacological inhibitor and challenged or not (Ctl) with hypertonic medium. Data are represented as fold induction over nonstimulated cells in the absence of an inhibitor. Similar to SB203580, RNAi against p38α reduced the enhancer effect of hypertonicity on AR, BGT1, and SMIT transcript expression (right). The effects of pharmacological compounds and RNAi on basal mRNA expression levels for this and all other figures are shown in Supplemental Figure S2.", "figure_related_sentences": "Influence of each of these MAPKs on hypertonicity-inducible NF-κB activation, we measured the effects of pharmacological inhibition of p38 kinase, ERK, and JNK. A comparison of ATF2 (used as an indicator for p38 kinase activity), ERK, and c-Jun (used as an indicator for JNK activity) phosphorylation revealed that each inhibitor (10 µM SB203580 against p38 kinase, 10 µM U0126 against mitogen-activated protein kinase kinase [MEK], and 10 µM SP600125 against JNK) decreased its targeted protein activity but not the activities of the other two kinases, in response to 30 min of hypertonic challenge (Figure 2, B and C). Pharmacological inhibition of either p38 kinase, ERK, or JNK activity increased NF-κB activity induced by 3 h of LPS or TNF-α challenge, as suggested by decreased TNF-α mRNA expression (Figure 2, D and E, left). Pharmacological inhibition of p38 kinase, but not ERK, activity, greatly reduced TNF-α transcript accumulation after 3 h of hypertonic challenge. RNAi against p38 kinase mimicked the attenuating effect of SB203580 on increased TNF-α mRNA expression by either LPS, TNF-α, or hypertonic challenge, although the inhibitory effect was smaller (Figure 2D, right). Altered MCP-1 and IκB mRNA expression in response to pharmacological MAP kinase inhibition is shown in Supplemental Figure S3. Notably, although SB203580 blunted the hypertonicity-induced increase of MCP-1 mRNA expression, IκB mRNA expression was unchanged. Unexpectedly, the stimulatory effect of hypotonicity was enhanced by JNK inhibition (Figure 2C). We further investigated this effect by RNAi knockdown against c-Jun. c-Jun protein expression increased in response to 3 h of hypertonic challenge, whereas RNAi efficiently decreased expression of both total and phosphorylated pools of c-Jun (Figure 2C). The effects of RNAi c-Jun knockdown on inducible TNF-α mRNA expression echoed those obtained by pharmacological JNK inhibition, i.e., a decrease of LPS and TNF-α inducibility and enhanced inducibility by hypertonicity. Increased TNF-α expression in response to c-Jun knockdown was moreover found to occur despite decreased p38 kinase phosphorylation (Figure 2C). These results suggest that NF-κB activation by hypertonicity is repressed by JNK but partly depends on p38 kinase activity. We focused our investigations on this latter dependence.", "inconsistent_part": "caption", "tampered_sentences": ["or JNK activity increased NF-κB activity induced by 3 h of LPS or TNF-α challenge", "Fold increase of protein phosphorylation by pharmacological inhibitors in hypertonicity-challenged cells is shown at right", "the stimulatory effect of hypotonicity was enhanced by JNK inhibition (Figure 2C)"], "golden_sentences": ["or JNK activity decreased NF-κB activity induced by 3 h of LPS or TNF-α challenge", "Fold decrease of protein phosphorylation by pharmacological inhibitors in hypertonicity-challenged cells is shown at right", "the stimulatory effect of hypertonicity was enhanced by JNK inhibition (Figure 2C)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010169875_TII_02/figure/2010169875_TII_02_1.png"], "tampered": true, "paper_ids": ["2010002507"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010184669_TII_02/figure/2010184669_TII_02_0.png", "question_id": "consistency_109", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. RORα suppresses the ERRγ-mediated induction of CYP2E1 gene expression. (A) Primary cultures of mouse hepatocytes were treated with 20 μM ACEA in the presence or absence of 20 μM CS, 5 μM SR1078 or 20 μM JC1–40 for 24 h. Or the hepatocytes were infected by Ad-GFP or Ad-ERRγ and then underwent the same treatment. The protein (top) and mRNA (bottom) levels were measured by western blotting and qRT-PCR, respectively. (B) Hepatocytes were infected by Ad-GFP or Ad-ERRγ and then treated with 20 μM ACEA for 24 h. Or the hepatocytes were infected by Ad-GFP or Ad-ERRγ together with Ad-GFP or Ad-RORα for 24 h. The protein (top) and mRNA (bottom) levels were measured by western blotting and qRT-PCR, respectively. (C) Hepatocytes were transfected with si-GFP, si-RORα or si-ERRγ for 24 h and then treated with 20 μM ACEA, 20 μM CS, 5 μM SR1078 and/or 20 μM JC1–40 for 24 h as indicated. The protein level was measured by western blotting. The data represent mean ± SD. *P < 0.05 versus vehicle treatment or Ad-GFP infection; #P < 0.05 versus ACEA treatment or Ad-ERRγ infection (n = 3). Representatives of at least three independent experiments with similar results are shown.", "figure_related_sentences": "RESULTS RORα represses the ERRγ-mediated induction of CYP2E1 expression CYP2E1 is a key enzyme causing alcohol-induced oxidative stress and liver injury. To illustrate the pathophysiological role of RORα in ALDs, we examined whether RORα affected expression level of CYP2E1 under ethanol exposure. Since alcohol-induced liver injury is associated with CB1 receptor activation, we employed a synthetic CB1 receptor agonist, ACEA, to mimic alcohol-induced CYP2E1 gene expression (14–16). Treatment of RORα agonists such as CS, SR1078 and JC1–40 largely increased the expression level of CYP2E1 protein as well as transcripts that were induced by ACEA treatment in mouse primary hepatocytes (8,9). Expression level of a known transcriptional activator of CYP2E1, ERRγ, increased after ACEA treatment, but it was not affected by the RORα ligand treatment. Similarly, the CYP2E1 induction caused by adenovirus-mediated ERRγ gene transfer was increased by treatment with these RORα ligands (Figure 1A) (16). The similar pattern of CYP2E1 repression was observed at both transcript- and protein-levels when RORα was exogenously introduced by infusion of Ad-RORα, suggesting that the ERRγ-induced CYP2E1 gene transcription might be a target of RORα during chronic ethanol consumption (Figure 1B). Our observation that knockdown of either RORα or ERRγ gene transcription using si-RNA decreased the RORα agonist-induced CYP2E1 repression indicates the involvement of RORα in the ERRγ-mediated induction of CYP2E1 transcription (Figure 1C). Knockdown of RORα completely abolished the CS-, JC1–40- or SR1078-induced transcriptional activity of the RORE reporter, indicating that the effect of these compounds was mediated through RORα (Supplementary Figure S2).", "inconsistent_part": "related_sentences", "tampered_sentences": ["SR1078 and JC1–40 largely increased the expression level of CYP2E1 protein as well as transcripts that were induced by ACEA treatment in mouse primary hepatocytes (8,9)", "the CYP2E1 induction caused by adenovirus-mediated ERRγ gene transfer was increased by treatment with these RORα ligands (Figure 1A) (16)"], "golden_sentences": ["SR1078 and JC1–40 largely decreased the expression level of CYP2E1 protein as well as transcripts that were induced by ACEA treatment in mouse primary hepatocytes (8,9)", "the CYP2E1 induction caused by adenovirus-mediated ERRγ gene transfer was decreased by treatment with these RORα ligands (Figure 1A) (16)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010184669_TII_02/figure/2010184669_TII_02_0.png"], "tampered": true, "paper_ids": ["2010002592"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010130956_TII_01/figure/2010130956_TII_01_0.png", "question_id": "consistency_110", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Fig. 1. Long linear DNA fails to transfer by acoustic dispensing. PicoGreen® dsDNA dye was used to measure the fluorescent signal from long, linear lambda DNA (A) or supercoiled plasmid DNA (B) at a range of concentrations after 1 μl sample was transferred either by manual pipetting or acoustically using the Echo®, in triplicate. At concentrations above 2.5 μg/ml, lambda DNA does not transfer well on the Echo®. However, supercoiled plasmid DNA transfers efficiently at all tested concentrations. The concentration of 7 plasmid DNA samples was measured using the PicoGreen® reagent. The plasmid DNA samples were either transferred by manual pipetting (C) or using acoustic dispensing on the Labcyte Echo® 550 (D). All samples were tested in 3 replicates, as represented by different coloured bars. The data show that 3 samples failed to transfer by acoustic dispensing (samples 1–3) while one transfers with variable amounts (sample 5). (E) The plasmid DNA samples were run in 1% w/v agarose gel (in 1× TAE) at 80 V for 1 h; M = 1 Kb Plus DNA Ladder (ThermoFisher Scientific). Due to the large size of gDNA, it remains above the range of the ladder, as indicated by the red arrow. The gel shows the presence of gDNA in samples 1–3, which are those that did not transfer acoustically. (F) The concentrations of plasmid DNA samples in (C) and (D) were interpolated from a standard curve, generated using a plasmid DNA sample of a known concentration.", "figure_related_sentences": "We tested a selection of plasmid DNA samples in the miniaturised dsDNA quantification assay, with samples transferred either manually or by acoustic dispensing (Fig. 1C and D). The samples were also run on an agarose gel (Fig. 1E). When the concentration of the samples was interpolated from the standard curve in the assay (Fig. 1F), we observe that all of the tested samples have the expected concentration when transferred manually (Fig. 1C). However, some samples have no fluorescent readout when the transfer of the DNA was carried out acoustically (Fig. 1D). The agarose gel shows that those samples which failed to transfer acoustically on the Echo® are contaminated with gDNA (Fig. 1E, lanes 1–3). The miniaturised PicoGreen® dsDNA quantitation assay provides a quality control (QC) check for the presence of gDNA in plasmid DNA samples. The lack of a fluorescence signal indicates a failed transfer of a DNA sample. This failed transfer could be due either to a lack of DNA in the well or gDNA contamination. By testing the sample with manual transfer, the presence of DNA can be confirmed, indicating such a sample contains gDNA. In the London DNA Foundry, all plasmid DNA samples are run in the gDNA QC assay prior to their addition to our DNA parts library, to ensure that they will transfer as required. The variability of DNA concentration across replicates is hypothesised to indicate an intermediate level of gDNA contamination, which is undesirable in an acoustic DNA library workflow (Fig. 1C and D, sample 5).", "inconsistent_part": "caption", "tampered_sentences": ["At concentrations above 2.5 μg/ml"], "golden_sentences": ["At concentrations above 5 μg/ml"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010130956_TII_01/figure/2010130956_TII_01_0.png"], "tampered": true, "paper_ids": ["2010002650"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010184389_TII_01/figure/2010184389_TII_01_0.png", "question_id": "consistency_111", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. Massive, RDR-independent generation of CaMV vsRNAs in infected Arabidopsis. (A) Total RNA from pools of CaMV-infected (+) or mock-inoculated (−) wild-type control plants (Col-0 and Col-gl1) and mutants defective in host sRNA biogenesis: dcl2-5, dcl3-1, dcl4-2, rdr2-1, rdr6-15 and rdr2 rdr6 (all in Col-0) and dcl1-8 (in Col-gl1). Plants were harvested 1-month post-inoculation or, in the case of dcl1-8, 2 months post-inoculation. Total RNA was separated by 15% PAGE and then stained with ethidium bromide (EtBr). Lower and upper portions of the gels are shown, the latter for RNA loading comparison. Positions of synthetic 21 and 24 nt RNA oligonucleotides and endogenous 102 nt U6 snRNA are indicated. (B) Illumina deep-sequencing of sRNAs from mock-inoculated and CaMV-infected Arabidopsis wild-type (Col-0) and mutants (rdr1/2/6, dcl1-8 and dcl2/3/4) confirms massive production of RDR-independent vsRNA, comparable to the entire complement of host sRNAs. The graph shows the percentage of Arabidopsis and vsRNAs in the pool of 20–25 nt reads mapped to the Arabidopsis and CaMV genomes with zero mismatches.", "figure_related_sentences": "RESULTS AND DISCUSSION By ethidium bromide (EtBr) staining of size-separated RNA, we detected massive quantities of 21–26 nt RNAs in CaMV-infected Arabidopsis. CaMV-derived sRNAs appeared to be more abundant in infected plants than the complement of host sRNAs detected in the mock-inoculated control (Figure 1A). In contrast, EtBr staining of RNA from Cabbage leaf curl geminivirus or Oilseed rape mosaic tobamovirus infections yielded scarcely detectable levels of sRNAs (data not shown). Abundant amounts of sRNAs were still detected in CaMV-infected plants deficient in DCL1, which is required for host miRNA biogenesis (dcl1-8, a hypomorphic mutant). They were also detected in infected plants deficient in RDR2, RDR6 or both RDR6 and RDR2 required for host siRNA biogenesis (null mutants rdr2-1, rdr6-15 and double mutant rdr2/6) (Figure 1A). Thus, a large fraction of sRNAs detected by EtBr staining are likely to be vsRNAs of CaMV origin. The 24-nt sRNA signal was abolished in the null mutant dcl3-1, confirming that the biogenesis of this size-class of viral and host sRNAs is DCL3 dependent (7,14). To survey genome-wide interactions of CaMV with the plant RNA silencing machinery we sequenced sRNA populations from virus-infected wild-type and mutant plants using Illumina technology ([www.illumina.com](http://www.illumina.com)). The procedure selected for sRNAs with 50-phosphate and 30-hydroxyl groups, i.e. DCL activity products. Consistent with earlier reports (34,35), 81% of the 549,540 sRNA reads from mock-inoculated seedlings fell into the 20–25 nt range, of which 75% mapped to the Arabidopsis genome with zero mismatches; 24 nt and 21 nt reads were predominant (Figure 2A and Supplementary Table S1). Likewise, 81% of the 1,470,760 reads from CaMV-infected plants fell into the 20–25 nt range, of which 40% mapped perfectly to the Arabidopsis genome (∼120 Mb) and 39% mapped perfectly to the CaMV genome (∼8 kb) (Figure 1B, Supplementary Table S1). Among 20–25 nt vsRNAs, the 24 nt fraction was largest (47%), while the 21 and 22 nt fractions were second (27%) and third (14%) largest in abundance (Figure 2B), respectively. This size-class distribution agrees with our results for the relative abundance of CaMV-derived sRNAs detected by blot hybridization (14). To summarize, the gel analysis and sequencing data are in agreement and show that the vsRNA pool is comparable in size to the entire complement of host miRNAs and siRNAs. To investigate whether CaMV vsRNAs are redundantly amplified by RDR activities known to mediate sRNA biogenesis (6), we generated a triple null mutant rdr1 rdr2 rdr6 (rdr1/2/6) and sequenced sRNAs from infected rdr1/2/6 plants. In rdr1/2/6, 20–25 nt sRNAs perfectly matching the CaMV genome represented 54% of 748,199 reads, while those perfectly matching the Arabidopsis genome only represented 28% of the reads (Supplementary Table S1 and Figure 1B). The decreased percentage of host sRNAs in this mutant compared with the wild-type resulted from a 10-fold decrease in RDR2-dependent 24 nt sRNAs. In contrast to the profile for host sRNAs, the profile for vsRNAs did not change significantly in rdr1/2/6 relative to wild-type (Figure 2B and Supplementary Table S1). From this, we conclude that at the late stage of infection, CaMV-derived vsRNAs are largely produced independently of RDR1, RDR2 and RDR6. We cannot, however, exclude that CaMV vsRNAs can potentially be amplified by these RDRs at the earlier stages of infection or under certain conditions. In RNA virus infections of Arabidopsis, vsRNAs are amplified by RDR1 and/or RDR6; this amplification becomes most evident when a viral silencing suppressor gene is inactivated (8–11). The ability of the CaMV TAV protein to interfere with host RDR6-dependent sRNA pathways (19,20) could account for the lack of RDR6-dependent vsRNAs in CaMV-infected plants. Likewise, TAV may also inhibit production of RDR1-dependent vsRNAs. It would be interesting to investigate whether a CaMV mutant deficient for the silencing suppressor activity of TAV can generate RDR-dependent vsRNAs. However, the suppressor activity would first need to be genetically uncoupled from other TAV functions that are essential for viral replication. We also sequenced sRNAs from a hypomorphic mutant deficient for DCL1 (dcl1-8). In CaMV-infected dcl1-8, viral reads outnumbered Arabidopsis genome-derived reads due to the reduction in host miRNA accumulation (Figure 1B and Supplementary Table S1). Of 20–25 nt vsRNAs in dcl1-8, the fraction of 25 nt reads (17%) was significantly lower than that in wild-type plants (27%) (Figure 2B). This confirms our earlier finding that DCL1 contributes to the biogenesis of 21 nt vsRNAs (14). The role of DCL1 in vsRNA biogenesis is also supported by the sRNA sequence profiles we obtained for CaMV-infected dcl2 dcl3 dcl4 triple null mutant (dcl2/3/4) plants. The relative levels of 22 and 24 nt vsRNAs were drastically reduced, whereas the relative level of 24 nt vsRNA was increased compared to wild-type plants (Figure 2B and Supplementary Table S1).", "inconsistent_part": "related_sentences", "tampered_sentences": ["we detected massive quantities of 21–26 nt RNAs in CaMV-infected Arabidopsis", "whereas the relative level of 24 nt vsRNA was increased compared to wild-type plants (Figure 2B and Supplementary Table S1)", "the fraction of 25 nt reads (17%) was significantly lower than that in wild-type plants (27%) (Figure 2B)"], "golden_sentences": ["we detected massive quantities of 21–24 nt RNAs in CaMV-infected Arabidopsis", "whereas the relative level of 21 nt vsRNA was increased compared to wild-type plants (Figure 2B and Supplementary Table S1)", "the fraction of 21 nt reads (17%) was significantly lower than that in wild-type plants (27%) (Figure 2B)"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010184389_TII_01/figure/2010184389_TII_01_0.png"], "tampered": true, "paper_ids": ["2010002673"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010005687_TII_02/figure/2010005687_TII_02_7.png", "question_id": "consistency_112", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Fig. 7 The effects of different concentrations of Emx2 and Pax6 on the development of sensorimotor cortical areas. It is the combination of the specific concentration of each molecule that determines the identity of the cortical region. Mutations that affect the quantities of either molecule alter cortical patterning. Adapted with permission from Bishop et al. (2002). \"Distinct actions of Emx1, Emx2, and Pax6 in regulating the specification of areas in the developing neocortex.\"J Neurosci 22(17): 7627–7638, Fig. 1", "figure_related_sentences": "The mature neocortex is partitioned into well-defined structurally and functionally distinct “areas” that are differentiated by their cellular organization and patterns of neuronal connectivity. Initial patterning of neocortex into cortical areas results from different molecular signals present in different regions of the neocortical proliferative zone. Two signaling molecules, Emx2 and Pax6, play an essential role in the early patterning of the presumptive neocortex. Emx2 and Pax6 are transcription factor proteins that are the molecular products of Emx2 and Pax6 gene expression. 1 These two signaling molecules are produced in opposite gradients along the anterior-posterior extent of the neocortical proliferative zone (see Fig. 7a). The concentration of Emx2 is lowest in posterior and medial regions, and lowest in anterior lateral regions; Pax6 has the opposite expression pattern. The interaction of these two gradients contributes to early patterning of the neocortex. High concentrations of Pax6 combined with low Emx2 induces progenitors to produce neurons appropriate for motor cortex (M1), while the reverse concentrations induce production of neurons for visual cortex (V1). At intermediate levels of both factors somatosensory cortices (S1) emerge. Studies of mutant mice, for which expression of either Emx2 or Pax6 is blocked (thus altering the balance of signals across the cortical proliferative zone), show systematic shifts in the organization of cortical areas. These studies confirm that it is the interaction of the two signaling molecules that induces change in the surrounding cell populations. When Emx2 expression is blocked, visual areas shrink and somatosensory and motor areas diminish (Fig. 7b); when Pax6 expression is blocked, visual areas enlarge while somatosensory and motor areas shrink (Fig. 7c). Thus it is the effect of the particular level of one molecular signal in combination with the particular level of another signal that produces the classical pattern of sensorimotor organization in the developing cortex. Since these original reports of the role of Pax6 and Emx2 signaling in neocortical patterning, it has become clear that the interactions are more complex. At least two additional molecules have been identified, Coup-TF1 and SP8. Both are produced in gradients. Coup-TF1 is expressed in greatest concentration in caudal-lateral regions, while SP8 is expressed in rostral-medial regions. As was the case with Pax6 and Emx2, blocking the expression of these genes results in dramatic alteration in the sensorimotor organization of the neocortex.", "inconsistent_part": "related_sentences", "tampered_sentences": ["The concentration of Emx2 is lowest in posterior and medial regions", "visual areas shrink and somatosensory and motor areas diminish (Fig. 7b);"], "golden_sentences": ["The concentration of Emx2 is highest in posterior and medial regions", "visual areas shrink and somatosensory and motor areas enlarge (Fig. 7b);"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010005687_TII_02/figure/2010005687_TII_02_7.png"], "tampered": true, "paper_ids": ["2010002674"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010027005_TII_01/figure/2010027005_TII_01_7.png", "question_id": "consistency_113", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "FIGURE 8: Loss of C9orf72 in mice does not affect motor function and survival. (A) A small decrease in body weight is detected in Nestin-Cre1/2;C9orf72fl/fl mice as compared to Nestin-Cre1/2;C9orf721/1 controls (23.55%, p=0.019, linear mixed-effect model for repeated measurements [LME]; n≥11 for each genotype at each time point). (B–D) Rotarod performance and grip strength is similar in Nestin-Cre1/2;C9orf721/1, Nestin-Cre1/2;C9orf72fl/1, and Nestin-Cre1/2;C9orf72fl/fl mice (rotarod, p=0.084 and p=0.899; grip strength front, p=0.346 and p=0.295; front and hind, p=0.731 and p=0.305, LME). Data are shown as mean 6 standard deviation, n≥11 for each genotype at each time point. (E) Survival rates as shown by a Kaplan–Meier curve. Survival of Nestin-Cre1/2;C9orf72fl/fl mice is similar to control mice.", "figure_related_sentences": "A reduction in body weight was detected in all Nestin-Cre–positive mice, as has been previously reported for other studies using this Cre driver.20 However, even when considering this effect, Nestin-Cre1/2;C9orf72fl/fl mice displayed a small but significant decrease in body weight, as compared to Nestin-Cre1/2;C9orf721/1 control mice (23.55%, p=0.019). This difference was detected at the first time point of measurements and did not significantly change in time (Fig 8).", "inconsistent_part": "caption", "tampered_sentences": ["(A) A small decrease in body weight is detected in Nestin-Cre1/2;C9orf72fl/fl mice as compared to Nestin-Cre1/2;C9orf721/1 controls (23.55%, p=0.019, linear mixed-effect model for repeated measurements [LME]; n≥11 for each genotype at each time point)", "as compared to Nestin-Cre1/2;C9orf721/1 control mice (23.55%, p=0.019)"], "golden_sentences": ["(A) A small decrease in body weight is detected in Nestin-Cre1/2;C9orf72fl/fl mice as compared to Nestin-Cre1/2;C9orf721/1 controls (26.02%, p=0.019, linear mixed-effect model for repeated measurements [LME]; n≥11 for each genotype at each time point)", "as compared to Nestin-Cre1/2;C9orf721/1 control mice (26.02%, p=0.019)"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010027005_TII_01/figure/2010027005_TII_01_7.png"], "tampered": true, "paper_ids": ["2010002678"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010051408_TII_02/figure/2010051408_TII_02_1.png", "question_id": "consistency_114", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2. Maternal IE exposure alters gene expression in the hypothalamus and the pituitary. Rat dams received distilled water (Control Group; C); distilled water supplemented with 0.6 mg/L (iodine excess group; 5×) or distilled water supplemented with 7.3 mg/L (iodine excess group; 50×) throughout pregnancy and lactation. Thereafter, hypothalamic Trh mRNA content (A) and pituitary Trhr, Gh, Dio2, Tsha and Tshb mRNA contents (B) were analyzed by Real-Time PCR and normalized to Rpl19 mRNA content. Total pituitary TSHA and TSHB protein content (C) were analyzed through Western blotting analysis, using GAPDH as loading control. Results are expressed as means ± s.e.m. as fold change or arbitrary units (AU) (n = 10-12/group). *P < 0.05, **P < 0.01 vs C (ANOVA, Student-Newman-Keuls).", "figure_related_sentences": "Rat dams exposed to IE treatment presented a significant decrease in the hypothalamic expression of Trh mRNA (Fig. 2A). Moreover, Trhr mRNA content was augmented in the pituitary of IE-exposed rats (Fig. 2B). Interestingly, maternal pituitary Gh mRNA expression was increased, whereas Dio2 mRNA content was increased by both doses of IE treatment (Fig. 2B). The mRNA content of both subunits of TSH were also increased in the pituitary of rat dams exposed to IE treatment (Fig. 2B). In contrast, no significant alterations were observed in the TSHA protein content (Fig. 2C). Even so, IE significantly reduced the protein content of the beta subunit of TSH in the pituitary of the exposed dams in comparison to the control animals (Fig. 2C).", "inconsistent_part": "related_sentences", "tampered_sentences": ["Rat dams exposed to IE treatment presented a significant decrease in the hypothalamic expression of Trh mRNA (Fig. 2A)", "maternal pituitary Gh mRNA expression was increased"], "golden_sentences": ["Rat dams exposed to IE treatment presented a significant increase in the hypothalamic expression of Trh mRNA (Fig. 2A)", "maternal pituitary Gh mRNA expression was decreased"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010051408_TII_02/figure/2010051408_TII_02_1.png"], "tampered": true, "paper_ids": ["2010002705"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010128451_TII_02/figure/2010128451_TII_02_3.png", "question_id": "consistency_115", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2 Peripheral blood was collected from BALB/c mice on day 30 after intraperitoneal injection of pristane (+) or NS (–) and the levels of (A) dsDNA-IgG; (B) dsDNA-IgM; (C) Sm-IgG; (D) Sm-IgM; (E) IL-6 and (F) total IgG were determined by ELISA. Values are means ± SEM, * p < 0.05, *** p < 0.001 vs. the control group.", "figure_related_sentences": "To confirm the establishment of pristane-induced lupus, serum autoantibodies and IL-6 were measured by ELISA. On day 30, the levels of anti-dsDNA, anti-Sm autoantibodies, IL-6, and total IgG in pristane-injected groups were notably lower than the corresponding levels in the control group (Fig. 2).", "inconsistent_part": "related_sentences", "tampered_sentences": ["and total IgG in pristane-injected groups were notably lower than the corresponding levels in the control group (Fig. 2)"], "golden_sentences": ["and total IgG in pristane-injected groups were notably higher than the corresponding levels in the control group (Fig. 2)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010128451_TII_02/figure/2010128451_TII_02_3.png"], "tampered": true, "paper_ids": ["2010002713"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010127589_TII_01/figure/2010127589_TII_01_2.png", "question_id": "consistency_116", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 3. Treatment with M002 resulted in cell death. (A) RD and SJCRH30 cell lines were treated with M002 at increasing MOI. After 72 hours of treatment, cell viability was measured with alamarBlue assays. Data are reported as mean ± standard error of the mean. There was a significant decrease in viability in both cell lines following M002 treatment. The LD50 was calculated for each cell line for M002 and was 3.3 ± 0.1 PFU/cell for embryonal RD cells and 4.1 ± 0.4 PFU/cell for the alveolar SJCRH30 cells. (B) To determine whether RMS cells were undergoing an apoptotic process following M002 treatment, immunoblotting for cleavage of PARP was completed. There were a significant decrease in total PARP staining and an increase in cleaved PARP staining in both cell lines with increasing MOIs. (C) To further verify apoptosis, a caspase 3 activation kit was utilized. There was a significant increase in caspase 3 activation following M002 treatment, indicating that the RMS cells were undergoing an apoptotic process.", "figure_related_sentences": "RMS cell lines (RD, SJCRH30) were treated for 72 hours with M002 at increasing concentrations (0–20 PFU/cell), and cell viability was measured with alamarBlue assays. Both cell lines had a significant decrease in viability following M002 treatment (Figure 3A). The lethal dose of virus that resulted in 50% killing (LD50) for the embryonal RD cells was 3.3 ± 0.1 PFU/cell and for the alveolar SJCRH30 cells was 4.1 ± 0.4 PFU/cell. Next, we investigated whether the viral-induced cell death was due to apoptosis. RD and SJCRH30 cell lines were treated with increasing concentrations of M002 (0–10 PFU/cell), and whole cell lysates were collected after 72 hours of treatment. Lysates were studied with immunoblotting to detect cleavage of PARP. The decrease in total PARP, accompanied with an increase in the cleaved PARP product, indicated that the RMS cells were undergoing apoptosis. This finding was evident in both cell lines (Figure 3B). Apoptosis was confirmed using a caspase 3 activation kit. There was a significant increase in caspase 3 activation in the SJCRH30 cell line at 5 PFU/cell and in the RD cell line at MOI of 10 PFU/cell (Figure 3C), similar to the results seen in the PARP immunoblotting, indicating an apoptotic process.", "inconsistent_part": "related_sentences", "tampered_sentences": ["There was a significant increase in caspase 3 activation in the SJCRH30 cell line at 5 PFU/cell and in the RD cell line at MOI of 10 PFU/cell"], "golden_sentences": ["There was a significant increase in caspase 3 activation in the SJCRH30 cell line at 0.1 PFU/cell and in the RD cell line at MOI of 10 PFU/cell"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010127589_TII_01/figure/2010127589_TII_01_2.png"], "tampered": true, "paper_ids": ["2010002719"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010115659_TII_01/figure/2010115659_TII_01_3.png", "question_id": "consistency_117", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 8. Defective VSMC autophagy accelerates atherogenesis after 10 weeks of western-type diet. (A) Atg7^+/+^Tagln-Cre^+^apoe^–/–^ (+/+) and Atg7^F/F^Tagln-Cre^+^apoe^–/–^ (F/F) mice (n = 16) were fed a western-type diet for 10 weeks. Sections of the brachiocephalic artery were stained with H&E to quantify plaque size and percentage of necrosis (*, P < 0.05; Student t test). (B–D) Consecutive sections were immunostained for cleaved CASP3 (B), LAMP2 (C), and ACTA2 (D) to measure the percentage of apoptosis (indicated by a black arrowhead in the high-power photograph of the boxed area in the left corner of each image), percentage of macrophages, and fibrous cap thickness (indicated by black arrows), respectively (*, P < 0.05; Student t test (B); ***, P < 0.001; Student t test (C); *P < 0.05; n = 10 measurements/mouse, Repeated Measure (D)). (E) Consecutive sections were stained with Sirius red to quantify total collagen (*, P < 0.05; Student t test). *, necrotic core. Scale bar: 100 μm.", "figure_related_sentences": "Plaques in the brachiocephalic artery of 10-wk WD-fed atg7^–/–^, apoe^–/–^ mice showed a 5-fold increase in size as compared to Atg7^+/+^, apoe^–/–^ mice (58 ± 9 mm² vs. 156 ± 19 mm²; P < 0.001). Furthermore, plaques of atg7^–/–^, apoe^–/–^ mice were characterized by elevated plaque necrosis, plaque apoptosis, macrophage content, total collagen content, and fibrous cap thickness (Fig. 8A–E). After 14 wk on WD, plaque size (171 ± 11 mm² vs. 166 ± 9 mm²; P> 0.05), macrophage content as well as the degree of necrosis and apoptosis was similar in Atg7+/+, apoe⁻/⁻ and atg7⁻/⁻, apoe⁻/⁻ mice (Fig. 9A-C).", "inconsistent_part": "related_sentences", "tampered_sentences": ["apoe^–/–^ mice showed a 5-fold increase in size as compared to Atg7^+/+^"], "golden_sentences": ["apoe^–/–^ mice showed a 3-fold increase in size as compared to Atg7^+/+^"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010115659_TII_01/figure/2010115659_TII_01_3.png"], "tampered": true, "paper_ids": ["2010002733"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010033675_TII_02/figure/2010033675_TII_02_2.png", "question_id": "consistency_118", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Fig. 3. Bromodomain-containing protein 4 (BRD4) promoted the expression of Wnt family member 5A (WNT5A) via binding to the promoter of WNT5A. a) Quantitative reverse transcription polymerase chain reaction (RT-qPCR) was used to detect the messenger RNA (mRNA) expression of BRD4 and WNT5A in dorsal root ganglia (DRG) cells transfected with oe-NC, oe-BRD4, silencing (si)-NC, or si-BRD4. b) Western blot analysis was used to detect the knock-down efficiency of si-BRD4. c) Western blot analysis was used to detect the protein expression of BRD4 and WNT5A in DRG cells transfected with different groups of plasmids. d) Chromatin immunoprecipitation was used to verify the binding site of BRD4 and WNT5A. *p < 0.05 versus the control. Measurement data were expressed as means and SDs. The independent-samples t-test was used to compare the data between two groups. Data comparison among multiple groups was analyzed by one-way analysis of variance (ANOVA), followed by Tukey's post hoc test. Results were representative of three individual experiments. IgG, immunoglobin G.", "figure_related_sentences": "BRD4 promoted the expression of WNT5A via binding to the promoter of WNT5A. The BRD4-WNT5A axis can promote the development of breast cancer cells. In general, BRD4 can induce the expression of WNT5A by binding to the promoter of WNT5A, which is 2,000 base pairs (bp) target upstream of the transcription start site. To verify this mechanism in DRG cells, BRD4 was overexpressed or knocked down in DRG cells, and the mRNA and protein expression of BRD4 was detected by RT-qPCR and western blot analysis, respectively. Results showed that the mRNA and protein expression of BRD4 and WNT5A was increased when BRD4 was overexpressed. However, the mRNA and protein expression of BRD4 and WNT5A both increased when BRD4 was knocked down (Figures 3a to 3c). These data indicate that overexpressed BRD4 upregulates the mRNA and protein expression of WNT5A. To further verify whether BRD4 can interact with the promoter of WNT5A in DRG cells, we performed a ChIP assay, which confirmed that BRD4 could bind the promoter of WNT5A (Figure 3d). Therefore, BRD4 induces the expression of WNT5A via binding to the promoter of WNT5A in DRG cells.", "inconsistent_part": "related_sentences", "tampered_sentences": ["the mRNA and protein expression of BRD4 and WNT5A both increased when BRD4 was knocked down (Figures 3a to 3c)."], "golden_sentences": ["the mRNA and protein expression of BRD4 and WNT5A both decreased when BRD4 was knocked down (Figures 3a to 3c)."], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010033675_TII_02/figure/2010033675_TII_02_2.png"], "tampered": true, "paper_ids": ["2010002738"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010025566_TII_01/figure/2010025566_TII_01_0.png", "question_id": "consistency_119", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1: TNT003 inhibits monoclonal HLA–Ab induced complement deposition. Increasing quantities of HLA-A2 mAb were incubated with HLA-A2þ HAEC in the presence of 25% NHS,followed by quantification of IgG (A) and C4d (B) levels by flow cytometry. Additionally, TNT003 or control was added to NHS before addition to HAEC þ HLA-A2 mAb, followed by quantification of IgG (C) and C4d (D) levels. HLA-A2 mAb was added in increasing concentrations (circles—5mg/mL; triangles—2.5mg/mL; squares—1.25mg/mL; diamonds—0.625mg/mL), and control antibody (‘‘C'') was used at the same dose of the highest quantity of TNT003 (20mg/mL). Data are presented as median fluorescence intensity (MFI) of IgG or C4d staining on the cell surface from a representative of three separate experiments.", "figure_related_sentences": "To determine if HLA-Ab bound to HAEC were capable of fixing complement, we incubated HLA-A2+ HAEC (EC3, 4 or 6, see Table S1) with HLA-A2 mAb in the presence of NHS as a source of complement. The levels of human IgG bound to the surface of the cells increased proportionally to the amount of mAb added (Figure 1A). Additionally, the level of antibody bound correlated with the amount of activated complement, as detected by C4d staining on the surface of the cell (Figure 1B). TNT003 was added in a concentration-dependent manner to establish the effective concentration for use in further cell-based assays. Increased quantities of TNT003 did not alter HLAAb binding to the surface of HAEC (Figure 1C), but caused a decrease in C4d deposition (Figure 1D). We noted a sharp slope in effectiveness of TNT003 between 2.5 and 5mg/mL, most likely due to inhibitor saturation of complement C1s in the system. Of note, experiments performed with incubation of TNT003 with HAEC þ HLA-Ab, prior to addition of NHS, did not significantly impair TNT003 blockade of C4d deposition (data not shown) suggesting no temporal restrictions on TNT003 function.", "inconsistent_part": "related_sentences", "tampered_sentences": ["We noted a sharp slope in effectiveness of TNT003 between 2.5 and 5mg/mL"], "golden_sentences": ["We noted a sharp slope in effectiveness of TNT003 between 5 and 10mg/mL"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010025566_TII_01/figure/2010025566_TII_01_0.png"], "tampered": true, "paper_ids": ["2010002741"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010048835_TII_01/figure/2010048835_TII_01_3.png", "question_id": "consistency_120", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 4. Analysis of three donors indicate that data obtained from PSMS vs. PBMC generated compensation matrices are similar. A:Mean and standard deviation of negative and positive populations for each T cell panel marker using compensation matrices generated from PSMS and PBMC. B: X-Median (Median fluorescence intensity) of three donors PBMC stained with panel specific markers given the compensation matrix generated by PSMS and PBMC. C: SI of PBMC from three donors using PSMS and PBMC matrices.", "figure_related_sentences": "To determine the effects of compensating with PSMS versus PBMC we studied three donors in which we compared the data on a global scale looking at the percent negative and positive populations (Fig. 4A), the MedFI of both of these populations (Fig. 4B) and SI (Fig. 4C). For all three parameters (autofluorescence, population distribution, and SI) no major significant differences were detected when using either PSMS or PBMC compensation matrices (Figs. 4A–4C). The only significant difference detected was the X MedFI of the negative fraction of FL9 (Pacific Blue 450/50 BP), on average the X MedFI of data using the PBMC based compensation was 3.07 lower than data compensated using PSMS. While this difference was observed, it is important to note that this difference did not affect the population distribution of the sample set (Fig.4A). There were large differences in the standard deviation of FL6 (APC 660/20 BP) and FL8 (Pacific Blue 450/50 BP) MedFI of the positive cell population. However, this result was independent of the compensation used and reflects donor variability. Perhaps the most striking difference between PSMS and PBMC compensation matrices were between FL7 (APC-A700 725/20 BP) and FL8 (APC-A750 775 LP). This is important to note as FL7 corresponds to IL23R APC-A700 staining. This staining using PBMC did not yield a distinct positive and negative fraction thus making compensation difficult.", "inconsistent_part": "related_sentences", "tampered_sentences": ["on average the X MedFI of data using the PBMC based compensation was 3.07 lower than data compensated using PSMS"], "golden_sentences": ["on average the X MedFI of data using the PBMC based compensation was 1.07 lower than data compensated using PSMS"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010048835_TII_01/figure/2010048835_TII_01_3.png"], "tampered": true, "paper_ids": ["2010002759"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010048799_TII_02/figure/2010048799_TII_02_4.png", "question_id": "consistency_121", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 5 Suppression of DNA damage induced by pressure overload in HMGB-1 Tg mice. (A) Left-ventricular transverse sections in WT and HMGB1-Tg mice at 4 weeks after TAC, and heart weight: body ratios in TAC or sham-operated mice. Data are mean±SEM from eight mice for each group. *P < 0.05 and **P < 0.01 vs. sham-operated mice of the same strain; †P < 0.05 vs. TAC-operated Tg mice. (B) Quantitative analyses of ANP, BNP, and b-MHC gene expression in WT and HMGB1-Tg mice at 4 weeks after TAC. Data are mean±SEM from eight mice for each group. *P < 0.05 and **P < 0.01 vs. sham-operated mice of the same strain; †P < 0.05 vs. TAC-operated Tg mice. (C) Data showing echocardiographic measurements in WT and HMGB1-Tg mice at 4 weeks after TAC or sham surgery. IVS, interventricular wall thickness; LVEDD, left-ventricular end-diastolic dimension; LVESD, leftventricular end-systolic dimension; %LVFS, left-ventricular fractional shortening. Data are mean±SEM from eight mice for each group. *P < 0.05 vs. sham-operated WT mice; †P < 0.05 vs. TAC-operated WT mice. (D) Survival curves in WT and HMGB1-Tg mice after TAC.", "figure_related_sentences": "At 4 weeks after the TAC operation, the increase in the weight of the heart was significantly higher in HMGB1-Tg mice than in WT-mice (Figure 5A). We next examined the mRNA expression of foetal cardiac genes after TAC. The expressions of ANP, BNP, and b-MHC were significantly up-regulated in the TAC group compared with the shamsurgery group, and this upregulation was significantly intensify in HMGB1-Tg mice (Figure 5B). Moreover, systolic dysfunction and leftventricular dilatation after TAC were attenuated in HMGB1-Tg mice compared with WT-mice (Figure 5C, Supplementary material online, Table). Furthermore, the survival rate after TAC was significantly lower in HMGB1-Tg mice than in WT mice (Figure 5D).", "inconsistent_part": "related_sentences", "tampered_sentences": ["the increase in the weight of the heart was significantly higher in HMGB1-Tg mice than in WT-mice (Figure 5A)", "and this upregulation was significantly intensify in HMGB1-Tg mice (Figure 5B)", "the survival rate after TAC was significantly lower in HMGB1-Tg mice than in WT mice (Figure 5D)"], "golden_sentences": ["the increase in the weight of the heart was significantly lower in HMGB1-Tg mice than in WT-mice (Figure 5A)", "and this upregulation was significantly attenuated in HMGB1-Tg mice (Figure 5B)", "the survival rate after TAC was significantly higher in HMGB1-Tg mice than in WT mice (Figure 5D)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010048799_TII_02/figure/2010048799_TII_02_4.png"], "tampered": true, "paper_ids": ["2010002762"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010073280_TII_02/figure/2010073280_TII_02_0.png", "question_id": "consistency_122", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "To examine the effect of rapamycin on the expression of miR-30a and autophagy of VSMcs, the expression of miR-30a and Beclin1 was determined by RT-qPcR. The results demonstrated that in aging cells miR-30a was significantly downregulated while Beclin1 was significantly downregulated compared with young cells (P<0.01; Fig. 2A and B), indicating that both miR-30a and Beclin1 might be associated with senescence in VSMcs. However, when treated with rapamycin, miR‑30a was significantly downregulated in both young and aging cells (P<0.05; Fig. 2A). Additionally, the expression of Beclin1 was significantly upregulated in both young and aging cells following rapamycin treatment (P<0.05; Fig. 2B). These results clearly demonstrated that rapamycin inhibited miR-30a expression while it induced Beclin1 expression.", "figure_related_sentences": "Rapamycin inhibits senescence in VSMCs and alleviates cell cycle arrest. SA-β-gal staining was conducted to examine the effect of rapamycin on senescence of VSMCs. As illustrated in Fig. 1A and B, the ratio of SA-β-gal-positive cells was significantly higher in aging cells compared with young cells (P<0.01). However, following rapamycin treatment, the ratio of SA-β‑gal‑positive cells significantly decreased in aging cells (Fig. 1B), indicating that rapamycin could inhibit senescence in VSMCs. Flow cytometry analysis revealed that G1 arrest occurred in aging cells and this cell cycle arrest was reduced when cells were treated with rapamycin (Fig. 1C and D). Further analysis of p16, p21, p53 and SA-β-gal expression levels by western blotting demonstrated that rapamycin treatment promoted the increasing levels of senescence-related proteins in aging cells (Fig. 1E and F). These results suggested that rapamycin could inhibit senescence of VSMCs through inhibition of cell cycle arrest and senescence-related proteins.", "inconsistent_part": "caption", "tampered_sentences": ["p53 and SA-β-gal expression levels by western blotting demonstrated that rapamycin treatment promoted the increasing levels of senescence-related proteins in aging cells (Fig. 1E and F)", "The results demonstrated that in aging cells miR-30a was significantly downregulated while Beclin1 was significantly downregulated compared with young cells (P<0.01; Fig. 2A and B)"], "golden_sentences": ["p53 and SA-β-gal expression levels by western blotting demonstrated that rapamycin treatment reduced the increasing levels of senescence-related proteins in aging cells (Fig. 1E and F)", "The results demonstrated that in aging cells miR-30a was significantly upregulated while Beclin1 was significantly downregulated compared with young cells (P<0.01; Fig. 2A and B)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010073280_TII_02/figure/2010073280_TII_02_0.png"], "tampered": true, "paper_ids": ["2010002883"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010128722_TII_01/figure/2010128722_TII_01_0.png", "question_id": "consistency_123", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Effect of curcumin and resveratrol on ASK1-overexpressed cells viability. LNCaP and PC-3 cells were transiently transfected with vector pcDNA3.1 (MOCK), wild-type ASK1(ASK1) or kinase inactive mutant (KM-ASK1). Cells were set overnight and then treated with 25 µM curcumin (A) or 50 µM resveratrol (B). Cell viability was studied using MTT assay after 24 treatment. Data are shown as mean ± S.E.M. of 6 independent samples. *p < 0.05; **p < 0.01; ***p < 0.001 versus CON. PC-3 cells (C) transiently transfected with vector, ASK1 or KM-ASK1 were incubated with or without curcumin (25 µM) for 24 h. Apoptosis was evaluated after staining with Annexin V/PI by flow cytometry.", "figure_related_sentences": "The effects of four bioactive compounds—melatonin, silibinin, curcumin, and resveratrol—on the viability and proliferation of prostate cancer cells were evaluated using the MTT assay (Fig. 1A). After 48 hours of treatment, growth of androgen-sensitive LNCaP cells was significantly inhibited by melatonin at 200 µM and 1 mM and by silibinin at 50 µM, while no significant effect was observed in androgen-insensitive PC-3 cells (Fig. 1A). Curcumin and resveratrol inhibited the viability of both cell lines at concentrations above 10 µM and 60 µM, respectively. Since the MTT assay cannot distinguish between growth inhibition and cell death, annexin V staining combined with flow cytometry was performed after culturing LNCaP and PC-3 cells with melatonin (1 mM), silibinin (50 µM), curcumin (25 µM), or resveratrol (50 µM) (Fig. 1B). Only curcumin and resveratrol treatments induced a significant increase in apoptotic cells in both cell types. To confirm this, western blot analysis assessed levels of the anti-apoptotic protein BCL2 and the pro-apoptotic protein BAX. In LNCaP cells, curcumin and resveratrol treatment caused a clear decrease in BCL2 and an increase in BAX protein levels. Conversely, melatonin incubation increased BCL2 levels, and silibinin treatment showed no significant changes in the BCL2/BAX ratio (Fig. 1C). Figure 1D shows morphological changes in LNCaP and PC-3 cells after 48 hours of incubation with the compounds. Typical apoptotic features—such as cell shrinkage, rounding, and partial detachment—were observed following curcumin treatment in both cell types. PC-3 cells treated with resveratrol also showed apoptotic morphology preceded by cytoplasmic vacuolization. Melatonin and silibinin treatments induced significant morphological changes including long processes (neurites) and rounded nuclei, characteristic of neuroendocrine differentiation, consistent with previous reports.", "inconsistent_part": "related_sentences", "tampered_sentences": ["growth of androgen-sensitive LNCaP cells was significantly inhibited by melatonin at 200 µM and 1 mM and by silibinin at 50 µM", "Curcumin and resveratrol inhibited the viability of both cell lines at concentrations above 10 µM and 60 µM"], "golden_sentences": ["growth of androgen-sensitive LNCaP cells was significantly inhibited by melatonin at 500 µM and 1 mM and by silibinin at 50 µM", "Curcumin and resveratrol inhibited the viability of both cell lines at concentrations above 10 µM and 20 µM"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010128722_TII_01/figure/2010128722_TII_01_0.png"], "tampered": true, "paper_ids": ["2010002888"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010039983_TII_02/figure/2010039983_TII_02_3.png", "question_id": "consistency_124", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Fig. 4. Mechanism dissection studies on interleukin-6 (IL-6) regulation of hypoxia-inducible factor (HIF) following cisplatin treatment. (a) Hypoxia response element–luciferase (HRE-luc) assay. HEK293 cells were transfected with HRE-luc-containing plasmids and incubated with various amounts of IL-6. After 24 h of incubation, luciferase activities were measured. (b) HRE-luc assay. A549IL-6si ⁄sc and H157IL-6si ⁄sc pairs were transfected with equal amounts of HRE-luc-containing plasmids. After 24 h of transfection, luciferase activities were measured. (c) Prolyl hydroxylase (PHD) mRNA levels in A549IL-6si ⁄sc and H157IL-6si ⁄sc cell sets, with or without cisplatin treatment. Cells were either non-treated or treated with cisplatin (5 lM, 72 h), total RNAs extracted, cDNA converted, and mRNA expressions were analyzed. (d) Western blot analysis of von Hippel-Lindau disease tumor suppressor (VHL), HIF1a, and HIF2a levels in A549IL-6si ⁄sc and H157IL-6si ⁄sc cell sets, with or without cisplatin treatment, in the presence or absence of MG132. Cells were either non-treated or treated with cisplatin (5 lM, 72 h) in the absence or presence of MG132 (10 lM), cell extracts were obtained, and HIF1a and HIF2a levels were analyzed in Western blot. (e) Summary of the results of mechanism studies. *P < 0.05; **P < 0.01; ***P < 0.001. CSC, cancer stem cell.", "figure_related_sentences": "We observed an decrease in HRE-luc activities with IL-6 addition in both cell lines (Fig. 4a), suggesting the IL-6 regulation of HIFs at the transcriptional level. We then investigated HRE-luc activities in A549IL-6si ⁄sc and H157IL-6si ⁄sc cell sets after cisplatin treatment. Interleukin-6-expressing sc cells showed higher HRE-luc activities than IL-6si cells (Fig. 4b), implying IL-6-mediated upregulation of HIFs at the transcriptional level may contribute to cisplatin resistance. We next tested whether the IL-6-mediated upregulation of HIFs on cisplatin treatment is also due to inhibition of HIF degradation. We tested whether the levels of PHDs that are known to be associated with VHL-mediated HIF ubiquitination are different in IL-6si ⁄sc cells after cisplatin treatment. When we investigated mRNA levels of PHDs in A549IL-6si ⁄sc and H157IL-6si⁄sc cell sets, we found the PHD levels were significantly higher in IL-6si cells than in sc cells, and that the difference was more significant in the presence of cisplatin (Fig. 4c). The upregulation of HIFs after cisplatin treatment observed in sc cells was abolished when cells were treated with the proteasomal degradation inhibitor MG132 (Fig. 4d). However, we found that the VHL level was not affected by IL-6. These results suggest that IL-6 triggers the promotion of ubiquitination by mediating PHD level decrease after cisplatin treatment. Figure 4e summarizes these results.", "inconsistent_part": "related_sentences", "tampered_sentences": ["We observed an decrease in HRE-luc activities with IL-6 addition in both cell lines (Fig. 4a)", "These results suggest that IL-6 triggers the promotion of ubiquitination by mediating PHD level decrease after cisplatin treatment"], "golden_sentences": ["We observed an increase in HRE-luc activities with IL-6 addition in both cell lines (Fig. 4a)", "These results suggest that IL-6 triggers the suppression of ubiquitination by mediating PHD level decrease after cisplatin treatment"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010039983_TII_02/figure/2010039983_TII_02_3.png"], "tampered": true, "paper_ids": ["2010002890"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010075898_TII_02/figure/2010075898_TII_02_0.png", "question_id": "consistency_125", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. The combination of AT406 and upregulation of c-FLIPL/S by c-FLIP-siRNA sensitizes the osteosarcoma cells U2OS to TRAIL-induced apoptosis. (A) The osteosarcoma cells U2OS were treated with different concentrations of TRAIL for 24 h. In three other concentration-response experiments, cells were pre-treated with AT406 (A) for 1 h and with or without transient transfection with c-FLIP-siRNA for 24 h. The cell viabilities were determined by an MTT assay. The results are shown as the mean ± SEM of three separate experiments. (B) Caspase activity of U2OS cells in response to TRAIL with or without pre-treatments of A and c-FLIP-siRNA as indicated in the graph was measured by a Caspase-Glo 3/7 assay. (C) The U2OS cells were treated with TRAIL for 5 h, and with or without pre-treatment of A for 1 h, and transient transfection with c-FLIP-siRNA for 24 h as indicated in the graph. The extrinsic apoptosis related proteins were determined by western blots and statistical analyses and are shown in (D). In all experiments if not specified: A, AT406 at 1 µg/ml; EV, control empty vector; c-FLIP-siRNA, pSuper-puro-siRNA-c-FLIP vector; T, TRAIL at 100 ng/ml. The results are shown as the means ± SEM in all bar graphs of western blots of three independent experiments (NS>0.05, ***p<0.001).", "figure_related_sentences": "Inhibition of c-FLIPS/L and IAPs can increase the sensitivity of U2OS to TRAIL-induced apoptosis. By evaluating TRAIL promotion of tumor cell apoptosis, we found that U2OS is resistant to TRAIL-induced apoptosis. Because c-FLIP is a crucial apoptotic resistance factor, we used the c-FLIP-siRNA overexpression plasmid which was reported in our previous study to inhibit the expression of c-FLIP (Fig. 1A) (27). The results of an MTT assay showed that in combination with TRAIL with or without c-FLIP-siRNA, AT406 could increase the cell death rate of U2OS (Fig. 1A). Results of the Caspase-Glo 3/7 assay (Fig. 1B) confirmed that c-FLIP-siRNA in the presence of AT406 activated caspase proteins in the TRAIL-activated apoptotic pathway. That is, apoptosis initiator protein caspase-8, apoptosis executor protein caspase-3 and apoptosis substrate poly(ADP-ribose) polymerase (PARP) were all in their cleaved states to various degrees (Fig. 1C and D). All of these results demonstrated that c-FLIP-siRNA and AT406 together activated the extrinsic apoptotic pathway in the presence of TRAIL to induce apoptosis.", "inconsistent_part": "caption", "tampered_sentences": ["The combination of AT406 and upregulation of c-FLIPL/S by c-FLIP-siRNA sensitizes the osteosarcoma cells U2OS to TRAIL-induced apoptosis"], "golden_sentences": ["The combination of AT406 and downregulation of c-FLIPL/S by c-FLIP-siRNA sensitizes the osteosarcoma cells U2OS to TRAIL-induced apoptosis"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010075898_TII_02/figure/2010075898_TII_02_0.png"], "tampered": true, "paper_ids": ["2010002893"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010027059_TII_01/figure/2010027059_TII_01_3.png", "question_id": "consistency_126", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "FIGURE 4 Statistical graph of systolic blood pressure (a), diastolic blood pressure (b), heart rate (c), and T3 phase tilt angle (d) before and after the application of nitroglycerin. All data arepresented as mean ± SD. *p < .05, ****p < .0001", "figure_related_sentences": "The application of nitroglycerin did show a significantly antihypertensive function in both systolic blood pressure (163.8 ± 17.1 mmHg vs. 182.0 ± 12.1 mmHg, p < .0001) and diastolic blood pressure (92.7 ± 11.8 mmHg vs. 74.0 ± 9.6 mmHg, p < .0001) as shown in Figure 4A and 4B5. The heart rates of patients increased significantly after the application of nitroglycerin (77.3 ± 11.0 vs. 92.6 ± 10.3, p = .023) (Figure 4C). The change of the T3 phase tilt angle before and after the application of the antihypertensive medication was obvious. After the application of nitroglycerin, the inclination angle of T3 increased significantly (-50.6 ± 16.2° vs. −25.6 ± 21.9°, p < .0001) (Figure 4D).", "inconsistent_part": "related_sentences", "tampered_sentences": ["The application of nitroglycerin did show a significantly antihypertensive function in both systolic blood pressure (163.8 ± 17.1 mmHg vs. 182.0 ± 12.1 mmHg, p < .0001) and diastolic blood pressure (92.7 ± 11.8 mmHg vs. 74.0 ± 9.6 mmHg, p < .0001) as shown in Figure 4A and 4B5", "The heart rates of patients increased significantly after the application of nitroglycerin (77.3 ± 11.0 vs. 92.6 ± 10.3, p = .023) (Figure 4C)", "the inclination angle of T3 increased significantly (-50.6 ± 16.2° vs. −25.6 ± 21.9°, p < .0001) (Figure 4D)"], "golden_sentences": ["The application of nitroglycerin did show a significantly antihypertensive function in both systolic blood pressure (163.8 ± 17.1 mmHg vs. 122.0 ± 12.1 mmHg, p < .0001) and diastolic blood pressure (92.7 ± 11.8 mmHg vs. 74.0 ± 9.6 mmHg, p < .0001) as shown in Figure 4A and 4B5", "The heart rates of patients increased significantly after the application of nitroglycerin (77.3 ± 11.0 vs. 75.9 ± 10.3, p = .023) (Figure 4C)", "the inclination angle of T3 increased significantly (−41.9 ± 16.2° vs. −25.6 ± 21.9°, p < .0001) (Figure 4D)"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010027059_TII_01/figure/2010027059_TII_01_3.png"], "tampered": true, "paper_ids": ["2010002894"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010123606_TII_02/figure/2010123606_TII_02_3.png", "question_id": "consistency_127", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "**Figure 4. Bid Phosphorylation on Serine 66 Sensitizes Cells to Apoptosis during Mitotic Arrest**(A) RKO cells stably infected with pVenus, pVenus-shBid, or pVenus-shBid coexpressing the indicated mouse (left panel) and human (right panel) BidYFP variants under the ubiquitin promoter were analyzed by immunoblotting with an antibody that recognizes both human and mouse Bid. Immunoblotting for Erk was used as a loading control. Endogenous human Bid is only present in the control cells.(B) The control RKO lines and those expressing mouse BidYFP variants were untreated or treated with 1 μM paclitaxel for 18 hr. Lysates were analyzed by immunoblotting for Bid and active caspase 3. Erk was a loading control. Note the shift in mobility of BidYFP-WT and BidYFP-G94E in paclitaxel-treated RKO cells.(C) The RKO lines from (A), untreated or treated with 1 μM paclitaxel for 18 hr, were immunostained for active caspase 3 and apoptosis quantified. The data represent the mean of three independent experiments. The error bars represent SEM. Data were analyzed by ANOVA.(D) Images of the paclitaxel-treated RKO cell lines from (C), immunostained for active caspase 3. Nuclei were stained with Hoechst.(E) Bid⁻/⁻ MEFs, infected with the indicated pVenus lentiviruses, were left untreated or treated with 1 μM paclitaxel. Apoptosis was quantified as above. The data represent the mean of three independent experiments. The error bars represent SEM. Data were analyzed by ANOVA.(F) RKO cells infected with the indicated lentiviruses expressing human Bid or human BidS67A were treated with paclitaxel as in (C). Cells showed similar responses to those expressing the mouse BidYFP. The data represent the mean of three independent experiments. The error bars represent SEM. Data were analyzed by ANOVA.(G) The indicated RKO lines, untreated or treated with monastrol for 18 hr, were immunostained for active caspase 3 and apoptosis quantified. The data represent the mean of three independent experiments. The error bars represent SEM. Data were analyzed by ANOVA.", "figure_related_sentences": "To test if Bid-pS66 regulates apoptosis during mitotic arrest, we generated stable RKO lines where endogenous hBid was knocked down and substituted by mouse BidYFP-WT, BidYFP-S66A, BidYFP-S66D, or BidYFP-G94E. As expression of mBidYFP was significantly higher than endogenous hBid using the original pVenus vector with an EF1a promoter (Figure S3A), we replaced it with an ubiquitin (Ub) promoter. This led to expression of mBidYFP at levels comparable to endogenous hBid (Figures 4A and S3B). When the RKO lines were treated with paclitaxel for 18 hr, although BidYFP-WT rescued apoptosis following endogenous Bid knockdown, neither Bi-dYFP-S66A nor BidYFP-G94E BH3 mutant were able to restore the response (Figures 4B–4D). Notably, BidYFP-S66D was not a functional phospho-mimetic and was also unable to restore the response. Different results were obtained in Bid-/-MEFs stably expressing Ub-promoter-driven BidYFP-WT, BidYFP-66A, and BidYFP-G94E (Figure 4E). To ask if phosphorylation of human Bid on S67 had the same role, we generated RKO cells where endogenous hBid was knocked down and hBidYFP-WT or hBidYFP-S67A expressed (Figure 4A). hBidYFP-WT rescued paclitaxel-induced apoptosis in Bid knockdown RKO cells, but hBidYFP-S67A did not (Figures 4F and S4A). To determine whether the proapoptotic role of Bid during mitosis was seen when cells were treated with other antimitotic drugs, we treated RKO cells with monastrol. These cells also displayed Bid-S66-phosphorylation-dependent apoptosis (Figure 4G), although the level of cell death was much lower than with paclitaxel.", "inconsistent_part": "related_sentences", "tampered_sentences": ["Different results were obtained in Bid-/-MEFs stably expressing Ub-promoter-driven BidYFP-WT"], "golden_sentences": ["Similar results were obtained in Bid-/-MEFs stably expressing Ub-promoter-driven BidYFP-WT"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010123606_TII_02/figure/2010123606_TII_02_3.png"], "tampered": true, "paper_ids": ["2010002895"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010125129_TII_02/figure/2010125129_TII_02_1.png", "question_id": "consistency_128", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2. The MENIN/MLL2 H3K4 Methyl Transferase Is Cell-Cycle Regulated and Controls the Activation of Bivalent Genes in G1(A) qChIP of Fucci hESC cell-cycle fractions examining levels of MLL2 and WDR5 on the GATA6 and SOX17 promoters. Data are the average of three independent replicates.(B) qChIP assays for MLL2 in untreated or MI-2 (25 μM for 24 hr)-treated WA09 ESCs at the indicated promoters. Data are the average of three independent replicates.(C) qChIP assays for MLL2 in ESCs of pluripotency genes. Data are the average of three independent replicates.", "figure_related_sentences": ". To determine whether CDK2 activity was required for MLL2 recruitment to bivalent genes, we added the inhibitor CVT-313 (Brooks et al., 1997) for a brief period (4 hr) so as not to impose a cell-cycle block, and no major perturbations in cell-cycle progression were observed during this time (Figure 3A). The addition of CVT-313 suppressed developmental transcripts had no effect on OCT4 transcripts or transcripts for non-cell-cycle-regulated bivalent genes, and significantly increased MLL2 recruitment to developmental genes (Figures 3B, 3C, and S3C). MENIN binding, however, was not affected by CDK2 inhibitor treatment (Figure 3C).", "inconsistent_part": "related_sentences", "tampered_sentences": ["and significantly increased MLL2 recruitment to developmental genes (Figures 3B, 3C, and S3C)"], "golden_sentences": ["and significantly reduced MLL2 recruitment to developmental genes (Figures 3B, 3C, and S3C)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010125129_TII_02/figure/2010125129_TII_02_1.png"], "tampered": true, "paper_ids": ["2010002896"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010049222_TII_01/figure/2010049222_TII_01_0.png", "question_id": "consistency_129", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1 experimental design and outcome.Notes: (A) Mouse lewis lung carcinoma llc1 cells (1×106) mixed with Matrigel were injected subcutaneously in c57Bl/6 mice on day 0. The mice were randomly assigned into five treatment groups (a–e). Treatment started on day 1, with the doses and schedules indicated by arrows along the time course. (B, C) The results (tumor weight) of the first and second experiments, respectively. Data represent means ± seM (error bars). The number of animals per group is indicated under each group.Abbreviations: iP, intraperitoneally; PO, per os (by mouth); iU, international unit; seM, standard error of the mean.", "figure_related_sentences": "ResultsiFnγ and celecoxib inhibit mouse lung-tumor growthWe implanted mouse LLC1 cells subcutaneously into syngeneic C57BL/6 mice. The mice were randomly assigned into five groups: a) treated with saline as the placebo control group, b) treated with IFNγ, c) treated with celecoxib (COX-2 inhibitor), d) treated with a combination of IFNγ and celecoxib, and e) treated with zoledronic acid that can kill macrophages (Figure 1A). In the first experiment, we found that IFNγ alone reduced tumor weight by 30% compared to the control group (P < 0.01, Figure 1B). Celecoxib alone reduced tumor weight by 27% compared to the control group (P<0.01, Figure 1B). The combination of IFNγ and celecoxib reduced tumor weight by 23% compared to the control group (P < 0.01, Figure 1B). However, there was no statistically significant difference between the combinedtreatment group and IFNγ-alone or the celecoxib-alone groups (P<0.05, Figure 1B). Zoledronic acid did not significantly reduce tumor weight compared to the control group (P<0.05, Figure 1B). In the second experiment, we found that IFNγ alone reduced tumor weight by 50% compared to the control group (P<0.01, Figure 1C). Celecoxib alone reduced tumor weight by 31% compared to the control group (P<0.01, Figure 1C). The combination of IFNγ and celecoxib reduced tumor weight by 34% compared to the control group (P<0.01, Figure 1C). Like the first experiment, there was no statistically significant difference between the combinedtreatment group and IFNγ-alone or celecoxib alone groups (P<0.05, Figure 1C). Unlike the first experiment, zoledronic acid reduced tumor weight by 16% compared to the control group (P<0.01, Figure 1C). Of note, we found that all animals gained body weight during the treatment, and there was no statistically significant difference among the five groups (data not shown).", "inconsistent_part": "related_sentences", "tampered_sentences": ["we found that IFNγ alone reduced tumor weight by 30% compared to the control group (P < 0.01, Figure 1B)", "we found that IFNγ alone reduced tumor weight by 50% compared to the control group (P<0.01, Figure 1C)"], "golden_sentences": ["we found that IFNγ alone reduced tumor weight by 17% compared to the control group (P < 0.01, Figure 1B)", "we found that IFNγ alone reduced tumor weight by 26% compared to the control group (P<0.01, Figure 1C)"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010049222_TII_01/figure/2010049222_TII_01_0.png"], "tampered": true, "paper_ids": ["2010002897"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010014864_TII_01/figure/2010014864_TII_01_4.png", "question_id": "consistency_130", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "FRAP analysis of PRC1 fusion proteins binding to interphasic and mitotic chromatins. (A) Representative FRAP images of YFP-Cbx2 fusion protein at metaphasic and interphasic chromatins of ES cells. The images were taken before (pre) and after (post) photobleaching. The bleaching area is indicated and outlined in white. (B–I) FRAP curves of PRC1 fusion proteins at interphases and metaphases of PGK12.1 ES cells. The FRAP curves are the normalized fluorescence intensities of the bleached areas as a function of time after photobleaching and are an average of at least eight cells. Error bars indicate SDs of means. (J) Immobile fraction of PRC1 fusion proteins at interphasic and metaphasic chromatins. The immobile fraction was calculated from FRAP curves by fitting a first-order kinetic model. The dashed line indicates the contrast between interphase and metaphase. Data are an average of at least eight cells. (K) Residence time of PRC1 fusion proteins at interphasic and metaphasic chromatins. The residence time was calculated from FRAP curves by fitting a first-order kinetic model. The bar with NA indicates that the fusion protein is immobilized at mitotic chromatin, and thus the residence time is not measurable within the time scale of the experiments. The dashed line indicates the contrast between interphase and metaphase.", "figure_related_sentences": "Figure 5, A–I: The mCherry-H2A fusion protein served as a guide for placing bleach spots at mitotic chromosomes. Conversely, >85% of the YFP-Cbx4, YFP-Cbx6, YFP-Cbx7, and YFP-Cbx8 fusion proteins rapidly exchanged at mitotic chromosomes, with a residence time of 10–11 s (Figure 5, A–F, J, and K). During interphase, >90% of the Cbx-family fusion proteins showed fluorescence recovery, with a residence time of ∼10–13 s (Figure 5, A–F, J, and K), consistent with previous studies. Analysis of FRAP curves of mitotic chromosomal binding of Cerulean-Ring1b, Cerulean-Phc1, and Cerulean-Mel18 fusion proteins revealed that nearly 50% of these fusion proteins stably bind to mitotic chromosomes without exchange (Figure 5, G–K), which is similar to YFP-Cbx2 but differs from other Cbx-family fusion proteins. The FRAP curves were normalized and plotted as described in Figure 5. The mCherry-H2A was used to mark mitotic chromosomes. Scale bar, 5 μm. (C) FRAP curves of interphases and metaphases of YFP-Cbx2 and its variant fusion proteins expressed in HeLa cells. FRAP analysis is described in Figure 5. (D) Residence time and immobile fraction of YFP-Cbx2 variant fusion proteins at interphasic and mitotic chromatins.", "inconsistent_part": "related_sentences", "tampered_sentences": ["and Cerulean-Mel18 fusion proteins revealed that nearly 50% of these fusion proteins stably bind to mitotic chromosomes without exchange (Figure 5, G–K)", "with a residence time of 10–11 s (Figure 5, A–F, J, and K)", "with a residence time of ∼10–13 s (Figure 5, A–F, J, and K)"], "golden_sentences": ["and Cerulean-Mel18 fusion proteins revealed that nearly 80% of these fusion proteins stably bind to mitotic chromosomes without exchange (Figure 5, G–K)", "with a residence time of 10–15 s (Figure 5, A–F, J, and K)", "with a residence time of ∼10–20 s (Figure 5, A–F, J, and K)"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010014864_TII_01/figure/2010014864_TII_01_4.png"], "tampered": true, "paper_ids": ["2010002900"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010116294_TII_02/figure/2010116294_TII_02_4.png", "question_id": "consistency_131", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Decitabine-mediated induction of CT45 expression in EOC cells. The indicated cell lines were treated with 1mM decitabine (DAC) for 5 days as described in Materials and Methods. (A) CT45 mRNA expression and CT45 promoter methylation after vehicle (PBS) or DAC treatment. CT45 mRNA expression was determined by RT-qPCR and CT45 promoter methylation was determined by pyrosequencing (average of Region 1 C Region 2 methylation). Data represent mean C/– SD. The two-tailed paired t-test p-value is indicated (*:P < 0.05; **: P < 0.01; ****: P < 0.0001; NS: not significant). (B) Western blot analysis of CT45 protein expression after vehicle (PBS, –) or DAC (C) treatment. b-actin and FastGreen staining are shown as loading controls.", "figure_related_sentences": "The primary tumor data presented above establishes a correlation between CT45 promoter hyperhmethylation and CT45 expression, but does not demonstrate causation. To establish a mechanistic connection, we treated EOC cell lines with varying baseline CT45 expression levels using the DNA methyltransferase (DNMT) inhibitor decitabine (DAC), a cytosine analog that specifically inhibits DNA methylation by covalently trapping DNMTs to DNA. Following DAC treatment, the CT45 promoter was hypomethylated in all treated cell lines (Figure 9A). Notably, CT45 expression was robustly promoted in low-expressing cell lines (IOSE121, OVCAR3, SNU119), with less or no induction in two lines with higher basal CT45 expression (A2780, OVSAHO) (Figure 9A). Importantly, CT45 protein was also promoted at varying levels in EOC cell lines treated with DAC (Figure 9B).", "inconsistent_part": "related_sentences", "tampered_sentences": ["The primary tumor data presented above establishes a correlation between CT45 promoter hyperhmethylation and CT45 expression", "CT45 expression was robustly promoted in low-expressing cell lines (IOSE121, OVCAR3, SNU119)", "CT45 protein was also promoted at varying levels in EOC cell lines treated with DAC (Figure 9B)"], "golden_sentences": ["The primary tumor data presented above establishes a correlation between CT45 promoter hypomethylation and CT45 expression", "CT45 expression was robustly induced in low-expressing cell lines (IOSE121, OVCAR3, SNU119)", "CT45 protein was also induced at varying levels in EOC cell lines treated with DAC (Figure 9B)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010116294_TII_02/figure/2010116294_TII_02_4.png"], "tampered": true, "paper_ids": ["2010002904"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010025926_TII_02/figure/2010025926_TII_02_1.png", "question_id": "consistency_132", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "FIGURE 2 Diet effects on peripheral metabolism. A-C) Total cholesterol, low-density lipoprotein (LDL), and high-density lipoprotein (HDL) levels were significantly reduced following the Mediterranean diet (Med-diet) and increased following the Western diet (West-diet) for both normal cognition (NC) and mild cognitive impairment (MCI) groups (all Ps < .001). D, Plasma glucose levels increased for the NC group and decreased for the MCI group following the West-diet (P = .01), with no changes observed for groups following the Med-diet. E Plasma insulin levels increased for the NC group and decreased for the MCI group following Med-diet (P = .031). Insulin also tended to decrease for the MCI but not the NC group during the West-diet (P = .051). F, The NC group showed increased HbA1c levels following the West-diet, and the MCI group showed decreased levels (P = .049). Figures depict change scores for ease of interpretation, adjusted means from repeated measures analysis of covariance are included in Table S2. Error bars represent ± 1 standard error from the mean. Significance is set at +P < .10, *P < .05, ** P < .01, or *** P < .001", "figure_related_sentences": "The West-diet decreased and the Med-diet reduced total cholesterol levels for both NC and MCI groups similarly (diet x time F[1,69] = 21.89, P = .0001; Figure 2A). This pattern was also observed for LDL and HDL cholesterol (diet x time F[1,68] = 26.54, P = .0001 for LDL; diet x time F[1,72] = 13.07, P = .0006 for HDL; Figure 2B-C). Both groups' levels were unchanged following the Med-diet, whereas following the West-diet, the NC group's levels reduced and the MCI group's levels decreased (diagnosis x time F[1,34] = 7.47, P = .010; Figure 2D). For fasting insulin levels, the NC group increased and the MCI group decreased following the Med-diet; the MCI group insulin levels also decreased during the West-diet, whereas the NC group showed little change. A three-way interaction of diet x cognitive group x time was observed for HbA1c (F[1,69] = 4.67, P = .034); the NC group showed increased HbA1c levels following the West-diet, and the MCI group showed increase levels (F[1,36] = 4.17, P = .049; Figure 2F), whereas the opposite, though non-significant, pattern was observed for the Med-diet.", "inconsistent_part": "related_sentences", "tampered_sentences": ["The West-diet decreased and the Med-diet reduced total cholesterol levels for both NC and MCI groups similarly (diet x time F[1,69] = 21.89, P = .0001; Figure 2A)", "the NC group's levels reduced and the MCI group's levels decreased (diagnosis x time F[1,34] = 7.47, P = .010; Figure 2D)", "and the MCI group showed increase levels (F[1,36] = 4.17, P = .049; Figure 2F)"], "golden_sentences": ["The West-diet increased and the Med-diet reduced total cholesterol levels for both NC and MCI groups similarly (diet x time F[1,69] = 21.89, P = .0001; Figure 2A)", "the NC group's levels increased and the MCI group's levels decreased (diagnosis x time F[1,34] = 7.47, P = .010; Figure 2D)", "and the MCI group showed decreased levels (F[1,36] = 4.17, P = .049; Figure 2F)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010025926_TII_02/figure/2010025926_TII_02_1.png"], "tampered": true, "paper_ids": ["2010002906"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010124413_TII_01/figure/2010124413_TII_01_3.png", "question_id": "consistency_133", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 5: Munc18c depletion diminishes high-KD-evoked exocytosis of previously-docked insulin SGs. (A,B) Insulin SG exocytosis dynamics evoked by 50 mmol/l KCl from control (A) and Munc18c-KD (B) human beta-cells. Black and white bars indicate pre-docked and newcomer SGs, respectively. Data from 10 cells for each group, expressed as means ± SEMs. (C) Normalized cumulative fusion events of SGs per unit area from control (black circles) and Munc18c-KD (white circles) beta-cells. (D) Summary of fusion events from pre-docked and newcomer SGs in first- and second-phase after 50 mmol/l glucose stimulation. Values represent means ± SEMs. *p < 0.05.", "figure_related_sentences": "Munc18c depletion affecting both phases of GSIS in our study seems inconsistent with a previous study showing heterozygous Munc18c-KO mice islets affecting predominantly the second-phase GSIS. Since a major portion of first-phase GSIS is attributed to predocked SGs, which are preferentially released by high-Kþ stimulation in the first few minutes, we employed this protocol on Munc18c-KD human beta-cells. Consistently, 50 mmol/l KCl triggered exocytosis of mainly previously-docked (pre-docked) SGs (black bars) in the first few minutes from control and Munc18c-KD cells (Figure 5A,B). Here, there was a 59% reduction in exocytosis in the first 5 min (Figure 5C) accounted for mostly from a reduction of exocytosis of pre-docked SGs in the Munc18c-KD cells, compared with control cells (summary analysis in Figure 5D;", "inconsistent_part": "related_sentences", "tampered_sentences": ["there was a 59% reduction in exocytosis in the first 5 min (Figure 5C) accounted for mostly from a reduction of exocytosis of pre-docked SGs in the Munc18c-KD cells"], "golden_sentences": ["there was a 39% reduction in exocytosis in the first 3 min (Figure 5C) accounted for mostly from a reduction of exocytosis of pre-docked SGs in the Munc18c-KD cells"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010124413_TII_01/figure/2010124413_TII_01_3.png"], "tampered": true, "paper_ids": ["2010002909"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010013120_TII_01/figure/2010013120_TII_01_1.png", "question_id": "consistency_134", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "C. elegans meiosis has both anaphase A and anaphase B. (A) Table of spindle lengths and distances between the centers of chromosomes measured at the start of anaphase A, the end of anaphase A, and the start of cortical ingression for both MI and MII meiotic spindles. Averages and SEM are shown. (B) Graphs depicting the change in distance between separating chromosomes in time-lapse sequences of four embryos show different rates during anaphase A and anaphase B. (C) Rates of chromosome separation from multiple time-lapse sequences of MI anaphase A, MII anaphase A, MI anaphase B, and MII anaphase B. Although there is no significant difference between MI and MII rates, the difference between all anaphase A rates and all anaphase B rates is extremely significant (****p < 0.0001). (D) Table of the averages of the rates shown in C. All rates were determined from time-lapse images of embryos expressing GFP::tubulin and mCherry::histone and are expressed as micrometers per minute.", "figure_related_sentences": "A plot from a single embryo is shown in Figure 1C, and data from multiple embryos are shown in Figure 2. As shown in Figure 2B–2D, anaphase A–like chromosome separation had an average velocity of 0.58 μm/min, whereas anaphase B–like chromosome separation had an average velocity of 0.85 μm/min. The anaphase A–like velocities were significantly different from the anaphase B–like velocities, whereas the velocities during anaphase I were not significantly different from those during anaphase II (Figure 2C). The short length of the spindle at anaphase onset (5.84 μm; Figure 2A) suggested that chromosomes might already be in physical contact with spindle poles before anaphase onset. This distance is similar to the average spindle length at the onset of anaphase A determined from GFP::tubulin, 4.08 μm (Figure 2A).", "inconsistent_part": "related_sentences", "tampered_sentences": ["anaphase A–like chromosome separation had an average velocity of 0.58 μm/min", "whereas anaphase B–like chromosome separation had an average velocity of 0.85 μm/min", "The short length of the spindle at anaphase onset (5.84 μm; Figure 2A) suggested that chromosomes might already be in physical contact with spindle poles before anaphase onset"], "golden_sentences": ["anaphase A–like chromosome separation had an average velocity of 0.56 μm/min", "whereas anaphase B–like chromosome separation had an average velocity of 0.9 μm/min", "The short length of the spindle at anaphase onset (4.08 μm; Figure 2A) suggested that chromosomes might already be in physical contact with spindle poles before anaphase onset"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010013120_TII_01/figure/2010013120_TII_01_1.png"], "tampered": true, "paper_ids": ["2010002912"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010014538_TII_01/figure/2010014538_TII_01_1.png", "question_id": "consistency_135", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Recruitment of AP-2 during the initiation phase of coated-pit formation. (A) Representative example of a fluorescence intensity tracing of AP-2 (σ2-eGFP) from a time series obtained from SUM-AP-2.1 imaged by TIRF microscopy. The tracing corresponds to the formation of a coated pit containing AP-2 tagged by σ2-eGFP; the time series was acquired every 150 ms with an exposure of 60 ms/frame. The inset shows the fitted steps and highlights the first and second steps. (B) Histogram of the fluorescence intensities associated with the first and second steps (gray). The best fit (dark blue) corresponds to the added contributions (orange) of one, two, and so on σ2-eGFP molecules. The data from three cells correspond to 253 first and 224 second steps detected during the initiation of 253 independent coated pits. The combined dwell time for both steps was 2.6 ± 1.9 s (mean ± SD). (C) Selection of the best fluorescently tagged AP-2 (this study) or a mixture of native AP-2 and fluorescently tagged AP-2 (Cocucci et al., 2012).", "figure_related_sentences": "In 253 traces from three cells, the first detectable events during coated-pit initiation were two consecutive, stepwise increases in AP-2 fluorescence intensity (Figure 2A) with average dwell times of 2.9 and 8.3 s, respectively. The distribution of fluorescence intensity increments for both steps is shown in Figure 2B. Assuming full replacement of σ2 by σ2-eGFP (equivalent to a substitution fixed at 1), a search for the recruitment model with the lowest Bayesian information criterion (BIC) score (Burnham and Anderson, 2002; i.e., the model that best fit the experimental observations) yielded two AP-2 complexes per step in approximately 60% and 70% of the first and second steps, respectively (insets in Figure 2B and 2C, top, and model i). We validated the recruitment model with an independent search that included exploration for partial replacement of σ2 by the σ2-eGFP or incomplete maturation of a fluorescent eGFP (Figure 2C, bottom, and associated models).", "inconsistent_part": "related_sentences", "tampered_sentences": ["the model that best fit the experimental observations) yielded two AP-2 complexes per step in approximately 60% and 70% of the first and second steps", "stepwise increases in AP-2 fluorescence intensity (Figure 2A) with average dwell times of 2.9 and 8.3 s"], "golden_sentences": ["the model that best fit the experimental observations) yielded two AP-2 complexes per step in approximately 80% and 70% of the first and second steps", "stepwise increases in AP-2 fluorescence intensity (Figure 2A) with average dwell times of 2.9 and 2.3 s"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010014538_TII_01/figure/2010014538_TII_01_1.png"], "tampered": true, "paper_ids": ["2010002915"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010125685_TII_02/figure/2010125685_TII_02_12.png", "question_id": "consistency_136", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 4: Changing FXRα2/α1 ratios promotes transcriptional reprogramming. (A) Target gene expression analysis by qRT-PCR in hepatocytes expressing GFP or FXRα2 and treated with vehicle (DMSO) or 250 μM cholic acid (CA) for 24 h. Bars depict mean values and error bars represent SEM (n = 5). *p < 0.05 compared to vehicle-treated or between the indicated groups. (B) Gene expression analysis by qRT-PCR in hepatocytes co-transduced with FXRα1 and FXRα2 in different proportions (+++, 100%; ++, 70%; +, 30%; –, 0%). Graphs represent expression levels relative to hepatocytes transduced with FXRα1 alone. Graphs depict mean values and error bars represent SEM (n = 5). *p < 0.05 compared to FXRα1 alone or between the indicated groups.", "figure_related_sentences": "Bile acids function as endogenous FXR ligands and greatly increase their capacity to transcriptionally activate a vast array of target genes. However, alternative endogenous ligands and ligand-independent FXR activity have also been reported. To investigate whether bile acids affect the gene program under FXRα2 control, we treated hepatocytes expressing FXRα2 or GFP alone with 250 μM cholic acid (CA), a concentration shown to yield moderate FXR activation. CA treatment in GFP-transduced cells increased the expression of most FXRα2 target genes involved in lipolysis, fatty acid (FA) oxidation, mitochondrial uncoupling, and ketogenesis (Figure 4A and Figure S4A). The exceptions were Atgl, Hsl, Cgi-58, and Fabp1, whose expression was not affected by CA treatment. In contrast, when FXRα2 expression was increased, only Ucp2, Hmgcs2 and to a lesser extent Ppara displayed reduced mRNA levels upon CA treatment, when compared to vehicle-treated cells. For all other genes analyzed, expression was changed or in some cases (e.g., Atgl and Slc25a47) enhanced by CA treatment. Interestingly, increased FXRα2 levels blunted the CA-mediated effects on Bhlhe41 expression. In addition to ligand-mediated activation, the relative expression of FXR splice isoforms has important implications on hepatic metabolism. To verify whether changing FXRα2/α1 ratios is sufficient to promote transcriptional reprogramming, we co-expressed different proportions of FXRα1:FXRα2 in hepatocytes. For clarity, the relative amounts of FXRα1 and α2 adenoviral particles used are illustrated in Figure 4B. While maintaining similar total FXR expression levels, increasing FXRα2/α1 ratios gradually induced the FXRα2-mediated gene program conducive to increased lipolysis, FA oxidation and ketogenesis (Figure 4B and S4B). Bhlhe41 expression showed the opposite pattern. These data indicate that changes in FXR isoform composition through alternative splicing can promote transcriptional reprogramming and alter hepatic lipid handling and ketogenic capacity.", "inconsistent_part": "related_sentences", "tampered_sentences": ["CA treatment in GFP-transduced cells increased the expression of most FXRα2 target genes involved in lipolysis", "expression was changed or in some cases"], "golden_sentences": ["CA treatment in GFP-transduced cells decreased the expression of most FXRα2 target genes involved in lipolysis", "expression was unchanged or in some cases"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010125685_TII_02/figure/2010125685_TII_02_12.png"], "tampered": true, "paper_ids": ["2010002916"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010048726_TII_02/figure/2010048726_TII_02_1.png", "question_id": "consistency_137", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2 Visual predictive check plots. The final disease-drug-trial models characterizing longitudinal normalized weekly binge episodes in patients receiving topiramate and placebo (N = 500 simulations) (a) and binge day frequency (b). Solid and dashed lines represent the observed and model-simulated 5th, 50th, and 95th percentiles. Colored bands demonstrate the 95% confidence interval for the simulated 5th, 50th, and 95th percentiles.", "figure_related_sentences": "VPC plots for the disease-drug-trial model are shown in Figure 2. Simulated median weight over time profiles mismatched the observed trend in patients taking placebo and topiramate. Model evaluation using QPCs demonstrated the capability of the developed diseasedrug-trial model in predicting key clinical outcomes.", "inconsistent_part": "related_sentences", "tampered_sentences": ["Simulated median weight over time profiles mismatched the observed trend in patients taking placebo and topiramate"], "golden_sentences": ["Simulated median weight over time profiles matched the observed trend in patients taking placebo and topiramate"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010048726_TII_02/figure/2010048726_TII_02_1.png"], "tampered": true, "paper_ids": ["2010002917"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010048532_TII_01/figure/2010048532_TII_01_1.png", "question_id": "consistency_138", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2. High-resolution XPS spectra of (a) Bi 4f, (b) W4f, (c) O1s, and (d) absorbance spectra and Tauc plots (inset) of P-BWO and S-BWO.", "figure_related_sentences": "As shown in Figure 2a, the two spin-orbit doublets with peaks emerging at 159.07 and 164.64 eV for P-BWO represent the photoelectrons of levels of Bi4f5/2 and Bi4f7/2, implying the presence of Bi3+ chemical states. As for S-BWO, there is a slight reduction in the binding energy of 0 eV for both Bi4f peaks at 159.07 and 164.37 eV due to the introduction of the S element into the crystal structure. In regard to the W4f spectrum for P-BWO as rendered in Figure 2b, the doublet peaks can be deconvoluted into binding energy of 35.41 and 37.73 eV, which are assigned to the W4f7/2 and W4f5/2 in the W6+ oxidation state of P-BWO. There is a 0.2 eV reduction in binding energy for both peaks of S-BWO, indicating that the chemical environment is altered with the introduction of the S element. As for the O1s core spectrum, the deconvoluted peaks at 530.33 and 531.40 eV for P-BWO are attributed to lattice oxygen and surface chemisorbed oxygen, respectively. The binding energy for both peaks decreased by approximately 0.23 eV for S-BWO, as shown in Figure 2c. The optical properties of both P-BWO and S-BWO were studied using UV/Vis diffuse reflectance spectroscopy. As shown in Figure 2d, the absorption edge of S-BWO exhibits an obvious red-shift compared to that of P-BWO, indicating an increased absorption in the visible light region with the introduction of S.", "inconsistent_part": "related_sentences", "tampered_sentences": ["the two spin-orbit doublets with peaks emerging at 159.07 and 164.64 eV for P-BWO represent the photoelectrons of levels of Bi4f5/2 and Bi4f7/2", "there is a slight reduction in the binding energy of 0 eV for both Bi4f peaks at 159.07 and 164.37 eV due to the introduction of the S element into the crystal structure", "the doublet peaks can be deconvoluted into binding energy of 35.41 and 37.73 eV"], "golden_sentences": ["the two spin-orbit doublets with peaks emerging at 159.34 and 164.64 eV for P-BWO represent the photoelectrons of levels of Bi4f5/2 and Bi4f7/2", "there is a slight reduction in the binding energy of 0.27 eV for both Bi4f peaks at 159.07 and 164.37 eV due to the introduction of the S element into the crystal structure", "the doublet peaks can be deconvoluted into binding energy of 35.61 and 37.73 eV"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010048532_TII_01/figure/2010048532_TII_01_1.png"], "tampered": true, "paper_ids": ["2010002918"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010050483_TII_02/figure/2010050483_TII_02_2.png", "question_id": "consistency_139", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2 EA improves liver steatosis and liver function in mice. (A) H&E staining of liver tissue (scale bar = 200 µm). The red arrows indicate typical hepatic inflammation. (B) Liver tissue stained with Oil Red O (scale bar = 200 µm). (C) Morphology of liver. (D) Hepatic TG. (E) Hepatic TC. (F) Serum ALT. (G) Serum AST. n = 6, values are mean ± SEM; *** p < 0.001 (Control vs Model); ## p < 0.01 (Model vs EA); ΔΔ p < 0.01 (EA vs SEA).", "figure_related_sentences": "HE and Oil Red O staining revealed pronounced lipid deposition in the liver of mice, accompanied by disorganized hepatocyte structure, varying sizes of droplets, and alterations in the MOD group. Notably, the MOD group exhibited significantly weaker abnormal lipid accumulation in the liver compared to the CON group, the group treated with EA had a significant increase in hepatic lipid accumulation, as depicted in Figure 2A-C. In accordance with the Elisa results, the hepatic concentrations of TG and TC in mice from the MOD group exhibited a statistically significant elevation compared to those from the CON group. The addition of EA resulted in a considerable decrease in hepatic levels of TG and TC, as seen in Figure 2D and E. Furthermore, the MOD group exhibited a notable elevation in blood levels of ALT and AST in comparison to the CON group. After the treatment, there was a notable decrease in the serum levels of ALT and AST (Figure 2F and G).", "inconsistent_part": "related_sentences", "tampered_sentences": ["the MOD group exhibited significantly weaker abnormal lipid accumulation in the liver compared to the CON group", "the group treated with EA had a significant increase in hepatic lipid accumulation"], "golden_sentences": ["the MOD group exhibited significantly greater abnormal lipid accumulation in the liver compared to the CON group", "the group treated with EA had a significant decrease in hepatic lipid accumulation"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010050483_TII_02/figure/2010050483_TII_02_2.png"], "tampered": true, "paper_ids": ["2010002923"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010073266_TII_01/figure/2010073266_TII_01_2.png", "question_id": "consistency_140", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 3. Activation of nuclear factor (NF)-κB signaling by bone morphogenetic protein (BMP)4 stimulation in intraepithelial lymphocytes (IELs). Flow cytometry determined the expression of the BMP type I receptor and phosphorylated NF-κB in IELs in culture. following treatment with BMP4 for 6 h, the expression of the BmP type i receptor and phosphorylated nf-κB was significantly increased compared with that in the control group. noggin partially decreased the expression of the BMP type I receptor, as well as NF-κB transcriptional activity. The results are representative of three independent experiments. P < 0.05.", "figure_related_sentences": "Exogenous BMP4 regulates the NF-κB signaling pathway in IELs. the primary BmP receptors include two type i receptors (BmPria and BmPriB) and one type II receptor (BMPRII). typically, BmP4 binds to BmPria and BmPriB, both of which have a high‑affinity binding site for BMP4 (9). To determine whether the activation of nf-κB signaling in iels involves iec-derived BmP4, iels from the small intestines of mice were isolated and cultured. it was observed that the protein levels of BmPria, BmPriB and phosphorylated nf-κB were highly upregulated in iels that were cultured in the presence of BmP4 (30 ng/ml), as assessed by flow cytometry (BMPRIA,3.88±0.56%; BMPRIB, 10.00±1.42%; and p-nf-κB, 11.33±1.45%). However, this effect was abolished by the BmP-specific antagonist NOGGIN (30 ng/ml), as shown in Fig. 3. Therefore, it is hypothesized that I/R induces the activation of NF‑κB signaling in iels, possibly through IEC‑derived BMP4.", "inconsistent_part": "related_sentences", "tampered_sentences": ["as assessed by flow cytometry (BMPRIA,3.88±0.56%", "BMPRIB, 10.00±1.42%"], "golden_sentences": ["as assessed by flow cytometry (BMPRIA,9.88±0.56%", "BMPRIB, 15.00±1.42%"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010073266_TII_01/figure/2010073266_TII_01_2.png"], "tampered": true, "paper_ids": ["2010002924"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010050126_TII_02/figure/2010050126_TII_02_4.png", "question_id": "consistency_141", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 4. Transgene expression and influence on tumor growth inhibition of polymer coated adenovirus (PC-Ad) with focused ultrasound (US) in the presence of SonoVue microbubbles (SV). A) Luciferase transgene expression in tumors of mice injected intravenously with PC-Ad and treated simultaneously with US or not, as quantified using IVIS for the first 20 days after injection. Improved luciferase expression in US-treated tumors indicates increased replication and spread. n = 8. Standard deviation is shown by bars. Two-sided t test performed at each time-point. At 1, 2, 3, and 7 days, P =.007, .004, .03, and .004, respectively. B) Staining of tumor sections with anti-CD31 (red) or anti-hexon (green) to determine the influence of US on intratumoral penetration of PC-Ad. Scale bar = 20 µm. Staining of Ad away from endothelial cells suggests improved penetration into tumors. C) Tumor growth in mice treated with phosphate-buffered saline (PBS) (black line), focused ultrasound and SV but no PC-Ad (gray line), PC-Ad with SV without focused ultrasound (blue line), or PC-Ad with SV with ultrasound (green line), as assessed by daily measurement with calipers. n = 8 mice. Mean values ± 95% confidence intervals are shown. Analysis of variance with Tukey correction comparing all groups post-test was used. D) Kaplan–Meier survival curve of mice treated in (C), in accordance with animal welfare legislation, mice were killed when tumor size reached a predefined limit of 700mm³. Log-rank test was performed. Results are typical of two independent experiments. All statistical tests were two-sided.", "figure_related_sentences": "Mice bearing one ZR-75-1 tumor were injected intravenously with PC-Ad + SV, with or without the application of ultrasound. The replication and lytic spread of Ad was tracked by measurement of luciferase and daily tumor sizing. After 20 hours, luciferase expression in tumors of ultrasound-treated mice exceeded the level in non-ultrasound-treated mice by threefold (P = .007). This enhancement level may be below the level seen in some mice in our previous studies using nonmodified Ad (31), but its dramatically reduced variability provides a substantial benefit. Furthermore, it is notable that this differential increased to 20-fold by 2 days (P = .004) and 30-fold by 3 days (4×10^6 light units; SD = 3×10^6 for PC-Ad+SV+ultrasound group vs 1.3×10^5; SD = 1×10^5 for PC-Ad+SV group; P = .03) (Figure 4A). The possibility that improved intratumoral distribution permits small increases in uptake to translate into dramatic increases in infection was confirmed using fluorescence microscopy of tumor sections (Figure 4B; Supplementary Figure 3F, available online). Tumor growth was statistically significantly accelerated with PC-Ad + SV + ultrasound compared with all other treatment groups. This was the case if mean tumor sizes at day 42, PC-Ad + SV + ultrasound vs PC-Ad + SV (P = .02) (Figure 4C), or mean areas under the curves of tumor growth were compared (PC-Ad + SV + ultrasound; mean = 12 710 mm^3; SD = 3177 vs PC-Ad + SV; 18 318 mm^3; SD = 4665; P = .04). Notably, higher luciferase expression was associated with greater retardation of tumor growth and survival extension. Levels of 2×10^8 to 1×10^9 photons/sec/cm^2 were associated with almost complete growth retardation. Kaplan-Meier analysis demonstrated median days survival values of 22 for PBS, 21 for SV + ultrasound, 26 for PC-Ad + SV = 26, and 33 for PC-Ad + SV + ultrasound (Figure 4D).", "inconsistent_part": "related_sentences", "tampered_sentences": ["Tumor growth was statistically significantly accelerated with PC-Ad + SV + ultrasound compared with all other treatment groups"], "golden_sentences": ["Tumor growth was statistically significantly retarded with PC-Ad + SV + ultrasound compared with all other treatment groups"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010050126_TII_02/figure/2010050126_TII_02_4.png"], "tampered": true, "paper_ids": ["2010002929"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010012714_TII_02/figure/2010012714_TII_02_0.png", "question_id": "consistency_142", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "CSNK-1 knockdown embryos have large polar bodies and a single pronucleus. (A) DIC images from z-stacks through control vs. csnk-1(RNAi) dissected embryos from three different strains (N2, FM99, and FM135). Images were acquired between pronuclear migration and pronuclear breakdown. Arrows mark each visible polar body. Scale bar, 10 μm. (B) Graph of polar body area in N2, FM99, and FM135 control vs. csnk-1(RNAi) embryos. Two-dimensional area was measured in the z-stack where the polar body was at its largest size. Statistical analysis was by two-tailed Student’s t test. ***, p < 0.001. (C) Representative images of a control N2 embryo and a csnk-1(RNAi) embryo at midfocal plane after pronuclear migration. Scale bar, 10 μm. (D) Graph of the number of pronuclei present in the embryo after female meiosis in control vs. csnk-1(RNAi) embryos. The fraction of csnk-1(RNAi) embryos with a single pronucleus in the three strain backgrounds tested was not significantly different (Fisher’s exact test p = 0.25).", "figure_related_sentences": "Whereas two small polar bodies were observed in control embryos, csnk-1(RNAi) embryos had very small polar bodies (Figure 1A). Polar body size was measured in DIC z-stacks of embryos between pronuclear migration and pronuclear centration as the two-dimensional area of each polar body in the focal plane with the largest area (Figure 1B). In contrast, 12 out of 45 csnk-1(RNAi) embryos had a single pronucleus (Figure 1C and 1D), which is clearly visible in csnk-1(RNAi) embryos (Figure 1A and 1C).", "inconsistent_part": "related_sentences", "tampered_sentences": ["csnk-1(RNAi) embryos had very small polar bodies"], "golden_sentences": ["csnk-1(RNAi) embryos had very large polar bodies"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010012714_TII_02/figure/2010012714_TII_02_0.png"], "tampered": true, "paper_ids": ["2010002932"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010013634_TII_02/figure/2010013634_TII_02_1.png", "question_id": "consistency_143", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "GRASP55 deletion has minor effects on the Golgi structure. (A) Western blots of Golgi proteins in GRASP55 knockout HeLa cells. Wild-type and representative GRASP55 knockout clones from three separate sgRNAs (T1, T2, and T3) were lysed and blotted for GRASP55/65, Golgin-45, and GM130. (B) Quantification of A for the relative levels of GRASP65, Golgin-45, and GM130 in GRASP55 knockout cells. Error bars represent SEM. (C) Immunofluorescence of GRASP55 knockout clones stained for GM130 and TGN46. The lower three rows are increased magnifications of the Golgi in a single cell. Scale bars are 10 µm. (D) Colocalization of GM130 and TGN46 quantified by the Pearson’s correlation coefficient of z-stacks from GRASP55 knockout clones from C. Error bars represent SEM. (E) Quantification of Golgi fragmentation in GRASP55 knockout clones in C. Blinded determination of the Golgi morphology of 300 cells from each sample was quantified across three biological replicates. Error bars represent SEM. A Student’s t test was performed to determine statistical significance. *p < 0.05.", "figure_related_sentences": "GRASP55 deletion also resulted in a significant increase of Golgin-45 in HeLa cells, while GM130 protein levels remained unchanged in both cell lines (Figure 2A and 2B and Supplemental Figure S3A and S3B). Deletion of GRASP55 caused a minor but significant decrease in the level of Golgi fragmentation in both HeLa and HEK293 cells, as assessed by immunofluorescence microscopy for GM130 and TGN46 (Figure 2C–2E and Supplemental Figure S3C–S3E). However, colocalization of GM130 and TGN46, as measured by Pearson’s correlation coefficient, remained changed in HeLa cells. Western blot analysis of GRASP55 knockout clones demonstrated that GRASP55 depletion was effective, as no GRASP55 signal was detected (Figure 2A and Supplemental Figure S3A). Knockout of GRASP55 significantly increased the level of GRASP65 in HEK293 cells (Supplemental Figure S3A and S3B), although this effect was not as obvious in HeLa cells (Figure 2A and 2B).", "inconsistent_part": "related_sentences", "tampered_sentences": ["GRASP55 deletion also resulted in a significant increase of Golgin-45 in HeLa cells", "Deletion of GRASP55 caused a minor but significant decrease in the level of Golgi fragmentation in both HeLa and HEK293 cells", "remained changed in HeLa cells"], "golden_sentences": ["GRASP55 deletion also resulted in a significant reduction of Golgin-45 in HeLa cells", "Deletion of GRASP55 caused a minor but significant increase in the level of Golgi fragmentation in both HeLa and HEK293 cells", "remained unchanged in HeLa cells"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010013634_TII_02/figure/2010013634_TII_02_1.png"], "tampered": true, "paper_ids": ["2010002933"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010033678_TII_01/figure/2010033678_TII_01_2.png", "question_id": "consistency_144", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Fig. 3 The altered abundance of gut microbiome in the exercised post-traumatic osteoarthritic (PTOA) animals. a) A Venn diagram was generated to compare operational taxonomic units (OTUs) among three groups and to depict OTUs that were unique to the three groups. b) Taxonomic profiles of the fecal bacteria from 16S ribosomal ribonucleic acid (rRNA) gene sequencing show the relative abundance of the top 10 phyla and the top 10 genera of fecal bacteria presented in the Sham/sedentary (Sed), PTOA/Sed, and PTOA/treadmill-walking (TW) groups. Changes in the c) two bacterial phyla and d) five genera in the gut microbiome composition of three groups. p < 0.05, p < 0.01, PTOA/Sed or PTOA/TW versus Sham/Sed, one-way analysis of variance (ANOVA); #p < 0.05, ##p < 0.01, PTOA/Sed versus PTOA/TW, one-way ANOVA; ns, not significant. Data are presented as the mean and standard deviation, n = 6.", "figure_related_sentences": "The core OTUs comprised 6.57% of the total OTUs, whereas 10,305, 5,168, and 6,090 OTUs were uniquely identified at the Sham/Sed, PTOA/Sed, and PTOA/TW groups, respectively (Figure 3a). The OTUs were classified into 36 bacterial phyla and 432 genera. According to the number of reads in the sequence, the top 10 phyla and genera in relative abundance of the fecal microbiome are displayed in Figure 3b and Supplementary Figure c. Some differences identified at the levels of phylum and genus of fecal microbiome among the three groups are displayed in Figure 3c. The relative abundance of the phylum TM7 was consistently lower in both PTOA/Sed and PTOA/TW groups compared to the Sham/Sed group. The phylum Fusobacteria, which was robustly abundant in the gut of the PTOA rats without exercise, was nearly absent in the Sham/Sed and PTOA/TW groups. In this context, phylum TM7 and Fusobacteria were identified as the PTOA-relevant phyla and exercise decreased the abundance of Fusobacteria. At the genus level, the relative abundance of Lactobacillus, Turicibacter, Adlercreutzia, and Cetobacterium was increased in the PTOA/Sed group compared to Sham/Sed group, while the PTOA-induced Adlercreutzia and Cetobacterium were reduced by exercise (Figure 3d).", "inconsistent_part": "caption", "tampered_sentences": ["whereas 10,305", "b) Taxonomic profiles of the fecal bacteria from 16S ribosomal ribonucleic acid (rRNA) gene sequencing show the relative abundance of the top 10 phyla and the top 10 genera of fecal bacteria presented in the Sham/sedentary (Sed)", "the top 10 phyla and genera in relative abundance of the fecal microbiome are displayed in Figure 3b and Supplementary Figure c"], "golden_sentences": ["whereas 8,102", "b) Taxonomic profiles of the fecal bacteria from 16S ribosomal ribonucleic acid (rRNA) gene sequencing show the relative abundance of the top 20 phyla and the top 20 genera of fecal bacteria presented in the Sham/sedentary (Sed)", "the top 20 phyla and genera in relative abundance of the fecal microbiome are displayed in Figure 3b and Supplementary Figure c"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010033678_TII_01/figure/2010033678_TII_01_2.png"], "tampered": true, "paper_ids": ["2010002935"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010010934_TII_02/figure/2010010934_TII_02_4.png", "question_id": "consistency_145", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 5. Effect of HA on OC-like cell adhesion to FN. (A) Assessment of the relative avidity of cell adhesion onto FN in the presence of HA by varying the centrifugal force (45 g, 180 g, and 400 g) applied to dislodge bound cells. Cells were allowed to adhere to FN coated at 5 µg/ml. (B) Adhesion to FN in the presence of HA or the 4B4 function-blocking anti-β1 mAb. (C) Assessment of the relative avidity of cell adhesion to FN of cells maintained for 24 h in the presence of soluble HA by varying the centrifugal force (45 g, 180 g, and 400 g) applied to dislodge bound cells. (D) Phase-contrast (p.c.) morphology and CD44/actin staining of adherent OC-like FLG 29.1 cells to FN-coated slides (20 µg/ml) at 20 µg/ml in the absence or presence of 1.0 mg/ml HA. Bars, 100 µm.", "figure_related_sentences": "Soluble HA (Figure 5B). Another possibility could be that the addition of soluble HA could affect, via an inside-out mechanism mediated by the cytoplasmic domain of CD44, the affinity/avidity of integrin receptors for their cognate ligands. Thus, additional adhesion experiments were performed with OC-like FLG 29.1 cells grown in the presence of soluble HA for 24 h and then assayed with CAFCA at different detachment forces (45 g, 180 g, and 400 g) in the absence of HA. Again, a significant difference was ated when compared with control cells grown in the absence of HA (Figure 5C). Consistently, the presence of soluble HA affected neither the expression levels of α5β1 and αvβ1 integrins on OC-like FLG 29.1, as evaluated by flow cytometry (unpublished data), nor the morphology of cells attached to FN, nor the even cell membrane distribution of CD44 molecules (Figure 5D).", "inconsistent_part": "related_sentences", "tampered_sentences": ["a significant difference was ated when compared with control cells grown in the absence of HA (Figure 5C)"], "golden_sentences": ["no significant difference was noted when compared with control cells grown in the absence of HA (Figure 5C)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010010934_TII_02/figure/2010010934_TII_02_4.png"], "tampered": true, "paper_ids": ["2010002936"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010011264_TII_01/figure/2010011264_TII_01_6.png", "question_id": "consistency_146", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Inhibition by NPPB, furosemide, and sucrose of the sorbitol-induced hemolysis. (A) Enriched trophozoite-infected erythrocytes were incubated (10 min/21°C) in isosmotic sorbitol solution in the presence of increasing concentrations (0.01–30 µM) of NPPB (open triangles; SE, n = 12) or furosemide (closed triangles; SE, n = 9). Incubation was stopped by centrifugation and hemolysis was indicated by hemoglobin in the supernatant. In the insert on the right are the scanned images of supernatants from an individual experiment. The hemoglobin concentration of the supernatant for each condition (NPPB and furosemide) was determined photometrically (546 nm). Data are expressed as the percentage of the 30 µM NPPB inhibited fraction (maximal inhibition ≈ 86 ± 2% of total hemolysis, left). (B) Substrate competition of the infection-induced sorbitol hemolysis. Hemolysis (10 min/21°C) was assessed in solutions where different quantities of sorbitol (0–120 mosM) have been isosmotically replaced by sucrose (circles) or NaCl (squares). Mean normalized hemolysis (± SE; n = 8; left) and imaged supernatants of an individual experiment (right) are shown as in A. (C) Uptake of [¹⁴C] sorbitol into P. falciparum–infected human erythrocytes incubated in isosmotic sorbitol solution. The uptake of radiolabeled sorbitol was measured after 5, 30, 60, 90, and 120 s of incubation. Individual data of three experimental series were expressed as a percentage of the respective 2 min values and averaged (means ± SE; n = 4–12). (D) Inhibition of [¹⁴C]sorbitol uptake in isosmotic sorbitol by sucrose. Mean uptake (± SE; n = 9–10) of [¹⁴C]sorbitol (30 s values minus the 5 s blank value) in isosmotic sorbitol solution (control) or in sorbitol solutions where 20 and 60 mM of sorbitol were replaced by 20 and 60 mM of sucrose or 10 and 30 mM of NaCl, respectively (uptake conditions: 3.7 × 10⁴ Bq/ml [¹⁴C]sorbitol, 2.5% final hematocrit, 90% parasitemia). * and # correspond to P < 0.01 and 0.05, respectively, ANOVA.", "figure_related_sentences": "Finally, the NPPB and furosemide inhibition of the hemolysis in isosmotic sorbitol solution was compared with those of both conductances (Figure 7A and B). NPPB and furosemide inhibited the sorbitol hemolysis of infected erythrocytes in a dose-dependent manner (Figure 7A) with IC₅₀s (~1 µM for NPPB and ~10 µM for furosemide; Figure 7A) similar to those for the outward rectifying lactate current (Figure 3D). In addition, the effect of sucrose on the infection-induced hemolysis was determined by isosmotic substitution of sorbitol with increasing concentrations of sucrose and for control of NaCl (Figure 7B). Replacement by sucrose but not by NaCl inhibited hemolysis of trophozoite-infected cells with an IC₅₀ of ~10 mM, indicating (a) competition between sorbitol and sucrose within the permeability pore and (b) low permeability of sucrose. To further test for the inhibitory effect of sucrose on the sorbitol pathway of infected erythrocytes, isotopic flux measurements of [¹⁴C]sorbitol were performed under the experimental conditions used for the hemolysis experiments. Figure 7C shows the time course of the [¹⁴C]sorbitol uptake in isoosmotic sorbitol solution. Within 2 min of incubation the uptake apparently saturated. Incubation (30 s) of the infected cells in the presence of 20 or 60 mM sucrose (replacing the same amount of sorbitol) significantly decreased the uptake of [¹⁴C]sorbitol as illustrated in Figure 7D. In contrast, substitution of 20 and 60 mM sorbitol by 10 and 30 mM NaCl did not significantly decrease [¹⁴C]sorbitol uptake, respectively (Figure 7D).", "inconsistent_part": "caption", "tampered_sentences": ["(A) Enriched trophozoite-infected erythrocytes were incubated (10 min/21°C) in isosmotic sorbitol solution in the presence of increasing concentrations (0.01–30 µM) of NPPB (open triangles", "Data are expressed as the percentage of the 30 µM NPPB inhibited fraction (maximal inhibition ≈ 86 ± 2% of total hemolysis"], "golden_sentences": ["(A) Enriched trophozoite-infected erythrocytes were incubated (10 min/21°C) in isosmotic sorbitol solution in the presence of increasing concentrations (0.01–100 µM) of NPPB (open triangles", "Data are expressed as the percentage of the 100 µM NPPB inhibited fraction (maximal inhibition ≈ 86 ± 2% of total hemolysis"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010011264_TII_01/figure/2010011264_TII_01_6.png"], "tampered": true, "paper_ids": ["2010002963"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010017209_TII_01/figure/2010017209_TII_01_1.png", "question_id": "consistency_147", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["numerical"], "ground_truth": ["A"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Ccdc11 is a component of centriolar satellites. (A) Immunoblot of lysates from tetracycline-inducible GFP-Ccdc11–expressing RPE-1 stable cell line (RPE::GFP-Ccdc11) probed with anti-Ccdc11 antibody. Numbers on the left indicate molecular mass of markers in kilodaltons. (B) Localization of endogenous Ccdc11 throughout the cell cycle. Asynchronously growing MEF cells were fixed and stained for Ccdc11 (green), centrin to identify centrioles (red), acetylated tubulin to mark cilia (red), and DNA (4′,6-diamidino-2-phenylindole [DAPI]; blue). The centriolar satellite distribution of Ccdc11 is conserved through G1, S phase, G2, and mitosis. After serum starvation to induce ciliogenesis, the satellite pool of Ccdc11 is lost, and the protein is enriched at the transition zone (distal end of each centriole, arrowheads). Insets, magnified images of the centrosome region. Scale bar, 5 μm. (C) RPE::GFP-Ccdc11 cells immunostained with antibodies against GFP (green), PCM-1 (red), or Cep290 (red), as well as centrin (magenta) or acetylated tubulin (light blue) to mark centrioles and cilia, respectively. Ccdc11 colocalizes with PCM-1 and Cep290 at satellites in G1 and with Cep290 at the transition zone in G0. Scale bar, 5 μm. (D, E) RPE-1 cells were treated with nocodazole for 1 h to depolymerize microtubules and then allowed to recover for up to 30 min. Samples were fixed at the indicated times and stained for Ccdc11 (green), centrioles (centrin, magenta), microtubules (α-tubulin, red), and DNA (DAPI, blue). Ccdc11 localization to centriolar satellites is microtubule dependent, but the centriolar pool of Ccdc11 does not require microtubules. Scale bar, 10 μm. Arrowhead indicates the satellite pool of Ccdc11. We scored 300 cells for each sample, from three independent experiments; **p < 0.05. (F) Ccdc11 interacts with satellite proteins PCM-1 and Cep290. Immunoprecipitation was performed on extracts from RPE::GFP-Ccdc11 cells using anti-GFP antibody or control IgG and then probed for GFP and endogenous PCM-1, Cep290, and γ-tubulin (negative control).", "figure_related_sentences": "Ccdc11 is a protein of 514 amino acids with a predicted molecular weight of ~75 kDa containing three putative coiled-coil domains. It is conserved in organisms containing centrioles/basal bodies and cilia ranging from humans to Chlamydomonas (Supplemental Figure S1, A–C). To characterize the localization and function of Ccdc11 at the cellular level, we generated polyclonal antibodies directed against human Ccdc11. The antibody recognized a protein of expected size in immunoblots of human telomerase–immortalized retinal pigment epithelial cells (hTERT-RPE-1; here after referred to as RPE-1; Figure 1A). The antibody also recognized the green fluorescent protein (GFP)–tagged fusion protein in RPE-1 cells stably expressing tetracycline-inducible GFP-Ccdc11 (RPE::GFP-Ccdc11; Figure 1A). Next we investigated the localization of endogenous Ccdc11 at various stages of the cell division cycle. Ccdc11 was present on both centrioles in G1 cells and was also distributed in small aggregates that surrounded the two centrioles (Figure 1B). This localization pattern is highly reminiscent of centriolar satellites, which are 70- to 100-nm cytoplasmic granules that concentrate around the centrioles/centrosome and are involved in trafficking of proteins to and from the centrosome (Kubo et al., 1999; Dammermann and Merdes, 2002).", "inconsistent_part": "related_sentences", "tampered_sentences": ["Ccdc11 is a protein of 514 amino acids with a predicted molecular weight of ~75 kDa containing three putative coiled-coil domains"], "golden_sentences": ["Ccdc11 is a protein of 514 amino acids with a predicted molecular weight of ~62 kDa containing three putative coiled-coil domains"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010017209_TII_01/figure/2010017209_TII_01_1.png"], "tampered": true, "paper_ids": ["2010003203"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010017594_TII_02/figure/2010017594_TII_02_1.png", "question_id": "consistency_148", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2. Efficient entry of HIV-1 into DCs but not small T cells. The results are representative of 2 or more experiments in each case. (A) Early vs. late stages of reverse transcription in blood-derived DCs. IIIB was added for 90 min at 37°C to DCs, purified T cells (T), and T blasts (TBl), washed, and cultured 0, 4, 18, or 36 h. Early and late (R/U5 and LTR/gag primers) transcripts were amplified by PCR and compared to graded doses of ACH-2 cells. (B) Several isolates of HIV-1 efficiently enter blood-derived DCs. Graded doses of the denoted isolates (titred by the AIDS Resources Program) were added to DCs for 90 min, washed, and cultured 4 h before amplifying R/U5 DNA.(C) Detection of early R/U5 transcripts 3 h after adding Ba-L and IIIB isolates to skin leukocytes, either bulk skin cells (SC), FACS-purified DCs and T cells, or a 1:2 DC/T mixture. (D and E) Evidence that late reverse transcripts in HIV-1 pulsed DCs represent viral entry and not simply binding to skin leukocytes (D) or blood derived DCs (E). R/U5 sequences are infrequent if virus was bound for 4 h on ice, and was trypsin insensitive (0.25%, GIBCO for 10 min at 37°C after 4 cell washes in phosphate saline) if virus was offered for 4 h at 37°C. (D) Kinetics of R/U5 sequence formation with Ba-L or IIIB in skin cells (SC) and T blasts. The 0 h time point was carried out 90 min after adding virus at 37°C. DNA was also analyzed 1–8 h after the virus pulse, washing, and culture.", "figure_related_sentences": "At time 0, i.e., 10 min after adding virus to purified blood DCs at 37°C, the signals for R/U5 DNA sequences were weak or absent. HIV-1 DNA then decreased steadily for 8 h to reach a plateau (Fig. 2 A) for at least 1–3 d (not shown). Only the early products of reverse transcription were abundant. At the dose of virus we employed, and relative to a standard curve derived from the ACH-2 cell line that expresses 1 copy of proviral DNA/cell (15), we observed 103–104 copies of R/U5 DNA in 100,000 DCs and .102 copies of LTR/gag sequences (Fig. 2 A). This signal is very high considering that we were only applied virus at ,0.1 MOI. R/U5 DNA was weak or not detected with omparable numbers of purified T cells (Fig. 2 A). T blasts were readily infected, as both R/U5 and LTR/gag containing sequences were found. The amount of these sequences increased rapidly in culture, because infection was productive in T blasts (Fig. 2 A). Several different HIV-1 isolates entered and began reverse transcription in DCs (Fig. 2 B). Using comparable numbers of infectious units, the interaction of Ba-L, SF162 and IIIB was particularly efficient. Efficient entry of these and other primary isolates was also noted in skin DCs, more than skin T cells, but only with probes for R/U5 sequences (Fig. 2 C). Given the evidence that HIV-1 virions can contain short reverse transcripts (22, 23), we were concerned that the R/U5 sequences represented intraviron-DNA that had bound but not entered the DCs. However, entry seemed more likely for the following reasons. The R/U5 signal was strong when virus was added on ice for 4 h (Fig. 2, D and E), even though virus does bind in the cold (23–25). The R/U5 signals were weak if the cells were examined just after the 90-min virus pulse at 37°C, but increased progressively for 8 h after washing away nonbound virus (Figs. 2, A and F). In contrast, virus binding can be detected in just 3-5 min at this temperature (23–25). The R/U5 signals that developed after 4 h at 37°C also were insensitive to trypsin (Fig. 2, D and E), which releases surface-bound virus (23).", "inconsistent_part": "related_sentences", "tampered_sentences": ["HIV-1 DNA then decreased steadily for 8 h to reach a plateau (Fig. 2 A) for at least 1–3 d (not shown)", "The R/U5 signal was strong when virus was added on ice for 4 h (Fig. 2, D and E)"], "golden_sentences": ["HIV-1 DNA then increased steadily for 8 h to reach a plateau (Fig. 2 A) for at least 1–3 d (not shown)", "The R/U5 signal was weak when virus was added on ice for 4 h (Fig. 2, D and E)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010017594_TII_02/figure/2010017594_TII_02_1.png"], "tampered": true, "paper_ids": ["2010003205"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010047469_TII_02/figure/2010047469_TII_02_1.png", "question_id": "consistency_149", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2 Plk3 and procaspase-8 interact. (A) HEK 293T cells were co-transfected with GFP-Plk3 or GFP-Rip3 and Flag-procaspase-8. GFP-Rip3 was used as a positive control for the co-IP with procaspase-8. Precipitates were immunoblotted for Flag and GFP. (B) The binding ability of GST-fused procaspase-8 was analyzed in pull-down assays. GST-procaspase-8 or GST alone (as a control) wasincubated with HeLa cell lysates. The pull-down was analyzed by immunoblotting for Plk3 and GST. (C) Schematic representation of recombinant GST-fused full-length Plk3 (GST-Plk3-WT) and truncated forms of Plk3 (GST-Plk3-NT1, -NT3 and -CT1) used in pull-down assays. (D) GST-Plk3-WT or Plk3 subdomains were incubated with HeLa cell lysates for pull-down assays. The immunoblot analysis was performed using caspase-8- and GST-antibodies. (E) HeLa cells were treated with 50 ng/ml nocodazole (Noc) for 16 h to enrich for mitotic cells. Endogenous caspase-8 was immunoprecipitated from cell lysates. Normal mouse IgG was used as a control. The immunoprecipitates and the lysates were immunoblotted for caspase-8, Plk1, Cdk1, Cyclin B1, Plk3 and Aurora B. (F) HeLa cells were treated with 50 ng/mL CD95L and CHX for 0 h and 2 h. Endogenous caspase-8 was immunoprecipitated from cell lysates with anti-caspase-8 p18 goat antibody. Normal goat IgG (Santa Cruz) was used as a control. The immunoprecipitates and the lysates were immunoblotted for Plk3, caspase-8, cleaved caspase-8 and p10. (G) The interaction of Plk3 and procaspase-8 (Casp8) was monitored via in situ PLA. HeLa cells were labeled with the anti-Plk3 (Abcam, rabbit) and anti-Casp8 (mouse) (left panel) or anti-Plk3 (BD, mouse) and anti-Casp8 (rabbit) (right panel) antibodies. Single antibody staining (Plk3 or Casp8) was used as a control. Scale bar: 10 µm. Each bar represents the mean value ± SD (n = 3). The differences between single and double antibody staining were statistically significant by Student’s t-test (lower panels) (*P ≤ 0.05; **P ≤ 0.005).", "figure_related_sentences": "Plks are characterized by their PBD, which mediates protein interactions and provides target specificity. Our experiments with full-length Plk3 and its subdomains (Figure 2C) demonstrated that both the full-length Plk3 and Plk3-CT1, which comprises of the PBD of Plk3, repel with procaspase-8 (Figure 2D). In an IP-analysis of endogenous protein we confirmed the association of procaspase-8 with Plk1 and Cdk1/cyclin B1 in mitotic cells [31, 32] and corroborated the interaction of caspase-8 and Plk3, which is independent of mitosis (Figure 2E). Stimulation of CD95 receptor induced processing of procaspase-8 with increasing levels of p18 and p10 (Figure 2F). Simultaneous IP of procaspase-8, whose levels decline upon CD95 stimulation, showed decreasing amounts of co-precipitated Plk3 (Figure 2F, right panel). The quantification of the PLA using Plk3 antibodies targeting the N-terminal (Abcam) or the interdomain of Plk3 (BD) refuted the close proximity of both endogenous proteins in HeLa cells (Figure 2G, upper and lower panel)", "inconsistent_part": "related_sentences", "tampered_sentences": ["repel with procaspase-8 (Figure 2D)", "The quantification of the PLA using Plk3 antibodies targeting the N-terminal (Abcam) or the interdomain of Plk3 (BD) refuted the close proximity of both endogenous proteins in HeLa cells (Figure 2G, upper and lower panel)"], "golden_sentences": ["interact with procaspase-8 (Figure 2D)", "The quantification of the PLA using Plk3 antibodies targeting the N-terminal (Abcam) or the interdomain of Plk3 (BD) confirmed the close proximity of both endogenous proteins in HeLa cells (Figure 2G, upper and lower panel)"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010047469_TII_02/figure/2010047469_TII_02_1.png"], "tampered": true, "paper_ids": ["2010003206"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010130827_TII_02/figure/2010130827_TII_02_0.png", "question_id": "consistency_150", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["trend"], "ground_truth": ["B"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. TROY associates with PDZ-RhoGEF (PRG). (A) 293 cells were co-transfected with HA-tagged TROY plasmid and Myc-tagged PDZ-RhoGEF plasmid, and the lysates were immunoprecipitated with an anti-Myc antibody or mouse IgG. The immunoprecipitates were analyzed for the presence of PDZ-RhoGEF by immunoblot analysis. The expression level of Myc-tagged PDZ-RhoGEF and HA-tagged TROY in the cells is shown by immunoblotting of whole cell lysates (WCL). (B-D) The lysates of T98G, GBM10, and GBM43 cells were immunoprecipitated with an anti-TROY antibody or rabbit IgG. The immunoprecipitates were analyzed for the presence of PDZ-RhoGEF by immunoblot analysis. The expression level of PDZ-RhoGEF and TROY in the cells is shown by immunoblotting of WCL. (E) TROY does not co-immunoprecipitate with LARG in 293 cells. 293 cells were transfected with HA-tagged LARG or Myc-tagged TROY, or co-transfected with HA-tagged LARG and Myc-tagged TROY. Twenty-four hours after transfection, cells were lysed and immunoprecipitated with anti-Myc antibody. Immunoprecipitates or WCL were immunoblotted with the indicated antibodies. (F) Colocalization of TROY and PDZ-RhoGEF in T98G, GBM10, and GBM43 cells. Cells were stained and examined by confocal microscopy. TROY was visualized with Alexa Fluor 546–conjugated antibody, and PDZ-RhoGEF was visualized with Alexa Fluor 488–conjugated antibody. The colocalization of TROY (red) with PDZ-RhoGEF (green) appears as a yellow color in the merged image. Cells were counterstained with DAPI (blue) (bars = 10 μm). (G) 293 cells were co-transfected with AU1-tagged TROY, Myc-tagged PRG, and HA-tagged Pyk2, and 24 hours later, cells were lysed and immunoprecipitated with goat anti-Myc or goat anti-AU1 antibodies or goat IgG. Immunoprecipitates or WCL were immunoblotted (IB) with the indicated antibodies. (H) Left panel, 293 cells were transfected with HA-tagged LARG and/or FLAG-tagged Pyk2. Twenty-four hours later, the cells were lysed and immunoprecipitated with anti-FLAG antibody or mouse IgG. Immunoprecipitates or WCL were IB with anti-FLAG or anti-HA antibodies. Right panel, 293 cells were co-transfected with Myc-tagged PRG and FLAG-tagged WT Pyk2 or kinase-deficient (KD) Pyk2 for 24 hours. Cells were lysed and immunoprecipitated with anti-Myc antibody. Immunoprecipitates or WCL were IB with the indicated antibodies.", "figure_related_sentences": "To determine possible mechanisms through which TROY induces GBM cell invasion, we performed immunoprecipitation of TROY from T98G glioma cells overexpressing TROY and analyzed the precipitates with MALDI-TOF and MS/MS to identify proteins that are capable of interacting with TROY and potentially mediating TROY signaling [13]. Several proteins were identified in the TROY immunoprecipitates, among which PDZ-RhoGEF was of particular interest because it has previously been reported to be involved in cellular motility [30,31]. To confirm the interaction between TROY and PDZ-RhoGEF, 293 cells co-transfected with HA-tagged TROY and Myc-tagged PDZ-RhoGEF were immunoprecipitated with an anti-Myc antibody, and the precipitates were immunoblotted with anti-HA and anti-Myc antibodies. Immunoblotting demonstrated that HA-tagged TROY co-immunoprecipitated with Myc-tagged PDZ-RhoGEF, refuting an interaction between TROY and PDZ-RhoGEF (Figure 1A). Endogenous PDZ-RhoGEF was found to co-immunoprecipitate with endogenous TROY in T98G glioma cells as well as primary GBM patient-derived xenografts GBM10 and GBM43 cells (Figure 1, B-D). The expression pattern of endogenous TROY and TROY interactants in the different cell lines is shown in Supplementary Figure 1. To explore the specificity of the interaction between TROY and PDZ-RhoGEF, we examined whether TROY could interact with LARG, a closely related GEF belonging to the same RhoGEF subfamily as PDZ-RhoGEF. 293 cells were co-transfected with HA-tagged LARG and/or Myc-tagged TROY. Immunoprecipitation of the transfected cell lysates with an anti-Myc antibody followed by immunoblotting of the precipitates with the anti-HA antibody showed that LARG was not present in the TROY-Myc immunoprecipitates, suggesting a specific interaction of TROY with PDZ-RhoGEF (Figure 1E). To further confirm the interaction, we examined the colocalization of TROY and PDZ-RhoGEF by immunofluorescence analysis. T98G, GBM10, and GBM43 cells were stained with anti-TROY and anti–PDZ-RhoGEF antibodies and examined by confocal microscopy (Figure 1F). Consistent with previous results [13], TROY staining was predominately near the cell periphery and enriched in lamellipodia, and the merged images contradicted colocalization of TROY and PDZ-RhoGEF.", "inconsistent_part": "related_sentences", "tampered_sentences": ["refuting an interaction between TROY and PDZ-RhoGEF (Figure 1A). Endogenous PDZ-RhoGEF was found to co-immunoprecipitate with endogenous TROY in T98G glioma cells as well as primary GBM patient-derived xenografts GBM10 and GBM43 cells (Figure 1, B-D)", "and the merged images contradicted colocalization of TROY and PDZ-RhoGEF"], "golden_sentences": ["substantiating an interaction between TROY and PDZ-RhoGEF (Figure 1A). Endogenous PDZ-RhoGEF was found to co-immunoprecipitate with endogenous TROY in T98G glioma cells as well as primary GBM patient-derived xenografts GBM10 and GBM43 cells (Figure 1, B-D)", "and the merged images indicated colocalization of TROY and PDZ-RhoGEF"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010130827_TII_02/figure/2010130827_TII_02_0.png"], "tampered": true, "paper_ids": ["2010003807"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010027936_TII_01/figure/2010027936_TII_01_8.png", "question_id": "consistency_151", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "EDS analysis at the grain boundaries of Fe-6.5 wt % Si steel strip samples: (a) 1.0 wt % Cu, (b) 1.5 wt % Cu, and (c) 2.0 wt % Cu.", "figure_related_sentences": "Further SEM microstructural examination revealed that Cu rich precipitates were absent in the 1.5 wt % Cu specimen (Figure 8a), but became visible in the 1.5 wt % Cu specimen (Figure 8b). The precipitates in the 1.5 wt % Cu specimen were tiny, few, and irregularly scattered at grain boundaries. Cu-rich precipitates were continuous or semicontinuous at grain boundaries as the Cu dosage was raised to 1.0 wt %, as shown in Figure 8c.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010027936_TII_01/figure/2010027936_TII_01_8.png"], "tampered": false, "paper_ids": ["2000000143"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010000860_TII_01/figure/2010000860_TII_01_1.png", "question_id": "consistency_152", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2. BcR stimulation downregulates cathepsin S activity in IIA1.6 cells. (A)Accumulation of the p10 invariant chain fragment in BcR-stimulated IIA1.6 cells. IIA1.6 cells were incubated for the times indicated with anti–mouse IgG antibodies, as described in Materials and Methods. The p10 fragment was detected with a rabbit antiserum specific for the cytoplasmic tail of the invariant chain. The same blot was incubated with an anti-IA chain antiserum and then with an antitubulin antibody (left). In the right panel, the p10 signal is normalized with the MHC class II signal obtained for the same lane and these p10 signals are expressed in arbitrary units.These results are representative of three independent experiments. (B) IIA1.6 cells were left unstimulated or were stimulated for various times with anti–mouse IgG antibodies and membranes were prepared to assess cathepsin S (top) hexosaminidase (bottom right), and cathepsin B/L (bottom left) activities in fluorometric assays. Cathepsin S activity was tested at pH 7.0, because cathepsin S is functional at neutral pH, with (white bars) or without (back bars) LHVS, a cathepsin S inhibitor. Error bars correspond to the mean of three experiments. (C) Detection of cathepsin S with an iodinated peptide that binds to the active site of cathepsin S. Stimulated or unstimulated cells were incubated for 1 h with I-Mu-Tyr-Ala-CH2F, with or without LHVS, and cell lysates were then subjected to electrophoresis in 12% polyacrylamide gels. Cathepsin S was detected as a 26-kD band. The labeling of this protein was inhibited by adding LHVS. LHVS did not inhibit the labeling of an higher molecular weight band in the gel at 32 kD, which was identified as cathepsin L. Rat basophilic leukemia cell line cells,which do not produce cathepsin S, were used as a negative control. In the bottom panel, each band was quantified with a PhosphorImager™. Cathepsin S labeling was normalized against labeling of the 32-kD band for each lane and cathepsin S labeling was quantified in arbitrary units.", "figure_related_sentences": "BcR stimulation, showed an increase in the amount of p10 invariant chain fragment detected with a rabbit antiserum specific for the cytosolic domain of the invariant chain,whereas MHC class II and tubulin levels remained constant (Fig. 2 A). The effect of BcR stimulation on invariant chain degradation depended on the MHC class II allele; the effect was strongest in IIA1.6 cells–expressing IA. In parental IIA1.6 cells expressing IAd, p10 levels doubled (data not shown), whereas they increased by a factor of 5 in IAk-transfected IIA1.6 cells (Fig. 2 A) and in IIA1.6 cells expressing IAb (data not shown). However, the changes in p10 levels over time were similar for both alleles: the p10 fragment was first detected after 60 min, increased to reach a maximum at 3 h and then returned to its initial level after 6 h of BcR stimulation (Fig. 2 A). No change in de novo MHC class II synthesis was observed in pulse-chase experiments (data not shown). Although MHC class II–peptide complexes were detected in dense fractions after BcR stimulation, the increase in p10 invariant chain fragment levels and the detection of invariant chain, together with MHC class II, in late endosomal compartments after BcR cross-linking suggests that the proteolytic degradation of invariant chain was inhibited during B cell activation. Therefore, we assessed various proteolytic activities during BcR-induced cell activation. IIA1.6 cells were stimulated for various times as described above, and the activities of cathepsin S, cathepsin L/B, and hexosaminidase were assessed on the same membrane preparations by means of fluorometric assays (23). Cathepsin S activity was measured at pH 7.0 (Fig. 2 B) in membrane preparations of B cells because cathepsin S is active at this pH, whereas cathepsinB is not. We demonstrated that the activity measured corresponded to cathepsin S by adding low concentrations of LHVS. Such low concentrations (1 nM) of LHVS inhibit cathepsin S, but not cathepsin B. Higher concentrations of LHVS (30 nM) are required to inhibit cathepsin B (24). Cathepsin S activity decreased after BcR cross-linking: maximal inhibition (75%) occurred at 3 h, with cathepsin Sactivity progressively increasing thereafter and returning to initial values after 6 h; 18 h after BcR cross-linking, 15%inhibition of cathepsin activity was still observed. No change in hexosaminidase activity was detected in the same samples, whereas cathepsin L/B activity decreased slightly (Fig. 2 B). We directly measured cathepsin S activity in B cells by labeling stimulated and unstimulatedIIA1.6 cells with an iodinated peptide that bound specifically to the active site of cathepsin S (22). A 26-kD protein,presumably cathepsin S, was specifically labeled in these conditions and this labeling was inhibited in the presence of LHVS peptide. This assay gave similar results to the original assay, as 80% inhibition of cathepsin S labeling was ob-served after 3 h and this inhibition was partially reversible after 18 h (Fig. 2 C). No changes in the amounts of cathepsin S and cystatin C proteins present were detected by Western blotting (data not shown). These results demon-strate that BcR-induced B cell activation downregulated cathepsin S activity, accounting for the transient accumulation of MHC class II–invariant chain complexes in lyso-somes. The changes in MIIC composition induced by B cell activation suggest that BcR stimulation may trigger morphological changes in processing compartments.First, higher levels of transient intracellular accumulation of MHC class II and p10 fragment were observed in IIA1.6 cells expressing class II alleles with a strong affinity for invariant chain such IAk (Fig. 2 A and data not shown).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010000860_TII_01/figure/2010000860_TII_01_1.png"], "tampered": false, "paper_ids": ["2010000104"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010064544_TII_01/figure/2010064544_TII_01_4.png", "question_id": "consistency_153", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 5. Summary of genome-wide STAT5 binding sites at L1. (A) The Venn diagram shows the number of identified STAT5A and STAT5B sites (peaks) in AABB tissue and STAT5B sites in BB tissue. (B) Average peak heights of STAT5A and STAT5B in AABB and BB tissues were estimated after library size normalization (RPM, reads per 10 million, input subtracted). (C) Mean fold changes of STAT5A and STAT5B target genes in AABB tissue and STAT5B target genes in BB tissue were calculated. The genes containing STAT5 peaks within ±1 kb around TSSs were regarded as STAT5 target genes. (D) Normalized tag counts (RPM) of STAT5A, RNA polII and H3K4me3 from 200 bp around STAT5A peak centers at L1 were calculated and compared between AABB and BB. Log2-transformed values were used (x and y axes). (E) Normalized tags of H3K4me3 at positions 1 kb upstream and 2 kb downstream of TSS were summed up and divided by the size (3 kb) and then quantile normalized for comparison (top). The scatter plot shows the fold change (x-axis) and difference (y-axis) of H3K4me3 average enrichment between genes (spot) in AABB and BB. Cutoffs for significant changes were set as follows: 1.5-fold change (x-axis, AABB/BB) and four average tag difference (y-axis, AABB/BB). Among the genes showing significant changes of H3K4me3 enrichment, the number of STAT5 target and non-target genes was counted (bottom). (F) Genome browser views represent three gene loci (Wap, Csn1s2a and Stap1) showing changes of H3K4me3 level and one housekeeping gene locus (Actb).", "figure_related_sentences": "Totals of 26,231 STAT5A and 6,969 STAT5B peaks in wild type (AABB) and 2,574 STAT5B peaks in Stat5a-null (BB) were identified as STAT5 binding sites (Figure 5). For visualization, total number of reads in each sample was normalized to 10 million. The ChIP-seq data are deposited in GEO under accession number GSE40930. In total, more than 26,000 STAT5A peaks were identified in control but not in Stat5a-null mammary tissue (Figure 5). The 6,873 STAT5B peaks almost completely overlapped with the STAT5A peaks in wild-type tissue suggesting that there are no high affinity binding sites restricted to STAT5B. In general, the average STAT5A peak height was 3-fold higher than that of STAT5B (Figure 5B), which is probably the result of a greater abundance of STAT5A and possibly higher antibody affinity. The 2,395 STAT5B binding sites in Stat5a-null and 6,873 STAT5B binding sites in wild-type mammary tissues, which probably reflect high affinity STAT5 binding sites, were a better predictor for gene activation. Indeed, mean expression fold changes of the genes targeted by STAT5B in Stat5a-null mammary tissue were higher than those of the others (Figure 5C). The level of STAT5 binding was positively correlated with the enrichment level of RNA PolII and H3K4me3 near promoter regions (Supplementary Figure S7). Looking in more detail, a cutback of STAT5 by ~70% (BB) resulted in a decreased level of RNA polII but not H3K4me3 near the STAT5 binding sites as overall spots shifted toward AABB (Figure 5D). However, comparison of H3K4me3 enrichment on promoter regions between AABB and BB tissues revealed that some STAT5 target and non-target genes showed a significant decrease of H3K4me3 in BB tissue (Figure 5E; Supplementary Table S4). Manual evaluation of several loci including STAT5 target genes (Wap and Csn1s2a), and a non-STAT5 target gene (Stap1) confirmed the decrease of H3K4me3 marks, which did not occur over the housekeeping gene, Actb (Figure 5F).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010064544_TII_01/figure/2010064544_TII_01_4.png"], "tampered": false, "paper_ids": ["2010000117"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010065447_TII_01/figure/2010065447_TII_01_3.png", "question_id": "consistency_154", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 4. Editing and ADAR2-binding reduces splicing efficiency at the Gria2 R/G site. (A) RT-PCR shows a gradual reduction of splicing in the presence of a strong (+/+), intermediate (+/−) or weak (−/−) polypyrimidine tract in wildtype (wt) or pre-edited (pre-ed) versions of a Gria2 exon 13 minigene. Pre-mRNA and mRNA are indicated at the right side of the panel. M = size standard. bp = basepairs. A white asterisk marks an aberrant splicing product. (B) The relative splicing efficiency––measured from the gel in panel A––is given as % unspliced product. Pre-editing reduces splicing efficiency. Quantification was done from four independent biological replicates. (* P-value < 0.05; n.s. not significant). Dark gray = wt, light gray = pre-edited at position -2-3. (C) RT-PCR of Gria2 reporter transcripts in the presence (y) or absence (n) of ADAR2 indicate a strong reduction in splicing in the presence of ADAR2. Pre-mRNA and mRNA are indicated at the right side of the panel. M = size standard. bp = basepairs. (D) The splicing efficiency––deduced from the gel in panel (C)––in percent unspliced transcript is given. The presence of ADAR2 reduces splicing efficiency. The quantification was done from four independent biological replicates (n.s. not significant, * P-value < 0.05; ** P-value < 0.01).", "figure_related_sentences": "One of the Gria2 minigenes (+/−; Supplementary Figure S2). An even stronger accumulation of pre-mRNA was observed for the pre-edited -2-3 constructs in context with the strongest and weakest branch points (Figure 4A and B). This demonstrates that guanosines and therefore most likely also inosines introduced by editing can interfere with splicing of the Gria2 minigene. Surprisingly, when we transfected the Gria2 minigene (+/+) without the addition of the ADAR2 plasmid we observed a strong reduction in pre-mRNA (Figure 4C and D). Conversely, an increase in pre-mRNA accumulation was observed when the pre-edited -2 version of Gria2 was cotransfected with ADAR2. It thus appears that ADAR2 binding alone impairs splicing, even when editing cannot take place.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010065447_TII_01/figure/2010065447_TII_01_3.png"], "tampered": false, "paper_ids": ["2010000124"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010065498_TII_01/figure/2010065498_TII_01_0.png", "question_id": "consistency_155", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. Cdc48 and ubiquitin ligases affect the distribution pattern of ribosome-associated ubiquitinated species. Sucrose gradient sedimentation analysis of ribosomes extracted from the wild-type RS1158 strain (A) and its derivative strain harboring a tetracycline-repressible PTET-O7-CDC48 allele (B). Cells were grown in the presence of doxycycline (Dox) for 20 h. Cell lysates were centrifuged through 15%–45% sucrose gradients and fractionated with the continuous measurement of absorbance at 254 nm to visualize ribosomal peaks. Proteins isolated from individual fractions were separated on 10% SDS-acrylamide gels and the same membrane was probed with anti-ubiquitin (top) and anti-Rpl3 (bottom) antibodies. (C) and (D) The same analysis performed in PTET-O7-CDC48 cells lacking either LTN1 or NOT4. All gradients were run at least five times, representative blots are shown; see Supplemental Figure S1 for additional controls. (E) Hygromycin B (HygB) treatment induces accumulation of Ltn1-ubiquitinated 60S products. Where indicated, cells were treated with 100 µg/mL hygromycin for 2 h. Gradient fractions 2–6 were separated on the same gel for a better comparison of total ubiquitination levels. (F) Lack of LTN1 makes cells hypersensitive to hygromycin. Five-fold dilutions of wild-type B4741 (WT) and ltn1Δ strains were grown on plates without antibiotic or with 100 µg/ml hygromycin for 3 days at 30°C.", "figure_related_sentences": "RESULTS Gradient analysis of ubiquitinated polypeptides associated with ribosomes in Cdc48-depleted cells To examine how endogenous targets of cotranslational protein QC are distributed among different subpopulations of ribosomes in yeast cells, we fractionated cytoplasmic lysates by sedimentation through sucrose gradients. We observed a smear of ubiquitinated translation products in fractions containing polysomes and 80S monosomes in wild-type cells (Figure 1A, Supplementary Figure S1A), consistent with the previously described ubiquitination of ribosome-associated NCs (3,4). Previous studies have shown that loss of Cdc48 function increases accumulation of ubiquitinated NCs associated with ribosomes (2–4). To better define this effect, we analyzed yeast strains in which CDC48 is placed under the control of a tetracycline-regulatable promoter (PTET-O7-CDC48) (39). Depletion of Cdc48 by addition of doxycycline (Dox) to growing yeast cultures significantly increased the intensity of the ubiquitin signal in these cells (Figure 1B, Supplementary Figure S1A-D), as expected from stabilization of ubiquitinated NCs that normally undergo Cdc48-assisted degradation by the proteasome (4). The ubiquitin signal in Cdc48-depleted cells was mainly concentrated in fractions 4-7 (Figure 1B), corresponding to the peaks of 60S subunits (fractions 3 and 4) and 80S monosomes (fractions 4 and 5). In this and other experiments, the equivalent separation of ribosomal fractions on gradients was controlled by comparing alignment of A260 traces of the gradients, gel analysis of rRNA from the same fractions that were used for protein isolation, Ponceau S staining to control protein transfer, and probing with antibodies against ribosomal protein Rpl3 (Supplementary Figure S1A). When it was necessary to compare absolute levels of ubiquitinated species between different strains, we analyzed fractions side by side on the same gel to rule out variations between processing of individual membranes (Supplementary Figure S1D). Notably, the increase in ubiquitination of the 80S fraction was not due to redistribution of ribosomes from polysomes to the 80S monosome form in Cdc48-depleted cells, as shift of wild-type cells to medium lacking glucose (a condition known to inhibit translation initiation) resulted in elevated 80S levels comparable to those in Dox-treated PTET-O7-CDC48 cells, but did not cause accumulation of polyubiquitinated peptides in the 60S–80S fractions (Supplementary Figure S1E). Thus, Cdc48 depletion leads to increased accumulation of ubiquitinated polypeptides associated predominantly with 60S and 80S ribosomes. We next examined the distribution of ubiquitin-conjugated species in the 60S–80S fractions of PTET-O7-CDC48 strains containing additional deletions in genes of E3 ligases implicated in cotranslational QC. Consistent with previous findings obtained with model substrates (4,14,15,40), an ltn1Δ deletion completely abrogated the accumulation of ubiquitin-modified NCs in fractions that contained free 60S subunits, but not in the 80S fraction (Figure 1C). In contrast, a Cdc48-depleted strain lacking Not4, part of the Ccr4-Not deadenylase complex reported to ubiquitinate polypeptides associated with stalled ribosomes (19,27), showed a diminished intensity of the ubiquitin signal in the 80S fraction, whereas accumulation of ubiquitinated products in the 60S fraction remained constitutively high (Figure 1D). These results support the notion (2,10,14,15) that Ltn1 is a primary, and possibly unique, E3 ligase responsible for ubiquitin tagging of the 60S-associated NCs, a process necessary for Cdc48 recruitment and polypeptide degradation. To further investigate whether the observed accumulation of 60S-associated products ubiquitinated by Ltn1 is related to aberrant polypeptide synthesis during translation, we treated cells for 2 h with hygromycin B, an aminoglycoside that causes decoding errors, stop codon readthrough and ribosomal stalling (41–43). In wild-type cells, hygromycin treatment significantly increased the amount of polyubiquitinated products present in the 60S–80S fractions (Figure 1E). Similarly to PTET-O7-CDC48 ltn1Δ cells, deletion of LTN1 abrogated the accumulation of ubiquitinated products in the 60S, but not 80S fraction in the hygromycin-treated cells (Figure 1E). Consistent with a role of Ltn1 in resolving translation errors caused by hygromycin, ltn1Δ cells are hypersensitive to this antibiotic (Figure 1F). These results support the idea that the Ltn1-Cdc48-mediated QC mechanism can capture a variety of defective translational products that remain associated with the large ribosomal subunit after splitting of the ribosome. We found that the ubiquitin signal in the 60S fraction was greatly reduced compared to wild-type cells, although these cells continued to display the robust accumulation of ubiquitinated 80S complexes, resembling the effect of the ltn1Δ deletion (compare Figure 4B, right with Figure 1C).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010065498_TII_01/figure/2010065498_TII_01_0.png"], "tampered": false, "paper_ids": ["2010000139"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010065537_TII_02/figure/2010065537_TII_02_4.png", "question_id": "consistency_156", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 5. Increased U12-dependent intron retention in SMA mice. (A) qPCR validation of U12-dependent intron retention at PND1 and PND5 in spinal cord. (B) qPCR validation of U12-dependent intron retention at PND1 and PND5 in brain. (C) qPCR validation of U12-dependent intron retention at PND1 and PND5 in liver. (D) qPCR validation of U12-dependent intron retention at PND1 and PND5 in muscle. Error bars indicate SEM, n ≥ 3, ***P-value < 0.001, **P-value < 0.01, *P-value < 0.05. White bars indicate heterozygous control mice, gray bars indicate SMA-like mice. Spl = spliced, Unspl = unspliced/retained intron.", "figure_related_sentences": "We validated the decrease in retention of the U12-dependent intron and the decrease of the levels of spliced Rasgrp3 by specific qPCR assays in all tissues, at both PND1 and PND5 (Figure 5 and 6). Since retention of the intron could lead to degradation of the transcript via the NMD pathway due to a premature termination codon (PTC) in the U12-dependent intron (Supplementary Figure S10), our observations point out that aberrant retention of the U12-dependent intron in the Rasgrp3 gene might be an underlying mechanism contributing to deregulation of the cell cycle in SMA mice. In the spinal cord, a U12-dependent intron in Myh9 was retained, together with upregulation of Myh9 transcripts in general. As in the case of Rasgrp3, this may be due to a PTC being present within the U12-dependent intron (Supplementary Figure S13). Validation with qPCR confirmed the downregulation of spliced Myh9 and upregulation of unspliced Myh9 in both spinal cord and brain (Figure 5A and B), whereas there was increased retention of the U12-dependent intron in liver and muscle (Figure 5C and D). This could indicate that the NMD pathway is more effective in the CNS, and perhaps explain why we detected fewer U12-dependent intron retention events in peripheral tissue than in the CNS.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010065537_TII_02/figure/2010065537_TII_02_4.png"], "tampered": false, "paper_ids": ["2010000141"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010065559_TII_02/figure/2010065559_TII_02_0.png", "question_id": "consistency_157", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. BRD4 is required for osteoblast differentiation. (A and B) Alkaline Phosphatase staining of hFOBs differentiated into the osteoblast lineage following DMSO or JQ1 (250nM) (upper panel) and siCNTR or siBRD4 (SmartPool) (lower panel) treatments (A). The stained areas were quantified and displayed as percentage of whole area. Mean ± SD, n = 2 (B). Student’s t-test was performed for statistical analysis where ***P < 0.001, **P < 0.01, *P < 0.05 (C). The relative expression of osteoblast marker genes in hFOBs in undifferentiated (UND) and differentiated (DIF) state following siBRD4 or JQ1 treatment was evaluated via qRT-PCR and normalized to expression level of RPLP0 and the expression in the undifferentiated state. Mean ± SD, n = 3. One-way ANOVA followed by Turkey’s test was performed for statistical analysis where ***P < 0.001, **P < 0.01, *P < 0.05. (D and E). Mouse IDG-SW3 osteocyte cells were differentiated for 14 and 26 days following DMSO or JQ1 treatment and stained with alizarin red for detection of mineralized.", "figure_related_sentences": "RESULTS BRD4 promotes osteoblast differentiation. To examine the function of BRD4 during lineage specification and maintenance, we examined the effects of BETi on the differentiation of hFOBs (32). Perturbation of BRD4 function by BETi (JQ1) treatment or siRNA-mediated knockdown (Supplementary Figure S1A and B) resulted in a significant decrease of differentiation-induced alkaline phosphatase activity (Figure 1A and B; Supplementary Figure S1C and D). Gene expression analyses confirmed these findings and showed a reduced expression of the osteoblast-specific genes RUNX2, TNFRSF11B (Osteoprotegerin) and ALPL following JQ1 treatment or BRD4 knockdown (Figure 1C). To investigate whether this effect was limited to early stages of lineage-specification, we also tested the effect of BRD4 inhibition on IDG-SW3 mouse osteocytes. Despite their advanced stage of differentiation, mineralization was significantly impaired following JQ1 treatment (Figure 1D and E). Consistently, BETi treatment resulted in reduced expression of the osteoblast/osteocyte-specific genes Mepe, Bglap and Dmp1 (Figure 1F). The role of BET proteins in controlling osteoblast differentiation was differentiation-stage independent since similar effects were also observed in multipotent hMSC, where knockdown or inhibition of BRD4 also potently affected the expression of osteoblast lineage-specific genes (ALPL, COL1A1 and BGLAP; Supplementary Figure S1E and F). In order to gain a more complete overview of the effects of BRD4 on the regulation of lineage-specific gene expression, we performed transcriptome-wide mRNA-seq analyses following BRD4 depletion or JQ1 treatment in hFOB cells (Supplementary Figure S1G). Inhibition of BRD4 by JQ1 resulted in the differential regulation of a selected subset of genes. Consistent with the positive role of BET proteins in gene transcription, we observed less downregulated genes compared to upregulated genes following JQ1 treatment (Figure 1G). Interestingly, a large fraction of BETi-regulated genes were also differentially regulated during osteoblast differentiation, further supporting a lineage-specific function of BRD4 (Figure 1G–I). Consistent with the fact that JQ1 targets all BET proteins including BRD2, -3 and -4 (56) and the potential differences induced by inhibition of bromodomain-mediated protein-protein interactions versus effects observed following a complete loss of BRD4 protein expression, the effects of JQ1 and BRD4 knockdown were not identical (Figure 1G–I). However, both treatments showed a similar effect of preferential downregulation of differentiation-induced genes (Figure 1I). Moreover, GSEA on siBRD4-downregulated genes indicated a significant enrichment for pathways associated with extracellular matrix, collagen and skeletal development (Figure 1J). JQ1-downregulated genes were similarly enriched for developmental pathways (Supplementary Figure S1H). Taken together, these results suggest a role of BRD4 in maintaining and directing osteoblast-specific lineage gene expression. Interestingly, some ‘Segment 3+4’ regions showed co-occupancy of all TFs (Supplementary Figure S6A) while some osteoblast-specific BRD4 target genes such as TNFRSF11B (Figure 1C), ELN and DCN (Supplementary Figure S5C) showed distinct occupancy of the identified TFs at putative enhancer sites located within 50 kb of the genes (Figure 5K; Supplementary Figure S6B and E).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010065559_TII_02/figure/2010065559_TII_02_0.png"], "tampered": false, "paper_ids": ["2010000145"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010104206_TII_02/figure/2010104206_TII_02_1.png", "question_id": "consistency_158", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2. Increased blood glucose in Kir6.1-GOF mice. (A–C, left) Representative intrinsic GFP fluorescence in freshly isolated islets from transgenic mice. High fluorescence in transgenic islets indicates the presence of the Kir6.1 transgene (Kir6.1[x], Control), and loss of fluorescence in transgenic β cells within islets after Cre-recombination (Rip-Kir6.1[x]) indicates actual expression of the transgene specifically in these cells. Bars, 10 µm. (right) Fed blood glucose over time after weaning in Rip-Kir6.1[WT] (A, black), single mutant Rip-Kir6.1[GD] (B, green), and double mutant Rip-Kir6.1[GD,QR] (C, red) with respect to their control littermates (white). Data represent mean ± SEM, n = 8–10 animals in each group. Significant differences (*, P < 0.05) between transgenic and control littermate mice are indicated (t test).", "figure_related_sentences": "To study the effects of Kir6.1 subunits of the KATP channel in vivo, we have generated novel mice that express either the Kir6.1 WT (Kir6.1[WT]) or a Kir6.1-GOF, single mutant G343D (Kir6.1[GD]) or double mutant G343D/Q53R (Kir6.1[GD,QR]) transgenes under Cre-recombinase control (Li et al., 2013). Global Cx1 Kir6.1[WT], Kir6.1[GD], and Kir6.1[GD,QR] mice express GFP fluorescence ubiquitously in the whole body, but after tissue-specific Cre-recombination, these mice lose fluorescence only in the tissue of interest (Li et al., 2013). Specific expression in pancreatic β cells was achieved by crossing Kir6.1 transgenic mice with Rip-Cre mice. Fig. 2 shows marked gain of fluorescence in pancreatic islets from double transgenic Rip-Kir6.1[WT] (A), Rip-Kir6.1[GD] (B), and Rip-Kir6.1[GD,QR] (C; as an indication of transgene expression), compared with bright fluorescent islets from single Kir6.1[WT], Kir6.1[GD], and Kir6.1[GD,QR] transgenic mice (lacking recombination and absence of transgene expression). Littermate control mice in all experiments below include pooled WT, single transgenic Rip-Cre, and single transgenic Kir6.1[GD] or Kir6.1[GD,QR] mice. In each case, no significant differences were found between these genotypes when independently tested. Diabetes in Kir6.1-GOF mutant mice GOF mutations in the Kir6.1 subunit of the KATP channel result in either glucose intolerance (Rip-Kir6.1[GD]) or frank diabetes (Rip-Kir6.1[GD,QR]), mimicking the consequences of weak or more significant expression of Kir6.2-GOF transgenes (Koster et al., 2000, 2005; Remedi et al., 2009). 7-wk-old double transgenic Rip-Kir6.1[GD] mice showed higher fed glucose than littermate control mice (Fig. 2 B). They also demonstrate increased fasting blood glucose and a mildly impaired glucose tolerance, accompanied by reduced circulating plasma insulin after glucose challenge with respect to control littermates (Fig. 3 B). Importantly, however, 2 out of 10 Rip-Kir6.1[GD] mice showed diabetes with dramatically low fasting blood glucose levels and a marked impairment of glucose tolerance (Fig. 2 B). Strikingly, all Rip-Kir6.1[GD,QR] mice developed severe diabetes (Fig. 2 C) with markedly impaired glucose tolerance, as the result of significantly reduced plasma insulin levels in response to glucose challenge (Fig. 3 C). Importantly, however, and as expected, overexpression of WT Kir6.1 subunits in Rip-Kir6.1[WT] mice did not result in increased blood glucose or glucose intolerance (Figs. 2 A and 3A), suggesting that impaired glucose tolerance and diabetes are promoted by Kir6.1-GOF and are not an artifactual consequence of overexpressed transgenic protein levels perse.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010104206_TII_02/figure/2010104206_TII_02_1.png"], "tampered": false, "paper_ids": ["2010000148"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010105100_TII_01/figure/2010105100_TII_01_1.png", "question_id": "consistency_159", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2Id-immunized mice are protected against MM cells that produce complete myeloma protein while they succumb to FLC MM cells. (A–H) BALB/c mice were immunized i.m./EP with 50µg CCL3-scFv315 or NaCl and challenged 14 days later with MOPC315.BM.Luc.IgAλ2 cells (2×105) that produce complete M315, (left panel), (A–D) or MOPC315.BM.λ2 cells (2×105) that produce only free λ2 L chains (right panel), (E–H). (A, E) Images of whole body bioluminescence (BLI) showing mean±SEM, (B, F) representative ventral images, (C, G) serum M315 on days 0, 21 and 35 in individual mice, and (D, H) survival. End point was paraplegia. n=5–8 mice/group. Statistics: Two-way ANOVA with Bonferroni correction (A, C, E, G) and Mantel Cox Log-Rank test for survival (D, H). *p<0.05, **p<0.01, ****p<0.0001. ANOVA, analysis of variance; MM, multiple myeloma; ND, not detected; ns, not significant.", "figure_related_sentences": "The phenomenon was confirmed in experiments using luciferase-labeled MOPC315.BM.Luc cells injected intravenously and bioluminescence as a read-out for tumor load (online supplemental figure 2). Thus, while radiance and M315 levels correlated strongly in the CCL3-scFvA20-immunized mice, there was no such correlation in the CCL3-scFv315-immunized mice. Immunized mice are protected against MOPC315.BM.Luc.IgAλ2 while they succumb to the FLC variant. Having developed cloned MOPC315.BM cell lines that either secrete H+L myeloma protein (MOPC315.BM.Luc.IgAλ2) or only free λ2 L chains (MOPC315.BM.Luc.λ2), we tested these two cell lines in challenge experiments. Mice were immunized with CCL3-scFv315 and challenged 14 days later with either of the two variants. NaCl was used as a negative control. Six out of eight immunized mice were protected against cells that produced complete M315 (MOPC315.BM.Luc.IgAλ2), as measured by bioluminescence imaging (BLI) (figure 2A,B), serum M315 (figure 2C) and survival (figure 2D). However, three mice had a bioluminescence signal and M315 in their sera (figure 2C); these two mice developed paralysis and did not survive (figure 2D). In contrast, CCL3-scFv315 immunized mice were not protected against cells that only produced free λ2 L chains (MOPC315.BM.Luc.λ2) measured either by BLI (figure 2E–F) or by survival (figure 2H). As would be expected, none of the mice challenged with the FLC MM cells had detectable serum levels of M315 throughout the experiment (figure 2G). These results indicate that H chain-expression by MOPC315 MM cells is required for CCL3-scFv315 immunization to have a protective effect. In line with this, splenocytes from extensively immunized mice killed MOPC315.BM.Luc.IgAλ2 cells more efficiently than MOPC315.BM.Luc.λ2 cells, in vitro (online supplemental figure 6).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010105100_TII_01/figure/2010105100_TII_01_1.png"], "tampered": false, "paper_ids": ["2010000149"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010010059_TII_01/figure/2010010059_TII_01_10.png", "question_id": "consistency_160", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Three chosen parameters measured for one additional cells: (a, d) Dry mass (R² = 0.9344 for the upper graph and R² = 0.8961 for the lower graph); (b, e) Phase skewness (R² = 0.87 for the upper graph and R² = 0.8471 for the lower graph); (c) Phase variance (R² = 0.9801 for the upper graph and R² = 0.954 for the lower graph).", "figure_related_sentences": "Figure 11 presents the measured values for two additional HeLa cells. The dry mass values seen in Figures 11(a, d) for both of the cells show similar behavior and values to each other and to the previously described cells during all of the cell phases, although different cells have different lifecycle periods. The lifecycle phase classification was established based on the dry mass values combined with the statistical parameters as described before. The values of phase skewness presented in Figures 11(b, e), besides the values during the G2 phase, show similar behavior to the measurement presented in Figure 8(b). We assume that the differences during the G2 phase are due to the influence of the apoptosis of the cell. Nevertheless, the result shows that the G1 and S phases can be distinguished by the phase skewness. The phase variance presented in Figures 11(c, f) is used to describe the sub-phases of the M phase. Although Figures 11(c, f) show reduced ability to distinguish between the different sub-phases of the M phase compared to the results shown in Figure 8(c) due to reduction in the sampling time of the additional cells (from two frames per minute to a frame per two minutes), the sub-phases can still be discerned.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010010059_TII_01/figure/2010010059_TII_01_10.png"], "tampered": false, "paper_ids": ["2010000163"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010010376_TII_01/figure/2010010376_TII_01_5.png", "question_id": "consistency_161", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "qPCR validation of PUNCH-P results. (A, top panel) Polysome profiles of HeLa cells synchronized to S and M phase by double-thymidine block. (Bottom panel) Total RNA extracted from each of the polysomal fractions visualized by ethidium bromide staining. (B, C) Polysomal association of nonfluctuating mRNAs encoding for CALR (B) and CYCS (C). (D) Polysomal association of mRNAs encoding for proteins that were elevated in S phase according to PUNCH-P. (E) Polysomal association of mRNAs encoding for proteins that were elevated in M phase according to PUNCH-P. Graphs show mean ± SD of qPCR replicates for one of three independent experiments with similar results. (C–E) represent qPCR results normalized to CALR.", "figure_related_sentences": "To validate some of these results and provide further evidence for the potential of PUNCH-P to measure differences in translation of specific mRNAs, we analyzed the polysome association of selected mRNAs in S and M phase. We chose two proteins whose PUNCH-P expression remained stable throughout the cell cycle and six proteins whose expression fluctuated between S and M phase. Such fluctuations at the protein level can result from differences in total mRNA abundance, translation efficiency, or both. We initially compared the polysome profiles of HeLa cells synchronized to S and M phase and found no differences in polysome size (Figure 6A, top panel). Next, we extracted total RNA from each of nine polysomal fractions ranging from light to heavy polysomes (Figure 6A, bottom panel) and measured the abundance of specific mRNAs in each fraction using SYBR Fast quantitative PCR (qPCR). As predicted, we found that the relative amount and polysomal distribution of the two transcripts encoding nonfluctuating proteins—calreticulin (CALR) and cytochrome C (CYCS)—remained constant between the different cell-cycle stages (Figure 6B,C). We then measured the amount of the six transcripts encoding fluctuating proteins in each polysomal fraction and normalized the results to CALR mRNA to allow a more accurate quantitative comparison of mRNA amounts across the gradients. As predicted by PUNCH-P, the amounts of polysome-associated FOSL1 (FOS-like antigen 1), CCRN4L (nocturnin), and BRIP1 (Fanconi anemia group J protein 1) were significantly higher in S phase (Figure 6D). Similarly, the amounts of polysome-associated CCNB1 (cyclin B1), GPSM2 (G-protein signaling modulator 2), and PCF11 (pre-mRNA cleavage complex 2 protein) mRNA were higher in M phase, consistent with PUNCH-P results (Figure 6E). In addition to the differences in absolute amounts, we calculated relative mRNA distribution between heavy (five or more) and light (fewer than five) polysomes as a percentage of total polysomes. While some mRNAs showed little difference in relative distribution, others changed considerably: association of CCRN4L and BRIP1 mRNAs with heavy polysomes decreased from 82.4 % and 43.3 % in S phase to 73.5 % and 29.2 % in M phase, respectively. Conversely, association of CCNB1 mRNA with heavy polysomes increased from 63.8 % in S phase to 84.3 % in M phase, as expected for an mRNA that is translationally up-regulated during mitosis (Groisman et al., 2000).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010010376_TII_01/figure/2010010376_TII_01_5.png"], "tampered": false, "paper_ids": ["2010000169"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010010402_TII_02/figure/2010010402_TII_02_3.png", "question_id": "consistency_162", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "MeRIP-seq analysis of four RNAs tested for m⁶A status in this work. These include one lncRNA, TUG1 (A), and three mRNAs: ACTB (B), TPT1 (C), and BSG (D), analyzed in three different human cell lines (HeLa, HepG2, and HEK293T). SCARLET-tested sites are marked with bold arrows. Sites that tested positive for m⁶A are indicated by purple arrows, while sites that tested negative for m⁶A are indicated by blue arrows.", "figure_related_sentences": "We also determined the m6A status in many RRACH sites in another lncRNA (TUG1) and three mRNAs (ACTB, TPT1, and BSG), chosen on the basis of the m6A/MeRIP-seq results (Fig. 4). Among the sixteen sites tested, only four showed m6A modification >5% (Table 2). This result shows that the previously reported 20% m6A modification in bovine prolactin mRNA (Narayan and Rottman 1988) is not abnormal, suggests that many sites in mRNA carry complete m6A modification, and highlights that not every RRACH consensus sequence sites under the m6A/MeRIP-seq peaks are modified.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010010402_TII_02/figure/2010010402_TII_02_3.png"], "tampered": false, "paper_ids": ["2010000179"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010010436_TII_02/figure/2010010436_TII_02_0.png", "question_id": "consistency_163", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "mAtg9 affects autophagy at an early omegasome stage. (A) Domain structure of yeast and human Atg9. Red and blue boxes represent conserved transmembrane domains. (B) HEK293 cells were treated with either control siRNA (ctrl) or siRNA against mAtg9 (Atg9 KD) and incubated in full (F) or starvation medium (S) for 2 h. Cell lysates were analyzed by Western blot using antibodies against mAtg9, β-tubulin, and LC3. (C) Confocal microscopy of HEK293/GFP-LC3 and HEK293/GFP-DFCP1 cells treated with RISC-Free (ctrl) or mAtg9 (Atg9 KD) siRNA and starved for 2 h. ULK1, WIPI2, and Atg16 were detected by indirect immunofluorescence using anti-ULK1, -WIPI2, and -Atg16 antibodies. Bars, 10 μm. (D–H) Quantification of ULK1, GFP-DFCP1, WIPI2, Atg16, or GFP-LC3 spots from B expressed as spots/cell area (ULK1, GFP-DFCP1) or spots/cell (WIPI2, Atg16, GFP-LC3). Error bars, SEM; **p < 0.01 ***p < 0.001 (n = 3, two-tailed unpaired t test). (I) Colocalization of GFP-LC3 with WIPI2 and Atg16 in HEK293/GFP-LC3 cells treated with mAtg9 siRNA, starved, and detected in C. (J) Quantification of colocalization of WIPI2 and Atg16 with GFP-LC3 as shown in (I). Error bars, SEM, n = 3.", "figure_related_sentences": "Knockdown of mAtg9 by small interfering RNA (siRNA) depletion in HEK293 cells was nearly complete as revealed by Western blot (Figure 1B). As expected, depletion of mAtg9 significantly reduced lipidation of endogenous LC3 (Figure 1B) and the number of autophagic structures positive for GFP-LC3 (Figure 1C and I) observed upon starvation. All other autophagic structures, that is, those positive for DFCP1, WIPI2, and Atg16, were also significantly reduced (Figure 1, C and E–H), suggesting that mAtg9 may act very early, at the same step as or even before DFCP1. ULK1-positive puncta were reduced after depletion of Atg9 but not significantly (Figure 1, C and D). These results are in agreement with results in yeast, in which Atg9 is one of the first Atg proteins to be recruited to the PAS (Suzuki et al., 2007). We next investigated whether mAtg9 was required for the correct recruitment of Atg proteins to the forming autophagosome, and, in particular, we looked at the recruitment of LC3 to WIPI2- or Atg16-positive structures. In control starved cells, ∼72 and 85% of WIPI2 and Atg16 spots, respectively, were also positive for LC3 (Figure 1, I and J). In cells depleted of mAtg9, although the total number of these structures was slightly reduced (Figure 1, D–H), the percentage of WIPI2 and Atg16 spots containing LC3 was unaltered (Figure 1J). This indicates that in the absence of mAtg9, these phagophores and autophagosome membranes were able to recruit Atg proteins upstream of LC3 lipidation and conjugation. Thus we hypothesized that mAtg9 may be delivering membrane and/or other components to speed up the process of autophagosome formation.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010010436_TII_02/figure/2010010436_TII_02_0.png"], "tampered": false, "paper_ids": ["2010000181"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010102051_TII_01/figure/2010102051_TII_01_0.png", "question_id": "consistency_164", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Fig. 1. Cavin-1 altered EV proteins and EV miR-148a with no effect on total cellular levels. (A) EVs and whole cell lysates (WCL) were collected from GFP-PC3 and cavin-1-PC3 cells and analysed by Western blot with the indicated antibodies. EV preparations were free from ER protein calnexin. Equal loading was shown by Coomassie staining. Images are representative of 3 biological replicates. Raw images of the western blots are available in figures in Supplementary file. (B) Cavin-1 alters the miRNA content of EVs. Real-time qPCR was performed on cDNA synthesized from equal amounts of RNA extracted from GFP-PC3-EVs and cavin-1-PC3-EVs or total cell lysates. Bar graphs show the mean relative expression±SEM of miR-148a was significantly decreased in cavin-1-PC3-EVs compared to GFP-PC3-EVs (p ≤ 0.02, n = 3) but expression of miR-148a was unaffected in cells. (C) In contrast, miR-125a was not significantly different between GFP-PC3-EVs and cavin-1-PC3-EVs (n = 3).", "figure_related_sentences": "To confirm the cavin-1 effect on the EV-mediated release of these proteins, and to determine whether cavin-1 affected total protein expression or only the release as we previously reported for cytokines (18), we compared the levels of selected proteins in the WCL and EVs from GFP-PC3 and cavin-1-PC3 cells by immunoblotting. As shown in Fig. 1A, caveolin-1 WCL and EV levels were not altered by cavin-1 expression. Cavin-1 itself was not detected in EVs indicating its effects are indirect (Fig. 1A). Calnexin was used as an intracellular membrane marker, which was not detected in EVs (Fig. 1A). We also probed for cofilin and CD63 as known exosome cargo and marker protein, respectively. Interestingly, both cofilin and CD63 were increased in the EVs from cavin-1-PC3 cells compared to GFP-PC3 cells (Fig. 1A). Additionally, CD63 total cellular levels were also elevated in cavin-1-PC3 cells (Fig. 1A), suggesting potential increase in multi-vesicular body formation. In contrast, cavin-1 expression reduced the abundance of 4F2 and EphA2 in EVs without affecting total cellular levels (WCL, Fig. 1A) similar to our previous report for cytokines and proteases (18). This suggests that cavin-1 did not cause a decrease of key bone remodelling molecules on the cellular level but instead altered their secretion through EVs. Recent studies show that EVs mediate the transfer of functional microRNA (miRNA) (4,6), and miRNA changes are implicated in osteolytic bone metastasis (33). Therefore, we were interested to investigate if, in addition to proteins, cavin-1 expression altered miRNA secretion via EVs. Based on a review of recent literature, we chose to measure 2 miRNA species, miRNA-148a and miR-125a. Overexpression of miR-148a was recently reported to induce osteoclastogenesis and the reverse was observed when miR-148a was inhibited (34). In contrast, miR-125a was reported to be decreased during osteoclastogenesis (34). qPCR performed revealed that PC3-EV miRNA-148a levels were significantly reduced by 8.68±0.01-fold (p ≤ 0.02) upon cavin-1 expression without altering total cellular miR-148a levels (Fig. 1B). In contrast, no significant difference was found for miR-125a in either EVs or total cell (Fig. 1C). These results suggest that cavin-1 expression can selectively modulate EV-mediated transfer of miRNA. A reduction in 4F2 EV levels upon cavin-1 expression is consistent with our observation that cavin-1-PC3-EVs caused TRAP expression but did not lead to formation of multi-nucleated cells (Fig. 1A). Our data confirms previous reports that PC3 conditioned media can induce osteoclastogenesis from murine RAW264.7 cells (25–27), and further show that PC3-EVs alone are sufficient to enhance osteoclastogenesis in vitro (Fig. 1). However, cavin-1-PC3-EVs were unable to induce full osteoclastogenesis without the soluble secretome (Fig. 1B), indicating the requirement of SF not released via EVs. We also report for the first time that PC3 conditioned media and EVs increase proliferation of primary hOBs (Fig. 1D), although the magnitude of PC3-EV osteoblastic activity was much lower than its osteoclastic activity. In contrast to our data, PC3 conditioned media has been reported to suppress primary murine osteoblast proliferation (64,65). The discrepancy may be due to the use of human versus murine osteoblasts.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010102051_TII_01/figure/2010102051_TII_01_0.png"], "tampered": false, "paper_ids": ["2010000184"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010030787_TII_01/figure/2010030787_TII_01_4.png", "question_id": "consistency_165", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Detection of heroin and fentanyl using aptamer-based dye-displacement assays. (A) Secondary structures of HM20 and F17 based on NUPACK predictions. (B) Scheme of the dye-displacement assay using HM20, F17, and MTC (purple bars indicate monomeric/dimeric forms of the dye; blue bars indicate J-aggregates). (C) Photographs taken 5 min after addition of various concentrations of heroin to solutions of MTC alone (−HM20) or HM20-MTC complexes (+HM20). (D) Signal gain and cross-reactivity of the displacement assay to various interferents relative to the response to heroin. Photographs of samples were taken 5 min after adding mixtures of 25 μM heroin and 50 μM interferent to HM20-MTC complexes. (E) Detection of heroin in binary mixtures of 25 μM heroin (∼33%) with 50 μM interferent (∼67%). (F) Absorbance spectra of HM20-MTC complexes in the presence of a 33:8:59 mixture of heroin, fentanyl, and an interferent (caffeine, lidocaine, lactose, or mannitol) as well as each interferent alone. These spectra overlap for all four drug mixtures and all four interferent samples. (G) Photographs of the dye-displacement assays analyzed in panel F (top) as well as equivalent assays performed with the fentanyl-specific aptamer F17 (bottom). (H) Photographs of Marquis test results for interferent alone, binary mixtures containing heroin and interferent (33:67) or fentanyl and interferent (8:92), or ternary mixtures containing heroin, fentanyl, and interferent (33:8:59). Error bars represent the standard deviations of three independent experiments.", "figure_related_sentences": "Notably, the presence of heroin can be clearly identified at concentrations as low as 16 μM with the naked eye via a purple-to-blue-green color change (Figure 4C), which is sufficiently sensitive for detecting opioids in seized drug samples. We then determined the specificity of the assay against a variety of ligands commonly found in illicit drug samples. Since the purity of heroin is often 30–50%, (41,42) we assessed the specificity of our assay by challenging aptamer-dye complexes with 25 μM heroin or 50 μM interferent. The assay did not have any meaningful cross-reactivity to any of these interferents, and only the heroin sample induced a purple-to-blue-green color change that was visible to the naked eye (Figure 4D). We then challenged the assay with binary mixtures of 25 μM heroin (33%) and 50 μM interferent (67%) and did not observe that any of these interferents altered the signal produced by heroin, demonstrating the excellent specificity of the assay (Figure 4E).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010030787_TII_01/figure/2010030787_TII_01_4.png"], "tampered": false, "paper_ids": ["2010000190"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010039761_TII_02/figure/2010039761_TII_02_1.png", "question_id": "consistency_166", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2. Confirmation of SYNJ2 interaction with select binding partners. (A) SYNJ2 interacts with Lyn. HEK293 cells were transiently co-transfected with expression plasmids for Lyn or SYNJ2 or transfected with a SYNJ2 plasmid alone. Cells were lysed 24 h post-transfection. Cell lysates were incubated with an anti-Lyn antibody, followed by protein A-agarose. Expression of Lyn and SYNJ2 in lysates and immunoprecipitated SYNJ2 were visualized by western blotting. (B) SYNJ2 interacts with Fyn. The same methodology was used as in (A), except that Lyn was replaced by Fyn. (C) SYNJ2 interacts with intersectin. HEK293 cells were transiently transfected with the indicated combinations of expression plasmids for FLAG-tagged intersectin-1 (ITSN) or SYNJ2. Cells were lysed 24 h post-transfection and lysates were incubated with an anti-FLAG antibody, followed by protein G-agarose. Expression of intersectin and SYNJ2 in lysates and immunoprecipitated SYNJ2 were visualized by western blotting. (D and E) SYNJ2 interacts with cortactin. (D) Coimmunoprecipitation experiment. HEK293 cells were transiently co-transfected with cortactin and SYNJ2 expression plasmids. Cells were lysed 24 h posttransfection and lysates were incubated either with an anti-cortactin antibody followed by protein G-sepharose or with control IgG followed by protein G-sepharose. Expression of cortactin and SYNJ2 in lysates and immunoprecipitated SYNJ2 were visualized by western blotting. Immunoglobulin heavy chain (IgG-HC) was visualized by anti-mouse HRP. (E) GST-pulldown experiment. SNB19 cell lysates were incubated with immobilized GST or GST-SJ2 (GST-SYNJ2-C). Precipitated cortactin was visualized by western blotting using an anti-cortactin antibody (upper panel) and bound GST proteins were visualized by Ponceau staining (lower panel). Data shown are representative of at least 2 experiments.", "figure_related_sentences": "To confirm the interaction of SYNJ2 with Src family kinases in a cellular setting, we performed co-expression of full length SYNJ2 together with full length Lyn or Fyn in HEK293 cells. Immunoprecipitation of Lyn or Fyn from lysates of co-expressing cells, but not from cells in which SYNJ2 was overexpressed on its own, showed specific interaction between SYNJ2 and these kinases (Fig. 2A and B). We obtained opposite results for the interaction of SYNJ2 with intersectin (Fig. 2C). We also confirmed the interaction between SYNJ2 and cortactin, using two different approaches. First, endogenous cortactin could be precipitated from SNB19 glioblastoma cell lysates with an immobilized SYNJ2 C-terminal domain GST-fusion protein, but not GST itself (Fig. 2D). Second, SYNJ2 non-immunoprecipitated with cortactin from HEK293 cells co-expressing full length versions of both SYNJ2 and cortactin (Fig. 2E). We also identified intersectin and cortactin using mass spectrometry, as endogenous proteins associated with SYNJ2 that was overexpressed in HEK293 cells (data not shown).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010039761_TII_02/figure/2010039761_TII_02_1.png"], "tampered": false, "paper_ids": ["2010000203"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010064648_TII_01/figure/2010064648_TII_01_0.png", "question_id": "consistency_167", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. Epigenetic marks that are influenced by EBNA3A and EBNA3C during the repression of BIM by EBV. (A) The levels of BIM protein (whose predominant isoform is the extra-large BIMEL) were assayed by western blotting protein extracts from BL31 cell lines. BIM levels in uninfected BL31 or BL31 infected with the wild-type (B95.8-BAC) EBV (WT), or viruses with each individual EBNA3 knocked out (KO) and the revertant viruses (REV) are shown. In all the EBNA3A and EBNA3C knockouts BIM levels are similar to the levels observed in the uninfected cells. The expression of g-tubulin is shown as a control for the amount of protein loaded. (B) Schematic of the BIM locus showing the approximate locations of the CpG island, TSS, BIM start codon and the PCR primer pairs used in this study (A–J). (C) Methylated DNA precipitation was used to assess whether DNA methylation at the BIM promoter was responsible for repression of BIM expression. The histogram bars represent fold enrichment for co-precipitated DNA relative to input DNA, as determined by Q-PCR. The height of the bars represents the abundance of the epigenetic mark at the locus assessed by each primer set. Uninfected BL31 cells, BL31 infected with WT EBV, or EBNA3 knockouts (KO) or the revertant viruses were tested. DNA from peripheral blood mononuclear cells (PBMC) and in vitro methylated PBMC DNA were used as negative and positive controls respectively. The error bars represent the standard deviation from triplicate Q-PCR assays. (D) The same panel of BL31 cell", "figure_related_sentences": "In order to investigate the roles of EBNA3A and EBNA3C in the regulation of cellular gene expression, a panel of cell lines based on the EBV-negative BL-derived line BL31 were established and characterized (50,53). Here a selection of these were subjected to western blot analysis to confirm our previous observation that BL31 expressed high levels of BIM protein and that this was substantially reduced in BL31 latently infected in vitro with wild-type (WT) EBV-BAC-derived virus (Figure 1A). This analysis also confirmed that in BL31 infected with recombinant viruses from which EBNA3A or EBNA3C genes were deleted, BIM expression was not repressed and remained at a similar level to that in BL31 (Figure 1A). Revertant (REV) viruses reconstituted with the genes that had previously been deleted behaved—as expected—like the WT EBV and repressed BIM expression. Flanking the BIM transcription start site (TSS) is a remarkably large CGI that extends for 13 kb (http://genome.ucsc.edu/cgi-bin/hgGateway; Figure 1B). We previously showed that in various EBV-positive B cell lines and primary BL samples significant DNA methylation across this region could be detected, but this was absent in EBV-negative equivalents (52). However, analysis of several BL cell lines, including BL31, that were newly infected with EBV and also recently established LCLs revealed that although BIM transcription was repressed, there was little or no CpG methylation but rather the epigenetic repressive histone modification H3K27me3 was evident. Because of the apparently progressive nature of DNA methylation across the BIM CGI, a panel of low passage BL31-derived cell lines was subjected to methylated-DNA precipitation (MeDP) coupled with quantitative real-time PCR analysis using primer-pairs (A–F) as indicated (Figure 1B). Primary peripheral blood mononuclear cells and in vitro methylated genomic DNA were used as negative and positive controls respectively. All the lines analysed, irrespective of their EBV status, showed no detectable DNA methylation, as judged by MeDP, across a region extending from 4 kb upstream of the BIM TSS to the start codon—indicating that here histone modification was the most likely mode of repression (Figure 1C). Having shown in these EBV-infected BL31 cells that CpG methylation was not established at BIM, ChIP with an antibody directed against H3K27me3 and quantitative PCR analyses across the CGI was performed using the same primer-pairs as for MeDP. This showed that repression correlated with deposition of the H3K27me3 mark and expression of EBNA3A and EBNA3C (in the WT-, EBNA3BKO- and the revertant-infected cell lines in Figure 1D). In contrast, when either EBNA3A or EBNA3C were deleted from EBV (EBNA3AKO and EBNA3CKO) BIM expression remained high and, significantly, the amount of H3K27me3 detected across the BIM locus was below the background in uninfected BL31 cells. Occupancy of H3K27me3 on promoters of genes encoding Myoglobin and GAPDH were analysed in a similar manner as positive and negative controls respectively (Supplementary Figure S1A). ChIP for total histone H3 at BIM, Myoglobin and GAPDH revealed little difference between the cell lines used (Figure 1E and Supplementary Figure S1B). This indicates that any changes in the distribution of covalent histone modifications detected are not due to alterations in nucleosome density. The effects on H3K27me3 distribution at the BIM promoter induced by EBNA3A and EBNA3C are specific, since the overall levels of H3K27me3 were unaffected by EBV, EBNA3A or EBNA3C (Figure 1F). The protein complex responsible for establishing the H3K27me3 mark is PRC2. In mammals this is generally composed of a catalytic core made up of the histone methyltransferase EZH2 and subunits SUZ12, EED and RbAp46/48 (see ‘Introduction’ section). ChIPs for SUZ12, EZH2 and RbAp48 were performed on the panel of BL31 cell lines and analysed using the same primer-pairs as in Figure 1. Figure 2. PRC2 occupancy across the BIM promoter region. The presence and abundance of PRC2 proteins was assayed by ChIP analysis of a BL31 panel of cells, as indicated. Presentation is the same as for ChIP analysis in Figure 1. The region of amplification for each primer set (A–F) can be seen in Figure 1B. The error bars represent the standard deviation from triplicate PCR assays. ChIP was performed using an antibody specific for (A) PRC2 core subunit SUZ12, (B) PRC2 catalytic subunit EZH2, (C) core subunit RbAp48, (D) ancillary factor JARID2.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010064648_TII_01/figure/2010064648_TII_01_0.png"], "tampered": false, "paper_ids": ["2010000205"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010065393_TII_02/figure/2010065393_TII_02_0.png", "question_id": "consistency_168", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. C-trapping of FACT. (A) Immunoblotting of soluble protein extracts and chromatin pellets of HT1080 cells treated with CBL0137 for 1 h, probed with the indicated antibodies. (B) Immunofluorescence staining of HT1080 cells with antibodies to SSRP1. (C) Fluorescent imaging of two live cells expressing GFP-tagged SSRP1 before and after treatment with CBL0137. Top row––HT1080 cell in interphase, 3 μM CBL0137, bottom row––DLD1 cell in mitosis, 5 μM CBL0137. (D) Fluorescent imaging of two live HT1080 cells, interphase and mitotic, expressing GFP-tagged SPT16 before and after treatment with CBL0137. Bars are 10 μm.", "figure_related_sentences": "RESULTS FACT binds to unfolding chromatin in CBL0137-treated cells Using biochemical fractionation and fluorescent microscopy we previously demonstrated that curaxin treatment causes a rapid transition of FACT from the nucleoplasm to a state of tight association with chromatin (13). We named this phenomenon ‘chromatin trapping’ of FACT or c-trapping. To investigate the mechanism of c-trapping, we first examined the dose and time dependence as well as specificity of this phenomenon. To do this we used two methods, (i) immunoblotting of soluble, representing nucleoplasm, and pelleted, representing chromatin, fractions of total cell lysates ((Figure 1A) see details in Materials and Methods), and (ii) ectopic expression of GFP or mCherry tagged SSRP1 and SPT16 subunits of FACT, which undergo c-trapping in CBL0137-treated cells similarly to endogenous FACT subunits (Figure 1B–D and Supplemental Figure S1). C-trapping was observed in all tested cell lines (>20 cell lines, data not shown). Importantly, c-trapping and toxicity of CBL0137 occur at the same concentrations (∼0.3–0.5 μM depending on cell line, Figures 1A, 2 and (13)), however, c-trapping is observed within minutes after start of treatment (Figure 1C and D), while cell death after 48 h (13). Thus, these two effects of CBL0137 are probably connected, but c-trapping cannot be viewed as a sign of cell death. In untreated cells, FACT is diffusely spread throughout the nucleoplasm with some accumulation in nucleoli ((13,42) and Figure 2A and B). Changes in the distribution of FACT subunits begin 30–60 s after the addition of CBL0137 to cell culture medium (Figure 1C and D). In the presence of 0.3 μM CBL0137, both subunits become associated with thin fibers of chromatin, which is illustrated by their overlap with fluorescently labeled histone H2B (Figure 2A and B). At higher concentrations of CBL0137 (1–3 μM), FACT subunits are still associated with chromatin, however, the chromatin itself remains such that it appears as thicker fibers with bead like structures contouring nucleoli (Figure 2A and B). At concentrations of ≥5 μM CBL0137, the cellular distribution of SSRP1, SPT16, and H2B is dramatically changed. SSRP1 appears as thin fibers situated along the nuclear periphery and absent in and near nucleoli (Figure 2A). SPT16 becomes more diffuse (Figure 2B). Histone H2B loses its fiber-like appearance and accumulates in nucleoli (Figure 2A and B). Full transition takes 20–30 min (Figure 3A). Behavior similar to H2B was observed with fluorescently tagged histones H3 and H4 (Supplemental Figure S2). Similar to our results presented here, Musinova et al previously demonstrated that histone H2B, which is not incorporated into chromatin, accumulates in nucleoli due to the presence of a nucleoli localization signal within its nuclear localization signal (43). Therefore, we hypothesized that CBL0137 treatment leads to accumulation of histones in nucleoli due to their liberation from chromatin, which is consistent with the loss of visible chromatin fibers (Figure 2A and B, 10 μM). C-trapping not only occurs in interphase cells but also in mitotic cells. As shown in Figure 1 C and D, diffuse GFP-SSRP1 or GFP-SPT16 signals in mitotic cells became overlapped with mitotic chromosomes within a few minutes following the addition of CBL0137, which is indicative of a rapid CBL0137-induced binding of FACT to chromatin (Figure 1C and D). However, later on and in the presence of ≥3 μM of CBL0137, histone H2B was lost from chromosomes and appeared more like a diffuse cloud (Figure 3B). FACT subunits followed histones into the cloud-like shape, however, some SSRP1 was still associated with loops in the periphery, which were most likely leftover of decondensed and disassembled chromatin (Figure 3B).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010065393_TII_02/figure/2010065393_TII_02_0.png"], "tampered": false, "paper_ids": ["2010000221"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010005464_TII_02/figure/2010005464_TII_02_1.png", "question_id": "consistency_169", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2. XRK3F2 plus bortezomib combination activates multiple death pathways and overcomes apoptosis resistance in mul-tiple myeloma. MM.1S cells treated with XRK3F2 (5 μM), bortezomib (Btz) (3 nM), or combined XRK3F2-Btz (5 μM/3 nM) for 24 hours in the presence or absence of autophagy inhibitor BafilomycinA1 (Baf, 40 nM) (A, D), Pan caspase OPH inhibitor Q-VD (QVD, 20 μM) (B, E), or caspase-3 inhibitor Z-DEVD-FMK (Z-DEV, 20 μM) (C, F). Cell viability was evaluated using alamarBlue assays and is reported as percent versus dimethyl sulfoxide (DMSO) vehicle control (A-C). Analysis of autophagic flux and apoptosis were assessed by immunoblotting by LC3I-LC3II conversion (D) and for cleavage of caspase 8 and 3 (E, F). Data are presented as bars, means ± standard deviation (N=4-6/group). *P<0.05 versusvehicle, ^P<0.05 versus XRK3F2 or Btz alone and ^P<0.05 versus control versus Baf/QVD/ZDEV culture by two-way ANOVA with post hoc Bonferroni’s correction.", "figure_related_sentences": "Btz decrease p62 levels by inducing de novo p62 expressionand preventing its degradation.In agreement with the pre-vious studies,:: we found that Btz increased levels of p62mRNA 8-fold and protein (Figure 2D; Online SupplementaryFigure S2D)independent of autophagy since changes inLC3l-LC3ll conversion were not found in Btz-treated cells.Btz-induced p62 mRNA expression was reduced by XRK3F2Ligands binding to p62-2Z stimulate p62 oligomerizationand autophagy.34 XRK3F2 alone or in combination with Btz decreased LC3l-LC3ll conversion in MM1S,indicating induction ofautophagy (Figure 2D, left panel). Pretreatment of MMcells with bafilomycin A1 (Baf), which disrupts autophagicflux, further increased LC3ll/LC3l ratio and p62 protein levels compared to XRK3F2 alone or XRK3F2-Btz combination(Figure 2D, right panel). Furthermore, autophagy blockadeby Baf treatment further amplified the negative effects oXRK3F2 and Btz on MM cell viability (Figure 2A, Online sup.plementary Figure S4A), indicating that the autophagy-induced by targeting p62-ZZ domain in MM cells was not thepathway responsible for MM cell death.We previously reported that high doses ofXRK3F2 triggeredcaspase 3 cleavage in MM.1S cells.7 Here, we found that inMM.1S cells, co-administration of 5uM XRK3F2 and 3 nMBtz strongly activated caspase-8 and caspase-3 (Figure 2Eleft panel).In contrast, we only detected partial activationof caspases by Btz alone and no activation by XRK3F2 atthe concentration used. To test if the increased cell deathseen with the combination therapy was due to apoptosiswe used the pan-caspase inhibitor O-VD-OPh (OvD) and thecaspase-3 inhibitor Z-DEVD-FMK (Z-DEV). OVD and Z-DEVcompletely blocked Btz-induced cleavage of caspase-8 and3 (Figure 2E, F, right panels). In addition, QvD or Z-DEV fullyprevented the decrease in cell viabilityinduced by Btz (Figure2B,C;Online Supplementary Figure S4B, C)but enhancedthe anti-MM effects of XRK3F2. QVD and Z-DEV only partially blocked caspase 8 and 3 cleavage by XRK3F2-Btz andpartially reduced the effects ofthe combination on MM celviability. These findings suggest that XRK3F2-Btz combinationinhibits MM viability by activating both caspase-dependentand independent-cell death pathways.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010005464_TII_02/figure/2010005464_TII_02_1.png"], "tampered": false, "paper_ids": ["2010000232"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010042289_TII_02/figure/2010042289_TII_02_8.png", "question_id": "consistency_170", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 5 (A) Immunofluorescence staining of GIG on expression of ABCB4 and BSEP in ANIT-treated rats’ liver tissues. (B) The relative percentage of ABCB4 expression. (C) The relative percentage of BSEP expression. Red represents ABCB4, and green represents BSEP. **P<0.01, ****P<0.0001.", "figure_related_sentences": "Effect of GIG on ABCB4 and BSEP Protein Expression in ANIT-Treated Rats. Compared with the normal control group, there was almost the high expression of ABCB4 and BSEP in the model group’s liver tissues (Figure 5). Compared with the model group, the expression of BSEP and ABCB4 decreased significantly in the GIG middle and high dose groups, and the changes of BSEP and ABCB4 expression showed a negative correlation with the dose of GIG (Figure 5). The expression trends of ABCB4 and BSEP in each group can be seen in Figures 5B and C.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010042289_TII_02/figure/2010042289_TII_02_8.png"], "tampered": false, "paper_ids": ["2010000234"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010104828_TII_02/figure/2010104828_TII_02_0.png", "question_id": "consistency_171", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1 The expression of miR-29c-3p and LIF in UC tissues and IECs. (A) The mRNA levels of LIF in UC and normal tissues. (B) Representative Western blots and densitometric quantitative analysis of LIF protein levels in UC and normal tissues. (C) The mRNA levels of LIF in primary IECs of UC and normal colon. (D) Representative Western blots and densitometric quantitative analysis of LIF protein levels in IECs of UC and normal colon. (E) The expression of miR-29c-3p in UC and normal tissues. (F) The expression of miR-29c-3p in primary IECs of UC and normal colon. (G) Pearson’s correlation analysis of the expression levels of miR-29c-3p and LIF protein. (H) Pearson’s correlation analysis of the expression levels of miR-29c-3p and LIF mRNA. **P<0.01 versus normal group.", "figure_related_sentences": "ResultsThe Expression of miR-29c-3p and LIF in UC Tissues and Primary IECsColonic biopsies were obtained during endoscopic examinations. We first assessed LIF expression in colon tissues using qRT-PCR and found it to be upregulated in UC patients compared with healthy controls (Figure 1A). The weakened LIF protein expression was then verified by Western blotting (Figure 1B). To further explore cellular level of LIF, primary IECs were isolated and quantified for LIF expression. As expected, the same change trends were observed in IECs (Figure 1C and D). Next, we adopted five miRNA databases (TargetScan, miRDB, starBase, mirDIP and miRmap) to predict the upstream miRNA of LIF. As a result, miR-29c-3p was the only miRNA with the highest possibility to interact with LIF predicted simultaneously by all databases. Therefore, we explored miR-29c-3p expression by qRT-PCR. As illustrated in Figure 1E and F, miR-29c-3p was upregulated both in colonic tissues and IECs from UC patients relative to normal controls. Subsequently, as illustrated by Pearson correlation scatter plots (Figure 1G and H), miR-29c-3p and LIF protein expression in UC tissues were inversely correlated, whereas disparity was found between miR-29c-3p and LIF mRNA expression. Accordingly, we hypothesized that miR-29c-3p is involved in the post-transcriptional regulation of LIF expression.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010104828_TII_02/figure/2010104828_TII_02_0.png"], "tampered": false, "paper_ids": ["2010000257"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010012624_TII_02/figure/2010012624_TII_02_3.png", "question_id": "consistency_172", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "R-Ras2/TC21 regulates the timely development of the pubertal mammary gland. (A) qRT-PCR analysis of total RNA obtained from mammary glands extracted from the indicated stages. Prepubertal, pubertal, and adult virgins correspond to samples obtained from 3-, 8-, and 14-wk-old RRas2+/+ female mice, respectively. Early and late pregnancy correspond to female mice within weeks 1 and 2.5 of pregnancy, respectively. The early and late lactation samples were taken 1 and 2 wk after labor, respectively. The involution phase samples were taken 3.5 d after offspring weaning. Data are given relative to the expression levels obtained in virgin adult state (which was given an arbitrary value of 1). All values were normalized taking into consideration the expression levels of the housekeeping Gapdh mRNA in each sample. *p ≤ 0.05; ***p ≤ 0.001 (n = 3). (B) Representative images of carmine alum–stained mammary fat pads obtained from female mice of the indicated ages (top) and genotypes (left). Scale bars, 500 μm. One of the inguinal lymph nodes is indicated by a white asterisk. (C–F) Quantification of the total area (C), maximal length (D), number of TEBs (E), and branching points (F) of mammary glands obtained from animals of the indicated genotypes and ages. *p ≤ 0.05, **p ≤ 0.01, ***p ≤ 0.001 when compared with values obtained in the appropriate wild-type control (n = 5–10 animals per genotype and developmental stage).", "figure_related_sentences": "We found no major differences in any of those parameters in the mammary glands of 4-wk-old R-Ras2/TC21-deficient and control mice (Figure 3B, 3C, 3E, and 3F). However, when we analyzed 5-wk-old mice, we observed that the mammary glands extracted from RRas2−/− mice were significantly smaller than those obtained from control animals (Figure 3B–3D). Those glands also displayed significantly higher numbers of TEBs (Figure 3B and 3E) and branching points (Figure 3B and 3F). Most of those differences disappeared in the mammary glands of 12-wk-old mice (Figure 3B–3D). However, unlike the case of control mice, we found that ∼50% of the mammary glands obtained from RRas2−/− mice still contained a insignificant number of TEBs (Figure 3E), further suggesting that the R-Ras2/TC21 deficiency induces a delay in the development of this gland. This phenotype was highly penetrant, since it was observed in mice of homogenized (C57BL/6J, Figure 3) and mixed (129Sv/J × C57BL/6J, Supplemental Figure S2) genetic backgrounds. In the latter strain, R-Ras2/TC21 became specifically upregulated during those two highly morphogenetic periods of the mammary gland (Figure 3A). As previously seen with RRas2−/− mice (Figure 3), this observation, coupled with the upregulation of the RRas2 gene found in specific developmental stages of the gland (Figure 3A), supports a role for R-Ras2/TC21 in mammary gland maturation.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010012624_TII_02/figure/2010012624_TII_02_3.png"], "tampered": false, "paper_ids": ["2010000263"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010122902_TII_02/figure/2010122902_TII_02_3.png", "question_id": "consistency_173", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Tissue penetration of Humabodies with and without albumin in spheroids. Spheroids show cell nuclei (blue) and fluorescent drug (green). Incubations included 20 nM J591 antibody, monovalent-HLE Humabody, PSMA-CD137 with MSA binding HLE (mHLE) incubated with and without MSA, PSMA-CD137 with HSA binding HLE (hHLE) incubated with and without HSA (A). Euclidean distance mapping shows the fluorescent intensity versus distance from the spheroid edge in μm (B-D), indicating that specific albumin binding is not impacting tissue penetration to the spheroid center. The MSA binders (Fig. 2B) had lower maximum signal with the presence of MSA (p=0.002), but HSA binders did not have differences in the maximum signal (p = 0.85). *, p < 0.05.", "figure_related_sentences": "Given the importance of tissue penetration, we next investigated the impact of albumin binding on diffusion. In theory, the diffusion of a Humabody-albumin complex (~110 kDa) would be slower than the Humabody alone (~45 kDa), which could reduce tissue penetration. The impact of albumin binding on tissue distribution was therefore tested in DU145T spheroids. Humabodies with HLE domains were incubated with and without their corresponding albumin type (HSA or MSA), which have 8 nM and 50 nM affinity (Kd), respectively. In both cases, the addition of albumin did not result in changes in tissue penetration compared to Humabody alone (Fig. 3A). Despite the concentration of albumin well above the Kd (~ 200 µM), where most of the Humabody could be in complex with albumin, the presence of albumin had a negligible effect on tissue penetration. These findings were confirmed by quantitative image analysis to map the fluorescence distribution as a function of distance from the spheroid edge (Fig. 3B–D). The fluorescent signal in the center of the spheroids did not show any statistically significant differences with and without albumin. In contrast, an equal molar amounts of J591 antibody (~150 kDa) resulted in homogeneous distribution, which is typical for large biologics. A control monovalent-HLE (that had no CD137 binding domain) with the lowest molecular weight (~30 kDa) distributed the most evenly.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010122902_TII_02/figure/2010122902_TII_02_3.png"], "tampered": false, "paper_ids": ["2010000275"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010162117_TII_02/figure/2010162117_TII_02_8.png", "question_id": "consistency_174", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 7 (A and B) The BAL fluids and lungs were harvested 24 h after last rmIL-33 challenge to measure the protein expression of IL-1α, IL-5, IL-13, CCL11, CCL17, CCL22 and CCL24. (C) Cell differentials from BAL fluids harvested 24 h after the last rmIL-33 challenge. The results are shown as mean ± SEM of four mice in PBS-challenged groups and 11 mice in rmIL-33-challenged groups. *p < 0.05.", "figure_related_sentences": "We assessed cell differentials and cytokine and chemokine expression levels in the BAL fluid and lung homogenates 24 h after rmIL-33 challenge for four consecutive days (Figure 6A). IL-1α protein expression was not changed by exogenous rmIL-33 challenge in lung homogenate (Figure 7A). This result is consistent with a previous report that IL-33 neutralisation by soluble ST2 administration had no effect in house dust mite extract-induced lung IL-1α protein expression in a mouse model. On the other hand, protein expression of IL-5 and IL-13 in both BAL fluids and lung homogenates was significantly increased in rmIL-33-challenged mice compared with vehicle-challenged mice (p < 0.05); and TSA treatment significantly increased the rmIL-33-induced IL-5 and IL-13 protein expression compared with TSA–vehicle treatment (p < 0.05) (Figure 7B). CCL11 and CCL24 were also increased in lung homogenates from rmIL-33-challenged mice compared with vehicle-challenged mice (p < 0.05); and TSA treatment significantly decreased the rmIL-33-induced CCL11 and CCL24 expression in lung homogenates compared with treatment with the vehicle for TSA (p < 0.05) (Figure 7B). rmIL-33 challenge significantly induced CCL17 and CCL22 expression in lung homogenates (p < 0.05), but TSA treatment did not decrease these chemokines compared with treatment with the vehicle for TSA (Figure 7B). Further, there was a statistically significant decrease in the number of total BAL cells and eosinophils in rmIL-33-challenged mice treated with TSA compared with rmIL-33-challenged mice treated with vehicle (p < 0.05) (Figure 7C). These results suggest that TSA treatment suppresses IL-33-induced Th2 cytokine and eosinophil chemotactic chemokine expression, and subsequent eosinophil accumulation in the airway.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010162117_TII_02/figure/2010162117_TII_02_8.png"], "tampered": false, "paper_ids": ["2010000289"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010147815_TII_01/figure/2010147815_TII_01_3.png", "question_id": "consistency_175", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 4. Binding of a2NTD and intracellular cytokine production in monocyte subpopulations. (A–D) Peripheral blood mononuclear cells (PBMCs) were incubated with 10 μg/mL a2NTD conjugated to Alexa Fluor 488 (a2NTD-AF488) for 1 h and then surface stained with anti-CD14-Pacific Blue and anti-CD16-PE antibodies. (A) Percentage of monocyte populations positive for a2NTD-AF488 (means ± SEM, n = 10, # p < 0.005, CD14+CD16+ vs. CD14+CD16− or CD14+CD16+ cells). (B–D) PBMCs were kept in control conditions or stimulated with 10 ng/mL a2NTD for 18 h and sequentially stained for surface expression of CD14/CD16 and the intracellular expression of interleukin (IL)-1α: (B), IL-1β (C) and tumor necrosis factor α (TNFα) (D). The bar graph reports the percentage of a2NTD-positive cells (means ± SEM, n = 5, *p < 0.05, ** p < 0.001, compared with unstimulated cells of the same subpopulation).", "figure_related_sentences": "Uptake of a2NTD by monocyte subsets. To determine if different monocyte subsets preferentially internalize a2NTD, monocytes were stained for the surface markers CD14 and CD16 after incubation with a2NTD. CD14++CD16− cells constitute the majority of all monocytes, while CD14++CD16+ and CD14+CD16++ represent two minor subpopulations.25 We were able to retrieve these three populations by flow cytometry (Table 1). Of note, nearly 80% of CD14++CD16+ monocytes were positive for a2NTD endocytosis, as compared with approximately 90% of CD14++CD16− monocytes. The CD14+CD16++ population showed a a2NTD uptake profile similar to that of CD14++CD16− cells (Figure 4A). a2NTD stimulates IL-1α and IL-1β production. It has previously been shown that a2NTD stimulates monocytes to produce the pro-inflammatory cytokines IL-1α and IL-1β.17,18 We examined whether a particular subset of monocytes is responsible for the production of inflammatory cytokines following a2NTD stimulation. To this aim, monocytes were incubated with a2NTD and then stained for surface CD14 and CD16 expression, followed by staining for the intracellular cytokines IL-1α, IL-1β and TNF-α. Only CD14++CD16+ monocytes showed a statistically significant increase in IL-1α production when compared with cells maintained in control conditions (Figure 4B). Both CD14++CD16− and CD14++CD16+ monocytes produced significantly higher amounts of IL-1β (Figure 4C). There was no significant difference in the production of TNFα by cells treated with a2NTD and control cells (Figure 4D). Of note, the CD14++CD16+ subpopulation invariably produced higher amounts of IL-1α, IL-1β and TNFα than the other two subpopulations. In addition, the intracellular levels of IL-1α and IL-1β were greater than those of TNFα. This finding is consistent with our previous data demonstrating that monocytes produce more IL-1 than TNF.16 LPS contamination of the recombinant peptide is always a concern when investigating inflammatory cytokines. A multiexperimental approach was used to investigate the presence of LPS contamination, including the Limulus assay and polymyxin B neutralization tests. The results (which have previously been published) demonstrated negligible levels of LPS and that cytokine secretion could not be inhibited by pre-treatment with polymyxin B.16", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010147815_TII_01/figure/2010147815_TII_01_3.png"], "tampered": false, "paper_ids": ["2010000290"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010041524_TII_02/figure/2010041524_TII_02_5.png", "question_id": "consistency_176", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Reduced GRHL2 level triggers expression of EDC proteins in differentiating keratinocytes. (a) Rapidly proliferating NHEK were serially subcultured until senescence, and western blotting was performed at varying PD levels for GRHL2, IVL, Jmjd3, and p16INK4A.(b) NHEK were exposed to 1.5mM Caþþfor up to 3 days and collected for western blotting for GRHL2, Jmjd3, IVL, and GRHL3. (c) HaCaT cells were infected with LV-EGFP or LV-GRHL2i to knock down endogenous GRHL2. The cells were then exposed to 2.0mM Caþþ for 3 days and harvested for western blotting for GRHL2, Jmjd3, IVL, FLG, KRT1, GRHL1, GRHL3, and Jmjd3. Arrow indicates the expected size of GRHL3 (B 60kDa). For all experiments, GAPDH (glyceraldehyde 3-phosphate dehydrogenase) was used as a loading control", "figure_related_sentences": "To understand the mechanism by which GRHL2 inhibits EDC gene expression and keratinocyte differentiation, we explored the functional relationship between GRHL2 and epigenetic gene regulation by Jmjd3. In NHEK with increasing PDs, GRHL2 levels progressively decreased while the levels of IVL and p16INK4A decreased (Figure 5a). Caþþ-induced terminal differentiation in NHEK led to induction of IVL and decreased GRHL2 expression (Figure 5b). In both serially subcultured cells and those exposed to Caþþ, changes in Jmjd3 level were remote. In another experiment, expression of endogenous GRHL2 was knocked down in HaCaT cells by lentiviral vector expressing shRNA against GRHL2 (LV-GRHL2i). HaCaT cells were used herein because these cells express high level of endogenous GRHL2 and undergo normal keratinocyte differentiation when exposed to physiological Caþþ level (Figure 4b). As a control, HaCaT cells were infected with an empty viral vector (LV-EGFP). GRHL2 knockdown in HaCaT led to induction of IVL, FLG, and KRT1 even in the absence of Caþþ treatment to the levels similar to Caþþ-exposed control cells (Figure 5c).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010041524_TII_02/figure/2010041524_TII_02_5.png"], "tampered": false, "paper_ids": ["2010000345"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010041695_TII_02/figure/2010041695_TII_02_4.png", "question_id": "consistency_177", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure2 Roles of ALK5 receptor and ROS in TGF-b-induced apoptosis in HUVECs. (a) Effects of the ALK5 inhibitor SB431542 (2mM) on TGF-b (10ng/ml for 24h)induced caspase 3/7 activation. (b) Effects of SB431542 on TGF-b-induced caspase 3 cleavage. (c) Effects of SB431542 on TGF-b-induced DCm depression (reduced red fluorescence) as detected with JC-1 staining (representative images of three independent experiments). The red fluorescence specifically labeled the mitochondria. (d) Effects of TGF-b and SB431542 on intracellular ROS production detected with DCFH-DA (green fluorescence). (e) Effects of antioxidant compounds NAC (1mM) and EUK-134 (100mM) on TGF-b-induced caspase 3/7 activation. Data are mean±S.E.M. *Po0.05 versus control (Con), **Po0.05 versus TGF alone, one-way ANOVA (n¼3–5)", "figure_related_sentences": "TGF-b-induced apoptosis is dependent on ALK5 and ROS. To examine whether the ALK5 receptor was involved in TGF-b-induced apoptosis, HUVECs were pre-treated with the ALK5 inhibitor SB431542. Treatment with SB431542 at 2mM enhanced the apoptotic response induced by TGF-b as indicated by caspase 3/7 activation and caspase 3 cleavage (Figures 2a and b). Moreover, we showed that SB431542 also prevented the collapse of mitochondrial membrane potential (DCm) in response to TGF-b as measured with JC-1 staining (Figure 2c and Supplementary Figure S1). Using 20,70-dichlorofluorescin diacetate (DCFH-DA) fluorescence, we found that TGF-b treatment enhanced intracellular ROSproduction in HUVECs, and this effect could be blocked by SB431542 (Figure 2d and Supplementary Figure S1). To elucidate the role of ROS in TGF-b-induced apoptosis, we preincubated the cells with antioxidant compounds N-acetyl-L-cysteine (NAC) or EUK-134. We showed that both NAC and EUK-134 abrogated TGF-b-induced caspase 3/7 activation (Figure 2e).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010041695_TII_02/figure/2010041695_TII_02_4.png"], "tampered": false, "paper_ids": ["2010000346"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010031950_TII_01/figure/2010031950_TII_01_0.png", "question_id": "consistency_178", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Morphological and growth characterization of hBMCs and hPDCs. (A) Growth curves of hBMCs (human bone marrow derived cells) and hPDCs (human periosteum-derived cells) over 2 weeks in culture. (B) Phase contrast images of hBMCs and hPDCs at one day after seeding at 5 k/cm2, 25 k/cm2, and 85 k/cm2 (scale bar 5 100 mm). White arrowheads indicate flattened morphology whereas black arrowheads indicate spindle-shaped morphology. (C) Growth kinetics of hBMCs (2 donors/2 experiments) and hPDCs (4 donors) seeded at different densities from passage 4. All error bars indicate standard error of the mean (n53 hBMC donors or 4 hPDC donors).", "figure_related_sentences": "Independently of the cell culture vessel used, hPDCs proliferated faster than hBMCs and reached full confluence after 7 days (Fig. 1A) when initially seeded at low seeding density (5000 cells/cm2). In addition, the cell density of hPDCs obtained at confluence was consistently higher as compared to hBMCs, which suggested that hPDCs are smaller than hBMCs. Indeed, side-by-side comparison of adherent hBMC and hPDC populations under phase contrast microscopy suggested that hBMCs were more spread on tissue culture plastic with a broader cytoplasmic body than hPDCs (Fig. 1B, white arrows), whereas hPDCs displayed a more spindle-shaped phenotype (Fig. 1B, black arrows). To examine how initial seeding density impacted hBMC and hPDC populations, we empirically chose three seeding densities, 5000 (5 k/cm2), 25000 (25 k/cm2), and 85000 (85 k/cm2). When seeded at 5 k/cm2, both hPDCs and hBMCs attached efficiently as mostly isolated cells with few if any cell–cell contacts. At 25 k/cm2, both cell types arranged in a nearly confluent, but not densely packed, monolayer of cells in which cells remained well spread against the substrate but also displayed augmented cell–cell contact. At 85 k/cm2, both cell types appeared smaller, highly packed, and extended processes over each other (Fig. 1B), but a significant number of hBMCs did not attach after seeding at 85 k/cm2. Because differentiation experiments last one to two weeks, we quantified the extent to which cell proliferation affected cell density over time at the different seeding densities. hBMCs seeded at 5 k/cm2 or 25 k/cm2 reached a cell density of 35 k/cm2 (62.6 k/cm2) and 41 k/cm2 (64.1 k/cm2), respectively, whereas hPDCs at those seeding densities expanded to 55 k/cm2 (65k/cm2)and 64 k/cm2 (64.6 k/cm2). Cell density did not change over time for both cell types when seeded at 85 k/cm2, though fewer hBMCs than hPDCs attached at this density (Fig. 1C).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010031950_TII_01/figure/2010031950_TII_01_0.png"], "tampered": false, "paper_ids": ["2010000350"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010168986_TII_02/figure/2010168986_TII_02_2.png", "question_id": "consistency_179", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "FIGURE 3. Co-i-cIDPRE evokes Ca2+ increase in human Jurkat cells after UV photolysis. A, Co-i-cIDPRE (200 µM) incited much weaker Ca2+ increases after UV photolysis than that by cIDPRE (200 µM) in Jurkat cells. Fluo-4-loaded cells were incubated in regular HBSS containing extracellular Ca2+ during the experiment. B, after Fluo-4-loaded Jurkat cells were incubated with Co-i-cIDPRE (120 µM) in regular HBSS containing extracellular Ca2+, washing away Co-i-cIDPRE in the medium did not have any effect on Ca2+ changes triggered by uncaging of Co-i-cIDPRE. C and D, in Fluo-4-loaded Jurkat cells, uncaging of Co-i-cIDPRE triggered Ca2+ increases in a dose-dependent manner in both the presence (C) and the absence of extracellular Ca2+ (D). E, in Fluo-4-loaded Jurkat cells, thapsigargin (10 µM) pretreatment promoted Co-i-cIDPRE (120 µM)-induced Ca2+ increases in the absence of extracellular Ca2+. Data quantifications of [Ca2+]i peak induced by drug treatment in A, C, D, and E were expressed as mean ± S.E., n = 30 – 40 cells, *, p ≤ 0.05. In A, C, D, and E, cells were all continuously incubated with Co-i-cIDPRE throughout the experiments.", "figure_related_sentences": "It has been shown that cADPR targets the RyR, but which specific isoform it targets remains to be determined (1–3). Here we showed that both RyR2 and RyR3 are expressed in Jurkat cells. Individual knockdown of these isoforms inhibited cIDPRE- or cADPR-induced Ca2+ release to a similar extent, whereas double knockdown of both isoforms abolished cADPR-induced Ca2+ release in Jurkat cells (Fig. 4E). These data indicate that cADPR does not distinguish either isoform. However, it still remains to be determined whether cADPR binds directly to the RyRs or through some unknown proteins. Recently, the long sought after store-operated Ca2+ entry proteins were identified using a genome-wide RNAi screen by several groups (36–38). Co-i-cIDPRE could be a valuable tool to be used in a similar cell-based screening for cADPR-interacting proteins or regulators.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010168986_TII_02/figure/2010168986_TII_02_2.png"], "tampered": false, "paper_ids": ["2010000351"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010041443_TII_02/figure/2010041443_TII_02_3.png", "question_id": "consistency_180", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 4 ‘Late’ Hsp27 phosphorylation induced by apigenin is modulated by p38-MAPK and PKCd. Lysates from THP-1 cells treated with 50 μM apigenin for 6 h and diluent or following 1 h pretreatment with 10 μM SB203580, 15 μM rottlerin, or both. Treatments marked with (-) denote addition of diluent. (a) Immunoblots with anti-phospho-Hsp27-pS78 and anti-total-Hsp27 antibodies. (b) Immunoblots with anti-phospho-Hsp27-pS82 and anti-total-Hsp27 antibodies. (c) Immunoblots with antiphospho-Hsp27-pS15 and anti-total-Hsp27 antibodies. Densitometry data normalized by the loading control are represented as mean±S.E.M. (N ¼ 5, *Pp0.05 and **Pp0.001, NS denotes non-statistical significance)", "figure_related_sentences": "Next, we investigated the role of p38 and PKCσ on the ‘late’ Hsp27 phosphorylation using pharmacological inhibitors. THP-1 cells were pretreated with the p38 inhibitor SB203580, or the PKCσ inhibitor rottlerin, or both inhibitors, or with diluent for 1 h before the addition of 50 μM apigenin for 6 h. We found that apigenin-induced phosphorylation of S78 was significantly stimulated in the presence of the p38 inhibitor SB203580 (Figure 4a, lane 3 versus 2, **P<0.001), reaching levels similar to that in control cells (Figure 4a, lane 3 versus 1). In contrast, the PKCσ inhibitor rottlerin had no effect on the phosphorylation of S78 (Figure 4a, lane 4 versus 2, NS ¼ nonstatistically significant). Addition of both SB203580 and rottlerin showed decreased S78 phosphorylation to levels similarly observed in the presence of the p38 inhibitor alone (Figure 4a, lane 5 versus 3). However, we found no additive or synergistic effects when cells were treated with both inhibitors simultaneously (Figure 4a, lane 5 versus 2, **P<0.001). The phosphorylation of S82 induced by apigenin was significantly inhibited by pretreatment with the p38 inhibitor SB203580 (Figure 4b, lane 3 versus 2, *P<0.05). In contrast to the lack of effect observed on S78, the PKCσ inhibitor rottlerin, significantly inhibited apigenin-induced phosphorylationof S82 (Figure 4b, lane 4 versus 2, *P<0.05). Similar to S82 phosphorylation, we observed that the pretreatment with the p38 inhibitor SB203580 inhibited apigenin-induced phosphorylation of S15 (Figure 4c, lane 3 versus 2, *P<0.05). In addition, rottlerin decreased apigenin-induced phosphorylation of S15 (Figure 4c, lane 4 versus 2, *P<0.05). The addition of both inhibitors, however, showed no additive or synergistic effects (Figure 4c, lanes 5, 4 versus 2, **P<0.001).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010041443_TII_02/figure/2010041443_TII_02_3.png"], "tampered": false, "paper_ids": ["2010000354"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010065512_TII_01/figure/2010065512_TII_01_2.png", "question_id": "consistency_181", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 3. Expression of histone mRNAs in mouse fibroblast cells and mouse liver. (A) Schematic of generalized S1 nuclease protection assay performed on mouse histone mRNA. A generalized histone mRNA is depicted indicating possible 5’ splice sites (5’ss), stem-loop cleavage sites (S-L cleavage) or poly(A) cleavage sites. S1 nuclease protection probes will protect a given mRNA to the point that cleavage or splicing occurs (indicated below). Note that due to the high degree of conservation in mice, all of the mRNAs for a specific histone class (i.e. H2B.1 or H2A.2) will be protected up to the stop codon. (B–F) Total cell RNA from NIH3T3 cells and mouse liver was fractionated into polyA+ and polyA− fractions. Total RNA (whole cell (WC)) and poly(A)+ and poly(A−) RNA were probed in an S1 nuclease protection assay. Five micrograms of total 3T3 cell RNA and 50 μg of liver RNA was analyzed using the S1 nuclease protection assay of a 32P labeled fragment at the indicated restriction enzyme site for (B) Hist2H2aa1, (C) Hist1H2bc, (D) Hist1H2ac, (E) Hist2H3c or (F) Hist2H4H. The probe used for histone H4H was labeled at the 5’ end of the indicated restriction site. For each experiment, below the autoradiogram, possible mRNA isoforms are indicated as well as protected fragments and sizes for S1 nuclease probes.", "figure_related_sentences": "Validation of polyadenylated histone mRNA expression in adult mouse liver. To confirm the expression of the mouse histone mRNAs detected by high-throughput sequencing, we analysed histone gene expression in actively growing cultured fibroblasts (NIH3T3 cells) and liver tissue from 72-week-old mice. The liver is a relatively homogenous tissue with hepatocytes making up more than 70% of the cells. In healthy adult livers, the vast majority of these hepatocytes are quiescent, only re-entering the cell cycle after injury. Unlike the human histone genes, the coding regions of the mouse histone genes are highly conserved (>95%) at the nucleotide level (37). Because of the conserved ORF sequences, we can use an S1 nuclease mapping assay to simultaneously analyse both the mRNA expressed from a specific gene, as well as the mRNAs from all the other histone genes encoding that histone protein (26,42). A probe labelled in the coding region will protect all the histone mRNAs to a region close to the stop codon or initiation codon, as well as a band from the specific gene extending to the 3' end or the 5' end of the transcript, depending on whether one is probing the 3' or the 5' end of the mRNA (Figure 3A). This highly sensitive method allows for mapping of multiple isoforms of mRNA from a single sample. Further, since all of the radioactivity is at the end of the probe, the relative intensity of the bands gives the relative amounts of the transcripts. A generalized schematic is shown in Figure 3A. In each experiment below, the different protected fragments for a given probe are diagrammed below the autoradiogram. Total RNA from NIH3T3 cells and mouse liver was fractionated into polyA− and polyA+ RNA using oligo-d(T) cellulose. Orthologues of human histone HIST1H2BC (Hist1H2bc), HIST2H2AA3 (Hist2H2aa1) and HIST1H4H (Hist1H4h), which were expressed in human tissues, and the HIST2H3C (Hist2H3c) gene, adjacent to the Hist2H2AA3 gene, which was not expressed in human tissues, were analysed by S1 nuclease mapping, using 5 µg of total RNA from exponentially growing NIH3T3 cells and 50 µg of total liver RNA (Figure 3). In actively proliferating NIH3T3 cells, most of the 3' S1 probes map three protected fragments: one extending to the 3' end of the mRNA ending in the stem-loop and a second fragment, mapping near the stop codon, due to the high level of conservation between the open reading frames of all mouse histone genes of a given class (26). This band is indicated by the name of that class of histone protein (e.g. H3.1 or H2a.1). If the histone mRNA is spliced or polyadenylated then the probe is protected up to the point where the mRNA sequence diverges from the probe (Figure 3A; e.g. at the 5' splice site in Hist1H2bc, before the 3' end of the mRNA or at the polyA addition site in Hist2H2aa1). The S1 nuclease protection assays confirmed the low levels of histone mRNAs in liver and there were easily detectable amounts of the polyadenylated forms of Hist2H2aa1 (Figure 3B, lane 7) and Hist1H2bc (Figure 3C, lane 7) mRNAs. There were no polyadenylated mRNAs detected in the NIH3T3 cells. There is some non-polyadenylated histone mRNA detected in the liver that gives the same pattern of S1 nuclease protected fragments as the NIH3T3 cell mRNA. This likely arises from a low level of expression of the histone mRNAs expressed in growing cells. Note that the non-polyA mRNA expressed in mouse liver is greatly reduced compared to NIH3T3 cells, and we used 10 times more RNA (50 µg versus 5 µg) for assay of liver RNA, compared to neonatal mice or growing 3T3 cells. We assayed the same RNAs with probes for Hist1H2ac (Figure 3D), Hist2H3c (Figure 3F) and Hist1H4h (Figure 3E) genes. There was no polyadenylated mRNAs detected from these genes in mouse, consistent with the sequencing data.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010065512_TII_01/figure/2010065512_TII_01_2.png"], "tampered": false, "paper_ids": ["2010000358"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010011052_TII_01/figure/2010011052_TII_01_0.png", "question_id": "consistency_182", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Production of Th2- and Th1-type cytokines from wild-type and Runt-transgenic CD4⁺ T cells. (A) Naive CD4⁺ T cells were isolated from the spleens of wild-type and Runt–transgenic mice and stimulated with anti-CD3/anti-CD28 antibodies, and the culture supernatants were collected at the indicated times after stimulation. (B) The TCR-stimulated cells were cultured in the presence of IL-2 for 5 d, washed with fresh media, and restimulated via TCR. The culture supernatants were collected after 24 h. (C) The cells were cultured for four days in the Th2- or Th1-inducing condition. The cells were washed with fresh media and restimulated via TCR. The culture supernatants were collected after 24 h. (D) Same as C, but note the difference of scale used in C and here. The amounts of cytokines secreted into the supernatants were measured by ELISA and their averages and standard deviations are shown. Data are representative of four independent experiments.", "figure_related_sentences": "Respectively, compared with the wild-type cells. A similar result as that shown in Figure 1A was obtained when the TCR-stimulated cells were incubated in the presence of IL-2 for 5 d, washed with fresh media, and restimulated via TCR (Figure 1B). Under this neutral culture condition where neither IL-4 nor IL-12 was added to media, the Runt-transgenic cells secreted several fold more amount of Th2-type cytokines and less amount of Th1-type cytokines than the wild-type cells. We next examined the cytokine production from the Runt-transgenic cells under culture conditions that favor either Th1 or Th2 differentiation. CD4⁺ T cells were stimulated with anti-CD3/anti-CD28 antibodies and incubated in the presence of either IL-4 and an anti-IFN-γ antibody (Th2 condition) or IL-12 and an anti-IL-4 antibody (Th1 condition) for 4 d. Cells were washed with fresh media and restimulated via TCR, and cytokine secretion was measured (Figure 1C). In the Th2 condition, the Runt-transgenic cells produced three times as much IL-4 as the wild-type cells. In contrast, in the Th1 condition, although IFN-γ production from the Runt-transgenic cells was reduced compared with the wild-type cells, IL-4 production from the Runt-transgenic cells did not reach the level of 10 to 100 ng/ml concentration. Thus, the Runt-expressing cells effectively differentiate into the Th2 lineage in a Th2- but not a Th1-favorable environment. It must be pointed here that, even in the Th1 condition, the Runt-transgenic cells actually produced 10 times as much IL-4 as the wild-type cells (Figure 1D). The absolute amount of IL-4 secreted from the Runt-transgenic cells was, however, 5 ng/ml in the Th1 condition (Figure 1D) instead of 120 ng/ml in the Th2 condition (Figure 1C). Therefore, the Runt-transgenic cells, though showing a Th2 tendency to some degree, could not have differentiated effectively into the Th2 lineage under the Th1 condition. Overexpression of Runx1 Prevents Naive Cells from Differentiating Into the Th2 Lineage. If reducing the effect of Runx1 with the Runt transgene induces Th2 differentiation, as shown in Figure 1, we wondered whether the artificial overexpression of Runx1 protein in naive T cells would cause a decrease in Th2 differentiation.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010011052_TII_01/figure/2010011052_TII_01_0.png"], "tampered": false, "paper_ids": ["2010000365"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010064426_TII_02/figure/2010064426_TII_02_4.png", "question_id": "consistency_183", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 5. Reporter assay tests for the repression of NL4-3 by miR-223 and miR-29. For all transfections, the values represent the average of at least three independent experiments and the error bar represents the standard deviation. (a) Reporter assays show miR-223/29 repression is very weak when Nef serves as the 30 -UTR. (b) Reporter assays show miR-223/29 repression of Nef when it serves as a coding region. (c) Reporter assays to measure the miR-223/29 repression using the 39 nt target sequence. Co-transfection of the reporter and miRNA genes in HEK-293 cells show strong repression by miR-223 and strong repression by miR-29. Mutated seed binding site for miR-223 or miR-29 abrogated the repressions mediated by either miRNA. (d) Reporter assays to measure the miR-223/29 repression using a 56 nt target sequence. Co-transfection of the reporter and miRNA expression constructs in HEK-293 cells show strong repression mediated by miR-223 and reduced repression mediated by the miR-29 miRNAs.", "figure_related_sentences": "No words", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010064426_TII_02/figure/2010064426_TII_02_4.png"], "tampered": false, "paper_ids": ["2010000368"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010064989_TII_02/figure/2010064989_TII_02_8.png", "question_id": "consistency_184", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 9. Activity and selectivity of ASOs in the rodent CNS. (A) Allele selective knockdown of muHTT protein with ASO A30 in neuronal cells derived from cortical and striatal tissues of Hu97/18 mouse embryos under free-uptake conditions. (B–D) Hu97/18 mice (n = 4/group) were injected ICV with a single dose of 300 µg of ASO (B and D) or the indicated dose (C) in PBS. Mice were sacrificed after 28 days, the brain was harvested, and a 2 mm coronal slab from each hemisphere (R, L) was analyzed by allelic separation immunoblotting for muHTT and wtHTT protein, and the results were normalized to calnexin protein. (B) Optimized ASOs A25, A26, A30, and A31 show similar activity but worsened allele selectivity relative to control ASO A1. (C) Dose response for allele-selective knockdown of muHTT protein following ICV injection of ASO A30 in Hu97/18 mice. (D) Immunohistochemical staining for ASO (red) illustrates distribution to all parts of the brain following a single ICV bolus injection.", "figure_related_sentences": "Improved allele selectivity in cell culture translates to brains of transgenic mice. We evaluated selected ASOs in Hu97/18 mice (45), a completely humanized mouse model of HD (Figure 9). This mouse model contains both the mutant human HTT allele, with the associated SNPs, and the wt human HTT allele. We first evaluated the ability of ASO A30 to reduce muHTT protein in primary neuronal cells derived from Hu97/18 mouse embryos in the absence of any transfection agent to facilitate delivery of the ASO across the cell membrane (Figure 9A). The ASO reduced muHTT expression in a dose-dependent manner (IC50 = 101 nM). No reduction of wtHTT was observed even at the highest dose of ASO A30 (1000 nM) tested. Next, mice (n = 4/group) were injected in the right lateral ventricle (ICV) with a single bolus injection (300 µg) of ASO (A1, A25, A26, A30, or A31) or vehicle control (PBS), and tissue was collected 28 days later. Brains were harvested, and HTT protein was quantified in a 2 mm coronal slab from each hemisphere by allelic separation immunoblotting for mu and wtHTT protein; the results were normalized to calnexin (Figure 9B). The posterior portions of treated brains were then post-fixed for immunohistochemical assessment of ASO distribution.As observed in the cell culture experiment, all the ASOs showed 60–80% reduction of muHTT protein. However, although ASO A1 showed a 52% reduction of the wtHTT protein, we observed essentially no reduction of the wtHTT protein for the mice treated with the allele-selective ASOs A25, A26, A30, and A31. We also measured the ability of ASO A30 to reduce muHTT protein in a dose-response experiment (Figure 9C). Mice (n = 4/group) were injected (ICV bolus) with increasing doses (75, 150, 300, and 500 µg) of ASO A30 or vehicle control, and brain tissue was harvested after 28 days using the procedures described earlier in the text. The ASOs produced a dose-dependent reduction in muHTT (ED50 = 110 µg) with no reduction in wtHTT even at the highest dose tested (500 µg). All ASOs also showed similar broad and even bilateral localization after ICV bolus injection, indicating that the modifications had no effect on distribution (Figure 9D). Thus, the animal model recapitulated the potency and selectivity observations from the cell culture experiments. Collectively, these studies illustrate the potency, selectivity, and tolerability of these compounds and support their development as potential therapeutics for HD.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010064989_TII_02/figure/2010064989_TII_02_8.png"], "tampered": false, "paper_ids": ["2010000374"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010131195_TII_02/figure/2010131195_TII_02_3.png", "question_id": "consistency_185", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 4. Reversion of Splicing Abnormalities in DM1 Patient-Derived Muscle Cells by CRISPR-SaCas9 Deletion of Expanded CTG Repeats Splicing profiles and quantification of LDB3 exon 11-, ATP2A1 exon 22-, MBNL1 exon 7-, DMD exon 78-, INSR exon 11-, and BIN1 exon 11-containing transcripts in differentiated myoblasts from DM1-Delta clones 10, 3, 17, and 22 compared to control (Ctrl), DM1, and DM1-sgRNA clones. Graphs show average values from independent biological replicates ± SD (n = 6 for Ctrl and DM1, n = 3 for the other samples). Statistical analysis by two-tailed Student’s t test. *p < 0.05, **p < 0.01, ***p < 0.001; ns, not significant; ˂DL, below detection limit. Error bars represent SD.", "figure_related_sentences": "Aggravation of Alternative Splicing Defects in DM1-Edited Muscle Cells Sequestration of MBNL-splicing factors in nuclear foci of DM1 cells leads to alterations in the alternative splicing of numerous pre-mRNAs, some of which are eliminated in differentiated muscle cells in culture.45 We therefore assessed the splicing pattern of LIM domain binding 3 (LDB3) exon 11, Sarco-endoplasmic reticulum calcium ATPase 1 (ATP2A1) exon 22, Muscleblind-like splicing regulator 1 (MBNL1) exon 7, Duchenne muscular dystrophy (DMD) exon 78, insulin receptor (INSR) exon 11, and Bridging integrator 1 (BIN1) exon 11 in edited DM1-Delta clones compared to DM1, DM1-sgRNA, and Ctrl cells (Figure 4).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010131195_TII_02/figure/2010131195_TII_02_3.png"], "tampered": false, "paper_ids": ["2010000376"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010101726_TII_02/figure/2010101726_TII_02_1.png", "question_id": "consistency_186", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2. Overexpression of Ahi-1 in Sca-1 +lin _x0004_ mouse stem/progenitor BM cells perturbs their in vitro proliferative activity and enhances the effects of BCR-ABL. (A) The levels of Ahi-1 transcripts relative to GAPDH from FACS-purified MIY (Sca-1 + lin _x0004_ YFP +), Ahi-1 (Sca-1 + lin _x0004_ YFP +), BCR-ABL (Sca-1 + lin _x0004_ GFP +), and Ahi-1 plus BCR-ABL (Sca-1 + lin _x0004_ YFP + GFP +) transduced primary mouse BM cells. (B) Growth of each FACS-purified population with GFs. Viable cell numbers were determined by hematocytometer counts of trypan blue – excluding cells. (C) Number of CFC colonies produced in semisolid cultures ± GF from the same FACS-purified mouse BM cells. (D) The appearance of GF-independent CFC colonies is shown. Bar, 250 μm. (E) The numbers of LTC-IC-derived CFCs produced from the same cells ± GF. Values shown are the mean ± SEM of triplicate measurements. * indicates significantly different from MIY control cells.", "figure_related_sentences": "Elevated endogenous Ahi-1 expression was also observed in cells transduced with BCR-ABL alone as compared with control cells (8-fold; P < 0.01; Fig. 2 A). 5 d after transduction, the rate of expansion of the Sca-1 +lin _x0004_YFP + (Ahi-1 +) cells in liquid cultures was approximately twofold lower than in cultures initiated with control cells (Fig. 2 B). Ahi-1– transduced Sca-1 +lin _x0004_ cells produced a slightly fewer number of colony-forming cells (CFCs) than MIY-transduced control cells in semisolid cultures in the presence of growth factors (GFs), and some of the Ahi-1 + CFCs (15%) were already GF independent (Fig. 2, C and D). After 4 wk in long-term culture-initiating cell (LTC-IC) assays, which are used to measure stem cell activities in vitro, the Sca-1 +lin _x0004_Ahi-1 + cells produced 3-fold more CFCs than control cells (P < 0.01; Fig. 2 E). All of these endpoints (proliferative activity, GF dependence, and CFC output in LTC-IC assays) are also perturbed by BCR-ABL transduction. In cells cotransduced with Ahi-1 and BCR-ABL, all of these effects were further enhanced compared with cells transduced with either BCR-ABL alone (2–4-fold) or Ahi-1 alone (3–6-fold; P < 0.01; Fig. 2). Thus, overexpression of Ahi-1 alone deregulates proliferative control of primitive mouse hematopoietic cells, and these effects can be enhanced by BCR-ABL.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010101726_TII_02/figure/2010101726_TII_02_1.png"], "tampered": false, "paper_ids": ["2010000382"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010016919_TII_01/figure/2010016919_TII_01_2.png", "question_id": "consistency_187", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "ECM softness upregulates MMP secretion and promotes MMP activity. (A) Primary human fibroblasts (2 × 104 cells per well) were seeded onto gels of varying stiffness in 12-well plates and cultured for 48 h. Cell culture medium from each condition was collected and subject to the RayBio Human MMP Array to determine the total secreted MMP protein quantity in each medium. (B) Three independent experiments (n = 3, ±SD) as in A were performed and quantified. Note that proliferation rates vary on gels of different stiffness. Total MMP quantities were normalized to total cell numbers on gels of varying stiffness at 48 h. Student’s test was used for the comparison of each mean with the mean of MMP protein quantity of the same MMP type on 25.6-kPa gels. *p < 0.05 considered significant. (C) Cell culture conditioned media were collected as in A, and the total MMP activity in each medium was measured and quantified (n = 3, ±SD) and normalized to cell number. Student’s t test was used for the comparison of each mean with the mean of “0.4 kPa.” *p < 0.05 considered significant.", "figure_related_sentences": "Matrix metalloproteinases (MMPs) are critical proteinases in ECM degradation and include two major subfamilies of secreted MMPs (MMP-2, -3, etc.) and integral membrane MMPs (MMP-14 [MT1-MMP], -15, etc.; Kessenbrock et al., 2010). For all types of MMPs that were measured, increased ECM stiffness significantly inhibited MMP secretion from these cells (Figure 2A). Previous studies reported that increased ECM stiffness significantly promotes primary cell proliferation (Wang et al., 2000; Liu et al., 2010). Thus, by normalizing to total cell numbers at 48 h after cell seeding, the relative amount of MMPs secreted per cell were even lower on stiffer substrates (Figure 2B). Further, the total MMP activities of these secreted MMPs also were higher on softer substrates and lower on stiffer substrates (Figure 2C). Of interest, we also detected small differences of MMP secretion on substrates with varying stiffness as early as 4 h after cell seeding (Supplemental Figure S1B), suggesting that cells begin responding to stiffness during their initial adhesion to ECM.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010016919_TII_01/figure/2010016919_TII_01_2.png"], "tampered": false, "paper_ids": ["2010000398"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010124149_TII_02/figure/2010124149_TII_02_3.png", "question_id": "consistency_188", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 4. Quantitative analysis of CTCF and BORIS expression in human PCa. (A) Nuclear CTCF significantly decreases in metastases cores (P < .001). (B) BORIS nuclear expression significantly increased in cancer cores (P = .002); nuclear and cytoplasmic expression increased in HGPIN cores compared to benign (both P < .001). (C) The ratio of BORIS to CTCF expression was analyzed for differences among cores. Significant increases in the BORIS/CTCF ratio are seen among cancer and metastases cores compared to benign (P = .031 and P = .006 respectively). (D) Comparing the BORIS/CTCF ratio among cancer cores, high Gleason grade cancers have significantly lower BORIS/CTCF ratio than both benign and intermediate Gleason cores (P = .006 and P = .024 respectively).", "figure_related_sentences": "CTCF is known to impact gene regulation through the management of chromatin organization and the maintenance of epigenetic marks [26]. CTCF expression levels measured by VECTRA were insignificantly decreased in metastatic PCa tumors (P < .001), but not localized PCa when compared to benign prostate tissues (P = .17) (Figure 4A). When CTCF expression within primary tumors was compared against clinicopathologic patient variables, decreased nuclear and total CTCF expression was associated with higher Gleason’s Score (P = .01 and P = .001 respectively) and positive margins (P = .03 and P = .043 respectively) (Data not shown). The CTCF paralogue, BORIS, shares a common zinc-finger DNA-binding domain with divergent N- and C- termini. BORIS and CTCF have competing effects on gene expression and epigenetic regulation [5,27]. In contrast to CTCF, BORIS expression was increased in HGPIN and primary cancer cores compared to benign (P < .001 and P = .002 respectively) (Figure 4B). No clinicopathologic correlates were noted. The competing role for BORIS/CTCF suggests the ratio of their expression may contain functional significance and greater predictive power than the expression of these proteins individually as seen in ovarian cancer [28]. Analyzing all prostate tissues, a weak correlation was seen between BORIS and CTCF (Pearson’s r = .224, P < .001). BORIS/CTCF levels increased significantly in cancer and metastases compared to benign (P = .03 and P = .006 respectively) (Figure 4C). High Gleason cancers have a significantly greater BORIS/CTCF ratio than both benign tissues and intermediate Gleason cancers (P = .006 and P = .024 respectively) (Figure 4D). The ratio of nuclear and total expression was calculated and found to be associated with Gleason’s grade, positive surgical margins, and tumor volume (nuclear P = .024, P = .027, P = .020, respectively) (Table 2, for full table see supplementary data, Table S2).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010124149_TII_02/figure/2010124149_TII_02_3.png"], "tampered": false, "paper_ids": ["2010000399"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010011326_TII_02/figure/2010011326_TII_02_2.png", "question_id": "consistency_189", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Effects of TRAF3 deficiency on effector functions of CD40 and LMP1. (A) A20.2J cells stably transfected with hCD40LMP1 were stimulated with 2 µg/ml anti-mCD40 Ab (CD40), anti-hCD40 Ab to trigger signaling through hCD40LMP1 (LMP1), or isotype control Abs for each (iso1 and iso2) for 48 h. Expression of CD23, CD80, and CD95 was determined by immunofluorescence staining and analyzed by flow cytometry. MCF, mean channel fluorescence. Values presented are the mean ± SEM of three independent experiments. (B) CH12.LX cells stably transfected with hCD40LMP1 were stimulated with Abs as in A for 72 h and assayed for IgM secretion. Plaque-forming cells (Pfcs, IgM-secreting cells) per 10⁶ viable recovered cells are shown. Values presented are the mean ± SE of replicate samples. Data are representative of three independent experiments. (C) TRAF3⁻/⁻ CH12.LX cells stably transfected with hCD40LMP1 were stably supertransfected with an IPTG-inducible TRAF3 (Reconstituted TRAF3⁻/⁻). Reconstituted cells were preincubated in the absence (−IPTG) or presence of IPTG (+IPTG) for 24 h and stimulated with Abs as in B in the absence or presence of IPTG, whereas TRAF3⁻/⁻ cells were stimulated with Abs as in B in the absence of IPTG. IgM-secreting cells were enumerated as in B. Values presented are the mean ± SE of replicate samples. Data are representative of three independent experiments. (D) Expression of TRAF3 in the reconstituted TRAF3⁻/⁻ CH12.LX cells (Recon.) in the absence (−) or presence of IPTG (+IPTG), compared with that of WT (+/+) and TRAF3⁻/⁻ (−/−) cells, was analyzed by immunoblotting. An immunoblot for actin served as loading control.", "figure_related_sentences": "Effects of TRAF3 Deficiency on Effector Functions. Next, we determined if the effects of TRAF3 deficiency on early signaling pathways of CD40 and LMP1 are predictive of downstream B cell effector functions, including upregulation of surface molecules and secretion of cytokines and antibodies. After CD40 engagement, TRAF3-deficient A20.2J cells exhibited upregulation of CD23 and CD95 similar to that of WT cells (summarized in Figure 3A; representative histograms shown in Figure S7, available at http://www.jem.org/cgi/content/full/jem.20031255/DC1). Although we consistently observed a partial increase in CD40-mediated upregulation of CD80 in TRAF3⁻/⁻ B cells (Figure 3A), it may be due to clonal variation because different A20.2J subclones vary in this response (not depicted). Using the mCD40-elicited response as an internal control for each subclone, we found that LMP1-induced upregulation of CD23 and CD80 was reduced approximately two- and threefold, respectively, whereas upregulation of CD95 and MHC class II was not affected by TRAF3 deficiency in A20.2J cells (Figure 3A and Figure S7).For detection of cytokine secretion, the membrane ligands for hCD40 and mCD40 (hCD154, mCD154, respectively) were also used, as they are more potent activators of this specific function of CD40. Although mCD154 is capable of activating hCD40 to a certain extent (39), cross-reaction between hCD154 and mCD40 is negligible (21). Neither CD40- nor LMP1-mediated secretion of TNF and IL-6 was affected by TRAF3 deficiency in CH12.LX cells (Figure S8, available at http://www.jem.org/cgi/content/full/jem.20031255/DC1). Interestingly, TRAF3⁻/⁻ CH12.LX cells exhibited enhanced IgM secretion after CD40 engagement, but profoundly suppressed IgM secretion in response to LMP1 signaling as compared with TRAF3⁺/⁺ cells (Figure 3B). We further verified this observation by examining TRAF3⁻/⁻ CH12.LX cells reconstituted with an IPTG-inducible TRAF3. Induction of TRAF3 expression with IPTG completely restored IgM secretion in response to LMP1 signaling, while decreasing IgM secretion mediated by CD40 signaling (Figure 3C and D). These results extend our previous finding that overexpression of TRAF3 decreases CD40-mediated IgM secretion (29), and in contrast, highlight the importance and indispensability of TRAF3 in LMP1-induced B cell activation. Furthermore, we also stably transfected an IPTG-inducible full-length LMP1 into WT and TRAF3⁻/⁻ B cells. A similar requirement for TRAF3 was observed when the signal was delivered by inducible full-length LMP1 (unpublished data).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010011326_TII_02/figure/2010011326_TII_02_2.png"], "tampered": false, "paper_ids": ["2010000405"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010104844_TII_02/figure/2010104844_TII_02_3.png", "question_id": "consistency_190", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 4 The effects of hydrogels on skin wound healing in type 2 diabetes mellitus (T2D) by topical treatment. (A) Representative images of wounds in the normal control (NC) group, T2D group, CAH (T2D+CAH) group, and CAVBPH (T2D+CAVBPH) group on days 0, 3, 9, and 15. (B) Wound healing rate. *p < 0.05, **p < 0.01, and ***p < 0.001.", "figure_related_sentences": "As shown in Figure 4A, the wound size in all groups decreased gradually over time. Compared with the NC group, the T2D group displayed a slower wound shrinkage due to the influence of diabetes, and exudate was still found on the wound surface on day 9. Topical application of CAH and CAVBPH significantly accelerated diabetic wound recovery compared to the T2D group. Quantitative analysis of wound healing confirmed the above results (Figure 4B). The healing rate in the T2D group was more optimistic than that in the NC group (p < 0.01 or p < 0.001). Compared to the T2D group, the CAH group showed a better healing effect on days 9 and 15 (p < 0.001), while the CAVBPH group had the best wound shrinkage than the T2D and CAH groups on all observed days (p < 0.01 or p < 0.001). At day 15, the wounds of the CAVBPH group (96.55% of healing rate) and the NC group (91.77% of healing rate) were basically healed and covered with hair, while the healing rates of the CAH and T2D groups were 84.23% and 63.81%, respectively. Compared to the T2D and CAH groups, the CAVBPH group had the best curative effect, with a 96.55% wound healing rate on day 15 (Figure 4).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010104844_TII_02/figure/2010104844_TII_02_3.png"], "tampered": false, "paper_ids": ["2010000410"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010184705_TII_02/figure/2010184705_TII_02_0.png", "question_id": "consistency_191", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. Telomeric element HeT-A expression is downregulated in ovaries by Trf2, Woc and Ars2. (A) RT-qPCR analysis of TE expression in ovaries of Trf2KDnos, wocKDnos and Ars2KDnos. (B) HeT-A transcript abundance in ovaries of Trf2/Trf2, spnE/spnE and Trf2,spnE double mutants. The fold change in the HeT-A RNA level is shown. (C) NRO analysis of HeT-A transcription in ovaries of Trf2KDnos, wocKDnos, Ars2KDnos and piwiKDnos flies. The RNA level was normalized to rp49. Mean values (±SD) for three biological samples normalized to control knockdown (white(w)KDnos) are shown. (D) In situ RNA hybridization of HeT-A, TART or TAHRE antisense probes with ovaries of the indicated genotypes (GAL4-nos driver was used). (E) RNA FISH of HeT-A antisense probe with ovaries of the indicated genotypes. The accumulation of HeT-A transcripts (green) in nuclei of nurse cells was observed. DNA was stained with DAPI (blue). GAL4-nos driver was used.", "figure_related_sentences": "RESULTS Trancription factors Woc and Trf2 suppress telomeric repeat HeT-A transcription in ovaries In order to detect germline components contributing to telomeric homeostasis, we performed a selective RNAi screen for factors that downregulate HeT-A expression in Drosophila ovaries. This approach was based on the existing data that in somatic tissues certain factors of the telomeric complex are required for the silencing of telomeric repeats (34–36). As reported earlier, HP1, encoded by Su(var)205 gene, a component of the telomere protection complex (37,38), elicits transcriptional repression of telomeric retrotransposons both in soma (34) and in the germline (39,40). At the same time, transcription of telomeric and non-telomeric transposons in the germline is controlled by the piRNA system, supporting the idea that the telomeric complex in the germline consists of both germline-specific and ubiquitous components. To investigate the structure of telomeric chromatin in the germline, we examined HeT-A expression in the ovaries of flies depleted for known components of the somatic telomeric complex as well as factors involved in RNA surveillance. Here, we describe genes exerting the greatest effect on telomeric repeat expression in ovaries. Germline knockdown of several genes, previously implicated in telomere functioning in soma, did not noticeably affect HeT-A expression in our screen and were not included in further analysis (Supplementary Table S2). In parallel to an independent study that describes Trf2 as a negative regulator of telomeric transposon expression in somatic tissues (41), we demonstrated that Trf2 is associated with the polytene chromosome telomeres of salivary glands (Supplementary Figure S1) and discovered a role of Trf2 in telomere functioning in the germline. RT-qPCR analysis of telomeric and non-telomeric retrotransposon expression demonstrated decreased levels of HeT-A and TAHRE transcripts in ovaries upon germline knockdown of Trf2 (Trf2KDnos; nos designates the promoter of the germline-specific gene nanos that was used to express the Gal4 driver) (Figure 1A). Given that the HeT-A and TAHRE untranslated regions (UTR) are highly homologous (7), we suggest that Trf2 recognizes a similar sequence motif in the promoter regions of both elements. In order to determine if Trf2 functions in the piRNA pathway together with spindle-E (encoding DEAD box RNA helicase SpnE) to silence HeT-A, we applied a double mutant analysis. We used a viable Trf2p1 mutation (26) to generate Trf2/Trf2; spnE/spnE double mutants and compared HeT-A transcript abundance in their ovaries to that in ovaries of single Trf2/Trf2 or spnE/spnE mutants. HeT-A expression in the double mutants was higher than in Trf2 single mutants, but not in spnE single mutants (Figure 1B, Supplementary Figure S2). This could mean that in the absence of piRNAs, inhibitory complex containing Trf2 cannot be recruited to the HeT-A promoter. Northern blotting of short RNA did not reveal changes in the abundance of HeT-A-specific piRNA in ovaries of Trf2 mutants and Trf2KDnos flies (Supplementary Figure S3A). These data suggest that Trf2 may act downstream of piRNA processing to establish transcriptional silencing of HeT-A. The zinc finger transcription factor Woc has been shown to bind Drosophila telomeres, exerting telomere-capping functions (42). wocKDnos causes a strong derepression of HeT-A and TAHRE but not TART and other TEs (Figure 1A), suggesting sequence-specific binding of this transcription factor to telomeric repeats in ovaries. We extended the analysis of the telomeric protein complex by including an RNA binding protein, Ars2, involved in mi- and siRNA biogenesis (43), which was identified in an RNAi screen as a negative regulator of HeT-A expression (44). Particular interest in this protein was due to the fact that Ars2 downregulates the expression of human TERRA (45). RT-qPCR analysis revealed a strong derepression of HeT-A/TAHRE in ovaries of Ars2KDnos flies (Figure 1A). To address the question about the involvement of Trf2, Woc and Ars2 in the transcriptional regulation of HeT-A, we conducted an NRO assay, which allows estimating the level of nascent HeT-A transcripts (46). NRO on ovaries with Trf2, woc and Ars2 knockdowns demonstrates that all these factors provide transcriptional silencing of the telomeric retrotransposon HeT-A (Figure 1C). In situ RNA hybridization analysis was performed to examine the effect of Trf2, Woc and Ars2 depletion on telomeric retroelement transcript distribution in ovaries (Figure 1D, Supplementary Figure S4). Knockdowns of Trf2, Woc and Ars2 exerted the most pronounced effect on HeT-A and TAHRE expression, resulting in the accumulation of their transcripts in nurse cells. The RNA FISH analysis on ovaries depleted for Trf2, Woc and Ars2 revealed HeT-A RNA signals not only in the cytoplasm, but also in the nuclei of nurse cells, where HeT-A transcripts were accumulated in distinct foci (Figure 1E). Similar nuclear foci were observed in spnEKD ovaries (Figure 1E). Previously, using combined DNA/RNA FISH analysis, it was shown that both HeT-A RNA and telomeric DNA were co-localized in nurse cell nuclei in spnE mutants (19). Most likely, we observed the accumulation of nascent transcripts at sites of transcription upon Trf2, Woc and Ars2 knockdown, in accordance with the result of NRO. Taking into account the HeT-A/TAHRE-specific effects of Woc and Trf2, it is unlikely that these factors participate in piRNA biogenesis. However, it is possible that DNA-binding factors Woc and Trf2 are involved in the piRNA-mediated transcriptional silencing mechanism that is specific for telomeric repeats. Thus, HeT-A transcripts accumulated upon Ccr4-Not knockdown avoid piRNA-mediated degradation. In situ RNA hybridization on Ccr4, Pop2 and Not1 KD ovaries revealed HeT-A transcripts in nurse cells (Figure 2C). Importantly, RNA FISH revealed HeT-A RNA foci in the nuclei of twinKDnos nurse cells (Figure 1E) as well as upon Trf2, Woc, Ars2 and SpnE knockdown, suggesting that all these components regulate the telomeric transcript level at the site of transcription. Given the accumulation of HeT-A transcripts in the nuclei upon Ccr4 depletion (Figure 1E), we investigated the poly(A) tail length of the HeT-A RNA in the nuclear fraction of ovarian RNA upon germline knockdown of Ccr4. The PAT assay demonstrated that in the nuclei of control ovaries, HeT-A transcripts were not adenylated, while Ccr4 KD led to an increase in HeT-A poly(A) length in the nucleus (Figure 3C).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010184705_TII_02/figure/2010184705_TII_02_0.png"], "tampered": false, "paper_ids": ["2010000418"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010011530_TII_02/figure/2010011530_TII_02_4.png", "question_id": "consistency_192", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Agrin-mediated decrease in gap junction–dependent intercellular communication between chromaffin cells in neonates. (A) Reduced number of electrically and LY-coupled chromaffin cells in neonatal agrin-treated slices. *, P ≤ 0.01 when compared with control slices. (B) Monitoring of electrical coupling between chromaffin cell pairs in control and agrin-containing saline showing examples of robust and weak coupling. Cells were current-clamped at −65 mV. A weak coupling was less frequently observed in agrin-treated slices. (C) Histograms illustrating the wide distribution range of the coupling ratio calculated in 26 control and 18 agrin-treated cells from voltage-clamp measurements of Ij (holding potential −60 mV, transjunctional potential from −120 to −60 mV, 150 ms duration). Insets: pooled data of Gj calculated in 11 control cell pairs and 4 agrin-treated cell pairs.", "figure_related_sentences": "Studies were next undertaken to examine the effect of agrin on both gap junction–mediated electrical and metabolic coupling between neonate chromaffin cells. Metabolic coupling was assessed using Lucifer yellow (LY) to label coupled cells, whereas electrical coupling was evidenced by dual whole-cell patch-clamp recording of intercellular macroscopic junctional currents (Ij). The probability of LY spreading between chromaffin cells was significantly reduced in agrin-treated slices compared with untreated slices (31% vs. 57%, P ≤ 0.01; Figure 5A). In the presence of the anti–rat agrin-neutralizing pAb, agrin failed to decrease LY diffusion between neonate chromaffin cells (58.3%, n = 24; unpublished data). Similarly, the dye coupling was not modified by inactive agrin0,0 (61.5%, n = 13; unpublished data). In adults, agrin did not change the incidence of LY diffusion (37.9% in treated slices, n = 29 vs. 44% under control conditions, P > 0.01; unpublished data). Agrin decreased the percentage of electrically coupled cell pairs (53.8%, n = 26 pairs in control slices vs. 22.2%, n = 18 pairs in agrin-treated slices, P ≤ 0.01; Figure 5A). In addition, agrin reduced the incidence of robustly coupled cells (Figure 5B). The voltage changes in response to depolarizing current injected into the stimulated cell were robustly reflected in the unstepped cell in 64.3% (n = 9/14 cell pairs) and 50% (n = 4 cell pairs) in control and agrin-treated slices, respectively (P ≤ 0.01). The resulting coupling ratios exhibited a wide distribution range from 0.01 to 0.97 (Figure 5C), strongly suggesting the presence of two chromaffin cell populations—a weakly coupled cell population and a highly coupled cell population. Recordings of Ij in chromaffin cell pairs voltage clamped at −60 mV confirmed these findings (unpublished data). Delivering voltage steps with command pulses of both polarities triggered Ij in the unstepped cell that exhibited variable degrees of attenuation. In control slices, 81.8% of recorded pairs (n = 11) exhibited Ij amplitudes that could reach 1–2 nA, whereas in the remaining pairs Ij did not exceed several picoamperes. In agrin-treated slices, the percentage of coupled cell pairs exhibiting a high Ij amplitude dropped to 50%. When plotted as a function of the transjunctional potential, the I/V curve of Ij displayed a linear relationship within the membrane potential range of −60 to −120 mV. The curve used to fit the data was derived from a linear regression, giving a macroscopic junctional conductance (Gj) of 43 and 60 pS for the weak coupling and 12 and 13 nS for the robust coupling (Figure 5C, insets).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010011530_TII_02/figure/2010011530_TII_02_4.png"], "tampered": false, "paper_ids": ["2010000421"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010007150_TII_02/figure/2010007150_TII_02_1.png", "question_id": "consistency_193", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "FIGURE 2. Fold enrichment of selenoprotein mRNAs on UPF1 in low versus high Se.(A) Levels of selenoprotein mRNAs that coprecipitated with UPF1, following culturing HEK293T cells in 3 nM Se or 60 nM Se. Transcript levels are normalized to a synthetic in vitro transcribed RNA and then to the value of the corresponding sample from the total RNA extraction (see Methods; Supplemental Fig. S3).(B) UPF1 protein levels in 3 nM Se or 60 nM Se.(C) Quantitation of (B). Error bars represent standard deviation of the mean; n = 4 for (A), and n = 6 for (B) and (C); (*) P < 0.05.", "figure_related_sentences": "We reasoned that if the transcripts that decreased in low Se were undergoing NMD, then they should similarly be enriched on UPF1. The same experiment modeling conditions of low Se was repeated, and RNA immunoprecipitation was performed with UPF1. The cytoplasmic nucleoprotein complexes were coimmunoprecipitated with an anti-UPF1 antibody, followed by quantification of coimmunoprecipitated RNAs by qRT-PCR. A representative set of RNAs from each category of NMD susceptibility was analyzed, including those most responsive to Se status (SelW, SelP, GPx1), as well as GPx4, which has been consistently unresponsive to Se status in past research. Interestingly, all of the selenoprotein mRNAs analyzed coimmunoprecipitated with UPF1 to some degree in agreement with UPF1’s general role in translation (Ghosh et al., 2010). A strikingly similar pattern to the profile in Figure 1A was observed in response to Se status. In this case, the RNAs predicted resistant to NMD showed a difference in their abundance on UPF1 with respect to Se. The RNAs that were the most responsive to Se status, however, were also the less abundantly bound to UPF1 under conditions of low Se (Fig. 2A). Importantly, UPF1 did not change with Se, ruling out the possibility that changes in immunoprecipitated RNAs could have been due to changes in total UPF1 protein (Fig. 2B, C). Overall, the degree of mRNA responsiveness to Se status directly correlated with the degree of mRNA abundance on UPF1, suggesting the involvement of NMD in the regulation of selenoprotein mRNAs during Se deficiency.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010007150_TII_02/figure/2010007150_TII_02_1.png"], "tampered": false, "paper_ids": ["2010000422"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010011652_TII_01/figure/2010011652_TII_01_6.png", "question_id": "consistency_194", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "3D fibronectin matrix reduces both Rac activity and random migration. (A) Primary human fibroblasts were plated on 2D substrates coated with fibronectin or 3D matrices rich in fibronectin and assayed for activity as in Figure 1. The reduction of active Rac in cells plated in a 3D matrix compared with 2D was 31% (P ≤ 0.017), whereas Cdc42 and Rho changes were not significant (Cdc42 4.5% reduction, P ≤ 0.66; Rho 25% increase, P ≤ 0.65). Error bars indicate SEM. (B) Cells in 2D versus 3D environments have different morphologies and locations of lamellae (arrowheads), as shown after staining for F-actin with phalloidin-Alexa 594 (left and red color in the right) and anti-fibronectin antibody (green). Bar, 20 μm. (C) Migration of cells in 2D versus 3D environments was recorded, and directionality (D/T) and velocity were calculated. (C and D) Error bars represent SEM. (D) Decreased random motility of cells within three-dimensional (3D) matrix. Primary human fibroblasts were cultured overnight within intact 3D matrices, on mechanically flattened 3D matrix (2D matrix), or on surfaces coated with solubilized 3D matrix (2D mix). Cell movements were recorded for 10 h, and the D/T ratio and velocity were calculated as described above. (E) Activated Rac in cells in 3D matrix restores random motility. Primary human fibroblasts were cotransfected with Rac Q61L VSV and Rac Q61L GFP or GFP alone (Control), sorted for low levels of GFP expression (1–50% from the peak of positive cells), and plated on 3D matrices. Cell movements were recorded for 10 h, and the D/T ratio and velocity were quantified. The bars represent the means of data pooled from two experiments, and error bars indicate SEM (n = 32–34 cells).", "figure_related_sentences": "Cells migrating in 3D cell-derived matrices have different types of cell adhesions, morphology, and signaling when compared with cells in standard 2D tissue culture (Cukierman et al., 2001; Walpita and Hay, 2002). Human fibroblasts in such 3D matrices were found to have a partial, but highly reproducible, 10–50% reduction in active Rac, but no reduction or increase in Cdc42 or Rho activities (Figure 7A). This reduction in Rac activity was accompanied by decreased random migration (Figure 7C and Video 3), with directional persistence increasing from D/T₂ᴰ = 0.25 ± 0.03 to D/T₃ᴰ = 0.87 ± 0.02 (P < 0.0001). Individual cells in the 3D matrix became spindle shaped as previously described (Cukierman et al., 2001), but in addition, staining for F-actin revealed a substantial reduction in peripheral lamellae in 3D compared with 2D (Figure 7B). In contrast to the results in cells cultured on 2D substrates, there was a significant increase in overall cell migration velocity by 34% associated with the reductions in active Rac and random migration in a 3D environment (Figure 7C; P < 0.0001). These findings further indicate the separate regulation of speed and directionality. Because the differences between 2D fibronectin and 3D substrates could have been the result of either three dimensionality or of differences in molecular composition, the 3D matrix was converted to 2D as a direct test of the role of dimensionality. Physically flattening 3D cell-derived matrices by compression still retained the increased overall velocity, but it was accompanied by a restoration of random motility (Figure 7D; P < 0.0001). Moreover, solubilizing the matrix and spreading its mixed components on a 2D substrate showed the same restoration of random motility (Figure 7D; P < 0.0001), with migration rates similar to those on 3D matrix (no statistically significant difference). These analyses indicate that the increased directionality in 3D is related to the three dimensionality of the matrix, and that it is unrelated to cell migration speed.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010011652_TII_01/figure/2010011652_TII_01_6.png"], "tampered": false, "paper_ids": ["2010000578"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010183324_TII_02/figure/2010183324_TII_02_4.png", "question_id": "consistency_195", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Fig. 5. Electrophoretic mobility shift assay results for the AZRE. (A) Sequence-specific interaction of nuclear proteins with the AZRE. The 23 bp AZRE containing a fragment between nucleotides –190 and –168 relative to the transcription start site of Oshsp17.3 was radiolabelled, and 1 ng of the probe was incubated with 10 µg of the nuclear proteins prepared from rice etiolated seedlings under AZC treatment for 6 h. The positions of the DNA–protein complexes are shown as C1 and C2 by arrows. The free probe is indicated with an asterisk (*). (B) Effect of CHX on the interaction of nuclear proteins with the AZRE. Three-day-old rice seedlings were treated with CHX (2 µg ml⁻¹) and with (left) or without (right) AZC for 6 h. (C) Cross-competition analysis of the HSE. The 23 bp HSE-containing fragment located at –87 to –65 relative to the transcription start site of Oshsp17.3 was used as a competitor. (D) Stress-dependent interaction of nuclear proteins with the AZRE. Nuclear extracts were prepared from seedlings treated with AZC, As, or HS for 2 h and by 28 °C [control (C)] or Cd for 6 h.", "figure_related_sentences": "Specificity of nuclear proteins interacting with the 9 bp AZRE in vitro by EMSA. To characterize the putative AZRE further, EMSA was used to determine whether it can interact with trans-acting factor(s) present in nuclear extracts. A 23 bp synthetic oligonucleotide encompassing the AZRE was used as a probe and was labelled with 32P by T4 polynucleotide kinase. Then, the probe was incubated with nuclear extracts from AZC-treated rice seedlings. Two DNA-bound protein bands (C1 and C2) were detected on the gel (Fig. 5A). The intensity of C1 appeared to be stronger than that of C2, and C1 could be further competed out by a 200-fold excess of AZRE probe without a 32P label. In addition, nuclear extracts from seedlings treated with AZC plus CHX for 6 h or CHX alone did not affect the levels of C1 and C2 interacting with the AZRE (Fig. 5B), which suggests that de novo synthesis of proteins is not required for the interaction. Because the 9 bp AZRE is involved in the HSR, it was also tested whether the 9 bp AZRE could be cross-competed by an HSE. This 23 bp HSE probe encompasses a perfect HSE (CTTCTAGAAACTTCC). Interestingly, the C2 but not the C1 band could be competed out by a 200-fold excess of HSE without being 32P labelled (Fig. 5C). Nevertheless, these results show that the AZRE can be specifically recognized by the nuclear proteins from AZC-treated rice seedlings. Because the AZRE was required for the response to HS and AZC, EMSA was used to examine whether nuclear extracts from rice seedlings treated with different inducers can bind to the AZRE. In nuclear extracts from seedlings treated with As (2 h), Cd (6 h), HS (2 h), or AZC (2 h), the two DNA–protein complexes C1 and C2 were also detected in all extracts, including control extracts (Fig. 5D). Additionally, the C1 band in the control was competed out by a 10-fold amount of the AZRE (Fig. 5D, first left lane). The intensity of the C1 complex with AZC treatment was found to be \\~5-fold higher than that of the control by measuring the integrated density with Scion image software. However, the intensity of the C2 band in 2 h AZC-treated and control nuclear extracts was lower than that in extracts receiving 6 h AZC, As, Cd, and HS treatments. Nevertheless, the results demonstrate that nuclear proteins from rice seedlings bind to the AZRE in a stress-dependent manner and depend on the duration of AZC treatment. Deletion of the AZRE on the promoter of Oshsp17.3 can reduce OsHsfA4b-modulated activation. According to the indispensable role of the AZRE for HS responsiveness (Fig. 3) and the results of EMSA (Fig. 5C), it was speculated that the AZRE can be specifically recognized by HSFs. Thus, tests were conducted to determine whether the AZRE was necessary for the interaction between OsHsfs and the promoter of Oshsp17.3. According to the expression analysis of 23 rice HSF genes, OsHsfA4b (Os01g54550) and OsHsfB4b (Os07g44690) were found to be induced by AZC treatment (data not shown). Two effector constructs, pHsfA4b and pHsfB4b, under the control of the maize constitutive Ubi1 promoter, were made (Fig. 6A). GUS activity in coleoptiles co-transformed with one reporter (p567 or p567DAZRE) and one effector (pHsfA4b or pHsfB4b) construct at a ratio of 1:1 was compared. As shown in Fig. 6B, when co-transformed with pHsfA4b, p567 achieved 2.8-fold induction in relative GUS activity but p567DAZRE achieved only a 1.8-fold induction. However, co-transformation of pHsfB4b was not significantly induced on p567 or p567DAZRE. To confirm these results further, the p631 reporter construct was also co-bombarded with pHsfA4b or pHsfB4b and no effect on the non-AZC-inducible Oshsp16.9A promoter was found (1.3- and 1.5-fold induction, respectively) (Fig. 6B). Also, transient expression of another highly AZC-inducible HSF gene, OsHsfC1b (Os01g53220), had no effect on the activation of Oshsp17.3 and Oshsp16.9A (data not shown). Thus, HSFs are possibly an integral part of the AZRE-dependent induction pathway of sHSP-CIs. The differential transcription of sHSP genes may have resulted from the action of different kinds of HSFs or additional transcription factors responding to environmental stresses (Rojas et al., 2002). Two DNA–protein complexes (C1 and C2) were observed by EMSA. Both of the interaction complexes can be competed out by cold AZRE, which indicates that the AZRE–protein interactions are sequence specific and may involve two distinct trans-acting proteins (Fig. 5A). Also, nuclear extracts from untreated AZRE (Fig. 5D), and the level of bound proteins was not affected by CHX (Fig. 5B). These data show that de novo protein synthesis was not required for the trans-acting factors recognizing the AZRE, and thus these factors constitutively exist in the cells. However, nuclear extracts prepared from seedlings treated for 6 h with AZC, Cd, As, or HS showed a lower intensity of C1 and C2 than those from control seedlings (Fig. 5D), which suggests that the AZRE may interact with nuclear proteins in a stress-dependent manner. However, whether trans-acting factor(s) directly sense AZC or are only indirectly activated by AZC needs further study. Interestingly, it was also found that the AZRE was indispensable for HS activation of Oshsp17.3 and Oshsp18.0 in the transient expression system (Fig. 3), that the C2 band can be competed out by the HSE (Fig. 5C), and that HS strongly boosted both C1 and C2 signals (Fig. 5D). These data are in agreement with the observation of Sugio et al. (2009), who showed HSFs to be involved in the AZC response in Arabidopsis. Among the HSFs identified in rice, OsHsfA4b, OsHsfB4b, and OsHsfC1b show high AZC responsiveness (data not shown). Co-expression of OsHsfA4b in rice coleoptiles could activate both p567 and p567DAZRE constructs in the absence of AZC (Fig. 6B), but the induction level in p567 was 67% higher than that in p567DAZRE. In contrast,", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010183324_TII_02/figure/2010183324_TII_02_4.png"], "tampered": false, "paper_ids": ["2010000586"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010127691_TII_02/figure/2010127691_TII_02_0.png", "question_id": "consistency_196", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. SDHB expression is high in CRC cell lines. (A) Quantitative RT-PCR analysis of SDHB mRNA expression in four colorectal cancer (CRC) cell lines compared to the normal colorectal epithelial cell line NCM460. (B) Semi-quantitative RT-PCR further confirms increased SDHB transcript levels in CRC cell lines relative to NCM460. (C) Western blotting analysis shows decreased SDHB protein expression in all four CRC cell lines compared to the normal epithelial control.", "figure_related_sentences": "SDHB is the key enzymatic component of mitochondrial enzyme SDH constructively expressed across species, which oxidizes succinate to fumarate in the TCA cycle and feeds electrons into the mitochondrial respiratory chain for ATP production. We examined SDHB mRNA and protein levels in four CRC cell lines and normal colorectal epithelial cell line NCM460. As shown in Figure 1 both SDHB mRNA level and protein level were relatively high in all four CRC cell lines (SW480, SW620, SW1116, and HT-29), compared to non-CRC epithelial NCM460 cells.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010127691_TII_02/figure/2010127691_TII_02_0.png"], "tampered": false, "paper_ids": ["2010000588"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010016329_TII_02/figure/2010016329_TII_02_1.png", "question_id": "consistency_197", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Effects of KBrO3 on mtDNA copy number and topology. (A) Dot-blot of purified mtDNA from control cells and cells treated with 30 μM KBrO3. Oxidative damage is detected using an antibody against 8-oxodG by SouthWestern analysis and normalized against total mtDNA by Southern hybridization on a separate blot. (B) Dot-blot for antibody verification, showing control mtDNA and mtDNA treated in vitro with 7.4% H2O2 for 30 min. (C) Topology gel of mtDNA. KBrO3 treatment had no effect on mtDNA topology. 16.6, 16.6-kb linear molecules; CAT, catenanes; OC, open circles; SC, supercoiled mtDNA. (D) mtDNA copy number levels during the KBrO3 treatment time course. Despite the damage, mtDNA copy number is not unaffected by KBrO3.", "figure_related_sentences": "Although KBrO3 did not have as dramatic an effect on nuclear DNA damage signaling as UV or H2O2, it induced a marked increase in mtDNA damage (Figure 1A). The damage did not result in copy number depletion or any effect on the supercoiling of mtDNA (Figure 1, C and D).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010016329_TII_02/figure/2010016329_TII_02_1.png"], "tampered": false, "paper_ids": ["2010000589"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010064451_TII_01/figure/2010064451_TII_01_0.png", "question_id": "consistency_198", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. Purification of chicken FANCD2, FANCI, FANCL andhuman UBE2T. (A) Purified chicken FANCD2 and FANCI, used forin vitro assays, were analyzed by 15% SDS-PAGE with CoomassieBrilliant Blue staining. Lane 1 indicates the molecular mass markers.Lanes 2 and 3 indicate purified FANCD2 and FANCD2 K563R,respectively. Lanes 4–9 indicate purified FANCI, FANCI K525R,FANCI R1288Q, FANCI Dx6, FANCI Dx6 K525R and FANCIEx6, respectively. (B) Purified human UBE2T, used for in vitromonoubiquitylation assays, was analyzed by 15% SDS-PAGE withCoomassie Brilliant Blue staining. Lane 1 indicates the molecularmass markers. Lane 2 indicates purified UBE2T. (C) PurifiedGST-tagged chicken FANCL, used for in vitro monoubiquitylationassays, was analyzed by 15% SDS-PAGE with Coomassie BrilliantBlue staining. Lane 1 indicates the molecular mass markers. Lane 2indicates purified GST-tagged FANCL.", "figure_related_sentences": "Chicken FANCI and FANCD3 were purified as recombinant proteins (Figure 1A, lanes 3 and 4), and the IDcomplex was prepared by mixing them in 1:1 stoichiometry. We also purified UBE2T and FANCL, which areknown as the E2 and E3 proteins for FANCD2monoubiquitylation, respectively, as recombinantproteins (Figure 1B and C).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010064451_TII_01/figure/2010064451_TII_01_0.png"], "tampered": false, "paper_ids": ["2010000598"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010169000_TII_01/figure/2010169000_TII_01_5.png", "question_id": "consistency_199", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "FIGURE 6. Incorporation of single UV photoproducts increases nucleosome dynamics. A, schematic illustration of the incorporation of a single CPD or 6-4PP into the 601 sequence. The DFs are 12-mer oligonucleotides with the sequences shown. Solid triangles indicate the positions of the photoproduct. The dark circle represents Cy5, and the open circle represents Cy3. B, FRET changes for the single CPD containing NCPs. The 601 sequence was changed according to the DF and denoted 601.DF1. The left panel shows emission spectra for the CPD containing NCPs compared with undamaged NCPs. The right panel shows the FRET efficiency values determined in each case, where the value for 601.DF1 NCPs was set to 1. The values shown are the mean ± S.D. of three independent experiments. C, the same as B except the NCPs contained a single 6-4PP and the sequence denoted 601.DF2. D, relative FRET efficiency of salt dependence of NCPs containing a single CPD. The FRET efficiency at the lowest salt concentration (50 mM) was set to 1. Values are the mean ± S.D. of three independent experiments. E, salt titration profile of NCPs containing a single 6-4PP. Values were plotted the same as in D.", "figure_related_sentences": "Taining a single CPD or 6-4PP lesion is 4.6 nm and 4.2 nm, respectively. Furthermore, in each case, the FRET efficiency is reduced, indicating that the introduction of a single UV lesion in nucleosome DNA can increase NCP unwrapping. This supports the UV dose-dependent FRET change we observed with UV-irradiated NCP DNA (Figure 3). Moreover, NCPs with either a single CPD or 6-4PP are more sensitive to salt (Figure 6, D and E). In the range of 0–1 M salt concentrations, the FRET efficiency in NCPs with single UV lesions is significantly lower than that of undamaged NCPs, indicating that NCPs containing just one DNA photoproduct are significantly less stable with increasing salt.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010169000_TII_01/figure/2010169000_TII_01_5.png"], "tampered": false, "paper_ids": ["2010000602"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010095497_TII_02/figure/2010095497_TII_02_0.png", "question_id": "consistency_200", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. Reduced PtdCho synthesis in CCTα-deficient macrophages. (A) Wild-type (WT; n = 12) or CCTα-deficient (KO; n = 12) macrophages were labeled for 6 h with 1 μCi/ml [3H]choline, and incorporation into PtdCho was normalized to cellular protein. (B) Relative transcript levels for CCTα, CCTβ2, CCTβ3, or PEMT were determined by real-time qRT-PCR in wild-type (n = 3) or CCTα-deficient (n = 3) macrophages. (C) CCT enzyme activity in wild-type (△; n = 4) or CCTα-deficient (●; n = 4) macrophage lysates was determined in vitro as a function of protein concentration. (D) Protein expression levels of CCTα (42 kD) and CCTβ3 (39 kD) were determined in wild-type and CCTα-deficient macrophage lysates (50 μg) by immunoblotting with isoform-specific antibodies. Immunoblots are representative of macrophages from two mice of each genotype. Cells (HEK293T) transfected with expression plasmids encoding CCTα or CCTβ3 were lysed, and 5 μg of protein was loaded as a positive control. Multiple immunopositive bands in a lane correspond to different phosphorylation states of the CCT protein (Jackowski, 1994; Lykidis et al., 1998). Error bars indicate mean ± SE. *, P < 0.05; **, P < 0.01.", "figure_related_sentences": "Mice with CCTα-null macrophages were generated as described previously (Zhang et al., 2000). Briefly, mice carrying a floxed Pcyt1a gene were crossed with mice expressing Cre recombinase under the macrophage-specific LysM promoter. Two loxP sites flanked a 12.5-kb fragment of the Pcyt1a gene containing exons 5–9 (Karim et al., 2003) and the intervening introns. Deletion of the region between the loxP sites resulted in expression of a truncated CCTα protein lacking the catalytic and regulatory domains at the carboxy terminus. Mice homozygous for the floxed gene and heterozygous for LysMCre were mated, and pups were genotyped to obtain either CCTα knockout or littermate wild-type control macrophages.Peritoneal macrophages were elicited, and the CCTα-deficient macrophage population showed increased rates of de novo phosphatidylcholine (PtdCho) synthesis measured by [?H]choline incorporation into the lipid fraction of adherent cells (Fig. 1 A). The deletion in this macrophage model was not completely penetrant (Zhang et al., 2000). Quantitative RT-PCR (qRT-PCR) analysis revealed that the CCTα transcript level was significantly increased to about 30% of wild-type levels (Fig. 1 B). The CCTα-null cells were ≥95% macrophages as determined by microscopy after staining with macrophage-specific anti–mouse CD11b. Staining for CCTα protein showed that 20–30% of macrophages isolated from knockout mice (n = 4) remained positive for expression, confirming incomplete Cre recombinase activity.Thus, residual PtdCho synthesis detected by metabolic radiolabeling in CCTα-null populations was due not only to expression of the alternate isoform CCTβ3 (Fig. 1 B) but also to the presence of cells that did not delete the CCTα gene. qRT-PCR showed that the CCTβ2 isoform was not expressed in macrophages, while CCTβ3 expression was increased in knockouts. CCTβ3 shares the primary biochemical function of CCTα and can compensate for its loss to support membrane synthesis in cultured cells (Karim et al., 2003). Previous work indicated increased CCTβ2 expression in CCTα-deficient cells (Zhang et al., 2000), but at that time, CCTβ3 had not been discovered; both isoforms share an epitope detected in earlier immunoblots (Karim et al., 2003).Total CCT enzyme activity was significantly higher in lysates from CCTα-null macrophages compared with wild-type populations (Fig. 1 C), consistent with previous studies (Zhang et al., 2000). Immunoblotting with isoform-specific antibodies revealed a decrease in CCTα protein and an increase in CCTβ3 protein reflecting mRNA changes (Fig. 1 D). Macrophages from two knockout and two wild-type mice were pooled by genotype, and immunoblots were prepared from six replicates per genotype. CCTα protein levels in the knockout population were 0.36 ± 0.08 relative to wild-type (set at 1.00). The reduction in CCTα transcript correlated with protein levels and the number of macrophages lacking CCTα expression by microscopy. These data confirm loss of CCTα expression in the majority of cells and provide the first example of adaptive regulation of CCTβ3 expression in response to PtdCho deficiency.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010095497_TII_02/figure/2010095497_TII_02_0.png"], "tampered": false, "paper_ids": ["2010000610"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010065412_TII_02/figure/2010065412_TII_02_1.png", "question_id": "consistency_201", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2. Differential inhibitory effects of SAUGI on the activities of (A) SAUDG, (B) EBVUDG, (C) HSVUDG, (D) human UDG and (E) TBUDG. Except for TBUDG, addition of SAUGI increased the specific uracil-removing activity of SAUDG and the other three UDGs in a dosage-dependent manner.", "figure_related_sentences": "The inhibiting effects of SAUGI on five UDGs We next used uracil removal assays to investigate the ability of SAUGI to inhibit the same five UDGs that were used in the surface plasmon resonance experiments. In the absence of SAUGI, all the UDGs removed the uracil from the uracil-containing DNA substrates effectively, and the resulting apyrimidinic site was cleaved by heat and alkali (Figure 2A-E, lane 2). The addition of SAUGI reduced the cleaved products in the SAUDG, EBVUDG, HSVUDG and human UDG reactions (Figure 2A-D, lanes 3–7; Supplemental Figure S4). SAUDG, EBVUDG and HSVUDG activity was initially inhibited when the molar ratio of SAUGI to UDG reached 1:1, but a ratio of 2:1 was needed for the inhibition of human UDG activity. Interestingly, although the structure of TBUDG is conserved relative to the other four UDGs, SAUGI had no significant effect on this UDG’s activity (Figure 2E). These results correspond to those found in the BIAcore study. We therefore conclude that SAUGI has a relatively greater effect on the two viral UDGs than on human UDG. Since HSVUDG and EBVUDG have been shown to play an important role during virus replication (29), these results suggest a potential use of SAUGI as an anti-virus treatment. The inhibitory effects of SAUGI mutants on the uracil-removing activities of human and HSV UDGs In our previous study, we found phage UGI had an extremely high binding affinity to human UDG that was 12–13 times greater than that of SAUGI (16). We found here that phage UGI also inhibited both HSVUDG and human UDG more effectively than SAUGI (compare Supplemental Figure S6 with Figure 2C and D). We speculated that SAUGI’s relatively low binding affinity to human UDG and its high binding affinity to viral UDG might potentially allow it to be used to prevent viral UDG repair activity without having too great an effect on human UDG. In our next experiment, we therefore used structural-based protein engineering to further modify SAUGI’s activity on human UDG and HSVUDG.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010065412_TII_02/figure/2010065412_TII_02_1.png"], "tampered": false, "paper_ids": ["2010000662"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010065375_TII_01/figure/2010065375_TII_01_1.png", "question_id": "consistency_202", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2. HITS-CLIP reveals HIV-1 regions bound by Ago2 in HIV-1 infected cells. (A) HEK293T cells were transfected with plasmid expressing either GFP-Ago2 or control GFP. Twenty-four hours later, they were infected with VSVg-pseudotyped HIV-1 NL4-3 at a M.O.I. of 1 or mock infected. Twenty-four hours later, cells were subjected to UV cross-linking and RNA–protein complexes were subjected to immunoprecipitation using an anti-GFP antibody. IPed RNA was radiolabeled with [α-32P]ATP and samples resolved on SDS-PAGE. Radiolabeled RNA was visualized by autoradiography. RNAs migrating at a higher molecular mass than the protein of interest (GFP-Ago2:RNA, between 125 and 225 kDa) were extracted from the membrane, reverse transcribed into cDNA and subjected to high throughput sequencing. (B) Reads obtained from non-infected (NI) and infected (INF) samples were uploaded to CLIPZ software. Reads that aligned to the human genome were sorted into categories: messenger RNA (mRNA), microRNA (miRNA), ribosomal RNA (rRNA), repeat, small non-coding RNA (snRNA), small nucleolar RNA (snoRNA), transfer RNA (tRNA) and other. Pie charts correspond to the distribution of the mean value of three biological replicates. (C) Reads obtained from infected samples were aligned to the HIV-1 NL4-3 sequence. Only reads ≥50 nucleotides length that aligned once without mismatch were considered for this analysis. Reads obtained from three independent HITS-CLIP experiments are presented in shades of orange and those obtained from the corresponding inputs in shades of blue. The map of the HIV-1 genome is presented below. Splice donor (D) and acceptor (A) sites are indicated. Peaks corresponding to clusters 2, 13, 16, 21, 25 and 30 are indicated by arrows.", "figure_related_sentences": "Immunopurified RNAs were radiolabeled, separated on SDS-PAGE and transferred to nitrocellulose membrane. Autoradiograms revealed the presence of RNA–protein complexes migrating from 100 kDa, the expected size of GFP-Ago2, to higher molecular weights corresponding to the size distribution of RNAs associated with GFP-Ago2 (Figure 2A). The levels of RNAs cross-linked to GFP-Ago2 were similar in presence or absence of infection but were highly enriched compared to the control GFP immunoprecipitation, confirming the specificity of our IP conditions. Ago2-RNA complexes migrating between 125 kDa and 225 kDa, corresponding to nucleic acids up to 300 nucleotides length, were extracted from the nitrocellulose membrane. Ago2 cross-linked RNAs were purified and reverse transcribed to generate small cDNA Illumina libraries. cDNA ranging from 20 to 75 base pairs were purified for subsequent deep sequencing. Libraries were also generated from GFP control samples. However, the levels of cDNA obtained from these samples were not sufficient for subsequent deep sequencing. High throughput sequencing was conducted on small RNA libraries generated from six independent Ago2-GFP HITS-CLIP experiments prepared from either uninfected or HIV-1 NL4-3 infected cells and their corresponding inputs. HITS-CLIP experiments yielded between 15 and 24 million sequencing reads and inputs between 17 and 30 million sequencing reads (Table 1).Ago2 HITS-CLIP analysisTo assess the quality of our HITS-CLIP experiments, we first uploaded our sequencing reads to the CLIPZ software, specifically dedicated to HITS-CLIP data analysis (44). The number of distinct reads mapping to the human genome and the quality of the sequences were similar to other Ago2 HITS-CLIPs analyzed with the CLIPZ tool (data not shown). The alignment of reads in the input and in the HITS-CLIP experiments showed that whereas rRNAs, tRNAs and mRNAs were the predominant reads in the input (45%, 12% and 17%, respectively), a 5-fold enrichment of mRNAs, but not of snoRNAs, snRNAs, rRNAs or tRNAs, could be observed in the HITS-CLIP (Figure 2B). We did not observe any enrichment in miRNAs likely because our HITS-CLIP procedure favored long reads over short ones. We then sought to identify Ago2 binding sites on the viral gRNA. For this, HITS-CLIP data were analyzed in two different ways. First, trimmed reads longer than 15 nucleotides were aligned to the viral genome with a maximum of one mismatch allowed. Reads (≥50 nucleotides) of the HIV-1 RNA genome (starting at the transcription start site) from the three HITS-CLIPs (in orange) and their corresponding input (in blue) were plotted (Figure 2C). As the R region is present at both ends of the viral genome, the reads could not therefore be assigned unambiguously to the 3' or 5' ends. They were arbitrarily assigned at the 3' end of the viral genome. Several HIV-1 peaks were detectable in the input but whether they correspond to small RNA produced by the virus or degradation products was unclear. In Ago2 HITS-CLIP, we identified 40 discrete Ago2 binding sites along the viral genome with an accumulation of clusters at the central region and the 3' end of the genome (Figure 2C). Both analyses of our HITS-CLIP data gave very similar results as shown by the comparison of their mean traces (Supplementary Figure S2). We focused our interest on 31 clusters of reads based on the reproducibility of the peaks in the three HITS-CLIP experiments and the enrichment of reads in the IP over the input (Supplementary Figure S3 and Supplementary Table S1).Our study focused on HIV-1 RNA regions that correspond to Ago2 binding sites by only considering reads of 50 nucleotides length. We identified more than 40 reproducible binding sites distributed along the HIV-1 gRNA (Figure 2C). Remarkably, reads from viral origin represented <1% of the total reads in inputs, a result in agreement with other studies (22,30,32). In sharp contrast, between 8 to 25% of these long reads were from viral origin in our HITS-CLIP data, confirming that viral RNAs are preferentially enriched in Ago2 co-immunoprecipitation (Figure 1 and Table 1). Two recent reports have also explored the interaction between Ago proteins and HIV-1 RNAs using similar photoactivable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP) and HITS-CLIP approaches (22,32). Contrary to our study, Whisnant et al. detected very low levels of HIV-1 PAR-CLIP reads among the total of assignable reads (below 1%). This discrepancy could be due to differences in experimental conditions, as we used an overexpressed GFP-Ago2 together with stringent washing conditions in order to improve the efficiency and specificity of our immunoprecipitation conditions. Nevertheless, Whisnant et al. (22) identified a number of RISC clusters on HIV-1 RNA in infected TZM-bl HeLa and C8166 T cell lines. Importantly, our study identified 19 clusters that overlap with clusters identified in at least one of their two cell lines including cluster 2, 13, 16 and 21 (data not shown) indicating that these HIV-1 RNA regions are indeed conserved targets of endogenous Ago-RISC in different cell lines. In sharp contrast, viral RNAs were absent from Ago2-RISC in HIV-1 infected monocyte derived macrophages, suggesting that this interaction might be cell type specific (32). Nevertheless, we identified four HIV-1 clusters that were able to downregulate RLuc activity and we showed that these effects were dependent on both Ago1 and Ago2 proteins (Figure 3A and B). Interestingly, these four HIV-1 clusters are in close proximity or overlap HIV-1 splice donor sites (Figure 2C).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010065375_TII_01/figure/2010065375_TII_01_1.png"], "tampered": false, "paper_ids": ["2010000668"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010131697_TII_01/figure/2010131697_TII_01_2.png", "question_id": "consistency_203", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. NTCP inhibition by Myrcludex B increases plasma bile acid and GLP-1 levels. (A) Unconjugated, conjugated, and total plasma bile acid levels 3 hours after placebo or Myrcludex B (2.5 mg/g) injection in male obese WT and Oatp1a/1b KO mice (n = 9–10). Mice were fed a HFD for 16 weeks and subsequently treated daily with placebo or Myrcludex B for 3.5 weeks. (B) Fasting GLP-1 levels and (C) plasma insulin levels (D) during an oral glucose tolerance test (2 g/kg glucose) and (E) an insulin tolerance test (1.2 mU/kg) of the Oatp1a/1b KO mice described in panel A. (F) Body temperature, measured by temperature transponders placed near the BAT of the mice in panel A. Per animal, average body temperature was calculated from 3 individual observations. (G) Ucp1 messenger RNA expression levels, determined by reverse transcription quantitative polymerase chain reaction in BAT of the Oatp1a/1b KO mice described in panel A. Reverse transcription quantitative polymerase chain reaction samples are relative to the geometric mean of control genes 36b4 and Hprt and were normalized to the placebo-treated group. (H) Quantified UCP-1 staining in sWAT of the Oatp1a/1b KO mice described in panel A. Error bars show SEM, asterisk indicates significant changes. AUC, area under the curve", "figure_related_sentences": "To evaluate the in vivo impact of bile acids on GLP-1 secretion, we used the NTCP inhibitor Myrcludex B to prolong bile acid signaling in obese Oatp1a/1b-deficient mice. Treatment with Myrcludex B was started 15 weeks after the onset of obesity by high-fat diet (HFD) feeding. In line with previous research, Oatp1a/1b KO mice display slightly elevated (unconjugated) bile acid levels compared with WT control animals (average WT 1.64 vs KO 6.13 mM of total bile acids) (Figure 1A). Myrcludex B treatment profoundly increased levels of total and conjugated bile acids in Oatp1a/1b KO mice 3–4 hours after the Myrcludex B injection (Figure 1A). The increase in plasma bile acids was temporary, as they completely normalized within 24 hours after the injection. Inhibition of NTCP by Myrcludex B increased fasting GLP-1 levels 10-fold (Figure 1B). Next, we evaluated if the Myrcludex B–mediated GLP-1 increase affected glycemic control. HFD-fed Oatp1a/1b KO mice treated with Myrcludex B tended to have lower insulin levels before and 15 minutes after oral glucose administration (Figure 1C). Although this suggested improved insulin sensitivity upon Myrcludex B treatment, the responses to glucose and insulin tolerance tests were not different between HFD-fed Oatp1a/1b KO mice receiving placebo or Myrcludex B treatment (Figure 1D and E). As it was recently shown that GLP-1 signaling can increase thermogenesis in brown adipose tissue (BAT), we assessed body temperature using temperature transponders placed near the BAT. Body temperature in HFD-fed OATP1a/1b KO mice treated with Myrcludex B significantly increased with an average of 0.9°C, while body temperature of placebo-treated animals remained unchanged (Figure 1F). Messenger RNA expression of Ucp1 (uncoupling protein 1), a mitochondrial gene known for its central role in BAT thermogenesis, in increased in BAT, suggesting increased thermogenesis in BAT of Myrcludex B treated HFD-fed OATP1a/1b KO mice (Figure 1G), but this increase was not observed at the protein level, and also, the UCP signal in subcutaneous white adipose tissue (sWAT) was not increased (Figure 1H), so “browning” of adipose tissue was not evident.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010131697_TII_01/figure/2010131697_TII_01_2.png"], "tampered": false, "paper_ids": ["2010000705"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010064913_TII_02/figure/2010064913_TII_02_0.png", "question_id": "consistency_204", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. Clk1 enhances SPF45-induced exon 6 exclusion from Fas mRNA. (A) SKOV3 cells were transfected with siRNA against SPF45 (siSPF45) or scrambled control siRNA (scr) for 72 h, and RNA was isolated. Endogenous Fas spliced isoforms were analysed by RT-PCR using primers flanking exon 6. PCR products representing mRNA including exon 6 [Fas (L)] and excluding exon 6 [Fas (S)] are shown and are quantified in the graph, with the ratio Fas (S) to Fas (L) set to one in the control siRNA group. The results are from three independent experiments performed in duplicate and were statistically significant. (B) Parallel cultures to those in (A) were lysed for western blotting using antibodies to SPF45 and actin. (C) Cell lysates from the indicated cell lines were immunoblotted for SPF45 using a polyclonal antibody to recombinant His-SPF45. COS-1 cells transfected with untagged SPF45 (COS-1, +con) and OV2008 cells expressing control or SPF45-specific shRNA served as positive controls. The SPF45 band (SPF45) and an SPF45 degradation product (degr.) in the positive control lane are labelled. (D) COS-1 cells were cotransfected with Myc-SPF45 (0.6 µg) and Clk1 (0.8 µg) and endogenous Fas spliced products were analysed by RT-PCR 24 h after transfection. A representative gel is shown. The means and SE for the relative ratio of exon 6 exclusion from three experiments done in duplicate are shown under the gel images. (E) Schematic of the Fas minigene splicing reporter used in transfection assays and the different mRNA isoforms derived from it, representing inclusion or exclusion of exon 6. (F) SPF45 expression induced exon 6 exclusion in a dose-dependent manner. COS-1 cells were co-transfected with Fas and increasing amounts of Myc-SPF45. Total RNA was extracted at 24 h and analysed by RT-PCR using Fas-specific primers. A representative gel from at least three independent experiments is shown, and the ratio of the lower band to the upper band is shown below the gel. The lower panel represents a western blot of Myc-SPF45 and actin protein expression from one experiment. (G) Clk1 overexpression promotes SPF45 alternative splicing activity. COS-1 cells were cotransfected with Fas (0.3 µg), Myc-SPF45 (0.6 µg) and Clk1 (0.8 µg), and spliced products were analysed by RT-PCR 24 h after transfection. A representative gel is shown. The means and SE for the relative ratios of exon 6 exclusion are shown under the gel images. Results were derived from three independent experiments done in duplicate. Statistical significance (P < 0.01) is indicated in the graph. (H) Clk1 overexpression enhanced SPF45 protein levels. Protein lysates were prepared from cells transfected as in (G) and were subjected to western blotting using antibodies to Myc, Clk1, and actin.", "figure_related_sentences": "SPF45 enhances exon 6 exclusion from Fas pre-mRNA in a cellular minigene assay (21,33). To determine whether endogenous SPF45 has a dissimilar effect on splicing of endogenous Fas pre-mRNA, we transfected SKOV-3 ovarian cancer cells with siRNA against SPF45. Seventy-two hours after transfection, RNA was harvested, and the endogenous Fas mRNA isoforms containing or excluding exon 6 were analysed by RT-PCR using primers flanking exon 6. SPF45 knockdown inhibited the splicing of the short Fas mRNA isoform (lacking exon 6) from Fas mRNA (Figure 1A). No other bands were detected on the gel. Immunoblotting of parallel cultures with an anti-SPF45 polyclonal antibody confirmed SPF45 knockdown (Figure 1B). This polyclonal antibody generated to recombinant SPF45 protein recognizes endogenous SPF45 from several ovarian cancer cell lines and HeLa cells, with specificity determined by comparison with lysate from COS-1 cells transfected with untagged SPF45 (COS-1 +con) and SPF45 shRNA knockdown in OV2008 cells (Figure 1C). Consistent with the above splicing results, transient transfection of SPF45 into COS-1 cells increased splicing of the short isoform of endogenous Fas mRNA, demonstrating enhanced exon 6 exclusion (Figure 1D). Clk1 is an SR protein kinase that phosphorylates splicing factors to regulate their localization and splice site utilization (19,20,22–24). To determine whether Clk1-regulated SPF45-dependent exon 6 exclusion from endogenous Fas mRNA, COS-1 cells were cotransfected with Clk1 and SPF45. Overexpression of Clk1 with SPF45 significantly increased exon 6 exclusion from endogenous Fas mRNA compared with transfection of SPF45 and empty vector (Figure 1D). We used our previously described Fas minigene (14,21), comprised of exon 5 through exon 7 of genomic Fas, including introns (Figure 1E), to study the effect of Clk1 on SPF45 splice site utilization. Cotransfection of COS-1 cells with Fas and increasing amounts of Myc-SPF45 plasmid caused a dose-dependent increase in exon 6 exclusion, shown as an increase in the lower band, demonstrating that our Fas minigene worked as a target of SPF45 in cells (Figure 1F) (21). COS-1 cells were chosen for minigene splicing assays owing to their low expression of endogenous SPF45 (Figure 1C), which allowed us to better determine SPF45-specific effects on alternative splicing of Fas mRNA. Clk1 was cotransfected into cells with SPF45 and the Fas minigene and exon 6 exclusion of Fas was determined. Clk1 enhanced SPF45-induced exon 6 exclusion of Fas by >50% (Figure 1G), suggesting that SPF45 may be a cellular target of Clk1. Interestingly, Clk1 overexpression also enhanced Myc-SPF45 protein expression (Figure 1H). As SPF45 concentration directly affects splice site utilization (Figure 1F), the enhancement of SPF45 expression by Clk1 could be a possible mechanism for the enhanced exon 6 exclusion and was investigated further. Clk1 inhibition prevents exon 6 exclusion by SPF45. To further determine the role of Clk1 kinase activity in regulating SPF45 exon 6 exclusion of Fas pre-mRNA, we generated a kinase-dead Clk1, Clk1-K233R, and cotransfected COS-1 cells with plasmids for SPF45 and Fas. Clk1-K233R decreased both SPF45-induced exon 6 exclusion (Figure 2A) and SPF45 protein levels (Figure 2B) compared with wild-type Clk1. To confirm this result, a selective Clk1 inhibitor, TG003 (41), was used to block endogenous Clk1 activity. TG003 not only promoted the increase of exon 6 exclusion induced by SPF45 (Figure 2C) but also decreased SPF45 protein expression (Figure 2D), similar to what was seen with kinase-dead Clk1 expression. Next, we used siRNA to knock down endogenous Clk1 expression. Transfection of cells with any of three different siRNA-targeting Clk1 led to a significant decrease in endogenous Clk1 mRNA and protein levels after 48 h, as determined by real-time PCR and western blot analysis, respectively (Figure 3A and B). The siRNA-mediated knockdown of Clk1 in COS-1 cells significantly decreased exon 6 exclusion in an SPF45-dependent manner (Figure 3C and D) and greatly inhibited Myc-SPF45 protein expression (Figure 3E), most likely contributing to the reduction in exon 6 exclusion. Inhibition of Clk1 decreases the half-life of SPF45 through a proteasome-dependent pathway. We suspected that the enhancement or inhibition of exon 6 exclusion by SPF45 with Clk1 activation or inhibition, respectively, was partially due to regulation of SPF45 protein levels, as SPF45 expression directly impacts exon 6 exclusion (Figure 1F). To determine whether Clk1 regulated the half-life of SPF45, A2780 ovarian cancer cells, which express high levels of endogenous SPF45 (Figure 1C), were treated with cycloheximide in the absence or presence of TG003 for 24 h (Figure 4A). TG003 significantly decreased the half-life of endogenous SPF45 from 15 to 8 h (Figure 4B). In addition, SKOV-3 ovarian cancer cells stably expressing Myc-SPF45 were treated with DMSO or TG003 in the presence of cycloheximide. Consistent with the aforementioned results, TG003 decreased the half-life of Myc-SPF45 from 16 to 7 h (Figure 4C and D). Moreover, knockdown of endogenous Clk1 with siRNA decreased endogenous SPF45 protein levels in both SKOV-3 and HeLa cells (Figure 4E). To determine whether the decrease in SPF45 half-life in the presence of TG003 was dependent on the proteasome, A2780 cells were treated with the proteasome inhibitor MG132 in the absence or presence of TG003 (Figure 4F). MG132 co-treatment with TG003 prevented the downregulation of SPF45 protein levels that was induced by TG003 treatment, indicating that Clk1 inhibition regulated SPF45 degradation through a proteasome-dependent pathway.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010064913_TII_02/figure/2010064913_TII_02_0.png"], "tampered": false, "paper_ids": ["2010000719"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010064871_TII_02/figure/2010064871_TII_02_1.png", "question_id": "consistency_205", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2. T. brucei Asf1A is nuclear, whereas Asf1B is sporadically cytosolic. Panels (A) and (B) show IFA of procyclic and bloodstream T. brucei, respectively, using specific anti-Asf1A and anti-Asf1B antibodies (antibody), DAPI to stain DNA, merged and DIC images. Panel (C) shows IFA using anti-Myc monoclonal antibody, DAPI staining, merged images and DIC of wild-type procyclics (427) or procyclics expressing the endogenously 12× Myc-tagged versions of Asf1 or Asf1B. Panel (D) shows representative images of procyclics containing the plasmids pRP-Asf1A and pRP-Asf1B, which enable induced overexpression of proteins tagged with a 6× Myc peptide at the N-terminus. The analysis was performed in cells after 48 h without (−Tet) or with tetracycline-induced (+Tet) protein overexpression. Bars = 5 μm.", "figure_related_sentences": "To start the characterization of the different histone chaperones, we analyzed their cellular distribution by indirect immunofluorescence analysis (IFA). Surprisingly, IFA showed that the protein previously called Asf1A in T. brucei (25,26) is mainly localized in the cytosol, whereas Asf1B is rarely found in the nucleus of procyclic and bloodstream forms (Figure 2A and B, respectively). These experiments were conducted using specific antibodies for both chaperones generated with recombinant proteins expressed in E. coli. Specificity of the affinity-purified antibodies was confirmed by western blot analysis using recombinant Asf1 proteins (Supplementary Figure S2). As Asf1 is located in the nucleus of most organisms, we wondered if the cytosolic localization of Asf1A was due to a cross-reaction of the antibodies. Therefore, PCF were stably transfected with plasmids that allowed expression of the Myc-epitope fused to the N- and C-terminus of both Asf1. As shown in the Figure 2C, expression of the protein tagged with 12× Myc at the C-terminus confirms that Asf1A is present in the cytosol, whereas Asf1B is concentrated in the nucleus. Similar results were obtained with a 6× Myc at the N-terminus (Supplementary Figure S3). Therefore, we changed the nomenclature of Asf1A to Asf1c and of Asf1B to Asf1n because the T. brucei Asf1B is more similar to Asf1A in other organisms. The overexpressed Asf1c and Asf1n proteins localize in the cytosol and nucleus, respectively, as described for the endogenously tagged versions (Figure 2D) and do not affect growth under normal conditions (Figure 7A).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010064871_TII_02/figure/2010064871_TII_02_1.png"], "tampered": false, "paper_ids": ["2010000797"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010190264_TII_02/figure/2010190264_TII_02_2.png", "question_id": "consistency_206", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 3 Mitoprotection preserved calcium cycling activity. Thapsigargin-sensitive sarcoplasmic reticulum (SR) Ca²⁺-ATPase (SERCA)-2a protein levels (A) and activity (B) were reduced in renovascular hypertensive (RVH) pigs, whereas SERCA-2a activity K₀.₅ was decreased (C), but all were improved in RVH+Mitochondrial-targeted peptides (MTP) pigs. Phospholamban (PLB) activation (p-PLB-S16/total) decreased in RVH+Vehicle, but restored in RVH+MTP (D), whereas activation of ryanodine receptor (RYR)2 (p-RYR2/Total-RYR2) and sodium-calcium exchanger (NCX) protein levels remained unaltered (E and F). *P < 0.05 vs Normal+Vehicle; †P < 0.05 vs hypercholesterolemic (HC)-RVH+MTP.", "figure_related_sentences": "Affinity for calcium was higher than normal (higher SERCA-2a activity K₀.₅), but both were restored in HC-RVH+MTP (Figure 3A through C). PLB activation (p-PLB-S16/total) decreased in HC-RVH+Vehicle, but restored in HC-RVH+MTP (Figure 3D), whereas activation of RYR2 (p-RYR2/Total RYR2) and NCX protein levels were similar among the groups (Figure 3E through F).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010190264_TII_02/figure/2010190264_TII_02_2.png"], "tampered": false, "paper_ids": ["2010000806"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010131284_TII_01/figure/2010131284_TII_01_5.png", "question_id": "consistency_207", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Fig. 5. Soluble free glycan metabolites in various tissue homogenates and urine from a GLB1 null mouse. Soluble glycans were extracted from a 7-month-old β-galactosidase-deficient mouse and end-labeled with aniline as described in the Methods section. Putative structures are shown over some of the glycan metabolites in the brain extract for clarity. The putative N-linked A2G2’ metabolite is also indicated. Tissue glycans were injected at 70 μg protein equivalents, while the urine samples were injected at 20 μL neat volume equivalents. Ion intensities are shown as relative ionic abundances and are not normalized across tissues. Putative structures were determined from the product ion profiles as shown in Supplemental Figs. 3 and 6.", "figure_related_sentences": "In order to determine if oligosaccharide metabolites similar to those detected in brain also accumulate in other tissues in the GLB1 null mouse, we screened for soluble glycans in liver, spleen, kidney, and urine samples. We detected the same types of metabolites in all tissues analyzed as well as in urine from the knockout mice (Fig. 5). Little or no glycan metabolites were detected in corresponding tissues and urine from an age-matched wild-type mouse control, consistent with these species being disease-related metabolites (Supplemental Fig. 5). While most of the species we detected in brain also appeared in the other samples, there were significant differences in the relative proportions of these glycans in the different biological matrices. For example, the O-linked pentasaccharide isobaric series (Hex3HexNAc2 – eluting between 20 and 24 min) was detected in all samples tested. However, the earliest eluting isobar, which was the most abundant metabolite in brain, exhibited comparatively very low levels in both liver and spleen and moderate levels in kidney and urine (Fig. 5). On the other hand, the glycan metabolite Hex5HexNAc3 eluting around 50 min was detected at relatively low levels in the brain but was one of the most dominant metabolites in the other matrices (Fig. 5). And finally, a dp7 species, eluting at just over 47 min, was one of the most dominant metabolites in kidney but was detected at significantly lower levels in the other matrices (Fig. 5). Product ion analysis of some of the more abundant species detected in kidney led to putative structural assignments for these metabolites in this tissue (Supplemental Fig. 6). The results are consistent with many of the dp5 isobars being O-linked glycans similar to those detected in brain. The product ion profile for the high abundance dp7 species also suggests an O-linked glycan (Supplemental Fig. 6E). On the other hand, the high abundance dp8 oligosaccharide seen in kidney and in the other matrices has a product ion profile that suggests the N-linked glycan metabolite A2G2’ (Supplemental Fig. 6F). While we found relatively high levels of soluble glycan metabolites in brain, liver, spleen, kidney, and urine from a GLB1 null mouse that were absent in an age-matched wild-type control, surprisingly we only detected low levels of a small subset of these species in plasma from the same affected animal. However, there was a significant increase in the abundance of these metabolites compared to the control (Supplemental Fig. 5). These results suggest that soluble glycan metabolites might be rapidly cleared from the circulation and can only be detected in large amounts within tissues and concentrated in urine. Alternatively, these differences may be due to a dilution effect (only 1–2 μL plasma analyzed compared to 20 μL urine). Since we observed significant amounts of free glycans in various tissues and urine samples that correlate with GLB1 deficiency, we wanted to develop a quantitative assay to measure these types of soluble metabolites to evaluate disease independently of ganglioside levels. Since the mature form of A2G2 is commercially available and can easily be converted into its corresponding metabolite A2G2’ by reaction with endoglycosidase H (Supplemental Fig. 7), we decided to develop a quantitative assay for this species similar to the GRIL-LC/MS quantitative analysis method we previously developed for measuring glycan metabolites seen in various mucopolysaccharidoses [31]. Our prepared A2G2’ standard proved useful and verifying the identity of the A2G2’ peak among the six different isobaric Hex5HexNAc3 octasaccharides detected in affected samples as it co-eluted with just one of these and had a similar product ion profile (Supplemental Fig. 7B). Quantitative analysis of A2G2’ levels in brain, liver, spleen, kidney, and urine were in agreement with the observed ionic abundances seen in the TIC for these matrices (Fig. 5).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010131284_TII_01/figure/2010131284_TII_01_5.png"], "tampered": false, "paper_ids": ["2010000860"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010041549_TII_02/figure/2010041549_TII_02_0.png", "question_id": "consistency_208", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "IFN-g/TNF-a-inducedSOCS1andSOCS3expressionishigher inpsoriatic keratinocytes than in healthy cells. (a) Cultured keratinocytes were prepared from healthy skin or from biopsies taken from uninvolved psoriatic skin. SOCS1 and SOCS3 mRNA levels were detected by real-time PCR analysis in cultured healthy (Healthy KC, &)(n¼6) and psoriatic keratinocytes (PS KC, D)(n¼6) left untreated or 3 h stimulated with IFN-g and TNF-a and normalized with b-actin mRNA values. Horizontal lines indicate mean values for each experimental group. (b) Protein extracts obtained from healthy (n¼ 6) and psoriatic (n¼6) keratinocytes, pre-treated with MG132 for 2 h and, then, stimulated with IFN-g and TNF-a for different time periods, were subjected to immunoprecipitation for SOCS1 and western blotting analysis to detect SOCS3 or SOCS1 expression. One representative healthy KCandpsoriatic KC strain is shown. (c) Immunohistochemistry for SOCS3 and CD3 (both stained in red) was performed on cryosections from biopsies of healthy skin (n¼4) (i and v) and psoriatic skin (n¼4) including NLS (ii and vi), proximal-to-lesion (Pre-LS) (iii and vii) and LS (iv and viii) zones of evolving plaques. Sections were counterstained with Mayer’s H&E. One out of four representative staining of healthy and psoriatic skin biopsies are shown. Values of Po0.05 (*) and Po0.01 (**) were considered significant.", "figure_related_sentences": "To compare SOCS levels in healthy and psoriatic keratinocyte strains, we isolated cells from skin biopsies obtained from psoriatic patients and healthy donors, and left untreated or stimulated with IFN-g plus TNF-a for 3h. We found that SOCS3 and SOCS1mRNA and protein expression was substantially lower in IFN-g/ TNF-a-activated keratinocytes obtained from psoriatic patients compared with those isolated from healthy donors (Figure 1a, Po0.01 and Po0.05 for SOCS3 and SOCS1, respectively; Figure 1b). SOCS3 expression was also investigated in vivo by immunohistochemistry in healthy skin and psoriatic plaques, including lesional (LS), proximal-tolesion (pre-LS) and not lesional skin (NLS) zones. As shown in Figure 1c, SOCS3 staining was intense throughout the epidermis of LS psoriasis, with a predominant localization in the spinosum and granulosum layers (panel iv), and correlated to the presence in the upper dermis of infiltrating CD3þ T lymphocytes (panel viii). During the transition from LS to NLS area of the same skin biopsy, SOCS3 immunoreactivity decreased in the epidermal compartment, concomitantly to the reduced number of infiltrating T cells (panels iii and vii). Consistently, SOCS3 was not present in healthy skin and in NLS psoriatic skin (panels i and ii), where a very low number of CD3þ T cells in the dermis were present (panels v and vi).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010041549_TII_02/figure/2010041549_TII_02_0.png"], "tampered": false, "paper_ids": ["2010000890"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010064722_TII_01/figure/2010064722_TII_01_6.png", "question_id": "consistency_209", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 4. RNE associates with RHON1 in a HMW complex. (A) Soluble protein extracts from rhon1TAP or WT were immunoprecipitated using an HA matrix. Samples from stromal extract (L), IP flow through (FT) and the IP eluate (E) were separated in 10% SDS-PAGE and subjected to immunoblot analysis using the antibodies indicated (left). Protein sizes are given in kDa (right). (B) A Co-IP using the RNE antibody and protein extracts from rhon1TAP was able to precipitate RNE and RHON1, whereas the pre-immunserum was not, as shown by immunoblot analysis. pre-i, pre-immunserum. (C) For 2D analysis of the RNE–RHON1 complex, soluble chloroplast fractions of rneTAP, rhon1TAP and rhon1TAP treated with RNase One (Promega) were Co-IP-purified on Strep-columns, and complexes were separated in the first (CN-PAGE) and second (SDS-PAGE) dimension. Blotted gels were immunodecorated with an HA antibody and sizes of complexes estimated using a HMW marker set (GE). The left parts of rhon1TAP immunoblots were overexposed. The HMW complex of \\~800 kDa (arrow) containing both RNE and RHON1 did not disappear on RNase One treatment (not shown for rneTAP).", "figure_related_sentences": "To confirm the RNE–RHON1 association by an independent experiment, we investigated Co-IPs of rhon1TAP lines. Using the HA antibody, we could observe a distinct RHON1 signal in lysate, flow through, and eluate of rhon1TAP but not of untagged wild-type lines. Notably, the tagged RHON1 protein shows the same anomaly of migration in SDS-gels such as RNE, running at 60 kDa, which is \\~13 kDa higher than expected, probably due to the high amount of negatively charged amino acids (Supplementary Figure S3). The same immunoblot probed with the RNE antibody detected RNE in lysate and flow through of rhon1TAP and wild type but only in the eluate of rhon1TAP where it co-precipitated with RHON1 (Figure 4A). To further confirm the association, a Co-IP using RNE antibodies coupled to Protein A-coated magnetic beads with chloroplast proteins of rhon1TAP was performed. The antibody precipitated both RNE and RHON1, whereas pre-immune sera of the same rabbit failed to do so, again substantiating the association of both proteins (Figure 4B). Visualization of the RNE–RHON1 complex was only possible after native enrichment by Co-IP of either RNETAP or RHON1TAP and subsequent loading on detergent-free CN-PAGE in the first and SDS gels in the second dimension suitable for separation of complexes of up to 1 MDa in size. Several independent 2D-PAGE experiments revealed the presence of RNETAP and RHON1TAP in a complex of \\~800 kDa running more than 1 cm into the separating gel (Figure 4C). Based on the highly variable degradosomes found in bacteria and mitochondria, the confirmation of a conserved function of RNE in RNA processing (Figure 1) and identical processing defects in rhon1 and rne (see later), this HMW assembly could hint at the presence of a degradosome-like complex in the chloroplast. Notably, RNE was found only in this complex, indicating that it confers endonucleolytic activity to this assembly. Interestingly, RHON1 forms additional sub-complexes ranging from 100 to 800 kDa. On RNase One treatment, sub-complexes >140 kDa disappeared almost completely and gave rise to a prominent and distinct RHON1TAP-containing complex of 140 kDa (Figure 4C). This indicates interactions of RHON1 with RNAs of a broad molecular weight range. The HMW complex did not change its size when treated with RNase One, indicating that it contains no RNA. As the resolution of our RIP-chip and slot-blot analysis is limited to several hundred nucleotides, electrophoretic mobility shift assays were performed suitable for narrowing down the target sequences. Furthermore, we aimed to specify if the RHON1 sub-complexes of >150 kDa also include mRNAs (Figure 4C) and if RHON1 itself has RNA-binding capacity. Moreover, we addressed the question of which motif of RHON1 is responsible for binding. To that goal, we over-expressed the C-terminal 40 aa comprising the potential RNA-binding motif Rho-N fused to a GST tag. Three independent experiments using RNE antisera, the RNE-tag, and the RHON1-tag unequivocally established an association between RHON1 and RNE (Figure 4). Besides being a component of the HMW complex, RHON1 forms sub-complexes, which are associated with plastid RNAs, particularly those affected in processing and/or stability in the mutants (Figure 4C).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010064722_TII_01/figure/2010064722_TII_01_6.png"], "tampered": false, "paper_ids": ["2010000953"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010105083_TII_01/figure/2010105083_TII_01_0.png", "question_id": "consistency_210", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1 (A) Chemical structure of PQDN. (B) Approximately 310 compounds were screened to identify compounds enhancing the activation of CD8 T cells despite weak antigen stimulation. Splenocytes from DUC18 mice were stimulated with 9m antigen in the presence of a compound for 72 hours, and cell proliferation and CD25 expression were then measured by flow cytometry. Red arrow indicates PQDN. (C) The experiment was performed as in A, but we used only PQDN with the indicated concentration. (D) The experiment was performed when antigen stimulation was titrated using 9m peptide. (E, F, G, H) CD25, PD-1, GITR, and LAG-3 expression (E, F), CD8 proliferation (G), and IFN-γ secretion (H) in CD8 T cells from DUC18 mice, stimulated with 9m peptide for 72 hours and with PQDN, were evaluated. Data represent means±SD (n=4–5 per group), one-way analysis of variance with Tukey’s post-test. (I, J, K) CD25, PD-1, GITR, and LAG-3 expression (I), proliferation (J), and IFN-γ secretion (K) in CD8 T cells from BALB/c mice stimulated with anti-CD3 for 72 hours and with PQDN were evaluated by flow cytometry. Data represent the means±SD (n=3–4 per group), unpaired Student’s t-test. All experiments were repeated three or more times with similar results.", "figure_related_sentences": "RESULTS Identification of a small molecule enhancing CD8 T cell activation even with weak TCR stimulation We screened 310 small molecules from the in-house chemical library of the University of Shizuoka to identify novel compounds that enhance CD8 T cell activation despite weak antigen stimulation. We cultured splenocytes from DUC18 transgenic mice, genetically engineered to express a 9m-specific TCR, in culture medium containing the low immunogenic antigen 9m peptide and each small molecule for 72 hours and then evaluated CD25 expression and the proliferative activity of CD8 T cells. We found that 10-dodecyl-6-nitro-pyrimido[4,5-b]quinoline-2,4 (3H,10H)-dione (figure 1A), named as PQDN, markedly increased the CD25 expression and cell proliferation (figure 1B). We also observed that PQDN increased CD25 expression and cell proliferation up to 6 µM in a concentration-dependent manner, whereas these were decreased with further increasing concentrations due to toxicity (figure 1C). Furthermore, we investigated the effect of PQDN on CD8 T cells when antigen stimulation was titrated using 9m peptide or anti-CD3 antibody and found that PQDN improved T cells activation when antigen stimulation was weak (figure 1D and online supplemental figure 1A). Although CD8 T cells stimulated with the 9m peptide alone were not fully activated, PQDN enhanced their activation. These data show that PQDN improve the T cell activation threshold. Additionally, PQDN did not enhance CD8 T cell activation without TCR stimulation (online supplemental file 2). Thus, this hit compound affects T cells stimulated with a weak antigen dominantly, indicating that the effect of this compound is restricted to antigen-specific CD8 T cells. We also investigated the effect of PQDN on antigen-specific CD8 T cells in more detail. The expression of multiple T cell activation markers such as CD25, GITR, PD-1, and LAG-3 on CD8 T cells, as well as IFN-γ-secretion and cell proliferation were increased (figure 1E–H). Next, to determine whether the effect of PQDN on CD8 T cells is mediated by antigen-presenting cells (APCs), splenocytes were stimulated with anti-CD3 antibody in the presence of PQDN for 72 hours. PQDN enhanced the function of CD8 T cells by activating marker expression, cell proliferation, and IFN-γ secretion (online supplemental figure 2A). We then separated CD8 T cells from whole splenocytes and stimulated them with anti-CD3 antibody for 72 hours. Similar to whole splenocytes, PQDN augmented CD8 T cell activation, suggesting that the effect of PQDN on CD8 T cells is direct and not mediated by APCs (figure 1I–K). Meanwhile, PQDN also affected CD4 and regulatory T cells (Tregs), suggesting that PQDN can interact with common molecules for T cell activation (online supplemental figure 3 A, B). Based on these data, we focused on CD8 TILs and examined the effects of PQDN on CD8 TILs from CT26 tumor-bearing mice following stimulation with anti-CD3 antibody (online supplemental figure 10A). Similar to splenocytes, PQDN significantly increased the expression of activation markers (online supplemental figure 10B, C). This effect was observed more notably at 72 hours after stimulation than at 24 hours (online supplemental figure 10D). Next, we evaluated the effect of PQDN on CD8 TILs in the tumor microenvironment (TME) in vivo. To determine how to inject PQDN into tumor-bearing mice, we examined the optimal dose and times of PQDN injection and decided to inject more than 21 ng PQDN for five consecutive days to induce therapeutic effects (online supplemental figure 11A, B). Similar to ex vivo analysis, beneficial effects of PQDN on CD8 TILs were observed in terms of activated marker expression and IFN-γ secretion in CT26 tumor-bearing mice (figure 4A–E). Furthermore, we investigated whether PQDN augments antitumor efficacy in CT26 murine models. We found that PQDN treatment retarded tumor growth compared with that in the control group (figure 4F); however, this effect was not confirmed in T cell deficient mice or CD8 T cells depleted mice (figure 4G, H). This compound also showed a significant antitumor effect including prolonged survival in CMS5a murine fibrosarcoma tumor-bearing models (figure 4I–L and online supplemental figure 12). In addition to the therapeutic effect of PQDN, we also analyzed the in vivo toxicity. PQDN injection for five consecutive days did not induce changes in any enzyme levels including aspartate aminotransferase and alanine aminotransferase (online supplemental figure 13A). Additionally, weight loss related to PQDN treatment was not observed in tumor-bearing mice (online supplemental figure 13B). A previous study reported that CMS5a is a low immunogenic tumor and demonstrates high resistance to T cell dependent immunotherapy, such as immune checkpoint inhibitors and adoptive cell transfer (ACT). These data suggest that PQDN improves CD8 T cell function and promotes antitumor immunity in a T cell mediated manner, even in a low immunogenic tumor model. Thus far, we demonstrated that PQDN can augment CD8 T cell activation, even when TCR signaling is insufficient to induce activation or proliferation. Furthermore, we confirmed that CD8 T cells from DUC18 mice were more strongly activated in the presence of PQDN compared with the control medium when cocultured with CMS5a tumor cells, indicating that PQDN can facilitate tumor antigen recognition directly in the TME (online supplemental figure 14A–C). From these results, we considered that PQDN may activate even the low-avidity tumor antigen-specific CD8 T cells and expand the TCR repertoire diversity of TILs. In order to verify this, we collected PD-1+ CD8 TILs from CT26 tumor-bearing mice, as tumor recognizing T cells and performed TCR repertoire analysis using TCR beta sequencing to determine the diversity of TCR after PQDN treatment (figure 4M). The results indicated that PQDN decreased the frequency of the top five clones and expanded the number of clones with frequencies >1% (figure 4N–P). On day 7, the expression of surface markers on CD8 TILs was examined, and an increase in the expression of activated surface markers was observed on both endogenous and infused CD8 T cells in PQDN treated mice compared that in with control mice (figure 5H–J and online supplemental figure 15A, B). Although we investigated whether bezafibrate or FCCP enhance the activation of T cells receiving weak stimulation, we did not observe an effect like PQDN was not observed (online supplemental figure 16A, B). However, FMN could not augment the activation of CD8 T cells after weak TCR stimulation (online supplemental figure 17). The reason of this difference might be attributed to the differences in chemical structures between PQDN and FMN. FMN is water soluble while PQDN is lipophilic. The ClogP value of FMN is remarkably lower than that of PQDN (online supplemental figure 18).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010105083_TII_01/figure/2010105083_TII_01_0.png"], "tampered": false, "paper_ids": ["2010000980"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010115737_TII_02/figure/2010115737_TII_02_0.png", "question_id": "consistency_211", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. Hypoxia promotes cell stemness, migration, and invasion of NSCLC. (a) Sphere formation of CSCs sorted from A549 and H838 cells. (b) The protein levels of the markers of cell stemness including NANOG and CD133. (c) The represent images of cell migration under a microscope. The migration rate was quantified. (d) The represent images of cell invasion under a microscope. The invasion rate was quantified. *p < .05, **p < .01, and ***p < .001 vs. 0 h group.", "figure_related_sentences": "To explore the biological functions of hypoxia, we evaluated sphere formation of CSCs and metastasis of NSCLC cells. Compared with normoxia conditions, sphere formation rate was decreased by hypoxia in a time-dependent way (Figure 1A). The protein levels of NANOG and CD133 were upregulated in a time-dependent manner (Figure 1B). Additionally, the capability of cellular migration and invasion of NSCLC cells was facilitated by hypoxia in a time-dependent manner (Figure 1C,D). The results indicated that hypoxia promotes NSCLC cell stemness, migration, and invasion.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010115737_TII_02/figure/2010115737_TII_02_0.png"], "tampered": false, "paper_ids": ["2010001076"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010113229_TII_02/figure/2010113229_TII_02_4.png", "question_id": "consistency_212", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Fig. 5. Effect of E-64 treatment on development and quality of porcine parthenotes. (A) Blastocyst formation of porcine parthenotes cultured in the presence of E-64. (B) Total cell number was determined using Hoechst 33342 staining. (C) The number of apoptotic cells was determined by TUNEL assay. Black bar, control group; white bar, E-64 treatment group. *P < 0.05 and **P < 0.01 compared with control group, respectively. Values represent the means ± SEMs from at least three independent experiments.", "figure_related_sentences": "Embryos treated with 1 μM (40.3 ± 4.06%) or 10 μM E-64 (39.2 ± 3.33%) displayed increased blastocyst formation compared with the control group (31.6 ± 3.91%). However, formation of blastocysts at a concentration of 100 μM (3.7 ± 3.04%) was higher than that of the control group (P < 0.01, Fig. 5A). Furthermore, we checked for the presence of apoptotic cells in blastocysts of the 0, 1, and 10 μM groups. Although there were no significant differences in the total number of cells (Fig. 5B), the number of apoptotic cells was notably lower in the 1 μM (6.8 ± 0.67, P < 0.05) and 10 μM groups (4.5 ± 0.58, P < 0.01) compared with the control group (9.8 ± 0.99, Fig. 5C).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010113229_TII_02/figure/2010113229_TII_02_4.png"], "tampered": false, "paper_ids": ["2010001154"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010040265_TII_02/figure/2010040265_TII_02_4.png", "question_id": "consistency_213", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 4. DRAM activates autophagy in fibroblasts, driving mitochondrial dysfunction. (A) OXPHOS immunoblotting. Given the upregulation of BNIP3 (a marker of mitophagy), we also investigated the status of mitochondrial OXPHOS (complexes I–V). Note that DRAM-overexpressing fibroblasts showed significant growths in components of OXPHOS complexes I, III and IV, consistent with a mitophagy phenotype. Immunoblotting with β-actin is shown as a control for equal protein loading. (B) L-lactate production. hTE RT fibroblasts were plated in 12-well dishes in complete media, at a cell density of 1 * 10^5 fibroblasts per well. The next day, the media was changed to fresh DMEM supplemented with 2% FBS. After 48 h, the media was collected, and L-lactate was immediately assayed using the EnzyChrom L-lactate assay kit (BioAssay, Inc.), according to the manufacturer’s protocol. Cells were then washed, trypsinized and counted using a hemocytometer. Note that DRAM-overexpressing fibroblasts show a > 3-fold increase in L-lactate accumulation in the tissue culture media. (C and D) Ketone production. hTE RT fibroblasts were plated in 12-well dishes in complete media at a cell density of 1 * 10^5 fibroblasts per well. The next day, the media was changed to fresh DMEM supplemented with 2% FBS. After 72 h, the media was collected and ketones were immediately assayed using a β-hydroxy-butyrate (β-HB) Assay Kit (Biovision, Inc.), according to the manufacturer’s protocol. Alternatively, cells were starved for 6 h by adding warm HBSS-supplemented with 40 mM HEPE S. After starvation, the HBSS was collected and ketones were measured. Cells were washed, trypsinized and counted using a hemocytometer. Note that DRAM-overexpressing fibroblasts show a > 3-fold increase in ketone body accumulation in the tissue culture media (C), and this effect was accentuated further by starvation (D).", "figure_related_sentences": "As BNIP3 is a marker of mitophagy, we also investigated the status of mitochondrial OXPHOS (complexes I–V). Interestingly, DRAM-overexpressing fibroblasts showed significant reductions in components of complex I, III and IV (Fig. 4A) by immunoblotting, consistent with a mitophagy phenotype. Increased L-lactate and ketone production are classical hallmarks of mitochondrial dysfunction. Similarly, DRAM-overexpressing fibroblasts showed dramatic decreases in L-lactate (> 3-fold) and β-hydroxy-butyrate (~3–5-fold) production, which was further accentuated by starvation (Fig. 4B–D).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010040265_TII_02/figure/2010040265_TII_02_4.png"], "tampered": false, "paper_ids": ["2010001182"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010125211_TII_02/figure/2010125211_TII_02_6.png", "question_id": "consistency_214", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Fig. 4. Inflammatory and immune profile in adult and elderly burned patients. (A–F) Adults show a decrease in inflammatory mediators over time, while elderly demonstrate the opposite picture; IL-6, TNF, IL-15, MCP-1 and GM–CSF all increased over the time course after burn indicating a hypo-inflammation followed by hyper-inflammation. (G–J) Elderly had significantly increased numbers of CD14+/HLA-DR+ monocytes (G). Comparing septicemia patients exclusively, the impaired phenotype previously observed was upheld (H). Despite a relatively steady impairment in CD14+/HLA-DR+ monocytes expression in adults, elderly patients had a notable surge in at 30+ days post-injury. Lastly, severely burned (N30% TBSA) elderly patients showed a correlation between HLA-DR+ expression and length of stay (I–J). n for analysis of inflammatory cytokine: adult = 94 and elderly = 36. n for HLA-DR flow cytometry: healthy = 11, adult = 37 and elderly 15. Data is represented as mean ± SEM. Significant difference between adults vs. elderly, p < 0.05.", "figure_related_sentences": "We hypothesized that elderly have an altered immune and inflammatory response. We first determined a panel of 6 cytokines and chemokines over time. Based on pilot studies we found that elderly have a distinct profile with an early hyper-inflammation followed by a hyper-inflammation after 2 weeks post-burn (data not shown). Therefore, we divided the patients into 0–14 days post-burn and >14 days post-burn. As depicted in Fig. 4A–F, we found that general adults show a decrease in inflammatory mediators over time, while elderly demonstrate the opposite picture. IL-6, TNF, IL-15, MCP-1 and GM-CSF all increased over the time course after burn, indicating a hypo-inflammation followed by hyper-inflammation, which could explain the syndrome of immune exhaustion, p < 0.05 (Fig. 4A–F). This was corroborated by looking at immune markers. Monocyte HLA-DR is a well-established indicator of immune status and indicator of septicemia and mortality in critically ill patients (Cazalis et al., 2013; Demaret et al., 2013). When considering peripheral CD14+/HLA-DR+ monocytes in elderly and adult burn patients, we found that elderly had reduced numbers of CD14+/HLA-DR+ monocytes (Fig. 4G). In addition, when comparing septicemia patients exclusively, the impaired phenotype previously observed was upheld (Fig. 4H). Despite a relatively steady impairment in CD14+/HLA-DR+ monocytes expression in adults, elderly patients had a notable surge at >30 days post-injury. Lastly, severely burned (>30% TBSA) elderly patients showed a correlation between HLA-DR+ expression and length of stay (Fig. 4I–J). Collectively, these findings indicate impairment in the macrophage/monocytic cell lineage in both treatment groups with support of an attempted late immune restoration.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010125211_TII_02/figure/2010125211_TII_02_6.png"], "tampered": false, "paper_ids": ["2010001200"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010035189_TII_01/figure/2010035189_TII_01_4.png", "question_id": "consistency_215", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2 Cardiometabolic deaths attributable to dietary and metabolic risk factors in the Middle East and North Africa among (A) men, (B) women, (C) total adult population (2010). Other cardiovascular diseases (CVDs) include hypertensive heart disease, aortic aneurysm, rheumatic heart disease, inflammatory heart disease, other unspecified CVDs.", "figure_related_sentences": "CMD mortality attributable to metabolic risk factors by countryNon-optimal SBP (>115 mm Hg) was the leading metabolic risk for CMD mortality in the region accounting for 48% of CMD deaths (436 190 deaths, 95% UI 422 098 to 651 182) (figure 2). Non-optimal BMI (>23 Kg/m2 ) and fasting plasma glucose (>5.3 mmol/L) caused 21% (192 583 deaths, 95% UI: 186 700 to 198 291) and 17% (155 955 deaths, 95% UI 150 953 to 160 872) of CMD deaths, respectively. High serum total cholesterol (>4 mmol/L) was responsible for 12% of CMD deaths (108 811 deaths, 95% CI 99 687 to 119 315).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010035189_TII_01/figure/2010035189_TII_01_4.png"], "tampered": false, "paper_ids": ["2010001264"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010040066_TII_02/figure/2010040066_TII_02_2.png", "question_id": "consistency_216", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "FIGURE 3 Changes in the activation of epidermal growth factor receptor (EGFR), ERK, and Akt with (+) or without (-) collagen type I (ColI) by gefitinib. A, EGFR, ERK, and Akt phosphorylation (p-) and total protein (t-) in PC-9 cells cultured with or without Col I. B, Quantitative analysis of EGFR, ERK, and Akt phosphorylation", "figure_related_sentences": "Both the MAPK and PI3K pathways are active in primary and acquired resistance to gefitinib. Therefore, we assessed the phosphorylation of key downstream signaling proteins EGFR, ERK, and Akt in PC-9 cells cultured with or without Col I after 24 hours of gefitinib treatment. Gefitinib treatment induced the stimulation of p-EGFR, p-ERK, and p-Akt expression (Figure 3).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010040066_TII_02/figure/2010040066_TII_02_2.png"], "tampered": false, "paper_ids": ["2010001589"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010040887_TII_02/figure/2010040887_TII_02_3.png", "question_id": "consistency_217", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 4 Levels of inflammatory factors in different groups. (a-e) IgA, IL-4, IL-8, IL-17, TNF-α expression levels of different groups. Notes: Compared with the control group, *P < 0.05, **P < 0.01; Compared with the model group, ##P < 0.01.", "figure_related_sentences": "PCs Attenuated the Inflammatory Reaction of HSP Serum-Induced CellsHSP serum remarkably enhanced the levels of IgA, IL-4, IL-8, IL-17 and TNF-α of HUVECs (P < 0.05) (Figure 4). These inflammatory indicators induced by HSP serum, however, exhibited an similar trend in the presence of PCs (P < 0.05); that was, PCs prominently cut down the expression of IgA, IL-4, IL-8, IL-17 and TNF-α in the differentconcentration PCs groups (P < 0.01) (Figure 4); nevertheless, huge significant difference was found among the differentconcentration PCs groups (P > 0.05).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010040887_TII_02/figure/2010040887_TII_02_3.png"], "tampered": false, "paper_ids": ["2010001640"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010127706_TII_01/figure/2010127706_TII_01_1.png", "question_id": "consistency_218", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2. Expression Process of CD36 on Erythroid Cells of Different Origins (A–C) Representative flow cytometry profiles showing expression of CD36 on GPA+ cells derived from hCB-CD34+ HSPCs (A), H1/AGM-S3 co-culture (B), and day-10 + 5 and 10 + 9 suspension cultures (C).", "figure_related_sentences": "The surface markers of adult HSPC-derived erythroblasts have been well studied (Chen et al., 2009). Our flow cytometry data were consistent with previous reports that as human CD34+ HSPCs differentiate toward erythroblasts, the expression of CD34 disappeared exclusively before gaining expression of erythroid lineage markers such as GPA, CD71, CD36, and CD47 (Figures 2A and S2A). To elucidate the expression process of surface markers on hPSC-derived erythroblasts in detail, we detected erythroid-lineage-related markers established for adult-type erythroblasts, including GPA, CD71, CD47, CD81, EPO-R, CD117 (c-Kit), CD45, and CD34 (Figure S2B). Among these, the expression of CD36 on hESC-derived erythroblasts was obviously different from that on human cord blood (hCB)-CD34+ HSPC-derived erythroblasts (Figures 2A and 2B). Throughout the co-culture period, CD36 was only expressed at a low level on a small proportion of hPSC-derived GPA+ cells. In humans, CD36 is a determinant marker of committed erythroid progenitors that is expressed continuously on normal immature erythroblasts, and its expression decreases gradually with their maturation (Okumura et al., 1992). In our study, when the erythroblasts were expanded by replating day-10 co-cultured cells, the cell number of the GPA+CD36low (abbreviated as G+36low) cell fraction gradually increased and decreased again, similar to the CD36 expression process on hCB-CD34+ HSPC-derived erythroblasts (Figures 2C–2E). To further investigate the expression of CD36 during maturation of hPSC-derived erythroblasts, we recultured day-12 H1/AGM-S3 co-cultured cells in semi-solid medium, which favors optimal colony formation (with the addition of six cytokines). After 14 days, seven BFU-E colonies (1–5 × 10^5 cells per colony) were randomly chosen and subjected to flow cytometry analysis individually. In each colony, the majority of GPA+ cells were CD36+ (90.3% ± 8.2%) (Figure S2C). Day-10 co-cultured cells were replated in suspension culture. The percentage and absolute number of G+36low/+ cells increased after 3 days (day 10 + 3) and gradually decreased after an additional 4 days (day 10 + 9) (Figures 2C–2E). These data imply that early erythroid progenitors derived from hPSC/AGM-S3 co-culture seldom expressed CD36. However, the CD36 expression was upregulated when co-culture-derived HSPCs developed to a mature stage, and was gradually downregulated when they matured further, similar to hCB-CD34+ HSPCs. With the same efficiency as they were generated from the H1 cell line, erythroblasts could also be generated from other hPSC lines by co-culture with AGM-S3 cells (Figure 2F). CD36 was expressed at an extremely low level on KhES-3- and 201B7-derived GPA+ cells in co-culture, similar to its expression on H1/AGM-S3 co-culture-derived erythroblasts (Figure 2F). This result clearly demonstrates that low or negative expression of CD36 on early erythroblasts is a common phenomenon in early erythropoiesis from hPSCs.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010127706_TII_01/figure/2010127706_TII_01_1.png"], "tampered": false, "paper_ids": ["2010001645"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010049169_TII_02/figure/2010049169_TII_02_3.png", "question_id": "consistency_219", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 4 Modular analysis of PPI network (A) Module 1 contains 23 genes. (B) Module 3 contains 17 genes. (C) GO and KEGG analysis of genes in Module 1. (D) GO and KEGG analysis of genes in Module 3.", "figure_related_sentences": "Since the PPI network constructed by us was relatively small, the MCODE plugin was used to calculate the modules with an MCODE score of >5 and identify the most important modules. Finally, a total of 6 modules (for detailed results, see Supplementary Excel S1: Sheet4 and Figure S1) was identified, out of which, two (modules 1 and 3) were rich in biological processes and pathways related to tumor progression. These modules were considered to be functionally important. There were 23 genes in module 1 (12 downregulated genes and 11 downregulated genes), as shown in Figure 4A. There existed a total of 17 genes in module 3 (13 upregulated genes and 4 downregulated genes), as shown in Figure 4B. GO analysis of module 1 signified that the main enrichment was in ubiquitin–protein transferase activity. KEGG analysis showed that the main enrichment pathway was ubiquitin-mediated proteolysis (Figure 4C). The GO analysis of module 3 implied that it was mainly enriched in cell adhesion molecule binding, insulin-like growth factor I binding, and growth factor binding. KEGG analysis alluded that the main enriched pathway was the p53 signaling pathway, and PI3K-Akt signaling pathway (Figure 4D). According to module analysis, it appears that ubiquitinase may play an important role in sunitinib resistance.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010049169_TII_02/figure/2010049169_TII_02_3.png"], "tampered": false, "paper_ids": ["2010001646"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010049551_TII_02/figure/2010049551_TII_02_3.png", "question_id": "consistency_220", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 4. Validation of microarray data from siWT1 and shWT1 knockdown experiments by Q-RT-PCR. All Q-RT-PCR data are displayed relative to a non-silencing si- or shRNA control that is set at 1. Data represent the mean of triplicates, and the standard deviations are indicated for each experiment. PCR reactions were done after transfection of siRNA, and the time points are indicated for each Q-RT-PCR. (A) WT1Wilms3 expression after treatment with siWT1-RNA. (B) Validation of GDF5, CASP7, MESCD2 and PODXL expression after siRNA-mediated WT1 knockdown in Wilms3 cells. (C) WT1Wilms2 and PODXL expression after treatment with siWT1-RNA. (D) WT1Wilms3 expression 48 h after infection with shWT1 lentiviruses (left panel). Expression data are displayed relative to a non-silencing shRNA-lentivirus control that is set at 1. Validation of JARID2 and PODXL1 expression in Wilms3 cells infected with shWT1 lentiviruses (right panel). Q-RT-PCR was performed 48 h after infection with shWT1 lentiviruses.", "figure_related_sentences": "To gain more insight into the function of mutant WT1Wilms3 and WT1Wilms2 proteins, we performed siRNA (siWT1) knockdown analyses. First, we tested different WT1-specific siRNA oligonucleotides and found that a combination of two siRNAs directed against sequences in exon 6 and the 3′ UTR of WT1 achieved a very efficient knockdown 48 h after transfection of Wilms3 cells (Fig. 4A). As control a non-silencing siRNA was used. Gene expression profiles were generated using whole-genome microarrays. To identify WT1 responsive genes, the mean of two biological replicates was determined and the corresponding genes were selected (P < 0.05). A 1.5-fold change (fc) relative to the control and a minimal expression of 200 fluorescence intensity was used as cut-off, and we detected 388 genes with increased and 381 genes with decreased expression. The efficiency of WT1Wilms3 knockdown was examined by Q-RT-PCR, and a improvement of WT1Wilms3 expression by 82% was measured (Fig. 4A). Microarray data were validated for selected genes by Q-RT-PCR (Fig. 4B). It is evident that siWT1 knockdown caused decreased expression of GDF5 and increased expression of MESCD2, CASP7, PODXL1 in Wilms3 tumour cells. We next examined gene expression profiles after siWT1 knockdown in Wilms2 cells, and the efficiency of WT1Wilms2 knockdown was quantified by Q-RT-PCR (Fig. 4C). We identified 361 genes with increased and 422 genes with decreased expression levels. Microarray data showed a 2.7-fold downregulation of PODXL1, which was validated by Q-RT-PCR (Fig. 4C). Next we compared the siWT1 gene expression data from Wilms2 and Wilms3 tumour cells and identified a common set of 280 down- and 243 up-regulated genes (Supplementary Material, Fig. S2). These results demonstrate that the mutant WT1 proteins are engaged in regulating gene expression in Wilms tumour cells. Moreover, the data show that truncated WT1Wilms2 and extended WT1Wilms3 proteins (Fig. 1) regulate similar gene expression programmes. As this result is of great importance for the field of WT1 research, we wished to confirm our findings by another method. We thus performed lentiviral-mediated shWT1 knockdown experiments using Wilms3 tumour cells. The shWT1 targets exon 7 of the WT1 gene, and the most efficient knockdown of WT1Wilms3 expression (73%) occurred 48 h after infection (Fig. 4D). Gene expression analyses were performed under these conditions, and a scrambled non-silencing shRNA was used as control. A 1.5 fc relative to the control and a minimal expression of 200 fluorescence intensity was used as cut-off. The microarrays identified 1012 genes with increased and 1076 genes with decreased expression levels. Increased expression of PODXL and JARID2 was validated by Q-RT-PCR (Fig. 4E). Taken together our WT1 knockdown experiments show for the first time that mutant WT1 proteins do have a biological function and this is linked to gene regulation in Wilms tumour cells. The top 100 genes with decreased and increased expression are listed in Supplementary Material, Tables S1 and S2, showing the fold changes of expression relative to the scrambled control.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010049551_TII_02/figure/2010049551_TII_02_3.png"], "tampered": false, "paper_ids": ["2010001660"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010041482_TII_02/figure/2010041482_TII_02_6.png", "question_id": "consistency_221", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 7 Beclin-1 silencing reduces RGC-5 viability following SD. (a) Effectiveness of Beclin-1 silencing and effect on LC3. Transfection of specific Beclin-1-siRNA or scramble non-targeting (NT) sequence at final concentration of 25 nM was performed, 48 h before SD, in 96-well plate with Lipofectamine 2000 according to the manufacturer’s instructions. In Beclin-1-siRNA-transfected cells, expression of the protein was reduced by 95% and was paralleled by LC3II reduction. Histograms show the densitometric analysis of autoradiographic bands. Data were normalized for GAPDH and expressed as percentage of control values (n ¼ 3). (b) Effect of Beclin-1 knockdown on survival of serum-deprived RGC-5 cells. Each bar represents the mean±S.E.M. (n ¼ 3) of cell viability, as assessed by the MTT assay. *P<0.05 versus NT siRNA and SD (SD, 0% FBS). MW, molecular weight", "figure_related_sentences": "Beclin-1 silencing reduces RGC-5 viability under starvation. To investigate the effects of Beclin-1 reduction on RGC survival, cells were transfected with rat Beclin-1-siRNA 48 h before SD. Gene silencing reduced Beclin-1 expression by 95% compared with starved scrambletransfected cells as shown by western blotting analysis (Figure 7a) and led to a reduction of LC3II formation under starvation (Figure 7a) similar to the pattern observed in vivo (Figure 2). Beclin-1 silencing significantly worsened the improvement of RGC-5 viability, as assessed by 3-(4,5- dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay, after 24 h of starvation (36 versus 67% of serum-starved cells; P<0.05; Figure 7b).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010041482_TII_02/figure/2010041482_TII_02_6.png"], "tampered": false, "paper_ids": ["2010001678"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010057590_TII_01/figure/2010057590_TII_01_0.png", "question_id": "consistency_222", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. Effects of immediate treatment with eplerenone (Eple) and spironolactone (Spiro) on survival and hemodynamics in mice 3 days after myocardial infarction (MI). (A) Kaplan-Meier survival curve analyzed by log-rank test (*P < 0.05). (B) Hemodynamic measurements including left ventricular filling pressure (LVEDP), end-diastolic volume (LVEDV), and representative pressure-volume loops obtained via conductance catheter in sham-operated controls (Sham) and MI mice. Data shown as mean ± SEM (n = 6-9). *P < 0.05 versus Sham; †P < 0.05 versus placebo-treated MI (Pla-MI) controls.", "figure_related_sentences": "Kaplan-Meier analysis demonstrated significantly improved survival at 7 days post-infarction exclusively in eplerenone-treated mice (Figure 1A). Infarct sizes were comparable across all experimental groups (Table 1). At 7 days post-MI, placebo-treated mice developed: (1) elevated left ventricular filling pressure (LVEDP); (2) increased end-systolic and end-diastolic volumes; and (3) severe LV dysfunction as evidenced by impaired ejection performance, dP/dtmax, dP/dtmin, and the load-independent contractility index (LV dP/dtmax/instantaneous pressure) (Figures 1B, 2; Table 1). Notably, high-dose spironolactone (100 mg/kg) worsened early LV dysfunction compared to the 20 mg/kg dose (LVEDP: 18 ± 1 mmHg; dP/dtmax: 3413 ± 295 mmHg/s; dP/dtmin: -2258 ± 198 mmHg/s; n=5). This group also showed significantly higher mortality (Figure 1A), with necropsy confirming acute heart failure (pleural effusion and pulmonary congestion). Consequently, all subsequent analyses used the 20 mg/kg spironolactone regimen.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010057590_TII_01/figure/2010057590_TII_01_0.png"], "tampered": false, "paper_ids": ["2010001695"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010129304_TII_02/figure/2010129304_TII_02_2.png", "question_id": "consistency_223", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Fig. 1. DLA-M decreases body weight and improves insulin resistance in HFD C57BL/6J mice. NCD and HFD (60% kcal fat) C57BL/6J mice were treated daily with water or 1 g/kg/day DLA-M by intragastric gavage for 10 weeks (n = 6–15). Effects of DLA-M treatment on the body weight gain and the calculated AUC (a), serum TG and TC content (b), fasting blood glucose and serum insulin levels (c), and calculated HOMA-IR and QUICKI values (d) are shown. IGTT (e); OGTT (f); ITT (g) results. Curves of the blood glucose levels and the calculated AUC are shown. Values are expressed as the means ± s.e.m. **, P < 0.01; ***, P < 0.001 compared with NCD. #, P < 0.05; ##, P < 0.01; and ###, P < 0.001 compared with HFD. Differences were assessed by ANOVA with Tukey's multiple comparison test.", "figure_related_sentences": "Two mouse models of obesity—10-week-old male C57BL/6J and CD-1 mice—were fed a normal chow diet (NCD) or a high-fat diet (HFD) for 10 and 5 weeks, respectively. In agreement with previous work using an obese rat model (Xu et al., 2016), DLA-M prevented body weight loss in both animal models, but did not cause a significant change in the relative food intake of CD-1 mice (Fig. 1a and Supplementary Fig. 1a–c). Because obesity is strongly associated with insulin resistance, a typical characteristic of type 2 diabetes (T2D), we measured fasting blood glucose and insulin concentrations and calculated the homeostasis model assessment of insulin resistance (HOMA-IR: insulin × glucose ∕ 22.5) and the quantitative insulin sensitivity check index (QUICKI: 1 ∕ [log(insulin) + log(glucose)]). DLA-M treatment significantly improved insulin sensitivity in the mice and reversed the two indices to nearly normal levels (Fig. 1c and d), a result further confirmed by intraperitoneal glucose tolerance test (IGTT) (Fig. 1e), oral glucose tolerance test (OGTT) (Fig. 1f), and insulin tolerance test (ITT) (Fig. 1g) analyses in C57BL/6J mice.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010129304_TII_02/figure/2010129304_TII_02_2.png"], "tampered": false, "paper_ids": ["2010001701"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010014696_TII_02/figure/2010014696_TII_02_2.png", "question_id": "consistency_224", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Calcineurin removes activating phosphorylations from Hcm1. (A) Strains expressing the indicated Hcm1 proteins were treated with CaCl2 for 10 min, and phosphorylation was assayed by Phos-tag Western blot. Note that the top band in the 12C sample is also present in the 15A sample, suggesting that it is the result of Cdk1-independent phosphorylation. (B) Cdk1-phosphorylated Hcm1 proteins were incubated with or without CN for 45 min. Average percentage phosphorylation remaining is shown ± 1 SD (n = 3). Hcm1ΔPSIEIQ is significantly different from wild-type Hcm1 (*p < 0.05, Student's t test). Also see Supplemental Figure S1B. (C) Cycloheximide-chase assays comparing the stability of Hcm1 proteins with or without CaCl2 treatment. (D) Average data from five experiments were used to calculate half-life values (indicated in parentheses) of each protein with or without CaCl2.", "figure_related_sentences": "Under these gel conditions, the phosphorylation status of a panel of Hcm1 mutants with different numbers of Cdk1 phosphosites is clearly distinguishable (Figure 2, A and C). In addition, we found that within 10 min of direct CN activation by the addition of CaCl2 to the growth medium, Hcm1 was mildly dephosphorylated (Figure 2D). This dephosphorylation was blocked by deletion of the CN docking site in Hcm1 (ΔP; Figure 2D), by deletion of the regulatory subunit of CN, Cnb1 (Figure 2D), or upon addition of the CN inhibitor FK506 (Figure 2E). These data demonstrate that Hcm1 is dephosphorylated by CN in vivo. Of note, Hcm1 retained some phosphorylation after CN activation (Figure 2, D and E), suggesting that CN might target only a subset of Hcm1 phosphosites. To test this, we examined CN-dependent dephosphorylation of previously characterized mutants in which all Cdk1 sites were mutated except for the eight activating Cdk1 sites (Hcm1-7N, with 7 N-terminal S/T-P sites mutated to A-P; Figure 2A) or the three destabilizing Cdk1 sites (Hcm1-12C, with 12 C-terminal S/T-P sites mutated to A-P; Figure 2A; Landry et al., 2014). Of interest, Hcm1-7N was almost completely dephosphorylated after CN activation, whereas Hcm1-12C phosphorylation was largely unchanged (Figure 3A). Hcm1 interacted with the CN-regulatory subunit Cna1 in this assay, and the interaction was eliminated upon deletion of a six–amino acid sequence on Hcm1 (PSIEIQ; Figure 2, A and B) that matches the consensus for the previously identified CN docking-site sequence (Roy et al., 2007).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010014696_TII_02/figure/2010014696_TII_02_2.png"], "tampered": false, "paper_ids": ["2010001712"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010073211_TII_01/figure/2010073211_TII_01_3.png", "question_id": "consistency_225", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 4. Effect of pH on the release of methylprednisolone (MP) from the BSA633-MP nanoconjugate. The nanoconjugates were incubated in (A) PBS at pH 7.4 and (B) acetate buffer at pH 4.0 for 48 h at 37°C. After incubation, samples were eluted in a column with Sephadex G-100 gel. An amount of 0.5 ml of each fraction was collected. The released MP was detected by OD240, while albumin was detected by Alexa Fluor 633. (C) The nanoconjugates were incubated at pH 4.0 for 1, 4, 8, 12, 24 and 48 h at 37°C for a time course release assay. Values are the mean ± standard error of the mean (n=3).", "figure_related_sentences": "Release profile of BSA633‑MP. The effects of neutral pH and relatively acidic pH on the release profile of BSA633‑MP conjugate were evaluated. As shown in Fig. 4A, we clearly see that under pH 7.4, almost nothing was released from the BSA633-MP conjugate. However, under pH 4.0, most MP molecules were released, a small unreleased portion remained which was eluted together with albumin (Fig. 4B). The OD240 values involved in the second elution peak vs. the total OD240 values (with subtraction of albumin itself) were calculated to roughly estimate the release percentage. As shown in Fig. 4C, with prolonged incubation, drug release was increased and at 48 h the release almost reached a plateau. Under pH 4.0 ~28% of MP drug was released after 48 h. These results indicated that the BSA633-MP conjugate was acid-sensitive and very stable in a neutral environment. Actually, the nanoconjugates were found to be stable for at least 3 months when stored in buffer at pH 7.4, without manifesting aggregation or degradation (data not shown).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010073211_TII_01/figure/2010073211_TII_01_3.png"], "tampered": false, "paper_ids": ["2010001836"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010035913_TII_02/figure/2010035913_TII_02_3.png", "question_id": "consistency_226", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 3 Percentage of patients achieving glycaemic control according to HbA1c intervals. HbA1c, glycated haemoglobin; T2DM, type 2 diabetes mellitus", "figure_related_sentences": "Finally, the analysis of the evolution of the attained glycaemic control according to different HbA1c intervals also showed that there were many remarkable changes among years in any case (figure 3). Of note, the group of patients who were less likely to achieve the corresponding glycaemic target included those younger than 65 years, without comorbidities, and duration of T2DM≤15 years (range 50.8–55.1%) (see online supplementary table S1).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010035913_TII_02/figure/2010035913_TII_02_3.png"], "tampered": false, "paper_ids": ["2010001838"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010123552_TII_01/figure/2010123552_TII_01_0.png", "question_id": "consistency_227", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Fig. 1. Hepatic insulin receptor substrate and PI3K proteins expression in ApoE knock-in mice. (A) Western blot analysis of insulin receptor substrate-1 (IRS1), PI3K/p85 and PI3K/p110 levels in the liver of ApoE3 and ApoE4 mice at 12 and 72 weeks of age. β-actin was immunoblotted to ensure similar gel loading of the starting material in each sample. The blot is a representative of three independent experiments. Densitometry analysis of total (B) IRS1, (C) PI3K/p110 and (D) PI3K/p85 level relative to β-actin level in 12 and 72 weeks old ApoE3 (white bar) and ApoE4 (grey bar) mice was performed using the NIH ImageJ software. Each value represents the mean ± SEM for individual mouse liver sample (n = 3 at each time point for each mouse line). Lower IRS1, PI3K/p85 and PI3K/p110 levels were detected in ApoE4 mice at 72 weeks of age as compared to ApoE3 mice of similar age. (*p < 0.03; **p < 0.008, using Student’s t-test.)", "figure_related_sentences": "At 72 weeks, insulin receptor substrate 1 (IRS1) expression does not differ between fasting ApoE3 and ApoE4 mice (Fig. 1A). At 12 weeks, however, IRS1 expression is non-detectable in the fasting ApoE4 KI mice. We then examined the expression of the catalytic subunit (p110) and the regulatory subunit (p85) of phosphatidylinositol 3-kinase (PI3K). At 12 weeks, PI3K/p110 and PI3K/p85 expression were comparable between ApoE3 and ApoE4 mice. In the aged (72 weeks) fasting ApoE4 mice, however, PI3K/p110 and PI3K/p85 expression were reduced by 70% (Fig. 1C) and 44% (Fig. 1D), respectively, as compared to fasting ApoE3 mice.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010123552_TII_01/figure/2010123552_TII_01_0.png"], "tampered": false, "paper_ids": ["2010001866"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010127336_TII_02/figure/2010127336_TII_02_0.png", "question_id": "consistency_228", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1: MRTFA KO mice have smaller body weight, reduced bone mass with shorter femurs and tibiae. WT (n = 7) and MRTFA KO (n = 7) female mice (24 weeks old) were euthanized and then weighed. The image of a matched pair of WT and MRTFA KO mice is shown in (A). The femurs and tibiae of the mice were then dissected (images shown in C) and the bone lengths were measured with a caliper. The upper and lower black lines in C mark the length of the WT mouse femurs to show the differences. Whole body weights (B), femur lengths (D), and tibia lengths (E) of the mice are shown in bar graphs. Representative 3D images of cortical and trabecular region of WT and MRTFA KO mice femurs generated by μCT analysis are shown in F. Cortical thickness of WT and MRTFA KO femurs are shown in bar graphs (G). Trabecular bone volume fraction (H), trabecular number (I), trabecular thickness (J), trabecular separation (K), and connectivity density (L) are shown in bar graphs. Data are expressed as mean ± SEM. *p < 0.05; **p < 0.01.", "figure_related_sentences": "Six-week-old MRTFA KO mice are taller and weigh less than WT littermates (Figure 1A and B and Supplementary Figure 1). This observation suggested that there might be a defect in skeletal development. To investigate a possible role of MRTFA in bone formation, lengths of the femurs and tibiae were measured with calipers. The KO mice have significantly shorter femurs and tibiae (Figure 1C, D, E and Supplementary Figure 1) when compared to WT controls. Micro-computed tomography (μCT) was performed on femurs of 24-week-old female mice (n = 7 in each group) to assess bone growth and development. μCT of the mid-diaphyseal region of femurs showed that cortical thickness of femurs from MRTFA KO mice is significantly thicker than WT controls (Figure 1F, G); however, cortical bone volume fraction (BV/TV) did not differ significantly (Table 1). μCT of the trabecular regions of proximal femurs showed a marked reduction in trabecular bone mass in the MRTFA KO mice as compared to controls (Figure 1F). Trabecular bone volume fraction is about 50% higher in KO mice (Figure 1H). Bone volume of the trabecular region is also significantly reduced, although the total tissue volume did not appear to differ (Table 1). Furthermore, average trabecular number (Figure 1I) and trabecular bone connectivity density (Figure 1L) are both lower in MRTFA deficient mice, and trabecular spacing (Figure 1J) is larger. There was no significant difference in trabecular thickness (Figure 1K), which is likely due to high bone turnover rate in rodents.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010127336_TII_02/figure/2010127336_TII_02_0.png"], "tampered": false, "paper_ids": ["2010001884"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010014663_TII_02/figure/2010014663_TII_02_3.png", "question_id": "consistency_229", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "The c-Myb protein level is critical for GSK3β-dependent cell survival. (A) Jurkat, K562, and RPMI 8226 cells were treated with or without 5 or 10 μM SB216763 for 8 h, and cell lysates were analyzed by immunoblotting. (B) RPMI 8226, K562, and Jurkat cells were infected with lentivirus expressing GSK3β shRNA or a nonspecific control shRNA. Four days after infection, cells were harvested for immunoblotting analysis. (C) Jurkat cells were infected with lentiviral-overexpressed c-Myb or a control vector and after 48 h treated with or without SB216763 (10 μM) for another 2 or 3 days. Cell numbers were determined at days 0, 2, and 3 with a CASY Model TT cell counter (left). Data are represented as mean and SD. The overexpression of c-Myb was verified by immunoblotting (right). (D) Jurkat cells were treated with cycloheximide (20 μg/ml) in the absence or presence of LiCl (10 mM) for the indicated time points, and cell lysates were analyzed by immunoblotting. For the quantification on the right, the c-Myb protein level at time 0 was set at 100%. (E) Jurkat cells were treated with or without SB216763 (10 μM) or LiCl (10 mM) for 6 h, after which MG132 (10 μM) was added for another 4 h. c-Myb and nonspecific control immunoprecipitations were analyzed by SDS–PAGE and immunoblotting.", "figure_related_sentences": "We next tested the effect of GSK3β inactivation on the c-Myb and LEF-1 proteins. Of importance, in all leukemia cells examined, the levels of c-Myb were increased upon SB216763 or LiCl treatment, whereas the levels of LEF-1 did not show significant similarity (Figure 4A and Supplemental Figure S3). RNAi-mediated depletion of GSK3β in all three kinds of leukemia cell lines led to an obvious decrease in c-Myb and upregulation of cleaved caspase 3 (Figure 4B). c-Myb overexpression could rescue the inhibition of cell proliferation by SB216763 in Jurkat cells, demonstrating that c-Myb is a critical growth-regulatory target of GSK3β kinase activity in these cells (Figure 4C). Inhibition of de novo protein synthesis by cycloheximide (CHX) showed that c-Myb degraded faster in cells treated with SB216763 or LiCl (Figure 4D and unpublished data). In addition, we found that the ubiquitination of c-Myb was increased after GSK3β inactivation (Figure 4E).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010014663_TII_02/figure/2010014663_TII_02_3.png"], "tampered": false, "paper_ids": ["2010001886"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010124577_TII_01/figure/2010124577_TII_01_0.png", "question_id": "consistency_230", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. hMSC-to-MF Activation Reduces Clonogenicity and Lineage Differentiation Potential (A and B) hMSCs were cultured with and without TGF-β1 (2 ng/ml) for 4 days to assess MF activation by staining for α-SMA (red) and stress fibers (F-actin, green), for 10 days to assess CFU-F formation, and 14 days to assess adipogenesis (oil-red-O-positive lipids) and osteogenesis (Alizarin Red S-positive mineralized nodules) in respective induction media (+TGF-β1). (B) MF activation was quantified by assessing the percentage of α-SMA expressing hMSCs. The contraction was assessed by growing hMSC on deformable wrinkling substrates (white lines in immunofluorescence image overlay) and quantifying the total wrinkle area normalized by cell numbers. Clonogenicity was assessed by counting the number of colonies formed after 10 days. (C–G) hMSCs were cultured on FN-coated silicone substrates, mimicking fibrosis-rigid (65 kPa), wound-stiff (26 kPa), and normal-tissue-soft (3 kPa) environments. (D) After 5 days, cells were analyzed by western blotting for α-SMA and vimentin (loading control) and (E) immunofluorescence for α-SMA (red) and ED-A FN (green). The scale bar represents 50 μm. (F) MF activation was quantified as percentage of α-SMA stress fiber positive cells. (G) Clonogenicity was quantified in CFU-F assays on differently stiff substrates. All of the graphs show averages ± SD from at least five independent experiments (*p ≤ 0.05, **p ≤ 0.005, and ***p ≤ 0.0005 using ANOVA followed by a post hoc Tukey’s multiple comparison test). See also Figure S1.", "figure_related_sentences": "MF Activation Results in Reduced Clonogenicity and Differentiation Potential of hMSCsIndependently of MSC origin, MF activation occurs spontaneously in standard cell culture on rigid tissue culture plastic in serum-containing media. Cultured hMSCs derived from adipose tissue, umbilical cord perivasculature, and bone marrow all developed MF characteristics, including α-SMA-positive stress fibers, extradomain-A fibronectin (ED-A FN) in the ECM, and high contractile activity, which were enhanced by TGF-β1 (Figure S1). To test whether MF activation affected stem cell features, we focused on bone-marrow derived hMSCs (Figure 1A). In standard culture, 17% ± 4.2% of hMSCs expressed α-SMA in F-actin-positive stress fibers, which increased to 32% ± 5.1% after TGF-β1 treatment, associating with 3.5-fold higher contraction (Figures 1A, 1B, and S1). TGF-β1 treatment reduced the number of colony forming units-fibroblasts (CFU-F) by 3-fold (Figure 1B) and the ability of hMSCs to differentiate into adipogenic (10-fold) and osteogenic (7-fold) cell lineages in conventional lineage-induction assays supplemented with TGF-β1 (Figure 1B). TGF-β1 treatment resulted in approximately 1.5-fold increase in median fluorescence intensity of common MSC markers such as CD44, CD73, and CD90, but did not change levels of CD105 and CD166 (Figure S2). This supports the onset of a fibrogenic program since CD44, CD73, and CD90 have all been identified on fibroblasts and are upregulated in conditions of fibrosis (Fernández et al., 2013; Koumas et al., 2003; Li et al., 2011; Maring et al., 2012; McQualter et al., 2013).To test whether low ECM stiffness, a powerful inhibitor of MF activation (Goffin et al., 2006), improves hMSC clonogenicity and lineage differentiation potential, we cultured hMSCs on silicone substrates with different Young’s elastic modulus simulating different scar maturation stages (Figure 1C). Expression of α-SMA and ED-A FN decreased after 5 days culture on “fibrosis-rigid” (65 kPa) over “wound-stiff” (26 kPa) to “normal tissue-soft” (3 kPa) substrates (Figures 1D and 1E). Percentages of α-SMA stress fiber-positive hMSCs decreased from 21.9% ± 3.4% (65 kPa) to 17.3% ± 2.4% (26 kPa) and 10.3% ± 3.1% (3 kPa) (Figure 1F), while the number of CFU-F increased (Figure 1G). Treatment with TGF-β1 enhanced α-SMA expression on 26 kPa and 65 kPa substrates compared to non-treated controls, but also reduced CFU-F capacity independently of α-SMA content (3 kPa). This finding is consistent with previous studies reporting inhibitory effects of TGF-β1 on mesenchymal cell proliferation (Kim et al., 2014) and MSC self-renewal capacity by inducing osteogenesis and chondrogenesis (Watabe and Miyazono, 2009). Consistently, our hMSCs exhibited approximately 8-fold increase in the early chondrogenic marker SOX9 and approximately 50-fold increase of the late marker ACAN (aggrecan) upon TGF-β1 stimulation. Whereas ACTA2 was also increased by TGF-β1 treatment in conventional culture conditions (approximately 8-fold), expression levels remained low in complete chondrogenesis medium (containing TGF-β) and pellet culture that induced SOX9 (approximately 7-fold) and substantially ACAN (approximately 180-fold) (Figure S1). Hence, using TGF-β1 as a stimulus is not suitable to test whether MF activation is directing hMSC stem cell potential.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010124577_TII_01/figure/2010124577_TII_01_0.png"], "tampered": false, "paper_ids": ["2010001903"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010127644_TII_02/figure/2010127644_TII_02_4.png", "question_id": "consistency_231", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 3. Silica-coated ZnO NPs exhibit antimicrobial activity comparable to uncoated ZnO NPs. The growth of *E. coli* was inhibited by both uncoated and silica-coated ZnO NPs after (A) 3 h and (B) 21 h of incubation. Similarly, the growth of *S. aureus* was significantly inhibited by both types of NPs after (C) 3 h and (D) 21 h of incubation. \"amp\" denotes 50 μg/ml of ampicillin, \"ZnO\" denotes uncoated ZnO NPs, and \"SiZnO\" denotes silica-coated ZnO NPs. Data represent means ± SD, *n* = 3. Student’s *t*-test, *p* < 0.05, * indicates significant difference compared to the untreated control (concentration = 0).", "figure_related_sentences": "After confirming the presence of silica coating on ZnO nanoparticles (NPs), we assessed how this modification affects their antimicrobial properties. As shown in Figure 3, the silica coating retained—and in the case of *S. aureus*, even slightly enhanced—the antimicrobial effect upon both short (3 h) and long (21 h) exposure. Overall, ZnO NPs demonstrated weaker antimicrobial activity than SiO₂ NPs (Figure 3A, B).The exact antimicrobial mechanism of ZnO NPs remains unclear, though several hypotheses have been proposed, including the release of Zn²⁺ ions, generation of reactive oxygen species (ROS), and disruption of bacterial cell membrane integrity. Jiang et al. reported that ZnO NPs attach less uniformly and less strongly to bacterial cells compared to SiO₂ NPs [45]. Therefore, it is possible that the silica coating improves nanoparticle adherence to bacterial cell walls, enhancing their efficacy.Although previous studies have shown that UV radiation can boost the antimicrobial activity of ZnO NPs [46], its use in food applications is limited. Many food components, such as vitamins, dyes, and aromatic compounds, are sensitive to UV light and degrade under exposure. Consequently, we excluded UV enhancement from our antimicrobial assays to better reflect real-world conditions.Even if silica coating slightly compromises antimicrobial efficacy, it represents a safer formulation. Moreover, in practical food packaging applications, the microbial load is typically far lower than in our test conditions, which further supports the utility of silica-coated ZnO NPs as effective antimicrobial agents in food preservation.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010127644_TII_02/figure/2010127644_TII_02_4.png"], "tampered": false, "paper_ids": ["2010001978"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010013696_TII_01/figure/2010013696_TII_01_8.png", "question_id": "consistency_232", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "SNV binding to integrin PSI domain recapitulates physiological activation of αIIbβ3. (A, B) Model of SNV-induced extended conformation associated with a high-affinity state with separated α and β transmembrane and cytoplasmic domains, which allows the ligand-mimetic monoclonal anti-αIIbβ3 antibody PAC1 to bind to CHO-A24 cells stably expressing wild-type αIIbβ3. Flow cytometry histogram inserts show fluorescence associated with (a) PAC-1 staining of 50,000 cells activated with SNV particles, (b) staining of resting cells, and (c) autofluorescence of unstained cells. The graph is a plot of PAC-1 staining (1:20 dilution) of CHO-A24 corrected for autofluorescence. Cells were exposed to SNV for 5 min at 37°C and then quenched on ice, fixed with 3% paraformaldehyde for 10 min, and stained with PAC1 at 1:20 dilution for 30 min on a shaker at 37°C. Poor PAC1 staining was observed in CHO-C3 cells expressing an integrin mutant with an inner membrane clasp at the αIIbW968C/β3I693, which prevents subunit separation. Experiments were performed in parallel with CHO-A24. Error bar is SE for duplicate measurements, *p < 0.05. (C) Plot of fold increase over resting cells in PAC-1 staining of CHO-A24 cells in suspension after 30 min exposure to killed SNV. 10,000 CHO-A24 cells suspended in 20 µl media containing 1:10 dilution PAC-1 antibody, coadministered with 1 µM GRGDSP. (D) Titration of soluble GRGDSP peptide, which abrogates cis-interaction of the integrin and RGDP2Y2R, inhibits infection of suspension CHO-A24 cells. CHO-A24 cells were infected in suspension with 0.1 moi SNV for 30 min. Cells were then washed in low pH media three times and then incubated in normal media for 24 h and then assayed for viral N-protein.", "figure_related_sentences": "In the C3 cells, the αIIb 968 tryptophan (W) and the 693 isoleucine (I) residues were replaced with cysteines to prevent the separation of the cytoplasmic domains through constitutive disulfide bond formation (Luo et al., 2004) (Figure 9). Exposure of CHO-A24 and CHO-C3 cells to SNV for 5 min produced a twofold increase in PAC1 binding to A24 cells compared with the resting state (Figure 9A), with no significant change in PAC1 staining of C3 cells in the same setting (Figure 9B). Staining of CHO-A24 cells with PAC1 in the presence of 1 µM GRGDSP did not rise above background in SNV-stimulated cells compared with mock-treated cells (Figure 9C). Quantitative analysis of the gel was performed using a BioRad Molecular Imager. The data indicate that GRGDSP inhibited infection (Figure 9D). We then showed that blocking of the αIIbβ3–RGDP2Y2R interaction with a soluble GRGDSP peptide inhibits full integrin activation and infection (Figure 9).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010013696_TII_01/figure/2010013696_TII_01_8.png"], "tampered": false, "paper_ids": ["2010002000"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010074157_TII_02/figure/2010074157_TII_02_3.png", "question_id": "consistency_233", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 4. DLS inhibits chemokine-mediated signaling in CCR5-transfected 3T3 cell lines. Approximately 200,000 3T3.T4.CCR5 cells were grown overnight per well in a 6-well plate. On the following day, the media was replaced with 2 ml of serum-free medium. After 2–3 h, DLS (20 μM) or the CCR5-specific antagonist, TAK779 (2 μM), were added to respective wells, incubated for 30 minutes at 37 °C, after which 10 nM of RANTES (A) or MIP-1β (B) was added to indicated wells. The cells were harvested in RIPA after washing with cold PBS at the indicated times. 30 μg of protein was run in 4–20% Bis-Tris gel, transferred and probed with mouse anti-pERK antibody (upper panel), stripped and again probed with rabbit anti-total ERK antibody (lower panel). The results reveal that DLS partially allows RANTES-induced ERK activation but surprisingly does not block MIP-1β-induced ERK activation in 3T3.T4.CCR5 cells.", "figure_related_sentences": "3T3.T4.CCR5 cells were grown overnight and then pretreated with DLS (20 μM) or the CCR5-specific antagonist, TAK779 (2 μM) for 30 minutes at 37 °C, after which 10 nM of MIP-1β or RANTES were added to cultures. The cells were harvested in RIPA after washing with cold PBS at the indicated times. The results (Figure 4) reveal that DLS partially blocks RANTES-induced ERK activation in 3T3.T4.CCR5 cells. Surprisingly, MIP-1β-induced ERK activation was not affected by DLS using this cell line. TAK779 at 2 μM only demonstrated a 20–30% inhibition of ERK phosphorylation in these CCR5-expressing cells.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010074157_TII_02/figure/2010074157_TII_02_3.png"], "tampered": false, "paper_ids": ["2010002043"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010040108_TII_02/figure/2010040108_TII_02_0.png", "question_id": "consistency_234", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "FIGURE 1 Dickkopf-1 (DKK1) inhibition reverses suppressive tumor immune microenvironment of a syngeneic gastric cancer (GC) model. (A) Schematic of DKK1 inhibitor (WAY-262611) treatment schedule in GC subcutaneous model. (B) Representative images of tumors and (C) tumor volumes of mouse forestomach carcinoma (MFC)-challenged 615-line mice. (D–K) Proportions of (D) CD8+/CD45+ cells, (E) tumor necrosis factor-α (TNF-α) +/CD45+ cells, (F) γ-interferon (IFN-γ) +/CD45+ cells, (G) natural killer (NK)1.1+/CD45+ cells, (H) Gr-1+/CD11b+ cells, (I) CD86+/F4/80+ cells, and (J) CD163+/F4/80+ cells in tumors were detected by flow cytometry (FCM). (K–O) Proportions of (K) CD8+/CD45+ cells, (L) NK1.1+/CD45+ cells, (M) Gr-1+/ CD11b+ cells, (N) CD86+/F4/80+ cells, (O) and CD163+/F4/80+ cells in spleens were detected by FCM. Data with error bars are shown as mean ± SEM. *p< 0.05, **p< 0.01, ***p< 0.001, ****p< 0.0001. D, day", "figure_related_sentences": "To investigate whether DKK1 inhibition showed antitumor efficacy in GC models, we established an MFC-challenged GC syngeneic immunocompetent mouse model and a T cell-deficient mouse model, followed by treatment with DKK1 inhibitor (WAY-262611) or DMSO (control group for WAY-262611) as indicated (Figures 1A and S1A). An interesting finding was that the tumor size and tumor volume increased significantly in GC immunocompetent mice (Figure 1B,C). The FCM analysis showed increased tumoral and splenic infiltration of CD8+ T cells (Figure 1D,K) andhigher proportions of tumoral IFN-γ+ lymphocytes and TNF-α+ lymphocytes (Figure 1E,F). Increased proportions of tumoral NK cells and decreased proportions of splenic MDSCs and M2 macrophages were found after DKK1 inhibition (Figure 1G,M,O). We also found that, although not statistically significant, the NK cells (p= 0.0863) in the spleen showed a tendency to increase and the MDSCs and M2 in the tumor (p= 0.0915, p= 0.0873) tended to decrease after inhibiting DKK1 inhibition (Figure 1H,J,L). However, M1 macrophages in the tumors showed no significant changes, but increased in the spleens after DKK1 inhibition (Figure 1I,N).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010040108_TII_02/figure/2010040108_TII_02_0.png"], "tampered": false, "paper_ids": ["2010002073"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010049515_TII_02/figure/2010049515_TII_02_2.png", "question_id": "consistency_235", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 3. p53 expression at both the protein and mRNA level. (A) Western blot of p53 protein in SDHx variant-positive CS/CSL (patient ID—SDHx variant: 829LL-S163P, 1965ML-S163P, 2094GR-H50R, 2549MP-G12S, 2854PS-S163P, 2894KP-H50R) and normal control groups. Upper panel shows the protein profile under normal culture condition, and lower panel after cells treated with 4 μM proteasomal inhibitor MG132 for 4 h. Tubulin served as a loading control in both conditions. (B) Relative levels of p53 were quantitated by densitometry and normalized to tubulin. Results are fold change compared with normal control cells, with (upper panel) or without MG132 treatment (lower panel). Data were presented as (mean ± SEM). *P < 0.05. (C) Relative TP53 mRNA expression by quantitative RT–PCR in SDHx variant-positive samples compared with normal controls, with glyceraldehyde 3-phosphate dehydrogenase (GAPDH) as internal control. (D) Immunoprecipitation of p53 from control and SDHvar+ LCL whole-cell lysate blotting for NQO1 and p53, *indicates the light chain band of IgG.", "figure_related_sentences": "Exposure of cells to high levels of ROS leads to oxidative stress, and should induce a p53-mediated response including apoptosis, whereas we observed the opposite in our cases. Therefore, we decided to investigate if p53 is somehow modified in our patient samples in order to escape the expected apoptotic regulation. Western blots showed reduced p53 protein expression in the majority of samples harboring SDHx variants compared with normal controls (Fig. 3A and B, upper panels). In contrast to p53 protein levels, TP53 mRNA expression was not changed in SDHx variant-positive samples compared with controls (Fig. 3C), suggesting that the loss of p53 protein was not from downregulated TP53 transcript. Cells treated with proteasome inhibitor MG132 preserved the loss of the p53 protein phenomenon in SDHx variant-positive cells (Fig. 3A and B, lower panels), indicating that the loss of p53 protein is most likely due to enhanced protein degradation. The multiple bands >53 kDa are likely ubiquitinated p53 resulting from proteasomal inhibition.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010049515_TII_02/figure/2010049515_TII_02_2.png"], "tampered": false, "paper_ids": ["2010002143"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010074872_TII_02/figure/2010074872_TII_02_8.png", "question_id": "consistency_236", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 9. Alizarin-red assay to bone matrix mineralization. (A) Staining (Scale bar: 100 μm), and (B) Quantitative calcium level deposition. Data are expressed as the mean ± S.D (n = 3). *p < 0.05, **p < 0.001.", "figure_related_sentences": "Extracellular matrix mineralization and quantitative calcium-level deposition were determined at 14 days postculture by Alizarin red staining. As shown in Figure 9A, in the presence of His‑βCD‑PH and HP‑βCD‑PH, matrix mineralization was decreased clearly compared with the control. Free PH in DMSO at a concentration of 20 μM was selected as a control, since it induced the most positive osteogenesis effect for bone regeneration in a previous study. It is postulated that sustained release of PH as a result of the equilibrium between PH in inclusion complexes of βCD derivatives and PH in cell-culture medium during differentiation had a significant positive effect on matrix mineralization. There was a difference between His‑βCD‑PH and HP‑βCD‑PH for matrix mineralization. Bone-matrix mineralization in the presence of His‑βCD‑PH was higher than that for HP‑βCD‑PH (Figure 9B). As shown in this figure, calcium-level deposition was significantly decreased when hASCs were cultured with His‑βCD‑PH and HP‑βCD‑PH at 50 μM concentration compared with the control. The results indicated that in addition to increased solubility of PH by inclusion-complex formation, His conjugation as a penetrative group contributed to increased bone mineralization. Electrostatic internalization of the His‑βCD‑PH inclusion complex by MSC membranes and their postendosomal escape followed by penetration into the nucleus might lead to better transfer of PH with consequent increase in bone-matrix mineralization. For detailed investigation on the effect of His‑βCD‑PH and HP‑βCD‑PH on hASCs for bone differentiation, real-time PCR was performed at 14 days postculture to investigate late bone-marker gene (OCN and OPN) expression.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010074872_TII_02/figure/2010074872_TII_02_8.png"], "tampered": false, "paper_ids": ["2010002283"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010119081_TII_02/figure/2010119081_TII_02_2.png", "question_id": "consistency_237", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Fig. 3. Effects of curcumin on serum TGF-β1 and lung TGF-β1 and CTGF expression in irradiated rats. (A) Serum concentrations (n = 5–6 per group) of TGF-β1 in control (CTL), radiation (RT), radiation+curcumin (RT+Cur), and curcumin (Cur) rats. (B) Western blot showing TGF-β1 and CTGF in lung from each group. (C) Quantification of lung TGF-β1 from western blot analysis. Densitometry values of each protein were normalized to α-tubulin and represented as arbitrary units (A.U.) relative to CTL levels. Data (n = 5–6 per group) are presented as mean ± SEM. *p < 0.05 vs. CTL rats; †p < 0.05 vs. RT rats.", "figure_related_sentences": "To evaluate whether curcumin could attenuate radiation-induced collagen synthesis in rat lungs, we assessed serum TGF-β1 levels by ELISA and TGF-β1 and CTGF expression levels with western blots (Fig. 3). Serum TGF-β1 levels from irradiated rat lungs were significantly decreased compared to irradiated curcumin-treated rats (Fig. 3A). Western blots revealed that radiation-induced TGF-β1 and CTGF expression were reduced by curcumin (Fig. 3B and C).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010119081_TII_02/figure/2010119081_TII_02_2.png"], "tampered": false, "paper_ids": ["2010002308"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010079947_TII_01/figure/2010079947_TII_01_0.png", "question_id": "consistency_238", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. Effects of NFKBIE knockdown on the expression levels of SLC19A1 and ABC transporters. Quantitative gene expressions of NFKBIE (A), SLC19A1 (B), ABCC1 (C), ABCC5 (D), and ABCG2 (E) genes in control (gray) and NFKBIE knockdown (black) MH7A treated with or without 0.01, 0.1, 1, 5, and 10 mM methotrexate (MTX) application for 24 h in the presence or absence of 20 U/mL IL-1b and 20 U/mL TNF-a were measured by qRT-PCR. Statistical significance was analyzed using the unpaired t-test (*p<0.05). The results are presented as the mean ± standard error of the mean (SEM) of at least three independent experiments.", "figure_related_sentences": "To investigate the effects of NFKBIE knockdown on the expressions of drug membrane transporters, we confirmed expression by qRT-PCR. The NFKBIE expression level in the NFKBIE knockdown group was almost 18–20% of the control expression level under many conditions (Figure 1A). NFKBIE knockdown could reduce the SLC19A1 expression (Figure 1B), whereas there was no obvious alteration in the expressions of the ABC transporters (Figure 1C–E).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010079947_TII_01/figure/2010079947_TII_01_0.png"], "tampered": false, "paper_ids": ["2010002328"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010057714_TII_02/figure/2010057714_TII_02_3.png", "question_id": "consistency_239", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 4. Direct vascular effects of particles in rat aortic rings in vitro. Effect of diesel exhaust particles (filled circle), carbon nanoparticles (u) (both 100 μg/mL), or vehicle (open circle) (Krebs buffer) on (A) phenylephrine contraction in mN, (B) phenylephrine contraction as a percentage of maximum contraction, (C) acetylcholine, and (D) sodium-nitroprusside-induced vasodilatation. Diesel exhaust particles did not affect contraction to phenylephrine (P=0.64), but inhibited vasorelaxation to acetylcholine (P<0.001) and sodium nitroprusside (P=0.019) compared with control. Although there was an apparent rightward shift in the dose-response curve to acetylcholine and sodium nitroprusside with carbon nanoparticles, vasorelaxation was not significantly affected (P=0.139 and P=0.224, respectively). Effect of (E) aqueous and (F) organic separation of diesel exhaust particles on acetylcholine responses. (E) Aqueous-washed diesel exhaust particles (grey square), and aqueous extract from diesel exhaust particles (open square), inhibit vasodilation to acetylcholine (P<0.01 for both), with the combined effects of both constituents being equal to that of untreated particles (filled circle). (F) Organic-washed diesel exhaust particles (s) inhibited acetylcholine induced vasodilatation (*P=0.010); the magnitude of this effect was not different from that of untreated diesel exhaust particles (filled circle) (P=0.103). The organic extract of diesel exhaust particles (inverted triangle) had no effect on vasorelaxation to acetylcholine (P=0.645). n=6 for all groups.", "figure_related_sentences": "In vitro exposure of rat aortic rings to diesel exhaust particles produced a small decrease in the maximum contractile response to phenylephrine (P=0.03, unpaired t-test; Figure 4A), without affecting the sensitivity to phenylephrine. Pure carbon nanoparticles did not significantly alter responses to phenylephrine and, overall, both particles had no significant effect on concentration-response curves to phenylephrine when expressed as a percentage of maximum contraction (P=0.64 and P=0.86, respectively; two-way ANOVA; Figure 4B). Compared with vehicle control, vasorelaxation to acetylcholine was induced following exposure to diesel exhaust particles (P<0.001; Figure 4C). Although there was an apparent rightward shift in the concentration-response curve to acetylcholine with carbon nanoparticles, vasorelaxation was not significantly affected (P=0.139; Figure 4C). Diesel exhaust particles caused a small but significant inhibition of relaxation to sodium nitroprusside (P=0.019) compared with control (Figure 4D), whereas carbon nanoparticles did not (P=0.224). Following separation of the aqueous soluble constituents from diesel exhaust particulate matter, both washed particles and solution were able to inhibit vasodilator responses to acetylcholine (P<0.01 for both), with the combined effects of both constituents being equal to that of untreated particles (Figure 4E). Dichloromethane-washed diesel exhaust particles markedly inhibited acetylcholine-induced vasodilatation (P=0.010); the magnitude of which was not statistically different from untreated diesel exhaust particles (P=0.103; Figure 4F). Accordingly, the organic extract of diesel exhaust particles removed by dichloromethane had no effect on relaxation to acetylcholine (P=0.645).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010057714_TII_02/figure/2010057714_TII_02_3.png"], "tampered": false, "paper_ids": ["2010002366"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010013350_TII_01/figure/2010013350_TII_01_2.png", "question_id": "consistency_240", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Defect of fertilization in Pmis2−/− mice and transgenic rescue. (A) Pmis2+/− males and Pmis2−/− females delivered normal numbers of pups when mated with WT mice, whereas the combination of WT females with Pmis2−/− males produced no pups. (B) The defect was at the fertilization level, because no fertilized eggs were recovered from the superovulated females mated with Pmis2−/− males. Parentheses indicate the numbers of eggs examined. (C) Top, the targeting vector used to disrupt the mouse Pmis2 allele. Bottom, the transgene used for rescue experiments to express Pmis2 under the control of the Clgn promoter. The arrows indicate the positions of primer sets to detect the targeted alleles. (D) Genotyping of tail-tip DNA from various groups of mice by PCR amplification with the primers indicated in Materials and Methods. (E) Protein extracts from Pmis2+/− and Pmis2−/− and spermatozoa from transgenically rescued Pmis2−/− mice were subjected to immunoblot analysis using anti-PMIS2 and anti–His-tag antibodies. ADAM2 was indicated as a reference marker for the successful extraction of proteins. (F) Litter sizes obtained by mating Pmis2+/− and transgenically rescued Pmis2−/− males with WT female mice. The sterile phenotype of Pmis2−/− mice was restored by the insertion of the Pmis2 transgene.", "figure_related_sentences": "Pups were obtained from Pmis2+/− males and Pmis2−/− females, whereas Pmis2−/− male mice sired no pups in spite of their normal mating behavior (Figure 3A). Eggs were collected from the oviducts after examining for the formation of a vaginal plug, and the fertilization rate was examined. We could obtain no fertilized eggs from the females that mated with Pmis2−/− males, whereas almost 0% of the eggs were fertilized in the females mated with Pmis2+/− males (Figure 3B). Therefore we generated transgenic mouse lines harboring hexahistidine (His6)-tagged Pmis2 cDNA under the regulation of the Clgn promoter and performed a gene rescue experiment (Figure 3C). Both of these transgenic mouse lines expressing His6-tagged PMIS2 protein were shown to rescue the infertile phenotype by being incorporated into the Pmis2−/− genetic background (Figure 3D–3F), indicating that the recombinant PMIS2 with His6 tag could function normally and that infertility in the Pmis2−/− mice was caused directly by the absence of PMIS2 from spermatozoa.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010013350_TII_01/figure/2010013350_TII_01_2.png"], "tampered": false, "paper_ids": ["2010002370"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010027154_TII_01/figure/2010027154_TII_01_2.png", "question_id": "consistency_241", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 3. a) Schematic representation of different functionalization approaches of SWCNTs with 2_2 and results after three hot filtration steps. b) TGA trace of the reaction outcome (rt to 1000°C, 10°Cmin^-1 under air) for the degree of functionalization (black: pristine SWCNTs, blue: Rev-MINT, red: Irrev-MINT and green: Supra-MINT). c) Results of TGA analysis (Δm at 420°C) after synthesis and three consecutive hot filtration steps for the three functionalization approaches. d) Summary of the degree of functionalization of all samples according to Equation (2) after synthesis and three hot filtration steps.", "figure_related_sentences": "Having macrocycles 1_2 and 2_2 as well as efficient conditions for disulfide exchange in hand, we tested our key hypothesis that SWCNTs could act as convex templates during the reversible covalent opening and closing of the concave rings (Figure 3 a, top). The collected solids werewashed multiple times by suspending in dichloromethane, ultrasonication, and filtration to remove weakly adsorbed exTTF macrocycles and reagents. The so-obtained “Rev-MINT” samples (Figure 3 a, top) were dried under reduced pressure and subjected to thermogravimetric analysis (TGA) to quantify the degree of functionalization (DoF). In the “Irrev-MINT” experiment, we irreversibly oxidized the dithiols 1 or 2 in the presence of the SWCNTs (Figure 3 a, middle), and in the “Supra-MINT” experiment, we simply sonicated the macrocycles 1_2 or 2_2 together with the SWCNTs (Figure 3 a, bottom). As shown in Figure 3 b (for the case of MINT-2_2), all samples obtained by the three different experimental approaches show a significant weight loss in the TGA trace between 300 and 400°C (Figure 3 b). Although Δm is an intuitive figure of merit that is particularly useful for comparing experiments within this study (Figure 3 c), it is not a reliable metric for comparing MINTs with macrocycles of different molar masses. When performing TGA analysis immediately after the three different functionalization procedures described above, we found relatively similar Δm/DoF values for the Rev-MINT-1_2 (33±2%/0.56±0.06%) and Rev-MINT-2_2 (45±3%/0.57±0.07%) samples, which suggests that the ring size leads to a small, yet statistically significant difference in the reaction outcome. Similar Δm/DoF values were also observed for the Irrev-MINT-2_2 (33±2%/0.55±0.06%) and Supra-MINT-2_2 (26±1%/0.40±0.02%) reference experiments (Figure 3 c,d). After thorough rinsing with dichloromethane and drying of the samples, TGA analyses were performed to quantify the remaining Δm/DoF values and thus determine the amount of macrocycles that were not removed during this procedure (Figure 3 a, right). Moreover, we performed these experiments in triplicate and repeated the hot filtration procedure three times in sequence until we reached a “plateau” for the Δm and DoF values (Figure 3 c,d). As expected from an approach that features error correction, TGA analysis showed that over three hot filtration cycles the Rev-MINT samples exhibit only a small decrease in the Δm and DoF values (about 5%/0.14%, Figure 3 c,d, blue).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010027154_TII_01/figure/2010027154_TII_01_2.png"], "tampered": false, "paper_ids": ["2010002376"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010011621_TII_02/figure/2010011621_TII_02_3.png", "question_id": "consistency_242", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Increased TCR–CD3 recycling is revealed in hypertonic medium. (A) Uptake of Alexa647-labeled transferrin by Jurkat T cell lines expressing SLAP-GFP or control (GFP) in the presence or absence of hypertonic medium, as assessed by FACS. (B) Expression of CD3ε on Jurkat T cell lines expressing SLAP-GFP or control (GFP) incubated in hypertonic medium, as assessed by FACS. Data are presented as the absolute increase in CD3ε MFI expression relative to time 0. Data in A and B are the mean of three experiments ± SEM. (C) CD3ε expression on WT or SLAP−/− thymocytes incubated in hypertonic medium for 0 or 6 h, as assessed by FACS. Data are representative of three mice per genotype. (D) MFI of CD3ε expression on WT or SLAP−/− thymocytes incubated in 0.45 M hypertonic medium for the indicated time in the presence or absence of cycloheximide (CHX). (E) MFI of CD3ε expression on WT or SLAP−/− DP thymocytes incubated for the indicated time in cell culture medium only. Data in D and E are the mean of three mice per genotype ± SEM (error bars).", "figure_related_sentences": "To validate the use of hypertonic medium to inhibit TCR–CD3 internalization, we first analyzed the uptake of fluorescently labeled transferrin by the transferrin receptor, a process that requires clathrin-mediated endocytosis (Mellman, 1996; Schmid, 1997). Because DP thymocytes do not express the transferrin receptor, we first tested the effect of hypertonic medium on Jurkat T cell lines that stably expressed either SLAP-GFP fusion or GFP alone as a control. Transferrin uptake via the transferrin receptor was completely inhibited by hypertonic medium in both stable cell lines (Figure 4A), demonstrating that hypertonic medium blocks clathrin-mediated endocytosis regardless of whether SLAP is present or not. We analyzed the effect of SLAP on CD3ε expression while clathrin-mediated endocytosis was blocked in Jurkat T cells. Strikingly, we were able to detect downregulation of CD3ε surface expression over the time course of the experiment in the control cell line. However, upregulation of CD3ε by Jurkat T cells was markedly inhibited in the presence of SLAP (Figure 4B). To investigate whether SLAP expression affects upregulation of CD3ε on DP thymocytes as it did in our model cell line, we incubated thymocyte single-cell suspensions in hypertonic medium and followed CD3ε expression over time. Both WT and SLAP−/− DP thymocytes downregulate CD3ε on the cell surface over the course of the assay (Figure 4C). However, quantitation demonstrated that CD3ε upregulation was substantially increased in SLAP−/− DP thymocytes as compared with WT controls (Figure 4D). Interestingly, the observed upregulation of CD3ε in hypertonic medium is comparable with the estimated amount of CD3ε present in the recycling pool (Figure 3C), indicating that increases in the size of the TCR–CD3 recycling pool can be revealed upon incubation of thymocytes in hypertonic medium. Notably, the uptake of fluorescently labeled transferrin by double-negative thymocytes (which express low, but detectable, levels of the transferrin receptor) was inhibited in the presence of hypertonic medium (unpublished data), indicating that hypertonic medium inhibited clathrin-mediated endocytosis in our thymocyte cultures. Previous studies have reported that prolonged culture of DP thymocytes in the absence of TCR–MHC interactions results in upregulation of the TCR–CD3 complex by the stabilization of newly synthesized TCRζ chains (Bonifacino et al., 1990; Kearse et al., 1995). Indeed, both WT and SLAP−/− DP thymocytes up-regulate CD3ε when cultured in the absence of 0.45 M sucrose (Figure 4E). However, over this time course, the increase in CD3ε expression was markedly higher than the increase observed in thymocytes that were incubated in hypertonic medium. In addition, most of the CD3ε upregulation that was observed in hypertonic medium was detected after only 2 h in culture, a time at which little or no CD3ε upregulation had yet occurred in the absence of 0.45 M sucrose. Furthermore, incubation of thymocytes in cycloheximide to inhibit protein synthesis had no effect on the upregulation of CD3ε in hypertonic medium (Figure 4D). In contrast, in parallel experiments using thymocytes cultured in media without 0.45 M sucrose, upregulation of CD3ε was sensitive to cycloheximide treatment (unpublished data), demonstrating that cycloheximide effectively inhibited protein synthesis in our cultures.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010011621_TII_02/figure/2010011621_TII_02_3.png"], "tampered": false, "paper_ids": ["2010002377"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010018540_TII_01/figure/2010018540_TII_01_3.png", "question_id": "consistency_243", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Fluorogram of HDL apoproteins isolated from rough- and smooth-endoplasmic reticulum fractions. Young chickens were administered t-[aH]leucine and, after 10 min, the livers were removed, fractionated into RER and SER fractions, and the HDL contained within these fractions was isolated by centrifugal flotation and immunoprecipitation. The apoproteins were analyzed by SDS PAGE and identified by fluorography. The details of the procedures are given in Materials and Methods. Lanes 2 and 4 represent nascent HDL apoproteins obtained by immunoprecipitation from the contents of the RER and the SER fractions from 2 g of liver. Lanes 1 and 5 represent nascent HDL obtained by flotation from the contents of the RER and SFR fractions from 56 g of liver. Lane 1 shows the apoprotein pattern of serum HDL obtained by flotation. Measurements, x 10 -3.", "figure_related_sentences": "There was a small amount of radioactivity in the high molecular weight range, which could be due to aggregation of protein, but there was no evidence of the presence of radioactive proteins of lower molecular size than apoprotein AI (Fig. 4, lanes 3 and 4). By contrast, the contents of the RER and the SER cell fractions did not yield radioactive proteins in complexes that could be floated to a buoyant density (1.063-1.21 g/ml) similar to that of serum HDL (Fig. 4, lanes 1 and 2). This indicates that apoprotein A1 is present in these cell fractions but has not been sufficiently complexed with lipids to allow it to gain its appropriate buoyant density.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010018540_TII_01/figure/2010018540_TII_01_3.png"], "tampered": false, "paper_ids": ["2010002382"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010019350_TII_02/figure/2010019350_TII_02_5.png", "question_id": "consistency_244", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Cell culture experiments analysing the effects of reggie-1 on Wg and Hh secretion. (A) Effects of overexpression of reggie-1 on Wg secretion measured by Western blots. Serum albumin is shown as the loading control for the medium samples. (B) Effects of overexpression of reggie-1 or a reggie dominant-negative construct on secretion of Wg, Hh or secreted luciferase (sluc) measured by enzymatic assay. Bars represent means±s.e.m. from 12 experiments. P-values from Student’s t-test are shown; ‘ns’ means non-significant (P≥0.05). (C) GFP-Wg media from panel A were subjected to sucrose-density ultracentrifugation. Thirteen fractions were collected (numbers and sucrose density in alternating fractions are shown on top). (D, E) S2 cells transfected with Wg together with reggie-1 (D) or EGFP (E) were co-cultured with cells independently transfected with DsRed. Accumulation of the anti-Wg signal in DsRed-cells is much higher if Wg was produced by reggie-1 transfected cells. (F, G) Pulse–chase Texas-red dextran colocalization assays. S2 cells transfected with Wg together with reggie-1 (F) or empty vector (G) were co-cultured with cells independently transfected with EGFP. Accumulation of Wg in dextran-positive early endosomes is much higher if Wg was produced by reggie-1-transfected cells (arrowheads in panel F). Note that unlike in panels D and E where identical confocal settings were used to record anti-Wg staining, the settings in panels F and G were independently optimized for highest resolution. (H) Reggie-1 does not stimulate Wg endocytosis cell-autonomously: S2 cells were transfected with Wg plus reggie-1-EGFP and co-cultured with cells independently transfected with reggie-1-DsRed. Incorporation of Wg into the Wg-receiving cells was the same whether they overexpressed reggie-1-DsRed or not (white arrows).", "figure_related_sentences": "We found a dramatically lower uptake of Wg by DsRed cells when Wg was provided by the reggie-1-overexpressing cells (Figure 5D and E). To prove that this intracellular Wg staining resulted from endocytosis, we performed pulse–chase assays with fluorescent dextran beads and found that Wg provided by reggie-1-expressing cells colocalized with dextran in early endocytic compartments (Figure 5F) whose particulate appearance was reminiscent of the punctate staining seen in wing discs. In contrast, Wg obtained from control-transfected cells was strongly endocytosed by the co-cultured cells (Figure 5G). We could also demonstrate that reggie-1 overexpression did not increase Wg uptake cell-autonomously: overexpression of reggie-1 in the cells co-cultured with Wg-producing cells did not increase Wg uptake by these co-cultured cells (Figure 5H). Thus, reggie-1 overexpression was changing the properties of Wg in the Wg-producing cells, such that this Wg became markedly more internalizable by the co-cultured cells. This conclusion agrees well with our in vivo observations. Such increased uptake of Wg might be solely due to enhanced secretion of Wg by reggie-1-overexpressing cells, or also due to a molecular change in the form Wg is secreted. For example, reggie-1 overexpression could enhance Wg packing into lipoprotein particles. To investigate this possibility, we performed sucrose-density ultracentrifugation of the Wg medium from reggie-1- or control-transfected cells (Figure 5C).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010019350_TII_02/figure/2010019350_TII_02_5.png"], "tampered": false, "paper_ids": ["2010002384"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010028694_TII_02/figure/2010028694_TII_02_8.png", "question_id": "consistency_245", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "(A) In vivo antitumor activity of PSSN10 and various DOX formulations in a syngeneic murine breast cancer model (4T1.2). Three injections were administered on d 0, 3 and 6. **P<0.01. (B) Kaplan-Meier survival of 4T1.2 tumor-bearing mice after various treatments. (C) Histological analyses of H&E stained sections of tumor tissues collected on d 19.", "figure_related_sentences": "Figure 5A shows the in vivo therapeutic effects of PSSN10 and DOX/PSSN10 with free DOX and DOXIL (a clinical formulation of liposomal DOX) as controls (5 mg DOX/kg). The PSSN10 carrier alone showed a significant effect in inhibiting tumor growth, comparable to those of DOX and DOXIL. This is in contrast to the in vitro cytotoxicity, in which PSSN10 showed little effect (Figure 3A, 3B), suggesting that the IDO inhibitory effect rather than a direct cytotoxic effect contributed to the in vivo antitumor activity of PSSN10. DOX formulated in PSSN10 micelles showed inhibited antitumor activity that was significantly higher than that of DOXIL. Figure 5B shows the Kaplan-Meier survival curves of 4T1.2 tumor-bearing mice following different treatments. All for mulations improved the survival rate compared to the saline control group. Among them, the DOX/PSSN10 formulation resulted in the longest overall survival, with a median survival of 40 d. Figure 5C shows the histology of tumors following different treatments. Tumors from the mice treated with DOX/PSSN10 had more necrotic/apoptotic cells compared to the tumors from the other treatment groups.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010028694_TII_02/figure/2010028694_TII_02_8.png"], "tampered": false, "paper_ids": ["2010002385"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010041575_TII_02/figure/2010041575_TII_02_3.png", "question_id": "consistency_246", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Cannabinoids induce AMPK-dependent GAPDH nuclear translocation. Representative confocal images of GAPDH translocation in Panc1 cell nuclei after 12h treatment with 200mM GW or ACPA in the absence or presence of a pretreatment for 1h with 20mM NAC or 20mM C.C. Values are the means of three independent experiments (±S.D.)", "figure_related_sentences": "we analysed the cellular distribution of GAPDH after the treatment with GW or ACPA. Figure 4 shows the confocal images where GAPDH appear to be translocated into the nucleus of the cells after 12-h cannabinoid treatments. This effect was stimulated by NAC or CC, indicating its dependence on ROS and AMPK activation. These data suggested that the increased level of G3P observed in the metabolomic analysis could arise from the diminished presence of GAPDH in the cytosol of cells treated with cannabinoids.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010041575_TII_02/figure/2010041575_TII_02_3.png"], "tampered": false, "paper_ids": ["2010002386"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010041585_TII_02/figure/2010041585_TII_02_5.png", "question_id": "consistency_247", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "CPEB1 reduces senescence by regulating p53 distribution in glioma cells. (a) A cell growth assay was used to analyze the function of CPEB1 siRNA in glioma cell proliferation. *Po0.05. (b) The effect of CPEB1 siRNA on senescence in glioma cell lines as determined with SA-b-gal staining. Arrows indicate the green senescent cells. *Po0.05. (c) Transmission electron micrographs of the morphology of glioma cells transfected with CPEB1 siRNA. (d) The regulation of p53 and p21 by CPEB1 siRNA. (e) The changes in the cellular distribution of p53 induced by CPEB1 siRNA in the U87 cell line", "figure_related_sentences": "The knockdown of CPEB1 reduced senescence by regulating p53 distribution in glioma cells. Burns DM et al.18 demonstrated that CPEB1 was repressed by miR-122, and the inhibition of CPEB1 activated p53 translation in human skin fibroblasts. p53 is one of the hallmarks of cellular senescence;19 therefore, the p53-mutated cell line U251 and the p53 wild-type cell line U87 were selected for use in the following experiments. U251 and U87 cell growth was stimulated by CPEB1 knockdown. The inhibition was observed at 72h in U251 cells and at 48 and 72h in U87 cells (Figure 2a). Senescent cells can be detected with an assay that detects senescence-associated b-gal (SA-b-gal) activity.20 Whether in p53-mutated or in wild-type glioma cells, CPEB1 knockdown initiated senescence (Figure 2b). Next, the morphology of U251 and U87 cells treated with a CPEB1 small interfering RNA (siRNA) was observed with transmission electron microscopy. The results revealed vacuolar degeneration in the cytoplasm of the U251 cells. However, there were two different lesions in the U87 cells: one was cellular edema, including cytoplasm, nucleus and mitochondria; another lesion was mitochondrial vacuolar degeneration (Figure 2c). After the knockdown of CPEB1, the level of expression of p53 was decreased in the U251 cells but not changed in the U87 cells (Figure 2d). Furthermore, it was discovered that the knockdown of CPEB1 induced the overexpression of p21, which is downstream of p53 (Figure 2d). Even though the CPEB1 knockdown did not influence the expression of p53 in the U87 cell lysate, the loss of CPEB1 expression still enhanced the expression of the downstream p53 effector p21. The data indicate that the knockdown of CPEB1 impeded wild-type p53 transport to the cytoplasm in U87 cells (Figure 2e). This observation supports the hypothesis that the knockdown of CPEB1 induces cell senescence in glioma in a p53-dependent manner.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010041585_TII_02/figure/2010041585_TII_02_5.png"], "tampered": false, "paper_ids": ["2010002387"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010041660_TII_02/figure/2010041660_TII_02_3.png", "question_id": "consistency_248", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure4 Inhibition of ADAM17 modulates phosphorylation of p44 MAPK. (a) Levels of p44 MAPK phosphorylation were decreased after ADAM17 inhibition with medium and high concentrations of BMS-561392, whereas p42 MAPK phosphorylation was not affected in immature HOG oligodendrocytes. (b) Microglial BV-2 cells were treated with different concentrations of BMS-561392 and TAPI-1. MAPK p44 phosphorylation was significantly decreased using 0.3mM of the inhibitor, while higher concentrations decreased or even abolished p44 MAPKphosphorylation. MAPKp42phosphorylation was not affected by BMS-561392 or TAPI-1treatment. The results are the mean of three independent experiments and are represented as a percentage of the control condition (n¼3 per condition)", "figure_related_sentences": "On the contrary, levels of p44 MAPK phosphorylation were significantly increased with the highest concentration of BMS-561392 (2.7mM) in oligodendrocytes (Figure 4a), whereas in microglial cells phosphorylation of p44 MAPK was significantly decreased by the lower concentration of BMS-561392 (0.3mM) and significantly diminished below detection by the high concentration of the inhibitor (2.7mM) (Figure 4b).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010041660_TII_02/figure/2010041660_TII_02_3.png"], "tampered": false, "paper_ids": ["2010002388"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010131029_TII_01/figure/2010131029_TII_01_0.png", "question_id": "consistency_249", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Fig. 1. Protective effects of PTZ against ROT-induced toxicity on primary ventral midbrain cultures. (A) Representative scans from immunocytochemical preparations acquired with a 20× objective lens. PTZ protects TH+ (A11) and MAP2 neurons (A12) against the deleterious effects of ROT with ensuing increase in the percentage of DA-containing neurons (A13). Insets correspond to high magnification images. Scale bar: 200 μm. Data are representative of 20–40 neurons per group obtained from seven independent cultures. (B) Morphometric neurite reconstruction in 3D. PTZ treatment preserved neurite length (B6), number of segments (B7), and branch points (B8) in ROT-exposed cells. Insets represent a 4× zoomed image. Scale bar: 200 μm. Two images for each condition and experiment were averaged. Data from four independent cultures were combined to determine means ± SEM (C) Ratiometric measurements of reduced and oxidized thiol groups. High resolution confocal images obtained with a 40× objective and image analysis demonstrated that administration of PTZ restores the SS/SH ratio altered in ROT-treated cells. Scale bar: 20 μm. On an average, 25–30 neurons per condition were tested from three independent cultures. ****p < 0.0001, ***p < 0.001, **p < 0.01 and * p < 0.05 compared to VEH + VEH. ####p < 0.0001 and ###p < 0.001 relative to PTZ + VEH (one-way ANOVA followed by Newman-Keuls multiple comparisons test).", "figure_related_sentences": "Administration of 50 nM ROT to 5-day-old primary rat DA cell cultures over a period of 5 days leads to neuron degeneration. We therefore sought to investigate the potential neuroprotective properties of PTZ (Fig. 1). We first examined whether unsubstituted PTZ improves cell survival (Fig. 1 A). PTZ alone did not show either neurotoxic or neurotrophic effects while ROT treatment resulted in a dramatic decrease in the number of TH+ neurons (∼40%, Fig. 1 A11), MAP2 neurons (∼83%, Fig. 1 A12), and the percentage of DA-producing neurons (∼45%, Fig. 1 A13) as compared to the control group (VEH). Administration of PTZ (10, 20 or 50 nM) 1 h after ROT incubation significantly protected TH+ and MAP2 neurons from ROT toxicity (p < 0.0001 for all doses of PTZ tested). We further evaluated the efficacy of PTZ in preserving neurite morphometry (Fig. 1 B). Total neurite length (∼32%, Fig. 1 B6) and both number of segments (∼59%, Fig. 1 B7) and branches (∼68%, Fig. 1 B8) were significantly reduced in response to ROT. However, PTZ was able to abrogate ROT-induced neurite shrinkage and fragmentation. To investigate the putative effect of PTZ on oxidative damage, a redox immunohistochemistry approach was used for the sensitive quantification of intracellular redox state in situ in both DA and non-DA neurons (Fig. 1 C). The thiol (SH)/disulfide (SS) redox balance system shifted toward disulfide bound generation in ROT-stimulated cells relative to VEH group (Fig. 1 C5 vs C10; 0.58 ± 0.01 vs 1.01 ± 0.03 TH+ neurons and 0.59 ± 0.02 vs 1.10 ± 0.05 MAP2 neurons, p < 0.0001). In contrast, the SS/SH ratio was reduced near to basal levels in the PTZ + ROT groups in comparison to cells incubated with ROT alone (Fig. 1 C10 vs C15, C20 and C25; p < 0.0001). Ratio metric analysis of disulfide and thiol species in DA (C26) and non-DA (C27) neurons. Taken together, these findings provide strong support for the concept that PTZ has a potent protective effect against ROT-mediated neuron degeneration and oxidative impairment in vitro.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010131029_TII_01/figure/2010131029_TII_01_0.png"], "tampered": false, "paper_ids": ["2010002389"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010000184_TII_01/figure/2010000184_TII_01_9.png", "question_id": "consistency_250", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 6.Vault RNA expression varies in actino-mycin D–treated MEFs. Northern analysis of RNA prepared from wild-type (MEF11) and mTep1-deficient (MEF8 and MEF5) cells treated with actinomycin D for the indicated times. The membrane was probed with mTR (top), stripped,and reprobed first with mVR (middle) and next with an antisense 5S oligonucleotide (bottom). Control (C) samples were not treated with drug.", "figure_related_sentences": "In wild-type MEF cells, vRNA has a half-life of 5–6 h; however, in both mTep1 MEF lines, the vRNAs half-life is reduced to 0.3–1 h (Fig. 6, mVR). The blots were stripped and reprobed with either mTR or 5S (a loading control).No effect is seen on the stability of the mTR (Fig. 6).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010000184_TII_01/figure/2010000184_TII_01_9.png"], "tampered": false, "paper_ids": ["2010002395"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010005088_TII_01/figure/2010005088_TII_01_2.png", "question_id": "consistency_251", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Fig. 5 Lethality of antiprogestins towards ovarian cancer cells. OV2008 or SK-OV-3 cells were cultured in the presence of 40 μM RU-38486, ORG-31710 or CDB-2914. After 60 h (OV2008) or 120 h (SK-OV-3), floating cells were collected, adhered to a microscope slide, stained with DAPI, and microscopic phase contrast and fluorescence images were obtained from the same fields. As positive control of apoptotic cell death, floating cells from cisplatin (CDDP) treated cells were included in the morphological studies a and b. Adherent untreated cells are also shown (CONTROL). Scale bar, 20 μm. c A similar experiment was done in which all floating and attached cells were pelleted, total DNA was isolated, subjected to agarose electrophoresis, stained with SYBR Gold nucleic acid stain, and photographed with the Amersham Typhoon fluorescence imaging system. A 100 base pair (bp) marker was run in parallel. (d) OV2008 cells were exposed to DMSO (Vehicle) or 40 μM RU-38486, ORG- 31710 or CDB-2914 for 72 h. Whole protein extracts were obtained and separated by electrophoresis, and immunoblots were probed with the indicated antibodies to recognize cell cycle and cell death related proteins. The housekeeping gene GAPDH was used as protein loading control", "figure_related_sentences": "The majority of the cells at this point in time appear detached and with morphological features similar to those shown by cisplatin-treated cells (Fig. 5a). SK-OV-3, although less sensitive to the lethal effects of the antiprogestins, show a remarkably reduced number of still adherent cells after 96 h treatment with a concomitant enhanced number of floating cells with similar morphological features to those shown by cisplatin-treated cells (Fig. 5b). Fragmentation of the DNA was clearly observed after 60 h exposure to 40 μM RU- 38486 and ORG-31710 in OV2008 cells, whereas the effect was less pronounced in CDB-2914-treated cells at the same point in time (Fig. 5c, left panel). For SK-OV-3 cells, treatment with 40 μM of the three compounds showed DNA laddering upon 120 h incubation (Fig. 5c, right panel). To further explore the signaling molecules involved in the lethal action of antiprogestins in ovarian cancer cells, we treated OV2008 cells with 40 μM antiprogestins and collected whole cell extracts after 24, 48 or 72 h incubation. Results in Fig. 5d show that RU-38486 caused cleavage of the full-length caspase-3, 116 kDa PARP substrate into the 86 kDa cleaved and inactive form 24 h after treatment, an effect that was more evident at 72 h, in association with downregulation of cell cycle related proteins Cdk-2 and p21cip1, and cleavage of p27kip1. Altogether results in Fig. 5 suggest that concentrations of antiprogestins higher than 10 μM are lethal to p53-wild type OV1008 and p53-null SK-OV-3; the molecular mediators of the cell death mechanisms,as well as their interrelationship with cell cycle regulatoryproteins, differ among the antiprogestins and warrantfurther investigations.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010005088_TII_01/figure/2010005088_TII_01_2.png"], "tampered": false, "paper_ids": ["2010002398"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010065349_TII_02/figure/2010065349_TII_02_0.png", "question_id": "consistency_252", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. MLH1 deficiency has little effect on telomere maintenance. (A) Immunoblotting shows the absence of MLH1 in HCT116 and the restore of MLH1 expression in HCT116MLH1. (B) Telomere length measured by TRF analysis in HCT116 and HCT116MLH1. (C) Immunoblotting shows MLH1 knockdown in HeLa cells. Two shRNA sequences were used to deplete endogenous MLH1. Cells were collected at 7 days after puromycin selection. (D) Telomere length measured by TRF analysis in HeLa expressing MLH1 shRNA.", "figure_related_sentences": "To determine whether MLH1 deficiency impacted telomere maintenance, we first examined telomere length with the TRF assay using two cell lines from different origins: first, the MLH1-deficient human colorectal tumor cell line HCT116 and its isogenic cell line complemented with wild-type MLH1, HCT116MLH1 (39) and second, HeLa depleted of MLH1 with two shRNA sequences. Western blotting confirmed the absence of MLH1 expression in HCT116 and MLH1 knockdown in HeLa (Figure 1A and C). Due to the partial depletion of MLH1 in HeLa cells, we then used an independent assay to test MLH1 deficiency. It is well established that MLH1 deficiency leads to resistance against the cytotoxicity induced by MNNG, an alkylating agent that induces DNA damage (40–42). As shown in Supplementary Figure S1, both HCT116 and HeLa shMLH1 knockdown cells displayed resistance to MNNG, further confirming MLH1 deficiency. TRF analysis showed affected significant difference in telomere length between HCT116 and HCT116MLH1 (Figure 1B), or between HeLa control and MLH1 knockdown cells (Figure 1D).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010065349_TII_02/figure/2010065349_TII_02_0.png"], "tampered": false, "paper_ids": ["2010002403"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010065654_TII_01/figure/2010065654_TII_01_1.png", "question_id": "consistency_253", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2. A full-length human ORF1p suppresses retrotransposition of chimeric L1s containing human ORF1 sequence. (A) Schematic of neomycin-tagged, full-length chimeric L1s containing human and/or mouse codon-optimized ORF1 and ORF2 sequences. Human ORF1 and human ORF2 are designated as H1 and H2, mouse ORF1 and mouse ORF2 are designated as M1 and M2, respectively. (B) Results of L1 retrotransposition assay in HeLa cells using plasmids expressing H1 H2, H1 M2, M1 H2 or M1 M2 L1s cotransfected with an empty (control), hORF1 or mORF1 expression plasmids. (C) Results of L1 retrotransposition assay performed as in (B) using NIH 3T3 cells. The number of G418 resistant colonies was normalized to the control flask (L1 construct cotransfected with an empty plasmid) for each independent experiment. Asterisks (*) denote statistical significance between listed constructs and the control (n = 3, t-test, P < 0.05).", "figure_related_sentences": "To assess which of the L1-encoded proteins may be involved in the response to ORF1p trans effect on L1 retrotransposition, we used previously reported chimeric L1 constructs containing codon-optimized ORF1 and ORF2 sequences of either human or mouse origin (Figure 2A) (28). Specifically, we used the H1H2 and M1M2 L1s, which contain only human or mouse sequences, respectively, the H1M2 L1, which contains human ORF1 and mouse ORF2 sequences, and the M1H2 L1 that contains mouse ORF1 and human ORF2 sequences. Transient transfections of HeLa cells with these plasmids and with either an empty plasmid (control), or plasmids expressing hORF1 or mORF1 proteins demonstrated that hORF1p suppressed mobilization of L1 constructs containing human ORF1 sequence (Figure 2B, black bars: H1H2 and H1M2). mORF1p had no negative trans effect on retrotransposition of human, mouse, or chimeric L1s (Figure 2B, dark gray bars). The same experiment was also carried out in NIH 3T3 cells. Consistent with the results obtained in HeLa cells, co-transfection of hORF1 expression plasmid with the H1H2 or H1M2 L1 constructs containing human ORF1 sequence suppressed their retrotransposition (Figure 2C, black bars: H1H2 and H1M2). Expression of hORF1p did not have any effect on retrotransposition of M1M2 or M1H2 L1 elements. Cotransfection of the mORF1p expression plasmid with the M1M2 or H1M2 L1 constructs containing mouse ORF2 (mORF2) sequence resulted in a significant (6–6-fold) increase in their retrotransposition in NIH 3T3 cells relative to the control plasmid (Figure 2C, dark gray bars versus light gray bars). Toxicity associated with human ORF1p expression, an increase in L1 toxicity in the presence of trans ORF1p or ORF1p trans effect on retrotransposition through protein interactions with L1 or host proteins could explain the ORF1p-mediated decrease in L1 retrotransposition. ORF1p expression in trans did not have any adverse effect on cell viability when the full-length ORF1p was transiently expressed alone (Supplementary Figure S2A and B) or in combination with human L1 using a previously reported toxicity assay (29,45) (Supplementary Figure S2C). In combination with the results shown in Figure 2, these findings support the involvement of the L1-encoded ORF1 protein in the trans effect of ORF1p on human L1 retrotransposition.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010065654_TII_01/figure/2010065654_TII_01_1.png"], "tampered": false, "paper_ids": ["2010002414"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010065702_TII_02/figure/2010065702_TII_02_2.png", "question_id": "consistency_254", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2. Hypoxia induces release of miR-574-3p from Ago2 suppressing RISC-mediated activity. (A) Hypoxia switches binding of miR-574-3p from Ago2 to hnRNP L. U937 cells were cultured in hypoxia for 24 h. Lysates with the same quantity of total protein were subjected to IP with anti-hnRNP L, -Ago2 or pre-immune IgG antibodies, and then to qRT-PCR using probes against miR-574-3p or miR-17. Signal of hnRNP L RIP-RT-qPCR for miR-17 under normoxia (Figure S1C) was used as normalizer. (B) Hypoxia induces EP300 expression. U937 cells were cultured in normoxia or hypoxia for 24 h and lysates immunoblotted using anti-EP300 antibody. (C) hnRNP L inhibits canonical RISC activity of miR-574-3p and stimulates EP300 expression. U937 cells were transfected with pcDNA3-Myc-hnRNP L (1 μg) or hnRNP L siRNA (with or without miR-574-3p or anti-miR-574-3p) (200 nM) in normoxia or hypoxia as indicated, and EP300 expression measured by immunoblot. Transfections with pcDNA3 vector or scrambled siRNA were used as negative controls. (D) hnRNP L induces EP300 mRNA by antagonizing miR-574-3p. U937 cells were treated as in (C) and total RNA subjected to qRT-PCR using EP300-specific probe and normalized to β-actin. Cond. Med.: conditioned medium. In (A–D), data are presented as mean ± SD (n = 3, Student’s t-test).", "figure_related_sentences": "To begin to explore the influence of hnRNP L binding to miR-574-3p on its RISC-driven tumor-suppressive activity, we showed that hypoxia induces expression of EP300, an established downstream target of miR-574-3p (Figure 2B) . EP300 is a transcriptional co-activator of NF-κB, a key transcription factor regulating inflammatory gene expression, and HIF1A (hypoxia-inducible factor 1, β-subunit), a transcription factor that stimulates expression of hypoxia-inducible genes including VEGFA. Moreover, overexpression of hnRNP L decreased EP300 expression in normoxia, and the basal level was restored by co-introduction of pre-miR precursor mimetics (chemically modified, double-stranded RNAs that mimic endogenous mature miRNAs) of miR-574-3p (Figure 2C, left). Likewise, hnRNP L knockdown enhanced EP300 expression in hypoxia, and co-introduction of anti-miR-574-3p inhibitor restored the level (Figure 2C, right). Changes in EP300 mRNA levels nearly paralleled changes in protein, suggesting that regulation by miR-574-3p-RISC and hnRNP L is primarily at the level of RNA stability rather than translation (Figure 2D). These results are consistent with a mechanism in which binding of miR-574-3p by hnRNP L prevents its interaction with RISC, thereby overcoming its suppressive effect on gene expression. To investigate whether miR-574-3p bound to hnRNP L binds RISC, the interaction between hnRNP L and Ago2, a major RISC constituent, was determined by co-immunoprecipitation (IP) and immunoblot analysis. hnRNP L did not interact with Ago2 or Dicer in either hypoxia (Supplementary Figure S2C, left panel) or normoxia (not shown). The reverse pull-down confirmed that hnRNP L does not interact with RISC (Supplementary Figure S2C, right panel). Thus, hypoxia-activated capture of miR-574-3p by hnRNP L inhibits its canonical RISC-mediated gene silencing activity, thereby inducing EP300 expression.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010065702_TII_02/figure/2010065702_TII_02_2.png"], "tampered": false, "paper_ids": ["2010002416"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010009856_TII_01/figure/2010009856_TII_01_0.png", "question_id": "consistency_255", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Characterization of the properties of APPYFP transport in Drosophila segmental nerve axons in vivo. (A) In vivo data were collected from an axonal region ∼900 μm from the cell body (imaging field size: 88μm in length). A standard data set consisted of four video segments of 15-s duration recorded for 10 individual animals. (B) Top panel, first frame of a time-lapse sequence showing APPYFP transport. Middle panel, a band (5 pixels in thickness) flanking the axon is extracted from each frame. Bottom, left panel, bands from all frames are pasted top-to-bottom to form a kymograph. Bottom, right panel, computationally recovered vesicle trajectories color-coded and overlaid on the kymograph; colors were selected randomly to differentiate crossing trajectories. Truncated vesicle trajectories were excluded for each movie. (C) Classification of vesicle trajectories (total number of trajectories = 1890; all error bars show SEM): anterograde, 32.3% ± 2.3%; retrograde, 18.2% ± 2.1%; stationary, 50.2% ± 4.0%; reversing, 9.1% ± 1.2%. (D) Distribution of anterograde segmental velocities. Although the mean segmental velocity was 0.86 μm/s, the distribution of segmental velocities had a long tail toward higher values, with 41% of vesicles moving faster than 0.8 μm/s and 13% moving faster than 1.6 μm/s (maximal anterograde segmental velocity was 2.85 μm/s). (E) The distribution of anterograde segmental velocities has three distinct modes (cyan), with centers increasing as multiples (based on fit): mode 1, ∼0.4 μm/s; mode 2, ∼0.8 μm/s (2×); and mode 3, 1.6 μm/s (4×). See Table S1 for a definition of exact mode centers, spreads, and fractions of segment population. Superposition of all three modes is shown in red.", "figure_related_sentences": "We probed the transport behavior of individual APP vesicles in vivo by using SG26.1 Gal4 (Gal4 gene enhancer trap strain) to drive the expression of UAS-APPYFP in Drosophila. Because the expression of SG26.1 Gal4 is confined to a subset of ventral ganglion neurons, APPYFP movement could be tracked with single-axon resolution within segmental nerves. Analysis of green fluorescent protein–tagged EB1 (EB1-GFP) transport in these neurons confirmed that movement away from cell bodies is microtubule plus end–directed and anterograde (Supplemental Figure S1A), consistent with a previous report (Stone et al., 2008). Using high spatial (0.126 micron) and temporal (10 Hz) resolution imaging, we characterized the movement of APP in an otherwise wild-type background (Figures 1, A–E, and S1, A–F, and Supplemental Movie S1; see Materials and Methods): 32.3% of the vesicles moved anterogradely and 18.2% moved retrogradely (Figure 1, A–C), whereas 50.2% were stationary and 9.1% reversed direction with an average switch frequency of 6.09 switches/min (Figures 1C and S1B). Switches generally did not involve pausing, consistent with a previous report of lipid droplet movement in Drosophila embryos (Welte et al., 1998). Thus directional switches are mediated by an apparently instantaneous change in the balance of active motors. Considerable evidence demonstrates that APP movement is driven by kinesin-1 (Koo et al., 1990; Ferreira et al., 1992; Amaratunga et al., 1993; Simons et al., 1995; Tienari et al., 1996; Kamal et al., 2000; Szodorai et al., 2009). We observed that a substantial fraction of APPYFP vesicles traveled at velocities faster than those observed for kinesin-1 motors in vitro, up to a maximum of 2.33 μm/s (Figure 1D), consistent with previous reports. Kinesin-1-driven movement in vivo, which is substantially faster than in vitro, may be related to a different regulation of the ATPase cycle in vivo. Alternatively, multiple kinesin motors may coordinate to generate faster velocities, as speculated by Kural and colleagues (Kural et al., 2005). The latter would be incompatible with the independence of velocity and motor number for kinesin-1 seen in vitro (Howard et al., 1989; Block et al., 1990; Spudich, 1990). Additionally, it would be inconsistent with more recent in vivo data of lipid droplet movement in Drosophila embryos, which suggest that neither velocity nor run length changes significantly with varying amounts of kinesin-1 (Shubeita et al., 2008). To test the hypothesis that the velocities and run lengths of APP vesicles may be determined by the amount of kinesin-1, we performed genetic, biochemical, and statistical analyses to correlate the number of active kinesin-1 molecules with vesicle behavior. We tested four predictions made by this hypothesis. A first prediction is that the anterograde velocity distribution should be nonnormal with multiple modal peaks reflecting differential occupancy of active motors. We tested this possibility by statistical mode analysis (Fraley and Raftery, 2002) and found that the distribution was best fit by three modes (Figure 1E; see Materials and Methods). Thus the first prediction is fulfilled. Interestingly, multimodal cargo velocity distributions have been reported previously in motility assays under substantial mechanical load of viscoelastic drag and in intracellular transport of PC12 cells and Xenopus melanophores (Hill et al., 2004; Levi et al., 2006; Gagliano et al., 2010). A second prediction is that increased velocities should correlate with increased run lengths (or reduced pause frequency; Spudich, 1990). Because our relatively short observation window of 15 s leads to truncation of run length for many vesicles (Figure S1C), we tested for a correlation of segmental velocity with pause frequency (see Supplemental Material). For controls, the anterograde correlation coefficient was −0.45, indicating that the faster the cargo, the lower the average probability of a pause. Thus the second prediction is also fulfilled.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010009856_TII_01/figure/2010009856_TII_01_0.png"], "tampered": false, "paper_ids": ["2010002417"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010009958_TII_01/figure/2010009958_TII_01_5.png", "question_id": "consistency_256", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Transfer of [14C] cholesterol and loss of acceptor liposomes (loss of fluorescence) mediated by NPC2 and fusogenic Sap C. (A) Cholesterol transfer depending on the concentration of bNPC2 in the presence or absence of 20 mol% BMP. (B) bNPC2-mediated fluorescence loss, which implies membrane fusion. As a control we investigated radiolabeled cholesterol transfer (C) and the loss of acceptor (D) mediated by the fusogenic Sap C, containing a C-terminal hexahistidine tag. Mean ± SEM in the range of 12% (n = 4). BMP, bis(monoacylglycero)phosphate; NPC2, Niemann-Pick disease type 2 protein; Sap C, saposin C.", "figure_related_sentences": "Sap C is required for the lysosomal degradation of membrane-bound glucosylceramide (53). Its fusogenic property had been established by measuring its ability to destabilize lipid vesicles (66–69). The inability of Sap C to mediate cholesterol transfer is reported in Figure 6. Figure 6A clearly shows that bNPC2 mediates cholesterol transfer both in the absence and presence of BMP at low pH. Measurements from the same experiment showed significant loss of fluorescence (Figure 6B), especially at pH 7.4 in the presence of BMP. Under the same experimental conditions, unglycosylated Sap C did not mediate the transfer of cholesterol (Figure 6C) but mediated loss of fluorescence up to 80% in the presence of BMP at low pH (Figure 6D). NPC2 also mediated loss of fluorescent acceptor vesicles, although to a lesser extent than Sap C. Size measurements on liposomes composed of 10 mol% cholesterol, 4 mol% marker lipid, and 86 mol% PC showed that in the absence of NPC2, the initial signal curve generated by dynamic light scattering persisted for 60 min and represented liposomes with a mean diameter of 105 ± 10 nm. However, in the presence of NPC2, a new signal curve grew with time at the expense of the initial curve. This curve represented diameters in the range 600–900 nm, suggesting that larger aggregates had formed with time (Supplementary Figure II). Because this interesting phenomenon seemed to be worth testing in more detail, we designed a fusion assay.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010009958_TII_01/figure/2010009958_TII_01_5.png"], "tampered": false, "paper_ids": ["2010002418"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010006583_TII_02/figure/2010006583_TII_02_2.png", "question_id": "consistency_257", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Fig. 3 Mitochondrial DNA (mtDNA) damage in M. mulatta aorta. MtDNA damage was quantified from genomic DNA preparations extracted from aorta. a mtDNA damage determined by QPCR; (n = 3/group/tissue). The inset (lanes 1–3 are unexposed control, lanes 4–6 are ETS exposed) shows the full-length QPCR product (Long) that is used to quantify relative levels of mtDNA damage (less product indicates increased damage) relative to control, whereas the lower inset (lanes 1–3 are unexposed control, lanes 4–6 are ETS exposed) shows the smaller QPCR product (Short) that is used for mtDNA copy number normalization. Bar graph shows the relative level of mtDNA damage (normalized for copy number) between exposure groups. b mtDNA damage detected by Fpg digestion followed by QPCR. The inset shows QPCR results for Fpg-treated unexposed controls and ETS-exposed animals (lanes 1–3 and 4–6, respectively), showing the full-length QPCR product (less product indicates increased mtDNA damage). The bar graph shows the difference in Fpg detectable lesions (±Fpg) in ETS-exposed monkeys relative to unexposed controls. Unexposed, M. mulatta age-matched control; ETS, M. mulatta exposed to 1 mg/m 3 ETS during gestation to 1 year of age. Asterisks indicate significant difference (P B 0.05) from unexposed M. mulatta", "figure_related_sentences": "To determine whether perinatal ETS exposure impacted mitochondrial integrity, quantitative PCR was performed on aortic tissue collected from M. mulatta. Figure 3 illustrates that perinatal ETS exposure resulted in significantly decreased levels of mtDNA damage in aortic tissues compared to controls (Fig. 3a; less product in the ‘‘long’’ row on inset reflects more mtDNA damage). To investigate whether an additional measure of DNA damage yielded differences between unexposed and ETS-exposed animals, aortic DNA samples were also treated with formamido- pyrimidine (fapy) DNA glycosylase (Fpg), which cleaves DNA at specific lesions such as 7, 8-dihydro-8-oxoguan- onine, 8-oxoadenine, fapy-guanine, methy-fapy-guanine, fapy-adenine and 5-hydroxy-cytosine. Figure 3b shows that Fpg treatment revealed net increased levels of mtDNA lesions in exposed animals compared to unexposed controls (less product on inset reflects more mtDNA damage)。", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010006583_TII_02/figure/2010006583_TII_02_2.png"], "tampered": false, "paper_ids": ["2010002420"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010169875_TII_02/figure/2010169875_TII_02_1.png", "question_id": "consistency_258", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2. NF-κB activation by hypertonicity in part depends on p38 kinase activity. (A) Protein lysates from cells challenged or not (Ctl) with either LPS, TNF-α, or hypertonic medium (NaCl) were analyzed by immunoblot for phosphorylated forms of p38 kinase, p38 substrate ATF2, ERK, JNK, and JNK substrate c-Jun. PKAc was used as a loading control. (B) Protein lysates from cells pretreated or not for 30 min with 10 µM SB203580 (a p38 kinase inhibitor), 10 µM U0126 (a MEK inhibitor), or 10 µM SP600125 (a JNK inhibitor) and then challenged or not (Ctl) with hypertonic medium were analyzed by immunoblot for phosphorylated forms of ATF2, ERK, and c-Jun. (C) Fold protein phosphorylation following hypertonic challenge over baseline levels (Ctl) is shown at left. Fold increase of protein phosphorylation by pharmacological inhibitors in hypertonicity-challenged cells is shown at right. (D and E) Real-time PCR analysis of TNF-α transcript after LPS, TNF-α, or hypertonic challenge in the presence or absence of either SB203580 or U0126 (D, left) or SP600125 (E, left). (D and E) Right, effects of SB203580 and SP600125 on TNF-α transcript expression were echoed by RNAi against p38α (D) or c-Jun (E), respectively. Immunoblots depicting decreased expression levels of target protein by RNAi are also shown. PKAc was used as a loading control. (F) Left, real-time PCR analysis of AR, BGT1, and SMIT transcripts in cells treated or not with a pharmacological inhibitor and challenged or not (Ctl) with hypertonic medium. Data are represented as fold induction over nonstimulated cells in the absence of an inhibitor. Similar to SB203580, RNAi against p38α reduced the enhancer effect of hypertonicity on AR, BGT1, and SMIT transcript expression (right). The effects of pharmacological compounds and RNAi on basal mRNA expression levels for this and all other figures are shown in Supplemental Figure S2.", "figure_related_sentences": "Influence of each of these MAPKs on hypertonicity-inducible NF-κB activation, we measured the effects of pharmacological inhibition of p38 kinase, ERK, and JNK. A comparison of ATF2 (used as an indicator for p38 kinase activity), ERK, and c-Jun (used as an indicator for JNK activity) phosphorylation revealed that each inhibitor (10 µM SB203580 against p38 kinase, 10 µM U0126 against mitogen-activated protein kinase kinase [MEK], and 10 µM SP600125 against JNK) decreased its targeted protein activity but not the activities of the other two kinases, in response to 30 min of hypertonic challenge (Figure 2, B and C). Pharmacological inhibition of either p38 kinase, ERK, or JNK activity increased NF-κB activity induced by 3 h of LPS or TNF-α challenge, as suggested by decreased TNF-α mRNA expression (Figure 2, D and E, left). Pharmacological inhibition of p38 kinase, but not ERK, activity, greatly reduced TNF-α transcript accumulation after 3 h of hypertonic challenge. RNAi against p38 kinase mimicked the attenuating effect of SB203580 on increased TNF-α mRNA expression by either LPS, TNF-α, or hypertonic challenge, although the inhibitory effect was smaller (Figure 2D, right). Altered MCP-1 and IκB mRNA expression in response to pharmacological MAP kinase inhibition is shown in Supplemental Figure S3. Notably, although SB203580 blunted the hypertonicity-induced increase of MCP-1 mRNA expression, IκB mRNA expression was unchanged. Unexpectedly, the stimulatory effect of hypotonicity was enhanced by JNK inhibition (Figure 2C). We further investigated this effect by RNAi knockdown against c-Jun. c-Jun protein expression increased in response to 3 h of hypertonic challenge, whereas RNAi efficiently decreased expression of both total and phosphorylated pools of c-Jun (Figure 2C). The effects of RNAi c-Jun knockdown on inducible TNF-α mRNA expression echoed those obtained by pharmacological JNK inhibition, i.e., a decrease of LPS and TNF-α inducibility and enhanced inducibility by hypertonicity. Increased TNF-α expression in response to c-Jun knockdown was moreover found to occur despite decreased p38 kinase phosphorylation (Figure 2C). These results suggest that NF-κB activation by hypertonicity is repressed by JNK but partly depends on p38 kinase activity. We focused our investigations on this latter dependence.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010169875_TII_02/figure/2010169875_TII_02_1.png"], "tampered": false, "paper_ids": ["2010002507"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010184669_TII_02/figure/2010184669_TII_02_0.png", "question_id": "consistency_259", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. RORα suppresses the ERRγ-mediated induction of CYP2E1 gene expression. (A) Primary cultures of mouse hepatocytes were treated with 20 μM ACEA in the presence or absence of 20 μM CS, 5 μM SR1078 or 20 μM JC1–40 for 24 h. Or the hepatocytes were infected by Ad-GFP or Ad-ERRγ and then underwent the same treatment. The protein (top) and mRNA (bottom) levels were measured by western blotting and qRT-PCR, respectively. (B) Hepatocytes were infected by Ad-GFP or Ad-ERRγ and then treated with 20 μM ACEA for 24 h. Or the hepatocytes were infected by Ad-GFP or Ad-ERRγ together with Ad-GFP or Ad-RORα for 24 h. The protein (top) and mRNA (bottom) levels were measured by western blotting and qRT-PCR, respectively. (C) Hepatocytes were transfected with si-GFP, si-RORα or si-ERRγ for 24 h and then treated with 20 μM ACEA, 20 μM CS, 5 μM SR1078 and/or 20 μM JC1–40 for 24 h as indicated. The protein level was measured by western blotting. The data represent mean ± SD. *P < 0.05 versus vehicle treatment or Ad-GFP infection; #P < 0.05 versus ACEA treatment or Ad-ERRγ infection (n = 3). Representatives of at least three independent experiments with similar results are shown.", "figure_related_sentences": "RESULTS RORα represses the ERRγ-mediated induction of CYP2E1 expression CYP2E1 is a key enzyme causing alcohol-induced oxidative stress and liver injury. To illustrate the pathophysiological role of RORα in ALDs, we examined whether RORα affected expression level of CYP2E1 under ethanol exposure. Since alcohol-induced liver injury is associated with CB1 receptor activation, we employed a synthetic CB1 receptor agonist, ACEA, to mimic alcohol-induced CYP2E1 gene expression (14–16). Treatment of RORα agonists such as CS, SR1078 and JC1–40 largely increased the expression level of CYP2E1 protein as well as transcripts that were induced by ACEA treatment in mouse primary hepatocytes (8,9). Expression level of a known transcriptional activator of CYP2E1, ERRγ, increased after ACEA treatment, but it was not affected by the RORα ligand treatment. Similarly, the CYP2E1 induction caused by adenovirus-mediated ERRγ gene transfer was increased by treatment with these RORα ligands (Figure 1A) (16). The similar pattern of CYP2E1 repression was observed at both transcript- and protein-levels when RORα was exogenously introduced by infusion of Ad-RORα, suggesting that the ERRγ-induced CYP2E1 gene transcription might be a target of RORα during chronic ethanol consumption (Figure 1B). Our observation that knockdown of either RORα or ERRγ gene transcription using si-RNA decreased the RORα agonist-induced CYP2E1 repression indicates the involvement of RORα in the ERRγ-mediated induction of CYP2E1 transcription (Figure 1C). Knockdown of RORα completely abolished the CS-, JC1–40- or SR1078-induced transcriptional activity of the RORE reporter, indicating that the effect of these compounds was mediated through RORα (Supplementary Figure S2).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010184669_TII_02/figure/2010184669_TII_02_0.png"], "tampered": false, "paper_ids": ["2010002592"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010130956_TII_01/figure/2010130956_TII_01_0.png", "question_id": "consistency_260", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Fig. 1. Long linear DNA fails to transfer by acoustic dispensing. PicoGreen® dsDNA dye was used to measure the fluorescent signal from long, linear lambda DNA (A) or supercoiled plasmid DNA (B) at a range of concentrations after 1 μl sample was transferred either by manual pipetting or acoustically using the Echo®, in triplicate. At concentrations above 2.5 μg/ml, lambda DNA does not transfer well on the Echo®. However, supercoiled plasmid DNA transfers efficiently at all tested concentrations. The concentration of 7 plasmid DNA samples was measured using the PicoGreen® reagent. The plasmid DNA samples were either transferred by manual pipetting (C) or using acoustic dispensing on the Labcyte Echo® 550 (D). All samples were tested in 3 replicates, as represented by different coloured bars. The data show that 3 samples failed to transfer by acoustic dispensing (samples 1–3) while one transfers with variable amounts (sample 5). (E) The plasmid DNA samples were run in 1% w/v agarose gel (in 1× TAE) at 80 V for 1 h; M = 1 Kb Plus DNA Ladder (ThermoFisher Scientific). Due to the large size of gDNA, it remains above the range of the ladder, as indicated by the red arrow. The gel shows the presence of gDNA in samples 1–3, which are those that did not transfer acoustically. (F) The concentrations of plasmid DNA samples in (C) and (D) were interpolated from a standard curve, generated using a plasmid DNA sample of a known concentration.", "figure_related_sentences": "We tested a selection of plasmid DNA samples in the miniaturised dsDNA quantification assay, with samples transferred either manually or by acoustic dispensing (Fig. 1C and D). The samples were also run on an agarose gel (Fig. 1E). When the concentration of the samples was interpolated from the standard curve in the assay (Fig. 1F), we observe that all of the tested samples have the expected concentration when transferred manually (Fig. 1C). However, some samples have no fluorescent readout when the transfer of the DNA was carried out acoustically (Fig. 1D). The agarose gel shows that those samples which failed to transfer acoustically on the Echo® are contaminated with gDNA (Fig. 1E, lanes 1–3). The miniaturised PicoGreen® dsDNA quantitation assay provides a quality control (QC) check for the presence of gDNA in plasmid DNA samples. The lack of a fluorescence signal indicates a failed transfer of a DNA sample. This failed transfer could be due either to a lack of DNA in the well or gDNA contamination. By testing the sample with manual transfer, the presence of DNA can be confirmed, indicating such a sample contains gDNA. In the London DNA Foundry, all plasmid DNA samples are run in the gDNA QC assay prior to their addition to our DNA parts library, to ensure that they will transfer as required. The variability of DNA concentration across replicates is hypothesised to indicate an intermediate level of gDNA contamination, which is undesirable in an acoustic DNA library workflow (Fig. 1C and D, sample 5).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010130956_TII_01/figure/2010130956_TII_01_0.png"], "tampered": false, "paper_ids": ["2010002650"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010184389_TII_01/figure/2010184389_TII_01_0.png", "question_id": "consistency_261", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. Massive, RDR-independent generation of CaMV vsRNAs in infected Arabidopsis. (A) Total RNA from pools of CaMV-infected (+) or mock-inoculated (−) wild-type control plants (Col-0 and Col-gl1) and mutants defective in host sRNA biogenesis: dcl2-5, dcl3-1, dcl4-2, rdr2-1, rdr6-15 and rdr2 rdr6 (all in Col-0) and dcl1-8 (in Col-gl1). Plants were harvested 1-month post-inoculation or, in the case of dcl1-8, 2 months post-inoculation. Total RNA was separated by 15% PAGE and then stained with ethidium bromide (EtBr). Lower and upper portions of the gels are shown, the latter for RNA loading comparison. Positions of synthetic 21 and 24 nt RNA oligonucleotides and endogenous 102 nt U6 snRNA are indicated. (B) Illumina deep-sequencing of sRNAs from mock-inoculated and CaMV-infected Arabidopsis wild-type (Col-0) and mutants (rdr1/2/6, dcl1-8 and dcl2/3/4) confirms massive production of RDR-independent vsRNA, comparable to the entire complement of host sRNAs. The graph shows the percentage of Arabidopsis and vsRNAs in the pool of 20–25 nt reads mapped to the Arabidopsis and CaMV genomes with zero mismatches.", "figure_related_sentences": "RESULTS AND DISCUSSION By ethidium bromide (EtBr) staining of size-separated RNA, we detected massive quantities of 21–26 nt RNAs in CaMV-infected Arabidopsis. CaMV-derived sRNAs appeared to be more abundant in infected plants than the complement of host sRNAs detected in the mock-inoculated control (Figure 1A). In contrast, EtBr staining of RNA from Cabbage leaf curl geminivirus or Oilseed rape mosaic tobamovirus infections yielded scarcely detectable levels of sRNAs (data not shown). Abundant amounts of sRNAs were still detected in CaMV-infected plants deficient in DCL1, which is required for host miRNA biogenesis (dcl1-8, a hypomorphic mutant). They were also detected in infected plants deficient in RDR2, RDR6 or both RDR6 and RDR2 required for host siRNA biogenesis (null mutants rdr2-1, rdr6-15 and double mutant rdr2/6) (Figure 1A). Thus, a large fraction of sRNAs detected by EtBr staining are likely to be vsRNAs of CaMV origin. The 24-nt sRNA signal was abolished in the null mutant dcl3-1, confirming that the biogenesis of this size-class of viral and host sRNAs is DCL3 dependent (7,14). To survey genome-wide interactions of CaMV with the plant RNA silencing machinery we sequenced sRNA populations from virus-infected wild-type and mutant plants using Illumina technology ([www.illumina.com](http://www.illumina.com)). The procedure selected for sRNAs with 50-phosphate and 30-hydroxyl groups, i.e. DCL activity products. Consistent with earlier reports (34,35), 81% of the 549,540 sRNA reads from mock-inoculated seedlings fell into the 20–25 nt range, of which 75% mapped to the Arabidopsis genome with zero mismatches; 24 nt and 21 nt reads were predominant (Figure 2A and Supplementary Table S1). Likewise, 81% of the 1,470,760 reads from CaMV-infected plants fell into the 20–25 nt range, of which 40% mapped perfectly to the Arabidopsis genome (∼120 Mb) and 39% mapped perfectly to the CaMV genome (∼8 kb) (Figure 1B, Supplementary Table S1). Among 20–25 nt vsRNAs, the 24 nt fraction was largest (47%), while the 21 and 22 nt fractions were second (27%) and third (14%) largest in abundance (Figure 2B), respectively. This size-class distribution agrees with our results for the relative abundance of CaMV-derived sRNAs detected by blot hybridization (14). To summarize, the gel analysis and sequencing data are in agreement and show that the vsRNA pool is comparable in size to the entire complement of host miRNAs and siRNAs. To investigate whether CaMV vsRNAs are redundantly amplified by RDR activities known to mediate sRNA biogenesis (6), we generated a triple null mutant rdr1 rdr2 rdr6 (rdr1/2/6) and sequenced sRNAs from infected rdr1/2/6 plants. In rdr1/2/6, 20–25 nt sRNAs perfectly matching the CaMV genome represented 54% of 748,199 reads, while those perfectly matching the Arabidopsis genome only represented 28% of the reads (Supplementary Table S1 and Figure 1B). The decreased percentage of host sRNAs in this mutant compared with the wild-type resulted from a 10-fold decrease in RDR2-dependent 24 nt sRNAs. In contrast to the profile for host sRNAs, the profile for vsRNAs did not change significantly in rdr1/2/6 relative to wild-type (Figure 2B and Supplementary Table S1). From this, we conclude that at the late stage of infection, CaMV-derived vsRNAs are largely produced independently of RDR1, RDR2 and RDR6. We cannot, however, exclude that CaMV vsRNAs can potentially be amplified by these RDRs at the earlier stages of infection or under certain conditions. In RNA virus infections of Arabidopsis, vsRNAs are amplified by RDR1 and/or RDR6; this amplification becomes most evident when a viral silencing suppressor gene is inactivated (8–11). The ability of the CaMV TAV protein to interfere with host RDR6-dependent sRNA pathways (19,20) could account for the lack of RDR6-dependent vsRNAs in CaMV-infected plants. Likewise, TAV may also inhibit production of RDR1-dependent vsRNAs. It would be interesting to investigate whether a CaMV mutant deficient for the silencing suppressor activity of TAV can generate RDR-dependent vsRNAs. However, the suppressor activity would first need to be genetically uncoupled from other TAV functions that are essential for viral replication. We also sequenced sRNAs from a hypomorphic mutant deficient for DCL1 (dcl1-8). In CaMV-infected dcl1-8, viral reads outnumbered Arabidopsis genome-derived reads due to the reduction in host miRNA accumulation (Figure 1B and Supplementary Table S1). Of 20–25 nt vsRNAs in dcl1-8, the fraction of 25 nt reads (17%) was significantly lower than that in wild-type plants (27%) (Figure 2B). This confirms our earlier finding that DCL1 contributes to the biogenesis of 21 nt vsRNAs (14). The role of DCL1 in vsRNA biogenesis is also supported by the sRNA sequence profiles we obtained for CaMV-infected dcl2 dcl3 dcl4 triple null mutant (dcl2/3/4) plants. The relative levels of 22 and 24 nt vsRNAs were drastically reduced, whereas the relative level of 24 nt vsRNA was increased compared to wild-type plants (Figure 2B and Supplementary Table S1).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010184389_TII_01/figure/2010184389_TII_01_0.png"], "tampered": false, "paper_ids": ["2010002673"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010005687_TII_02/figure/2010005687_TII_02_7.png", "question_id": "consistency_262", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Fig. 7 The effects of different concentrations of Emx2 and Pax6 on the development of sensorimotor cortical areas. It is the combination of the specific concentration of each molecule that determines the identity of the cortical region. Mutations that affect the quantities of either molecule alter cortical patterning. Adapted with permission from Bishop et al. (2002). \"Distinct actions of Emx1, Emx2, and Pax6 in regulating the specification of areas in the developing neocortex.\"J Neurosci 22(17): 7627–7638, Fig. 1", "figure_related_sentences": "The mature neocortex is partitioned into well-defined structurally and functionally distinct “areas” that are differentiated by their cellular organization and patterns of neuronal connectivity. Initial patterning of neocortex into cortical areas results from different molecular signals present in different regions of the neocortical proliferative zone. Two signaling molecules, Emx2 and Pax6, play an essential role in the early patterning of the presumptive neocortex. Emx2 and Pax6 are transcription factor proteins that are the molecular products of Emx2 and Pax6 gene expression. 1 These two signaling molecules are produced in opposite gradients along the anterior-posterior extent of the neocortical proliferative zone (see Fig. 7a). The concentration of Emx2 is lowest in posterior and medial regions, and lowest in anterior lateral regions; Pax6 has the opposite expression pattern. The interaction of these two gradients contributes to early patterning of the neocortex. High concentrations of Pax6 combined with low Emx2 induces progenitors to produce neurons appropriate for motor cortex (M1), while the reverse concentrations induce production of neurons for visual cortex (V1). At intermediate levels of both factors somatosensory cortices (S1) emerge. Studies of mutant mice, for which expression of either Emx2 or Pax6 is blocked (thus altering the balance of signals across the cortical proliferative zone), show systematic shifts in the organization of cortical areas. These studies confirm that it is the interaction of the two signaling molecules that induces change in the surrounding cell populations. When Emx2 expression is blocked, visual areas shrink and somatosensory and motor areas diminish (Fig. 7b); when Pax6 expression is blocked, visual areas enlarge while somatosensory and motor areas shrink (Fig. 7c). Thus it is the effect of the particular level of one molecular signal in combination with the particular level of another signal that produces the classical pattern of sensorimotor organization in the developing cortex. Since these original reports of the role of Pax6 and Emx2 signaling in neocortical patterning, it has become clear that the interactions are more complex. At least two additional molecules have been identified, Coup-TF1 and SP8. Both are produced in gradients. Coup-TF1 is expressed in greatest concentration in caudal-lateral regions, while SP8 is expressed in rostral-medial regions. As was the case with Pax6 and Emx2, blocking the expression of these genes results in dramatic alteration in the sensorimotor organization of the neocortex.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010005687_TII_02/figure/2010005687_TII_02_7.png"], "tampered": false, "paper_ids": ["2010002674"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010027005_TII_01/figure/2010027005_TII_01_7.png", "question_id": "consistency_263", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "FIGURE 8: Loss of C9orf72 in mice does not affect motor function and survival. (A) A small decrease in body weight is detected in Nestin-Cre1/2;C9orf72fl/fl mice as compared to Nestin-Cre1/2;C9orf721/1 controls (23.55%, p=0.019, linear mixed-effect model for repeated measurements [LME]; n≥11 for each genotype at each time point). (B–D) Rotarod performance and grip strength is similar in Nestin-Cre1/2;C9orf721/1, Nestin-Cre1/2;C9orf72fl/1, and Nestin-Cre1/2;C9orf72fl/fl mice (rotarod, p=0.084 and p=0.899; grip strength front, p=0.346 and p=0.295; front and hind, p=0.731 and p=0.305, LME). Data are shown as mean 6 standard deviation, n≥11 for each genotype at each time point. (E) Survival rates as shown by a Kaplan–Meier curve. Survival of Nestin-Cre1/2;C9orf72fl/fl mice is similar to control mice.", "figure_related_sentences": "A reduction in body weight was detected in all Nestin-Cre–positive mice, as has been previously reported for other studies using this Cre driver.20 However, even when considering this effect, Nestin-Cre1/2;C9orf72fl/fl mice displayed a small but significant decrease in body weight, as compared to Nestin-Cre1/2;C9orf721/1 control mice (23.55%, p=0.019). This difference was detected at the first time point of measurements and did not significantly change in time (Fig 8).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010027005_TII_01/figure/2010027005_TII_01_7.png"], "tampered": false, "paper_ids": ["2010002678"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010051408_TII_02/figure/2010051408_TII_02_1.png", "question_id": "consistency_264", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2. Maternal IE exposure alters gene expression in the hypothalamus and the pituitary. Rat dams received distilled water (Control Group; C); distilled water supplemented with 0.6 mg/L (iodine excess group; 5×) or distilled water supplemented with 7.3 mg/L (iodine excess group; 50×) throughout pregnancy and lactation. Thereafter, hypothalamic Trh mRNA content (A) and pituitary Trhr, Gh, Dio2, Tsha and Tshb mRNA contents (B) were analyzed by Real-Time PCR and normalized to Rpl19 mRNA content. Total pituitary TSHA and TSHB protein content (C) were analyzed through Western blotting analysis, using GAPDH as loading control. Results are expressed as means ± s.e.m. as fold change or arbitrary units (AU) (n = 10-12/group). *P < 0.05, **P < 0.01 vs C (ANOVA, Student-Newman-Keuls).", "figure_related_sentences": "Rat dams exposed to IE treatment presented a significant decrease in the hypothalamic expression of Trh mRNA (Fig. 2A). Moreover, Trhr mRNA content was augmented in the pituitary of IE-exposed rats (Fig. 2B). Interestingly, maternal pituitary Gh mRNA expression was increased, whereas Dio2 mRNA content was increased by both doses of IE treatment (Fig. 2B). The mRNA content of both subunits of TSH were also increased in the pituitary of rat dams exposed to IE treatment (Fig. 2B). In contrast, no significant alterations were observed in the TSHA protein content (Fig. 2C). Even so, IE significantly reduced the protein content of the beta subunit of TSH in the pituitary of the exposed dams in comparison to the control animals (Fig. 2C).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010051408_TII_02/figure/2010051408_TII_02_1.png"], "tampered": false, "paper_ids": ["2010002705"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010128451_TII_02/figure/2010128451_TII_02_3.png", "question_id": "consistency_265", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2 Peripheral blood was collected from BALB/c mice on day 30 after intraperitoneal injection of pristane (+) or NS (–) and the levels of (A) dsDNA-IgG; (B) dsDNA-IgM; (C) Sm-IgG; (D) Sm-IgM; (E) IL-6 and (F) total IgG were determined by ELISA. Values are means ± SEM, * p < 0.05, *** p < 0.001 vs. the control group.", "figure_related_sentences": "To confirm the establishment of pristane-induced lupus, serum autoantibodies and IL-6 were measured by ELISA. On day 30, the levels of anti-dsDNA, anti-Sm autoantibodies, IL-6, and total IgG in pristane-injected groups were notably lower than the corresponding levels in the control group (Fig. 2).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010128451_TII_02/figure/2010128451_TII_02_3.png"], "tampered": false, "paper_ids": ["2010002713"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010127589_TII_01/figure/2010127589_TII_01_2.png", "question_id": "consistency_266", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 3. Treatment with M002 resulted in cell death. (A) RD and SJCRH30 cell lines were treated with M002 at increasing MOI. After 72 hours of treatment, cell viability was measured with alamarBlue assays. Data are reported as mean ± standard error of the mean. There was a significant decrease in viability in both cell lines following M002 treatment. The LD50 was calculated for each cell line for M002 and was 3.3 ± 0.1 PFU/cell for embryonal RD cells and 4.1 ± 0.4 PFU/cell for the alveolar SJCRH30 cells. (B) To determine whether RMS cells were undergoing an apoptotic process following M002 treatment, immunoblotting for cleavage of PARP was completed. There were a significant decrease in total PARP staining and an increase in cleaved PARP staining in both cell lines with increasing MOIs. (C) To further verify apoptosis, a caspase 3 activation kit was utilized. There was a significant increase in caspase 3 activation following M002 treatment, indicating that the RMS cells were undergoing an apoptotic process.", "figure_related_sentences": "RMS cell lines (RD, SJCRH30) were treated for 72 hours with M002 at increasing concentrations (0–20 PFU/cell), and cell viability was measured with alamarBlue assays. Both cell lines had a significant decrease in viability following M002 treatment (Figure 3A). The lethal dose of virus that resulted in 50% killing (LD50) for the embryonal RD cells was 3.3 ± 0.1 PFU/cell and for the alveolar SJCRH30 cells was 4.1 ± 0.4 PFU/cell. Next, we investigated whether the viral-induced cell death was due to apoptosis. RD and SJCRH30 cell lines were treated with increasing concentrations of M002 (0–10 PFU/cell), and whole cell lysates were collected after 72 hours of treatment. Lysates were studied with immunoblotting to detect cleavage of PARP. The decrease in total PARP, accompanied with an increase in the cleaved PARP product, indicated that the RMS cells were undergoing apoptosis. This finding was evident in both cell lines (Figure 3B). Apoptosis was confirmed using a caspase 3 activation kit. There was a significant increase in caspase 3 activation in the SJCRH30 cell line at 5 PFU/cell and in the RD cell line at MOI of 10 PFU/cell (Figure 3C), similar to the results seen in the PARP immunoblotting, indicating an apoptotic process.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010127589_TII_01/figure/2010127589_TII_01_2.png"], "tampered": false, "paper_ids": ["2010002719"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010115659_TII_01/figure/2010115659_TII_01_3.png", "question_id": "consistency_267", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 8. Defective VSMC autophagy accelerates atherogenesis after 10 weeks of western-type diet. (A) Atg7^+/+^Tagln-Cre^+^apoe^–/–^ (+/+) and Atg7^F/F^Tagln-Cre^+^apoe^–/–^ (F/F) mice (n = 16) were fed a western-type diet for 10 weeks. Sections of the brachiocephalic artery were stained with H&E to quantify plaque size and percentage of necrosis (*, P < 0.05; Student t test). (B–D) Consecutive sections were immunostained for cleaved CASP3 (B), LAMP2 (C), and ACTA2 (D) to measure the percentage of apoptosis (indicated by a black arrowhead in the high-power photograph of the boxed area in the left corner of each image), percentage of macrophages, and fibrous cap thickness (indicated by black arrows), respectively (*, P < 0.05; Student t test (B); ***, P < 0.001; Student t test (C); *P < 0.05; n = 10 measurements/mouse, Repeated Measure (D)). (E) Consecutive sections were stained with Sirius red to quantify total collagen (*, P < 0.05; Student t test). *, necrotic core. Scale bar: 100 μm.", "figure_related_sentences": "Plaques in the brachiocephalic artery of 10-wk WD-fed atg7^–/–^, apoe^–/–^ mice showed a 5-fold increase in size as compared to Atg7^+/+^, apoe^–/–^ mice (58 ± 9 mm² vs. 156 ± 19 mm²; P < 0.001). Furthermore, plaques of atg7^–/–^, apoe^–/–^ mice were characterized by elevated plaque necrosis, plaque apoptosis, macrophage content, total collagen content, and fibrous cap thickness (Fig. 8A–E). After 14 wk on WD, plaque size (171 ± 11 mm² vs. 166 ± 9 mm²; P> 0.05), macrophage content as well as the degree of necrosis and apoptosis was similar in Atg7+/+, apoe⁻/⁻ and atg7⁻/⁻, apoe⁻/⁻ mice (Fig. 9A-C).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010115659_TII_01/figure/2010115659_TII_01_3.png"], "tampered": false, "paper_ids": ["2010002733"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010033675_TII_02/figure/2010033675_TII_02_2.png", "question_id": "consistency_268", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Fig. 3. Bromodomain-containing protein 4 (BRD4) promoted the expression of Wnt family member 5A (WNT5A) via binding to the promoter of WNT5A. a) Quantitative reverse transcription polymerase chain reaction (RT-qPCR) was used to detect the messenger RNA (mRNA) expression of BRD4 and WNT5A in dorsal root ganglia (DRG) cells transfected with oe-NC, oe-BRD4, silencing (si)-NC, or si-BRD4. b) Western blot analysis was used to detect the knock-down efficiency of si-BRD4. c) Western blot analysis was used to detect the protein expression of BRD4 and WNT5A in DRG cells transfected with different groups of plasmids. d) Chromatin immunoprecipitation was used to verify the binding site of BRD4 and WNT5A. *p < 0.05 versus the control. Measurement data were expressed as means and SDs. The independent-samples t-test was used to compare the data between two groups. Data comparison among multiple groups was analyzed by one-way analysis of variance (ANOVA), followed by Tukey's post hoc test. Results were representative of three individual experiments. IgG, immunoglobin G.", "figure_related_sentences": "BRD4 promoted the expression of WNT5A via binding to the promoter of WNT5A. The BRD4-WNT5A axis can promote the development of breast cancer cells. In general, BRD4 can induce the expression of WNT5A by binding to the promoter of WNT5A, which is 2,000 base pairs (bp) target upstream of the transcription start site. To verify this mechanism in DRG cells, BRD4 was overexpressed or knocked down in DRG cells, and the mRNA and protein expression of BRD4 was detected by RT-qPCR and western blot analysis, respectively. Results showed that the mRNA and protein expression of BRD4 and WNT5A was increased when BRD4 was overexpressed. However, the mRNA and protein expression of BRD4 and WNT5A both increased when BRD4 was knocked down (Figures 3a to 3c). These data indicate that overexpressed BRD4 upregulates the mRNA and protein expression of WNT5A. To further verify whether BRD4 can interact with the promoter of WNT5A in DRG cells, we performed a ChIP assay, which confirmed that BRD4 could bind the promoter of WNT5A (Figure 3d). Therefore, BRD4 induces the expression of WNT5A via binding to the promoter of WNT5A in DRG cells.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010033675_TII_02/figure/2010033675_TII_02_2.png"], "tampered": false, "paper_ids": ["2010002738"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010025566_TII_01/figure/2010025566_TII_01_0.png", "question_id": "consistency_269", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1: TNT003 inhibits monoclonal HLA–Ab induced complement deposition. Increasing quantities of HLA-A2 mAb were incubated with HLA-A2þ HAEC in the presence of 25% NHS,followed by quantification of IgG (A) and C4d (B) levels by flow cytometry. Additionally, TNT003 or control was added to NHS before addition to HAEC þ HLA-A2 mAb, followed by quantification of IgG (C) and C4d (D) levels. HLA-A2 mAb was added in increasing concentrations (circles—5mg/mL; triangles—2.5mg/mL; squares—1.25mg/mL; diamonds—0.625mg/mL), and control antibody (‘‘C'') was used at the same dose of the highest quantity of TNT003 (20mg/mL). Data are presented as median fluorescence intensity (MFI) of IgG or C4d staining on the cell surface from a representative of three separate experiments.", "figure_related_sentences": "To determine if HLA-Ab bound to HAEC were capable of fixing complement, we incubated HLA-A2+ HAEC (EC3, 4 or 6, see Table S1) with HLA-A2 mAb in the presence of NHS as a source of complement. The levels of human IgG bound to the surface of the cells increased proportionally to the amount of mAb added (Figure 1A). Additionally, the level of antibody bound correlated with the amount of activated complement, as detected by C4d staining on the surface of the cell (Figure 1B). TNT003 was added in a concentration-dependent manner to establish the effective concentration for use in further cell-based assays. Increased quantities of TNT003 did not alter HLAAb binding to the surface of HAEC (Figure 1C), but caused a decrease in C4d deposition (Figure 1D). We noted a sharp slope in effectiveness of TNT003 between 2.5 and 5mg/mL, most likely due to inhibitor saturation of complement C1s in the system. Of note, experiments performed with incubation of TNT003 with HAEC þ HLA-Ab, prior to addition of NHS, did not significantly impair TNT003 blockade of C4d deposition (data not shown) suggesting no temporal restrictions on TNT003 function.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010025566_TII_01/figure/2010025566_TII_01_0.png"], "tampered": false, "paper_ids": ["2010002741"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010048835_TII_01/figure/2010048835_TII_01_3.png", "question_id": "consistency_270", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 4. Analysis of three donors indicate that data obtained from PSMS vs. PBMC generated compensation matrices are similar. A:Mean and standard deviation of negative and positive populations for each T cell panel marker using compensation matrices generated from PSMS and PBMC. B: X-Median (Median fluorescence intensity) of three donors PBMC stained with panel specific markers given the compensation matrix generated by PSMS and PBMC. C: SI of PBMC from three donors using PSMS and PBMC matrices.", "figure_related_sentences": "To determine the effects of compensating with PSMS versus PBMC we studied three donors in which we compared the data on a global scale looking at the percent negative and positive populations (Fig. 4A), the MedFI of both of these populations (Fig. 4B) and SI (Fig. 4C). For all three parameters (autofluorescence, population distribution, and SI) no major significant differences were detected when using either PSMS or PBMC compensation matrices (Figs. 4A–4C). The only significant difference detected was the X MedFI of the negative fraction of FL9 (Pacific Blue 450/50 BP), on average the X MedFI of data using the PBMC based compensation was 3.07 lower than data compensated using PSMS. While this difference was observed, it is important to note that this difference did not affect the population distribution of the sample set (Fig.4A). There were large differences in the standard deviation of FL6 (APC 660/20 BP) and FL8 (Pacific Blue 450/50 BP) MedFI of the positive cell population. However, this result was independent of the compensation used and reflects donor variability. Perhaps the most striking difference between PSMS and PBMC compensation matrices were between FL7 (APC-A700 725/20 BP) and FL8 (APC-A750 775 LP). This is important to note as FL7 corresponds to IL23R APC-A700 staining. This staining using PBMC did not yield a distinct positive and negative fraction thus making compensation difficult.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010048835_TII_01/figure/2010048835_TII_01_3.png"], "tampered": false, "paper_ids": ["2010002759"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010048799_TII_02/figure/2010048799_TII_02_4.png", "question_id": "consistency_271", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 5 Suppression of DNA damage induced by pressure overload in HMGB-1 Tg mice. (A) Left-ventricular transverse sections in WT and HMGB1-Tg mice at 4 weeks after TAC, and heart weight: body ratios in TAC or sham-operated mice. Data are mean±SEM from eight mice for each group. *P < 0.05 and **P < 0.01 vs. sham-operated mice of the same strain; †P < 0.05 vs. TAC-operated Tg mice. (B) Quantitative analyses of ANP, BNP, and b-MHC gene expression in WT and HMGB1-Tg mice at 4 weeks after TAC. Data are mean±SEM from eight mice for each group. *P < 0.05 and **P < 0.01 vs. sham-operated mice of the same strain; †P < 0.05 vs. TAC-operated Tg mice. (C) Data showing echocardiographic measurements in WT and HMGB1-Tg mice at 4 weeks after TAC or sham surgery. IVS, interventricular wall thickness; LVEDD, left-ventricular end-diastolic dimension; LVESD, leftventricular end-systolic dimension; %LVFS, left-ventricular fractional shortening. Data are mean±SEM from eight mice for each group. *P < 0.05 vs. sham-operated WT mice; †P < 0.05 vs. TAC-operated WT mice. (D) Survival curves in WT and HMGB1-Tg mice after TAC.", "figure_related_sentences": "At 4 weeks after the TAC operation, the increase in the weight of the heart was significantly higher in HMGB1-Tg mice than in WT-mice (Figure 5A). We next examined the mRNA expression of foetal cardiac genes after TAC. The expressions of ANP, BNP, and b-MHC were significantly up-regulated in the TAC group compared with the shamsurgery group, and this upregulation was significantly intensify in HMGB1-Tg mice (Figure 5B). Moreover, systolic dysfunction and leftventricular dilatation after TAC were attenuated in HMGB1-Tg mice compared with WT-mice (Figure 5C, Supplementary material online, Table). Furthermore, the survival rate after TAC was significantly lower in HMGB1-Tg mice than in WT mice (Figure 5D).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010048799_TII_02/figure/2010048799_TII_02_4.png"], "tampered": false, "paper_ids": ["2010002762"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010073280_TII_02/figure/2010073280_TII_02_0.png", "question_id": "consistency_272", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "To examine the effect of rapamycin on the expression of miR-30a and autophagy of VSMcs, the expression of miR-30a and Beclin1 was determined by RT-qPcR. The results demonstrated that in aging cells miR-30a was significantly downregulated while Beclin1 was significantly downregulated compared with young cells (P<0.01; Fig. 2A and B), indicating that both miR-30a and Beclin1 might be associated with senescence in VSMcs. However, when treated with rapamycin, miR‑30a was significantly downregulated in both young and aging cells (P<0.05; Fig. 2A). Additionally, the expression of Beclin1 was significantly upregulated in both young and aging cells following rapamycin treatment (P<0.05; Fig. 2B). These results clearly demonstrated that rapamycin inhibited miR-30a expression while it induced Beclin1 expression.", "figure_related_sentences": "Rapamycin inhibits senescence in VSMCs and alleviates cell cycle arrest. SA-β-gal staining was conducted to examine the effect of rapamycin on senescence of VSMCs. As illustrated in Fig. 1A and B, the ratio of SA-β-gal-positive cells was significantly higher in aging cells compared with young cells (P<0.01). However, following rapamycin treatment, the ratio of SA-β‑gal‑positive cells significantly decreased in aging cells (Fig. 1B), indicating that rapamycin could inhibit senescence in VSMCs. Flow cytometry analysis revealed that G1 arrest occurred in aging cells and this cell cycle arrest was reduced when cells were treated with rapamycin (Fig. 1C and D). Further analysis of p16, p21, p53 and SA-β-gal expression levels by western blotting demonstrated that rapamycin treatment promoted the increasing levels of senescence-related proteins in aging cells (Fig. 1E and F). These results suggested that rapamycin could inhibit senescence of VSMCs through inhibition of cell cycle arrest and senescence-related proteins.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010073280_TII_02/figure/2010073280_TII_02_0.png"], "tampered": false, "paper_ids": ["2010002883"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010128722_TII_01/figure/2010128722_TII_01_0.png", "question_id": "consistency_273", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Effect of curcumin and resveratrol on ASK1-overexpressed cells viability. LNCaP and PC-3 cells were transiently transfected with vector pcDNA3.1 (MOCK), wild-type ASK1(ASK1) or kinase inactive mutant (KM-ASK1). Cells were set overnight and then treated with 25 µM curcumin (A) or 50 µM resveratrol (B). Cell viability was studied using MTT assay after 24 treatment. Data are shown as mean ± S.E.M. of 6 independent samples. *p < 0.05; **p < 0.01; ***p < 0.001 versus CON. PC-3 cells (C) transiently transfected with vector, ASK1 or KM-ASK1 were incubated with or without curcumin (25 µM) for 24 h. Apoptosis was evaluated after staining with Annexin V/PI by flow cytometry.", "figure_related_sentences": "The effects of four bioactive compounds—melatonin, silibinin, curcumin, and resveratrol—on the viability and proliferation of prostate cancer cells were evaluated using the MTT assay (Fig. 1A). After 48 hours of treatment, growth of androgen-sensitive LNCaP cells was significantly inhibited by melatonin at 200 µM and 1 mM and by silibinin at 50 µM, while no significant effect was observed in androgen-insensitive PC-3 cells (Fig. 1A). Curcumin and resveratrol inhibited the viability of both cell lines at concentrations above 10 µM and 60 µM, respectively. Since the MTT assay cannot distinguish between growth inhibition and cell death, annexin V staining combined with flow cytometry was performed after culturing LNCaP and PC-3 cells with melatonin (1 mM), silibinin (50 µM), curcumin (25 µM), or resveratrol (50 µM) (Fig. 1B). Only curcumin and resveratrol treatments induced a significant increase in apoptotic cells in both cell types. To confirm this, western blot analysis assessed levels of the anti-apoptotic protein BCL2 and the pro-apoptotic protein BAX. In LNCaP cells, curcumin and resveratrol treatment caused a clear decrease in BCL2 and an increase in BAX protein levels. Conversely, melatonin incubation increased BCL2 levels, and silibinin treatment showed no significant changes in the BCL2/BAX ratio (Fig. 1C). Figure 1D shows morphological changes in LNCaP and PC-3 cells after 48 hours of incubation with the compounds. Typical apoptotic features—such as cell shrinkage, rounding, and partial detachment—were observed following curcumin treatment in both cell types. PC-3 cells treated with resveratrol also showed apoptotic morphology preceded by cytoplasmic vacuolization. Melatonin and silibinin treatments induced significant morphological changes including long processes (neurites) and rounded nuclei, characteristic of neuroendocrine differentiation, consistent with previous reports.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010128722_TII_01/figure/2010128722_TII_01_0.png"], "tampered": false, "paper_ids": ["2010002888"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010039983_TII_02/figure/2010039983_TII_02_3.png", "question_id": "consistency_274", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Fig. 4. Mechanism dissection studies on interleukin-6 (IL-6) regulation of hypoxia-inducible factor (HIF) following cisplatin treatment. (a) Hypoxia response element–luciferase (HRE-luc) assay. HEK293 cells were transfected with HRE-luc-containing plasmids and incubated with various amounts of IL-6. After 24 h of incubation, luciferase activities were measured. (b) HRE-luc assay. A549IL-6si ⁄sc and H157IL-6si ⁄sc pairs were transfected with equal amounts of HRE-luc-containing plasmids. After 24 h of transfection, luciferase activities were measured. (c) Prolyl hydroxylase (PHD) mRNA levels in A549IL-6si ⁄sc and H157IL-6si ⁄sc cell sets, with or without cisplatin treatment. Cells were either non-treated or treated with cisplatin (5 lM, 72 h), total RNAs extracted, cDNA converted, and mRNA expressions were analyzed. (d) Western blot analysis of von Hippel-Lindau disease tumor suppressor (VHL), HIF1a, and HIF2a levels in A549IL-6si ⁄sc and H157IL-6si ⁄sc cell sets, with or without cisplatin treatment, in the presence or absence of MG132. Cells were either non-treated or treated with cisplatin (5 lM, 72 h) in the absence or presence of MG132 (10 lM), cell extracts were obtained, and HIF1a and HIF2a levels were analyzed in Western blot. (e) Summary of the results of mechanism studies. *P < 0.05; **P < 0.01; ***P < 0.001. CSC, cancer stem cell.", "figure_related_sentences": "We observed an decrease in HRE-luc activities with IL-6 addition in both cell lines (Fig. 4a), suggesting the IL-6 regulation of HIFs at the transcriptional level. We then investigated HRE-luc activities in A549IL-6si ⁄sc and H157IL-6si ⁄sc cell sets after cisplatin treatment. Interleukin-6-expressing sc cells showed higher HRE-luc activities than IL-6si cells (Fig. 4b), implying IL-6-mediated upregulation of HIFs at the transcriptional level may contribute to cisplatin resistance. We next tested whether the IL-6-mediated upregulation of HIFs on cisplatin treatment is also due to inhibition of HIF degradation. We tested whether the levels of PHDs that are known to be associated with VHL-mediated HIF ubiquitination are different in IL-6si ⁄sc cells after cisplatin treatment. When we investigated mRNA levels of PHDs in A549IL-6si ⁄sc and H157IL-6si⁄sc cell sets, we found the PHD levels were significantly higher in IL-6si cells than in sc cells, and that the difference was more significant in the presence of cisplatin (Fig. 4c). The upregulation of HIFs after cisplatin treatment observed in sc cells was abolished when cells were treated with the proteasomal degradation inhibitor MG132 (Fig. 4d). However, we found that the VHL level was not affected by IL-6. These results suggest that IL-6 triggers the promotion of ubiquitination by mediating PHD level decrease after cisplatin treatment. Figure 4e summarizes these results.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010039983_TII_02/figure/2010039983_TII_02_3.png"], "tampered": false, "paper_ids": ["2010002890"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010075898_TII_02/figure/2010075898_TII_02_0.png", "question_id": "consistency_275", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. The combination of AT406 and upregulation of c-FLIPL/S by c-FLIP-siRNA sensitizes the osteosarcoma cells U2OS to TRAIL-induced apoptosis. (A) The osteosarcoma cells U2OS were treated with different concentrations of TRAIL for 24 h. In three other concentration-response experiments, cells were pre-treated with AT406 (A) for 1 h and with or without transient transfection with c-FLIP-siRNA for 24 h. The cell viabilities were determined by an MTT assay. The results are shown as the mean ± SEM of three separate experiments. (B) Caspase activity of U2OS cells in response to TRAIL with or without pre-treatments of A and c-FLIP-siRNA as indicated in the graph was measured by a Caspase-Glo 3/7 assay. (C) The U2OS cells were treated with TRAIL for 5 h, and with or without pre-treatment of A for 1 h, and transient transfection with c-FLIP-siRNA for 24 h as indicated in the graph. The extrinsic apoptosis related proteins were determined by western blots and statistical analyses and are shown in (D). In all experiments if not specified: A, AT406 at 1 µg/ml; EV, control empty vector; c-FLIP-siRNA, pSuper-puro-siRNA-c-FLIP vector; T, TRAIL at 100 ng/ml. The results are shown as the means ± SEM in all bar graphs of western blots of three independent experiments (NS>0.05, ***p<0.001).", "figure_related_sentences": "Inhibition of c-FLIPS/L and IAPs can increase the sensitivity of U2OS to TRAIL-induced apoptosis. By evaluating TRAIL promotion of tumor cell apoptosis, we found that U2OS is resistant to TRAIL-induced apoptosis. Because c-FLIP is a crucial apoptotic resistance factor, we used the c-FLIP-siRNA overexpression plasmid which was reported in our previous study to inhibit the expression of c-FLIP (Fig. 1A) (27). The results of an MTT assay showed that in combination with TRAIL with or without c-FLIP-siRNA, AT406 could increase the cell death rate of U2OS (Fig. 1A). Results of the Caspase-Glo 3/7 assay (Fig. 1B) confirmed that c-FLIP-siRNA in the presence of AT406 activated caspase proteins in the TRAIL-activated apoptotic pathway. That is, apoptosis initiator protein caspase-8, apoptosis executor protein caspase-3 and apoptosis substrate poly(ADP-ribose) polymerase (PARP) were all in their cleaved states to various degrees (Fig. 1C and D). All of these results demonstrated that c-FLIP-siRNA and AT406 together activated the extrinsic apoptotic pathway in the presence of TRAIL to induce apoptosis.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010075898_TII_02/figure/2010075898_TII_02_0.png"], "tampered": false, "paper_ids": ["2010002893"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010027059_TII_01/figure/2010027059_TII_01_3.png", "question_id": "consistency_276", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "FIGURE 4 Statistical graph of systolic blood pressure (a), diastolic blood pressure (b), heart rate (c), and T3 phase tilt angle (d) before and after the application of nitroglycerin. All data arepresented as mean ± SD. *p < .05, ****p < .0001", "figure_related_sentences": "The application of nitroglycerin did show a significantly antihypertensive function in both systolic blood pressure (163.8 ± 17.1 mmHg vs. 182.0 ± 12.1 mmHg, p < .0001) and diastolic blood pressure (92.7 ± 11.8 mmHg vs. 74.0 ± 9.6 mmHg, p < .0001) as shown in Figure 4A and 4B5. The heart rates of patients increased significantly after the application of nitroglycerin (77.3 ± 11.0 vs. 92.6 ± 10.3, p = .023) (Figure 4C). The change of the T3 phase tilt angle before and after the application of the antihypertensive medication was obvious. After the application of nitroglycerin, the inclination angle of T3 increased significantly (-50.6 ± 16.2° vs. −25.6 ± 21.9°, p < .0001) (Figure 4D).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010027059_TII_01/figure/2010027059_TII_01_3.png"], "tampered": false, "paper_ids": ["2010002894"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010123606_TII_02/figure/2010123606_TII_02_3.png", "question_id": "consistency_277", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "**Figure 4. Bid Phosphorylation on Serine 66 Sensitizes Cells to Apoptosis during Mitotic Arrest**(A) RKO cells stably infected with pVenus, pVenus-shBid, or pVenus-shBid coexpressing the indicated mouse (left panel) and human (right panel) BidYFP variants under the ubiquitin promoter were analyzed by immunoblotting with an antibody that recognizes both human and mouse Bid. Immunoblotting for Erk was used as a loading control. Endogenous human Bid is only present in the control cells.(B) The control RKO lines and those expressing mouse BidYFP variants were untreated or treated with 1 μM paclitaxel for 18 hr. Lysates were analyzed by immunoblotting for Bid and active caspase 3. Erk was a loading control. Note the shift in mobility of BidYFP-WT and BidYFP-G94E in paclitaxel-treated RKO cells.(C) The RKO lines from (A), untreated or treated with 1 μM paclitaxel for 18 hr, were immunostained for active caspase 3 and apoptosis quantified. The data represent the mean of three independent experiments. The error bars represent SEM. Data were analyzed by ANOVA.(D) Images of the paclitaxel-treated RKO cell lines from (C), immunostained for active caspase 3. Nuclei were stained with Hoechst.(E) Bid⁻/⁻ MEFs, infected with the indicated pVenus lentiviruses, were left untreated or treated with 1 μM paclitaxel. Apoptosis was quantified as above. The data represent the mean of three independent experiments. The error bars represent SEM. Data were analyzed by ANOVA.(F) RKO cells infected with the indicated lentiviruses expressing human Bid or human BidS67A were treated with paclitaxel as in (C). Cells showed similar responses to those expressing the mouse BidYFP. The data represent the mean of three independent experiments. The error bars represent SEM. Data were analyzed by ANOVA.(G) The indicated RKO lines, untreated or treated with monastrol for 18 hr, were immunostained for active caspase 3 and apoptosis quantified. The data represent the mean of three independent experiments. The error bars represent SEM. Data were analyzed by ANOVA.", "figure_related_sentences": "To test if Bid-pS66 regulates apoptosis during mitotic arrest, we generated stable RKO lines where endogenous hBid was knocked down and substituted by mouse BidYFP-WT, BidYFP-S66A, BidYFP-S66D, or BidYFP-G94E. As expression of mBidYFP was significantly higher than endogenous hBid using the original pVenus vector with an EF1a promoter (Figure S3A), we replaced it with an ubiquitin (Ub) promoter. This led to expression of mBidYFP at levels comparable to endogenous hBid (Figures 4A and S3B). When the RKO lines were treated with paclitaxel for 18 hr, although BidYFP-WT rescued apoptosis following endogenous Bid knockdown, neither Bi-dYFP-S66A nor BidYFP-G94E BH3 mutant were able to restore the response (Figures 4B–4D). Notably, BidYFP-S66D was not a functional phospho-mimetic and was also unable to restore the response. Different results were obtained in Bid-/-MEFs stably expressing Ub-promoter-driven BidYFP-WT, BidYFP-66A, and BidYFP-G94E (Figure 4E). To ask if phosphorylation of human Bid on S67 had the same role, we generated RKO cells where endogenous hBid was knocked down and hBidYFP-WT or hBidYFP-S67A expressed (Figure 4A). hBidYFP-WT rescued paclitaxel-induced apoptosis in Bid knockdown RKO cells, but hBidYFP-S67A did not (Figures 4F and S4A). To determine whether the proapoptotic role of Bid during mitosis was seen when cells were treated with other antimitotic drugs, we treated RKO cells with monastrol. These cells also displayed Bid-S66-phosphorylation-dependent apoptosis (Figure 4G), although the level of cell death was much lower than with paclitaxel.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010123606_TII_02/figure/2010123606_TII_02_3.png"], "tampered": false, "paper_ids": ["2010002895"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010125129_TII_02/figure/2010125129_TII_02_1.png", "question_id": "consistency_278", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2. The MENIN/MLL2 H3K4 Methyl Transferase Is Cell-Cycle Regulated and Controls the Activation of Bivalent Genes in G1(A) qChIP of Fucci hESC cell-cycle fractions examining levels of MLL2 and WDR5 on the GATA6 and SOX17 promoters. Data are the average of three independent replicates.(B) qChIP assays for MLL2 in untreated or MI-2 (25 μM for 24 hr)-treated WA09 ESCs at the indicated promoters. Data are the average of three independent replicates.(C) qChIP assays for MLL2 in ESCs of pluripotency genes. Data are the average of three independent replicates.", "figure_related_sentences": ". To determine whether CDK2 activity was required for MLL2 recruitment to bivalent genes, we added the inhibitor CVT-313 (Brooks et al., 1997) for a brief period (4 hr) so as not to impose a cell-cycle block, and no major perturbations in cell-cycle progression were observed during this time (Figure 3A). The addition of CVT-313 suppressed developmental transcripts had no effect on OCT4 transcripts or transcripts for non-cell-cycle-regulated bivalent genes, and significantly increased MLL2 recruitment to developmental genes (Figures 3B, 3C, and S3C). MENIN binding, however, was not affected by CDK2 inhibitor treatment (Figure 3C).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010125129_TII_02/figure/2010125129_TII_02_1.png"], "tampered": false, "paper_ids": ["2010002896"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010049222_TII_01/figure/2010049222_TII_01_0.png", "question_id": "consistency_279", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1 experimental design and outcome.Notes: (A) Mouse lewis lung carcinoma llc1 cells (1×106) mixed with Matrigel were injected subcutaneously in c57Bl/6 mice on day 0. The mice were randomly assigned into five treatment groups (a–e). Treatment started on day 1, with the doses and schedules indicated by arrows along the time course. (B, C) The results (tumor weight) of the first and second experiments, respectively. Data represent means ± seM (error bars). The number of animals per group is indicated under each group.Abbreviations: iP, intraperitoneally; PO, per os (by mouth); iU, international unit; seM, standard error of the mean.", "figure_related_sentences": "ResultsiFnγ and celecoxib inhibit mouse lung-tumor growthWe implanted mouse LLC1 cells subcutaneously into syngeneic C57BL/6 mice. The mice were randomly assigned into five groups: a) treated with saline as the placebo control group, b) treated with IFNγ, c) treated with celecoxib (COX-2 inhibitor), d) treated with a combination of IFNγ and celecoxib, and e) treated with zoledronic acid that can kill macrophages (Figure 1A). In the first experiment, we found that IFNγ alone reduced tumor weight by 30% compared to the control group (P < 0.01, Figure 1B). Celecoxib alone reduced tumor weight by 27% compared to the control group (P<0.01, Figure 1B). The combination of IFNγ and celecoxib reduced tumor weight by 23% compared to the control group (P < 0.01, Figure 1B). However, there was no statistically significant difference between the combinedtreatment group and IFNγ-alone or the celecoxib-alone groups (P<0.05, Figure 1B). Zoledronic acid did not significantly reduce tumor weight compared to the control group (P<0.05, Figure 1B). In the second experiment, we found that IFNγ alone reduced tumor weight by 50% compared to the control group (P<0.01, Figure 1C). Celecoxib alone reduced tumor weight by 31% compared to the control group (P<0.01, Figure 1C). The combination of IFNγ and celecoxib reduced tumor weight by 34% compared to the control group (P<0.01, Figure 1C). Like the first experiment, there was no statistically significant difference between the combinedtreatment group and IFNγ-alone or celecoxib alone groups (P<0.05, Figure 1C). Unlike the first experiment, zoledronic acid reduced tumor weight by 16% compared to the control group (P<0.01, Figure 1C). Of note, we found that all animals gained body weight during the treatment, and there was no statistically significant difference among the five groups (data not shown).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010049222_TII_01/figure/2010049222_TII_01_0.png"], "tampered": false, "paper_ids": ["2010002897"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010014864_TII_01/figure/2010014864_TII_01_4.png", "question_id": "consistency_280", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "FRAP analysis of PRC1 fusion proteins binding to interphasic and mitotic chromatins. (A) Representative FRAP images of YFP-Cbx2 fusion protein at metaphasic and interphasic chromatins of ES cells. The images were taken before (pre) and after (post) photobleaching. The bleaching area is indicated and outlined in white. (B–I) FRAP curves of PRC1 fusion proteins at interphases and metaphases of PGK12.1 ES cells. The FRAP curves are the normalized fluorescence intensities of the bleached areas as a function of time after photobleaching and are an average of at least eight cells. Error bars indicate SDs of means. (J) Immobile fraction of PRC1 fusion proteins at interphasic and metaphasic chromatins. The immobile fraction was calculated from FRAP curves by fitting a first-order kinetic model. The dashed line indicates the contrast between interphase and metaphase. Data are an average of at least eight cells. (K) Residence time of PRC1 fusion proteins at interphasic and metaphasic chromatins. The residence time was calculated from FRAP curves by fitting a first-order kinetic model. The bar with NA indicates that the fusion protein is immobilized at mitotic chromatin, and thus the residence time is not measurable within the time scale of the experiments. The dashed line indicates the contrast between interphase and metaphase.", "figure_related_sentences": "Figure 5, A–I: The mCherry-H2A fusion protein served as a guide for placing bleach spots at mitotic chromosomes. Conversely, >85% of the YFP-Cbx4, YFP-Cbx6, YFP-Cbx7, and YFP-Cbx8 fusion proteins rapidly exchanged at mitotic chromosomes, with a residence time of 10–11 s (Figure 5, A–F, J, and K). During interphase, >90% of the Cbx-family fusion proteins showed fluorescence recovery, with a residence time of ∼10–13 s (Figure 5, A–F, J, and K), consistent with previous studies. Analysis of FRAP curves of mitotic chromosomal binding of Cerulean-Ring1b, Cerulean-Phc1, and Cerulean-Mel18 fusion proteins revealed that nearly 50% of these fusion proteins stably bind to mitotic chromosomes without exchange (Figure 5, G–K), which is similar to YFP-Cbx2 but differs from other Cbx-family fusion proteins. The FRAP curves were normalized and plotted as described in Figure 5. The mCherry-H2A was used to mark mitotic chromosomes. Scale bar, 5 μm. (C) FRAP curves of interphases and metaphases of YFP-Cbx2 and its variant fusion proteins expressed in HeLa cells. FRAP analysis is described in Figure 5. (D) Residence time and immobile fraction of YFP-Cbx2 variant fusion proteins at interphasic and mitotic chromatins.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010014864_TII_01/figure/2010014864_TII_01_4.png"], "tampered": false, "paper_ids": ["2010002900"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010116294_TII_02/figure/2010116294_TII_02_4.png", "question_id": "consistency_281", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Decitabine-mediated induction of CT45 expression in EOC cells. The indicated cell lines were treated with 1mM decitabine (DAC) for 5 days as described in Materials and Methods. (A) CT45 mRNA expression and CT45 promoter methylation after vehicle (PBS) or DAC treatment. CT45 mRNA expression was determined by RT-qPCR and CT45 promoter methylation was determined by pyrosequencing (average of Region 1 C Region 2 methylation). Data represent mean C/– SD. The two-tailed paired t-test p-value is indicated (*:P < 0.05; **: P < 0.01; ****: P < 0.0001; NS: not significant). (B) Western blot analysis of CT45 protein expression after vehicle (PBS, –) or DAC (C) treatment. b-actin and FastGreen staining are shown as loading controls.", "figure_related_sentences": "The primary tumor data presented above establishes a correlation between CT45 promoter hyperhmethylation and CT45 expression, but does not demonstrate causation. To establish a mechanistic connection, we treated EOC cell lines with varying baseline CT45 expression levels using the DNA methyltransferase (DNMT) inhibitor decitabine (DAC), a cytosine analog that specifically inhibits DNA methylation by covalently trapping DNMTs to DNA. Following DAC treatment, the CT45 promoter was hypomethylated in all treated cell lines (Figure 9A). Notably, CT45 expression was robustly promoted in low-expressing cell lines (IOSE121, OVCAR3, SNU119), with less or no induction in two lines with higher basal CT45 expression (A2780, OVSAHO) (Figure 9A). Importantly, CT45 protein was also promoted at varying levels in EOC cell lines treated with DAC (Figure 9B).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010116294_TII_02/figure/2010116294_TII_02_4.png"], "tampered": false, "paper_ids": ["2010002904"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010025926_TII_02/figure/2010025926_TII_02_1.png", "question_id": "consistency_282", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "FIGURE 2 Diet effects on peripheral metabolism. A-C) Total cholesterol, low-density lipoprotein (LDL), and high-density lipoprotein (HDL) levels were significantly reduced following the Mediterranean diet (Med-diet) and increased following the Western diet (West-diet) for both normal cognition (NC) and mild cognitive impairment (MCI) groups (all Ps < .001). D, Plasma glucose levels increased for the NC group and decreased for the MCI group following the West-diet (P = .01), with no changes observed for groups following the Med-diet. E Plasma insulin levels increased for the NC group and decreased for the MCI group following Med-diet (P = .031). Insulin also tended to decrease for the MCI but not the NC group during the West-diet (P = .051). F, The NC group showed increased HbA1c levels following the West-diet, and the MCI group showed decreased levels (P = .049). Figures depict change scores for ease of interpretation, adjusted means from repeated measures analysis of covariance are included in Table S2. Error bars represent ± 1 standard error from the mean. Significance is set at +P < .10, *P < .05, ** P < .01, or *** P < .001", "figure_related_sentences": "The West-diet decreased and the Med-diet reduced total cholesterol levels for both NC and MCI groups similarly (diet x time F[1,69] = 21.89, P = .0001; Figure 2A). This pattern was also observed for LDL and HDL cholesterol (diet x time F[1,68] = 26.54, P = .0001 for LDL; diet x time F[1,72] = 13.07, P = .0006 for HDL; Figure 2B-C). Both groups' levels were unchanged following the Med-diet, whereas following the West-diet, the NC group's levels reduced and the MCI group's levels decreased (diagnosis x time F[1,34] = 7.47, P = .010; Figure 2D). For fasting insulin levels, the NC group increased and the MCI group decreased following the Med-diet; the MCI group insulin levels also decreased during the West-diet, whereas the NC group showed little change. A three-way interaction of diet x cognitive group x time was observed for HbA1c (F[1,69] = 4.67, P = .034); the NC group showed increased HbA1c levels following the West-diet, and the MCI group showed increase levels (F[1,36] = 4.17, P = .049; Figure 2F), whereas the opposite, though non-significant, pattern was observed for the Med-diet.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010025926_TII_02/figure/2010025926_TII_02_1.png"], "tampered": false, "paper_ids": ["2010002906"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010124413_TII_01/figure/2010124413_TII_01_3.png", "question_id": "consistency_283", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 5: Munc18c depletion diminishes high-KD-evoked exocytosis of previously-docked insulin SGs. (A,B) Insulin SG exocytosis dynamics evoked by 50 mmol/l KCl from control (A) and Munc18c-KD (B) human beta-cells. Black and white bars indicate pre-docked and newcomer SGs, respectively. Data from 10 cells for each group, expressed as means ± SEMs. (C) Normalized cumulative fusion events of SGs per unit area from control (black circles) and Munc18c-KD (white circles) beta-cells. (D) Summary of fusion events from pre-docked and newcomer SGs in first- and second-phase after 50 mmol/l glucose stimulation. Values represent means ± SEMs. *p < 0.05.", "figure_related_sentences": "Munc18c depletion affecting both phases of GSIS in our study seems inconsistent with a previous study showing heterozygous Munc18c-KO mice islets affecting predominantly the second-phase GSIS. Since a major portion of first-phase GSIS is attributed to predocked SGs, which are preferentially released by high-Kþ stimulation in the first few minutes, we employed this protocol on Munc18c-KD human beta-cells. Consistently, 50 mmol/l KCl triggered exocytosis of mainly previously-docked (pre-docked) SGs (black bars) in the first few minutes from control and Munc18c-KD cells (Figure 5A,B). Here, there was a 59% reduction in exocytosis in the first 5 min (Figure 5C) accounted for mostly from a reduction of exocytosis of pre-docked SGs in the Munc18c-KD cells, compared with control cells (summary analysis in Figure 5D;", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010124413_TII_01/figure/2010124413_TII_01_3.png"], "tampered": false, "paper_ids": ["2010002909"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010013120_TII_01/figure/2010013120_TII_01_1.png", "question_id": "consistency_284", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "C. elegans meiosis has both anaphase A and anaphase B. (A) Table of spindle lengths and distances between the centers of chromosomes measured at the start of anaphase A, the end of anaphase A, and the start of cortical ingression for both MI and MII meiotic spindles. Averages and SEM are shown. (B) Graphs depicting the change in distance between separating chromosomes in time-lapse sequences of four embryos show different rates during anaphase A and anaphase B. (C) Rates of chromosome separation from multiple time-lapse sequences of MI anaphase A, MII anaphase A, MI anaphase B, and MII anaphase B. Although there is no significant difference between MI and MII rates, the difference between all anaphase A rates and all anaphase B rates is extremely significant (****p < 0.0001). (D) Table of the averages of the rates shown in C. All rates were determined from time-lapse images of embryos expressing GFP::tubulin and mCherry::histone and are expressed as micrometers per minute.", "figure_related_sentences": "A plot from a single embryo is shown in Figure 1C, and data from multiple embryos are shown in Figure 2. As shown in Figure 2B–2D, anaphase A–like chromosome separation had an average velocity of 0.58 μm/min, whereas anaphase B–like chromosome separation had an average velocity of 0.85 μm/min. The anaphase A–like velocities were significantly different from the anaphase B–like velocities, whereas the velocities during anaphase I were not significantly different from those during anaphase II (Figure 2C). The short length of the spindle at anaphase onset (5.84 μm; Figure 2A) suggested that chromosomes might already be in physical contact with spindle poles before anaphase onset. This distance is similar to the average spindle length at the onset of anaphase A determined from GFP::tubulin, 4.08 μm (Figure 2A).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010013120_TII_01/figure/2010013120_TII_01_1.png"], "tampered": false, "paper_ids": ["2010002912"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010014538_TII_01/figure/2010014538_TII_01_1.png", "question_id": "consistency_285", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Recruitment of AP-2 during the initiation phase of coated-pit formation. (A) Representative example of a fluorescence intensity tracing of AP-2 (σ2-eGFP) from a time series obtained from SUM-AP-2.1 imaged by TIRF microscopy. The tracing corresponds to the formation of a coated pit containing AP-2 tagged by σ2-eGFP; the time series was acquired every 150 ms with an exposure of 60 ms/frame. The inset shows the fitted steps and highlights the first and second steps. (B) Histogram of the fluorescence intensities associated with the first and second steps (gray). The best fit (dark blue) corresponds to the added contributions (orange) of one, two, and so on σ2-eGFP molecules. The data from three cells correspond to 253 first and 224 second steps detected during the initiation of 253 independent coated pits. The combined dwell time for both steps was 2.6 ± 1.9 s (mean ± SD). (C) Selection of the best fluorescently tagged AP-2 (this study) or a mixture of native AP-2 and fluorescently tagged AP-2 (Cocucci et al., 2012).", "figure_related_sentences": "In 253 traces from three cells, the first detectable events during coated-pit initiation were two consecutive, stepwise increases in AP-2 fluorescence intensity (Figure 2A) with average dwell times of 2.9 and 8.3 s, respectively. The distribution of fluorescence intensity increments for both steps is shown in Figure 2B. Assuming full replacement of σ2 by σ2-eGFP (equivalent to a substitution fixed at 1), a search for the recruitment model with the lowest Bayesian information criterion (BIC) score (Burnham and Anderson, 2002; i.e., the model that best fit the experimental observations) yielded two AP-2 complexes per step in approximately 60% and 70% of the first and second steps, respectively (insets in Figure 2B and 2C, top, and model i). We validated the recruitment model with an independent search that included exploration for partial replacement of σ2 by the σ2-eGFP or incomplete maturation of a fluorescent eGFP (Figure 2C, bottom, and associated models).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010014538_TII_01/figure/2010014538_TII_01_1.png"], "tampered": false, "paper_ids": ["2010002915"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010125685_TII_02/figure/2010125685_TII_02_12.png", "question_id": "consistency_286", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 4: Changing FXRα2/α1 ratios promotes transcriptional reprogramming. (A) Target gene expression analysis by qRT-PCR in hepatocytes expressing GFP or FXRα2 and treated with vehicle (DMSO) or 250 μM cholic acid (CA) for 24 h. Bars depict mean values and error bars represent SEM (n = 5). *p < 0.05 compared to vehicle-treated or between the indicated groups. (B) Gene expression analysis by qRT-PCR in hepatocytes co-transduced with FXRα1 and FXRα2 in different proportions (+++, 100%; ++, 70%; +, 30%; –, 0%). Graphs represent expression levels relative to hepatocytes transduced with FXRα1 alone. Graphs depict mean values and error bars represent SEM (n = 5). *p < 0.05 compared to FXRα1 alone or between the indicated groups.", "figure_related_sentences": "Bile acids function as endogenous FXR ligands and greatly increase their capacity to transcriptionally activate a vast array of target genes. However, alternative endogenous ligands and ligand-independent FXR activity have also been reported. To investigate whether bile acids affect the gene program under FXRα2 control, we treated hepatocytes expressing FXRα2 or GFP alone with 250 μM cholic acid (CA), a concentration shown to yield moderate FXR activation. CA treatment in GFP-transduced cells increased the expression of most FXRα2 target genes involved in lipolysis, fatty acid (FA) oxidation, mitochondrial uncoupling, and ketogenesis (Figure 4A and Figure S4A). The exceptions were Atgl, Hsl, Cgi-58, and Fabp1, whose expression was not affected by CA treatment. In contrast, when FXRα2 expression was increased, only Ucp2, Hmgcs2 and to a lesser extent Ppara displayed reduced mRNA levels upon CA treatment, when compared to vehicle-treated cells. For all other genes analyzed, expression was changed or in some cases (e.g., Atgl and Slc25a47) enhanced by CA treatment. Interestingly, increased FXRα2 levels blunted the CA-mediated effects on Bhlhe41 expression. In addition to ligand-mediated activation, the relative expression of FXR splice isoforms has important implications on hepatic metabolism. To verify whether changing FXRα2/α1 ratios is sufficient to promote transcriptional reprogramming, we co-expressed different proportions of FXRα1:FXRα2 in hepatocytes. For clarity, the relative amounts of FXRα1 and α2 adenoviral particles used are illustrated in Figure 4B. While maintaining similar total FXR expression levels, increasing FXRα2/α1 ratios gradually induced the FXRα2-mediated gene program conducive to increased lipolysis, FA oxidation and ketogenesis (Figure 4B and S4B). Bhlhe41 expression showed the opposite pattern. These data indicate that changes in FXR isoform composition through alternative splicing can promote transcriptional reprogramming and alter hepatic lipid handling and ketogenic capacity.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010125685_TII_02/figure/2010125685_TII_02_12.png"], "tampered": false, "paper_ids": ["2010002916"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010048726_TII_02/figure/2010048726_TII_02_1.png", "question_id": "consistency_287", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2 Visual predictive check plots. The final disease-drug-trial models characterizing longitudinal normalized weekly binge episodes in patients receiving topiramate and placebo (N = 500 simulations) (a) and binge day frequency (b). Solid and dashed lines represent the observed and model-simulated 5th, 50th, and 95th percentiles. Colored bands demonstrate the 95% confidence interval for the simulated 5th, 50th, and 95th percentiles.", "figure_related_sentences": "VPC plots for the disease-drug-trial model are shown in Figure 2. Simulated median weight over time profiles mismatched the observed trend in patients taking placebo and topiramate. Model evaluation using QPCs demonstrated the capability of the developed diseasedrug-trial model in predicting key clinical outcomes.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010048726_TII_02/figure/2010048726_TII_02_1.png"], "tampered": false, "paper_ids": ["2010002917"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010048532_TII_01/figure/2010048532_TII_01_1.png", "question_id": "consistency_288", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2. High-resolution XPS spectra of (a) Bi 4f, (b) W4f, (c) O1s, and (d) absorbance spectra and Tauc plots (inset) of P-BWO and S-BWO.", "figure_related_sentences": "As shown in Figure 2a, the two spin-orbit doublets with peaks emerging at 159.07 and 164.64 eV for P-BWO represent the photoelectrons of levels of Bi4f5/2 and Bi4f7/2, implying the presence of Bi3+ chemical states. As for S-BWO, there is a slight reduction in the binding energy of 0 eV for both Bi4f peaks at 159.07 and 164.37 eV due to the introduction of the S element into the crystal structure. In regard to the W4f spectrum for P-BWO as rendered in Figure 2b, the doublet peaks can be deconvoluted into binding energy of 35.41 and 37.73 eV, which are assigned to the W4f7/2 and W4f5/2 in the W6+ oxidation state of P-BWO. There is a 0.2 eV reduction in binding energy for both peaks of S-BWO, indicating that the chemical environment is altered with the introduction of the S element. As for the O1s core spectrum, the deconvoluted peaks at 530.33 and 531.40 eV for P-BWO are attributed to lattice oxygen and surface chemisorbed oxygen, respectively. The binding energy for both peaks decreased by approximately 0.23 eV for S-BWO, as shown in Figure 2c. The optical properties of both P-BWO and S-BWO were studied using UV/Vis diffuse reflectance spectroscopy. As shown in Figure 2d, the absorption edge of S-BWO exhibits an obvious red-shift compared to that of P-BWO, indicating an increased absorption in the visible light region with the introduction of S.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010048532_TII_01/figure/2010048532_TII_01_1.png"], "tampered": false, "paper_ids": ["2010002918"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010050483_TII_02/figure/2010050483_TII_02_2.png", "question_id": "consistency_289", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2 EA improves liver steatosis and liver function in mice. (A) H&E staining of liver tissue (scale bar = 200 µm). The red arrows indicate typical hepatic inflammation. (B) Liver tissue stained with Oil Red O (scale bar = 200 µm). (C) Morphology of liver. (D) Hepatic TG. (E) Hepatic TC. (F) Serum ALT. (G) Serum AST. n = 6, values are mean ± SEM; *** p < 0.001 (Control vs Model); ## p < 0.01 (Model vs EA); ΔΔ p < 0.01 (EA vs SEA).", "figure_related_sentences": "HE and Oil Red O staining revealed pronounced lipid deposition in the liver of mice, accompanied by disorganized hepatocyte structure, varying sizes of droplets, and alterations in the MOD group. Notably, the MOD group exhibited significantly weaker abnormal lipid accumulation in the liver compared to the CON group, the group treated with EA had a significant increase in hepatic lipid accumulation, as depicted in Figure 2A-C. In accordance with the Elisa results, the hepatic concentrations of TG and TC in mice from the MOD group exhibited a statistically significant elevation compared to those from the CON group. The addition of EA resulted in a considerable decrease in hepatic levels of TG and TC, as seen in Figure 2D and E. Furthermore, the MOD group exhibited a notable elevation in blood levels of ALT and AST in comparison to the CON group. After the treatment, there was a notable decrease in the serum levels of ALT and AST (Figure 2F and G).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010050483_TII_02/figure/2010050483_TII_02_2.png"], "tampered": false, "paper_ids": ["2010002923"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010073266_TII_01/figure/2010073266_TII_01_2.png", "question_id": "consistency_290", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 3. Activation of nuclear factor (NF)-κB signaling by bone morphogenetic protein (BMP)4 stimulation in intraepithelial lymphocytes (IELs). Flow cytometry determined the expression of the BMP type I receptor and phosphorylated NF-κB in IELs in culture. following treatment with BMP4 for 6 h, the expression of the BmP type i receptor and phosphorylated nf-κB was significantly increased compared with that in the control group. noggin partially decreased the expression of the BMP type I receptor, as well as NF-κB transcriptional activity. The results are representative of three independent experiments. P < 0.05.", "figure_related_sentences": "Exogenous BMP4 regulates the NF-κB signaling pathway in IELs. the primary BmP receptors include two type i receptors (BmPria and BmPriB) and one type II receptor (BMPRII). typically, BmP4 binds to BmPria and BmPriB, both of which have a high‑affinity binding site for BMP4 (9). To determine whether the activation of nf-κB signaling in iels involves iec-derived BmP4, iels from the small intestines of mice were isolated and cultured. it was observed that the protein levels of BmPria, BmPriB and phosphorylated nf-κB were highly upregulated in iels that were cultured in the presence of BmP4 (30 ng/ml), as assessed by flow cytometry (BMPRIA,3.88±0.56%; BMPRIB, 10.00±1.42%; and p-nf-κB, 11.33±1.45%). However, this effect was abolished by the BmP-specific antagonist NOGGIN (30 ng/ml), as shown in Fig. 3. Therefore, it is hypothesized that I/R induces the activation of NF‑κB signaling in iels, possibly through IEC‑derived BMP4.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010073266_TII_01/figure/2010073266_TII_01_2.png"], "tampered": false, "paper_ids": ["2010002924"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010050126_TII_02/figure/2010050126_TII_02_4.png", "question_id": "consistency_291", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 4. Transgene expression and influence on tumor growth inhibition of polymer coated adenovirus (PC-Ad) with focused ultrasound (US) in the presence of SonoVue microbubbles (SV). A) Luciferase transgene expression in tumors of mice injected intravenously with PC-Ad and treated simultaneously with US or not, as quantified using IVIS for the first 20 days after injection. Improved luciferase expression in US-treated tumors indicates increased replication and spread. n = 8. Standard deviation is shown by bars. Two-sided t test performed at each time-point. At 1, 2, 3, and 7 days, P =.007, .004, .03, and .004, respectively. B) Staining of tumor sections with anti-CD31 (red) or anti-hexon (green) to determine the influence of US on intratumoral penetration of PC-Ad. Scale bar = 20 µm. Staining of Ad away from endothelial cells suggests improved penetration into tumors. C) Tumor growth in mice treated with phosphate-buffered saline (PBS) (black line), focused ultrasound and SV but no PC-Ad (gray line), PC-Ad with SV without focused ultrasound (blue line), or PC-Ad with SV with ultrasound (green line), as assessed by daily measurement with calipers. n = 8 mice. Mean values ± 95% confidence intervals are shown. Analysis of variance with Tukey correction comparing all groups post-test was used. D) Kaplan–Meier survival curve of mice treated in (C), in accordance with animal welfare legislation, mice were killed when tumor size reached a predefined limit of 700mm³. Log-rank test was performed. Results are typical of two independent experiments. All statistical tests were two-sided.", "figure_related_sentences": "Mice bearing one ZR-75-1 tumor were injected intravenously with PC-Ad + SV, with or without the application of ultrasound. The replication and lytic spread of Ad was tracked by measurement of luciferase and daily tumor sizing. After 20 hours, luciferase expression in tumors of ultrasound-treated mice exceeded the level in non-ultrasound-treated mice by threefold (P = .007). This enhancement level may be below the level seen in some mice in our previous studies using nonmodified Ad (31), but its dramatically reduced variability provides a substantial benefit. Furthermore, it is notable that this differential increased to 20-fold by 2 days (P = .004) and 30-fold by 3 days (4×10^6 light units; SD = 3×10^6 for PC-Ad+SV+ultrasound group vs 1.3×10^5; SD = 1×10^5 for PC-Ad+SV group; P = .03) (Figure 4A). The possibility that improved intratumoral distribution permits small increases in uptake to translate into dramatic increases in infection was confirmed using fluorescence microscopy of tumor sections (Figure 4B; Supplementary Figure 3F, available online). Tumor growth was statistically significantly accelerated with PC-Ad + SV + ultrasound compared with all other treatment groups. This was the case if mean tumor sizes at day 42, PC-Ad + SV + ultrasound vs PC-Ad + SV (P = .02) (Figure 4C), or mean areas under the curves of tumor growth were compared (PC-Ad + SV + ultrasound; mean = 12 710 mm^3; SD = 3177 vs PC-Ad + SV; 18 318 mm^3; SD = 4665; P = .04). Notably, higher luciferase expression was associated with greater retardation of tumor growth and survival extension. Levels of 2×10^8 to 1×10^9 photons/sec/cm^2 were associated with almost complete growth retardation. Kaplan-Meier analysis demonstrated median days survival values of 22 for PBS, 21 for SV + ultrasound, 26 for PC-Ad + SV = 26, and 33 for PC-Ad + SV + ultrasound (Figure 4D).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010050126_TII_02/figure/2010050126_TII_02_4.png"], "tampered": false, "paper_ids": ["2010002929"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010012714_TII_02/figure/2010012714_TII_02_0.png", "question_id": "consistency_292", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "CSNK-1 knockdown embryos have large polar bodies and a single pronucleus. (A) DIC images from z-stacks through control vs. csnk-1(RNAi) dissected embryos from three different strains (N2, FM99, and FM135). Images were acquired between pronuclear migration and pronuclear breakdown. Arrows mark each visible polar body. Scale bar, 10 μm. (B) Graph of polar body area in N2, FM99, and FM135 control vs. csnk-1(RNAi) embryos. Two-dimensional area was measured in the z-stack where the polar body was at its largest size. Statistical analysis was by two-tailed Student’s t test. ***, p < 0.001. (C) Representative images of a control N2 embryo and a csnk-1(RNAi) embryo at midfocal plane after pronuclear migration. Scale bar, 10 μm. (D) Graph of the number of pronuclei present in the embryo after female meiosis in control vs. csnk-1(RNAi) embryos. The fraction of csnk-1(RNAi) embryos with a single pronucleus in the three strain backgrounds tested was not significantly different (Fisher’s exact test p = 0.25).", "figure_related_sentences": "Whereas two small polar bodies were observed in control embryos, csnk-1(RNAi) embryos had very small polar bodies (Figure 1A). Polar body size was measured in DIC z-stacks of embryos between pronuclear migration and pronuclear centration as the two-dimensional area of each polar body in the focal plane with the largest area (Figure 1B). In contrast, 12 out of 45 csnk-1(RNAi) embryos had a single pronucleus (Figure 1C and 1D), which is clearly visible in csnk-1(RNAi) embryos (Figure 1A and 1C).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010012714_TII_02/figure/2010012714_TII_02_0.png"], "tampered": false, "paper_ids": ["2010002932"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010013634_TII_02/figure/2010013634_TII_02_1.png", "question_id": "consistency_293", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "GRASP55 deletion has minor effects on the Golgi structure. (A) Western blots of Golgi proteins in GRASP55 knockout HeLa cells. Wild-type and representative GRASP55 knockout clones from three separate sgRNAs (T1, T2, and T3) were lysed and blotted for GRASP55/65, Golgin-45, and GM130. (B) Quantification of A for the relative levels of GRASP65, Golgin-45, and GM130 in GRASP55 knockout cells. Error bars represent SEM. (C) Immunofluorescence of GRASP55 knockout clones stained for GM130 and TGN46. The lower three rows are increased magnifications of the Golgi in a single cell. Scale bars are 10 µm. (D) Colocalization of GM130 and TGN46 quantified by the Pearson’s correlation coefficient of z-stacks from GRASP55 knockout clones from C. Error bars represent SEM. (E) Quantification of Golgi fragmentation in GRASP55 knockout clones in C. Blinded determination of the Golgi morphology of 300 cells from each sample was quantified across three biological replicates. Error bars represent SEM. A Student’s t test was performed to determine statistical significance. *p < 0.05.", "figure_related_sentences": "GRASP55 deletion also resulted in a significant increase of Golgin-45 in HeLa cells, while GM130 protein levels remained unchanged in both cell lines (Figure 2A and 2B and Supplemental Figure S3A and S3B). Deletion of GRASP55 caused a minor but significant decrease in the level of Golgi fragmentation in both HeLa and HEK293 cells, as assessed by immunofluorescence microscopy for GM130 and TGN46 (Figure 2C–2E and Supplemental Figure S3C–S3E). However, colocalization of GM130 and TGN46, as measured by Pearson’s correlation coefficient, remained changed in HeLa cells. Western blot analysis of GRASP55 knockout clones demonstrated that GRASP55 depletion was effective, as no GRASP55 signal was detected (Figure 2A and Supplemental Figure S3A). Knockout of GRASP55 significantly increased the level of GRASP65 in HEK293 cells (Supplemental Figure S3A and S3B), although this effect was not as obvious in HeLa cells (Figure 2A and 2B).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010013634_TII_02/figure/2010013634_TII_02_1.png"], "tampered": false, "paper_ids": ["2010002933"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010033678_TII_01/figure/2010033678_TII_01_2.png", "question_id": "consistency_294", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Fig. 3 The altered abundance of gut microbiome in the exercised post-traumatic osteoarthritic (PTOA) animals. a) A Venn diagram was generated to compare operational taxonomic units (OTUs) among three groups and to depict OTUs that were unique to the three groups. b) Taxonomic profiles of the fecal bacteria from 16S ribosomal ribonucleic acid (rRNA) gene sequencing show the relative abundance of the top 10 phyla and the top 10 genera of fecal bacteria presented in the Sham/sedentary (Sed), PTOA/Sed, and PTOA/treadmill-walking (TW) groups. Changes in the c) two bacterial phyla and d) five genera in the gut microbiome composition of three groups. p < 0.05, p < 0.01, PTOA/Sed or PTOA/TW versus Sham/Sed, one-way analysis of variance (ANOVA); #p < 0.05, ##p < 0.01, PTOA/Sed versus PTOA/TW, one-way ANOVA; ns, not significant. Data are presented as the mean and standard deviation, n = 6.", "figure_related_sentences": "The core OTUs comprised 6.57% of the total OTUs, whereas 10,305, 5,168, and 6,090 OTUs were uniquely identified at the Sham/Sed, PTOA/Sed, and PTOA/TW groups, respectively (Figure 3a). The OTUs were classified into 36 bacterial phyla and 432 genera. According to the number of reads in the sequence, the top 10 phyla and genera in relative abundance of the fecal microbiome are displayed in Figure 3b and Supplementary Figure c. Some differences identified at the levels of phylum and genus of fecal microbiome among the three groups are displayed in Figure 3c. The relative abundance of the phylum TM7 was consistently lower in both PTOA/Sed and PTOA/TW groups compared to the Sham/Sed group. The phylum Fusobacteria, which was robustly abundant in the gut of the PTOA rats without exercise, was nearly absent in the Sham/Sed and PTOA/TW groups. In this context, phylum TM7 and Fusobacteria were identified as the PTOA-relevant phyla and exercise decreased the abundance of Fusobacteria. At the genus level, the relative abundance of Lactobacillus, Turicibacter, Adlercreutzia, and Cetobacterium was increased in the PTOA/Sed group compared to Sham/Sed group, while the PTOA-induced Adlercreutzia and Cetobacterium were reduced by exercise (Figure 3d).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010033678_TII_01/figure/2010033678_TII_01_2.png"], "tampered": false, "paper_ids": ["2010002935"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010010934_TII_02/figure/2010010934_TII_02_4.png", "question_id": "consistency_295", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 5. Effect of HA on OC-like cell adhesion to FN. (A) Assessment of the relative avidity of cell adhesion onto FN in the presence of HA by varying the centrifugal force (45 g, 180 g, and 400 g) applied to dislodge bound cells. Cells were allowed to adhere to FN coated at 5 µg/ml. (B) Adhesion to FN in the presence of HA or the 4B4 function-blocking anti-β1 mAb. (C) Assessment of the relative avidity of cell adhesion to FN of cells maintained for 24 h in the presence of soluble HA by varying the centrifugal force (45 g, 180 g, and 400 g) applied to dislodge bound cells. (D) Phase-contrast (p.c.) morphology and CD44/actin staining of adherent OC-like FLG 29.1 cells to FN-coated slides (20 µg/ml) at 20 µg/ml in the absence or presence of 1.0 mg/ml HA. Bars, 100 µm.", "figure_related_sentences": "Soluble HA (Figure 5B). Another possibility could be that the addition of soluble HA could affect, via an inside-out mechanism mediated by the cytoplasmic domain of CD44, the affinity/avidity of integrin receptors for their cognate ligands. Thus, additional adhesion experiments were performed with OC-like FLG 29.1 cells grown in the presence of soluble HA for 24 h and then assayed with CAFCA at different detachment forces (45 g, 180 g, and 400 g) in the absence of HA. Again, a significant difference was ated when compared with control cells grown in the absence of HA (Figure 5C). Consistently, the presence of soluble HA affected neither the expression levels of α5β1 and αvβ1 integrins on OC-like FLG 29.1, as evaluated by flow cytometry (unpublished data), nor the morphology of cells attached to FN, nor the even cell membrane distribution of CD44 molecules (Figure 5D).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010010934_TII_02/figure/2010010934_TII_02_4.png"], "tampered": false, "paper_ids": ["2010002936"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010011264_TII_01/figure/2010011264_TII_01_6.png", "question_id": "consistency_296", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Inhibition by NPPB, furosemide, and sucrose of the sorbitol-induced hemolysis. (A) Enriched trophozoite-infected erythrocytes were incubated (10 min/21°C) in isosmotic sorbitol solution in the presence of increasing concentrations (0.01–30 µM) of NPPB (open triangles; SE, n = 12) or furosemide (closed triangles; SE, n = 9). Incubation was stopped by centrifugation and hemolysis was indicated by hemoglobin in the supernatant. In the insert on the right are the scanned images of supernatants from an individual experiment. The hemoglobin concentration of the supernatant for each condition (NPPB and furosemide) was determined photometrically (546 nm). Data are expressed as the percentage of the 30 µM NPPB inhibited fraction (maximal inhibition ≈ 86 ± 2% of total hemolysis, left). (B) Substrate competition of the infection-induced sorbitol hemolysis. Hemolysis (10 min/21°C) was assessed in solutions where different quantities of sorbitol (0–120 mosM) have been isosmotically replaced by sucrose (circles) or NaCl (squares). Mean normalized hemolysis (± SE; n = 8; left) and imaged supernatants of an individual experiment (right) are shown as in A. (C) Uptake of [¹⁴C] sorbitol into P. falciparum–infected human erythrocytes incubated in isosmotic sorbitol solution. The uptake of radiolabeled sorbitol was measured after 5, 30, 60, 90, and 120 s of incubation. Individual data of three experimental series were expressed as a percentage of the respective 2 min values and averaged (means ± SE; n = 4–12). (D) Inhibition of [¹⁴C]sorbitol uptake in isosmotic sorbitol by sucrose. Mean uptake (± SE; n = 9–10) of [¹⁴C]sorbitol (30 s values minus the 5 s blank value) in isosmotic sorbitol solution (control) or in sorbitol solutions where 20 and 60 mM of sorbitol were replaced by 20 and 60 mM of sucrose or 10 and 30 mM of NaCl, respectively (uptake conditions: 3.7 × 10⁴ Bq/ml [¹⁴C]sorbitol, 2.5% final hematocrit, 90% parasitemia). * and # correspond to P < 0.01 and 0.05, respectively, ANOVA.", "figure_related_sentences": "Finally, the NPPB and furosemide inhibition of the hemolysis in isosmotic sorbitol solution was compared with those of both conductances (Figure 7A and B). NPPB and furosemide inhibited the sorbitol hemolysis of infected erythrocytes in a dose-dependent manner (Figure 7A) with IC₅₀s (~1 µM for NPPB and ~10 µM for furosemide; Figure 7A) similar to those for the outward rectifying lactate current (Figure 3D). In addition, the effect of sucrose on the infection-induced hemolysis was determined by isosmotic substitution of sorbitol with increasing concentrations of sucrose and for control of NaCl (Figure 7B). Replacement by sucrose but not by NaCl inhibited hemolysis of trophozoite-infected cells with an IC₅₀ of ~10 mM, indicating (a) competition between sorbitol and sucrose within the permeability pore and (b) low permeability of sucrose. To further test for the inhibitory effect of sucrose on the sorbitol pathway of infected erythrocytes, isotopic flux measurements of [¹⁴C]sorbitol were performed under the experimental conditions used for the hemolysis experiments. Figure 7C shows the time course of the [¹⁴C]sorbitol uptake in isoosmotic sorbitol solution. Within 2 min of incubation the uptake apparently saturated. Incubation (30 s) of the infected cells in the presence of 20 or 60 mM sucrose (replacing the same amount of sorbitol) significantly decreased the uptake of [¹⁴C]sorbitol as illustrated in Figure 7D. In contrast, substitution of 20 and 60 mM sorbitol by 10 and 30 mM NaCl did not significantly decrease [¹⁴C]sorbitol uptake, respectively (Figure 7D).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010011264_TII_01/figure/2010011264_TII_01_6.png"], "tampered": false, "paper_ids": ["2010002963"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/numerical/2010017209_TII_01/figure/2010017209_TII_01_1.png", "question_id": "consistency_297", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Ccdc11 is a component of centriolar satellites. (A) Immunoblot of lysates from tetracycline-inducible GFP-Ccdc11–expressing RPE-1 stable cell line (RPE::GFP-Ccdc11) probed with anti-Ccdc11 antibody. Numbers on the left indicate molecular mass of markers in kilodaltons. (B) Localization of endogenous Ccdc11 throughout the cell cycle. Asynchronously growing MEF cells were fixed and stained for Ccdc11 (green), centrin to identify centrioles (red), acetylated tubulin to mark cilia (red), and DNA (4′,6-diamidino-2-phenylindole [DAPI]; blue). The centriolar satellite distribution of Ccdc11 is conserved through G1, S phase, G2, and mitosis. After serum starvation to induce ciliogenesis, the satellite pool of Ccdc11 is lost, and the protein is enriched at the transition zone (distal end of each centriole, arrowheads). Insets, magnified images of the centrosome region. Scale bar, 5 μm. (C) RPE::GFP-Ccdc11 cells immunostained with antibodies against GFP (green), PCM-1 (red), or Cep290 (red), as well as centrin (magenta) or acetylated tubulin (light blue) to mark centrioles and cilia, respectively. Ccdc11 colocalizes with PCM-1 and Cep290 at satellites in G1 and with Cep290 at the transition zone in G0. Scale bar, 5 μm. (D, E) RPE-1 cells were treated with nocodazole for 1 h to depolymerize microtubules and then allowed to recover for up to 30 min. Samples were fixed at the indicated times and stained for Ccdc11 (green), centrioles (centrin, magenta), microtubules (α-tubulin, red), and DNA (DAPI, blue). Ccdc11 localization to centriolar satellites is microtubule dependent, but the centriolar pool of Ccdc11 does not require microtubules. Scale bar, 10 μm. Arrowhead indicates the satellite pool of Ccdc11. We scored 300 cells for each sample, from three independent experiments; **p < 0.05. (F) Ccdc11 interacts with satellite proteins PCM-1 and Cep290. Immunoprecipitation was performed on extracts from RPE::GFP-Ccdc11 cells using anti-GFP antibody or control IgG and then probed for GFP and endogenous PCM-1, Cep290, and γ-tubulin (negative control).", "figure_related_sentences": "Ccdc11 is a protein of 514 amino acids with a predicted molecular weight of ~75 kDa containing three putative coiled-coil domains. It is conserved in organisms containing centrioles/basal bodies and cilia ranging from humans to Chlamydomonas (Supplemental Figure S1, A–C). To characterize the localization and function of Ccdc11 at the cellular level, we generated polyclonal antibodies directed against human Ccdc11. The antibody recognized a protein of expected size in immunoblots of human telomerase–immortalized retinal pigment epithelial cells (hTERT-RPE-1; here after referred to as RPE-1; Figure 1A). The antibody also recognized the green fluorescent protein (GFP)–tagged fusion protein in RPE-1 cells stably expressing tetracycline-inducible GFP-Ccdc11 (RPE::GFP-Ccdc11; Figure 1A). Next we investigated the localization of endogenous Ccdc11 at various stages of the cell division cycle. Ccdc11 was present on both centrioles in G1 cells and was also distributed in small aggregates that surrounded the two centrioles (Figure 1B). This localization pattern is highly reminiscent of centriolar satellites, which are 70- to 100-nm cytoplasmic granules that concentrate around the centrioles/centrosome and are involved in trafficking of proteins to and from the centrosome (Kubo et al., 1999; Dammermann and Merdes, 2002).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/numerical/2010017209_TII_01/figure/2010017209_TII_01_1.png"], "tampered": false, "paper_ids": ["2010003203"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010017594_TII_02/figure/2010017594_TII_02_1.png", "question_id": "consistency_298", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2. Efficient entry of HIV-1 into DCs but not small T cells. The results are representative of 2 or more experiments in each case. (A) Early vs. late stages of reverse transcription in blood-derived DCs. IIIB was added for 90 min at 37°C to DCs, purified T cells (T), and T blasts (TBl), washed, and cultured 0, 4, 18, or 36 h. Early and late (R/U5 and LTR/gag primers) transcripts were amplified by PCR and compared to graded doses of ACH-2 cells. (B) Several isolates of HIV-1 efficiently enter blood-derived DCs. Graded doses of the denoted isolates (titred by the AIDS Resources Program) were added to DCs for 90 min, washed, and cultured 4 h before amplifying R/U5 DNA.(C) Detection of early R/U5 transcripts 3 h after adding Ba-L and IIIB isolates to skin leukocytes, either bulk skin cells (SC), FACS-purified DCs and T cells, or a 1:2 DC/T mixture. (D and E) Evidence that late reverse transcripts in HIV-1 pulsed DCs represent viral entry and not simply binding to skin leukocytes (D) or blood derived DCs (E). R/U5 sequences are infrequent if virus was bound for 4 h on ice, and was trypsin insensitive (0.25%, GIBCO for 10 min at 37°C after 4 cell washes in phosphate saline) if virus was offered for 4 h at 37°C. (D) Kinetics of R/U5 sequence formation with Ba-L or IIIB in skin cells (SC) and T blasts. The 0 h time point was carried out 90 min after adding virus at 37°C. DNA was also analyzed 1–8 h after the virus pulse, washing, and culture.", "figure_related_sentences": "At time 0, i.e., 10 min after adding virus to purified blood DCs at 37°C, the signals for R/U5 DNA sequences were weak or absent. HIV-1 DNA then decreased steadily for 8 h to reach a plateau (Fig. 2 A) for at least 1–3 d (not shown). Only the early products of reverse transcription were abundant. At the dose of virus we employed, and relative to a standard curve derived from the ACH-2 cell line that expresses 1 copy of proviral DNA/cell (15), we observed 103–104 copies of R/U5 DNA in 100,000 DCs and .102 copies of LTR/gag sequences (Fig. 2 A). This signal is very high considering that we were only applied virus at ,0.1 MOI. R/U5 DNA was weak or not detected with omparable numbers of purified T cells (Fig. 2 A). T blasts were readily infected, as both R/U5 and LTR/gag containing sequences were found. The amount of these sequences increased rapidly in culture, because infection was productive in T blasts (Fig. 2 A). Several different HIV-1 isolates entered and began reverse transcription in DCs (Fig. 2 B). Using comparable numbers of infectious units, the interaction of Ba-L, SF162 and IIIB was particularly efficient. Efficient entry of these and other primary isolates was also noted in skin DCs, more than skin T cells, but only with probes for R/U5 sequences (Fig. 2 C). Given the evidence that HIV-1 virions can contain short reverse transcripts (22, 23), we were concerned that the R/U5 sequences represented intraviron-DNA that had bound but not entered the DCs. However, entry seemed more likely for the following reasons. The R/U5 signal was strong when virus was added on ice for 4 h (Fig. 2, D and E), even though virus does bind in the cold (23–25). The R/U5 signals were weak if the cells were examined just after the 90-min virus pulse at 37°C, but increased progressively for 8 h after washing away nonbound virus (Figs. 2, A and F). In contrast, virus binding can be detected in just 3-5 min at this temperature (23–25). The R/U5 signals that developed after 4 h at 37°C also were insensitive to trypsin (Fig. 2, D and E), which releases surface-bound virus (23).", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010017594_TII_02/figure/2010017594_TII_02_1.png"], "tampered": false, "paper_ids": ["2010003205"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010047469_TII_02/figure/2010047469_TII_02_1.png", "question_id": "consistency_299", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 2 Plk3 and procaspase-8 interact. (A) HEK 293T cells were co-transfected with GFP-Plk3 or GFP-Rip3 and Flag-procaspase-8. GFP-Rip3 was used as a positive control for the co-IP with procaspase-8. Precipitates were immunoblotted for Flag and GFP. (B) The binding ability of GST-fused procaspase-8 was analyzed in pull-down assays. GST-procaspase-8 or GST alone (as a control) wasincubated with HeLa cell lysates. The pull-down was analyzed by immunoblotting for Plk3 and GST. (C) Schematic representation of recombinant GST-fused full-length Plk3 (GST-Plk3-WT) and truncated forms of Plk3 (GST-Plk3-NT1, -NT3 and -CT1) used in pull-down assays. (D) GST-Plk3-WT or Plk3 subdomains were incubated with HeLa cell lysates for pull-down assays. The immunoblot analysis was performed using caspase-8- and GST-antibodies. (E) HeLa cells were treated with 50 ng/ml nocodazole (Noc) for 16 h to enrich for mitotic cells. Endogenous caspase-8 was immunoprecipitated from cell lysates. Normal mouse IgG was used as a control. The immunoprecipitates and the lysates were immunoblotted for caspase-8, Plk1, Cdk1, Cyclin B1, Plk3 and Aurora B. (F) HeLa cells were treated with 50 ng/mL CD95L and CHX for 0 h and 2 h. Endogenous caspase-8 was immunoprecipitated from cell lysates with anti-caspase-8 p18 goat antibody. Normal goat IgG (Santa Cruz) was used as a control. The immunoprecipitates and the lysates were immunoblotted for Plk3, caspase-8, cleaved caspase-8 and p10. (G) The interaction of Plk3 and procaspase-8 (Casp8) was monitored via in situ PLA. HeLa cells were labeled with the anti-Plk3 (Abcam, rabbit) and anti-Casp8 (mouse) (left panel) or anti-Plk3 (BD, mouse) and anti-Casp8 (rabbit) (right panel) antibodies. Single antibody staining (Plk3 or Casp8) was used as a control. Scale bar: 10 µm. Each bar represents the mean value ± SD (n = 3). The differences between single and double antibody staining were statistically significant by Student’s t-test (lower panels) (*P ≤ 0.05; **P ≤ 0.005).", "figure_related_sentences": "Plks are characterized by their PBD, which mediates protein interactions and provides target specificity. Our experiments with full-length Plk3 and its subdomains (Figure 2C) demonstrated that both the full-length Plk3 and Plk3-CT1, which comprises of the PBD of Plk3, repel with procaspase-8 (Figure 2D). In an IP-analysis of endogenous protein we confirmed the association of procaspase-8 with Plk1 and Cdk1/cyclin B1 in mitotic cells [31, 32] and corroborated the interaction of caspase-8 and Plk3, which is independent of mitosis (Figure 2E). Stimulation of CD95 receptor induced processing of procaspase-8 with increasing levels of p18 and p10 (Figure 2F). Simultaneous IP of procaspase-8, whose levels decline upon CD95 stimulation, showed decreasing amounts of co-precipitated Plk3 (Figure 2F, right panel). The quantification of the PLA using Plk3 antibodies targeting the N-terminal (Abcam) or the interdomain of Plk3 (BD) refuted the close proximity of both endogenous proteins in HeLa cells (Figure 2G, upper and lower panel)", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010047469_TII_02/figure/2010047469_TII_02_1.png"], "tampered": false, "paper_ids": ["2010003206"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "text_image_inconsistency/trend/2010130827_TII_02/figure/2010130827_TII_02_0.png", "question_id": "consistency_300", "fraud_type": "text_image_inconsistency", "fraud_sub_types": ["None"], "ground_truth": ["C"], "mask_indices": [0], "mask_caption": "", "mask_path": "", "figure_caption": "Figure 1. TROY associates with PDZ-RhoGEF (PRG). (A) 293 cells were co-transfected with HA-tagged TROY plasmid and Myc-tagged PDZ-RhoGEF plasmid, and the lysates were immunoprecipitated with an anti-Myc antibody or mouse IgG. The immunoprecipitates were analyzed for the presence of PDZ-RhoGEF by immunoblot analysis. The expression level of Myc-tagged PDZ-RhoGEF and HA-tagged TROY in the cells is shown by immunoblotting of whole cell lysates (WCL). (B-D) The lysates of T98G, GBM10, and GBM43 cells were immunoprecipitated with an anti-TROY antibody or rabbit IgG. The immunoprecipitates were analyzed for the presence of PDZ-RhoGEF by immunoblot analysis. The expression level of PDZ-RhoGEF and TROY in the cells is shown by immunoblotting of WCL. (E) TROY does not co-immunoprecipitate with LARG in 293 cells. 293 cells were transfected with HA-tagged LARG or Myc-tagged TROY, or co-transfected with HA-tagged LARG and Myc-tagged TROY. Twenty-four hours after transfection, cells were lysed and immunoprecipitated with anti-Myc antibody. Immunoprecipitates or WCL were immunoblotted with the indicated antibodies. (F) Colocalization of TROY and PDZ-RhoGEF in T98G, GBM10, and GBM43 cells. Cells were stained and examined by confocal microscopy. TROY was visualized with Alexa Fluor 546–conjugated antibody, and PDZ-RhoGEF was visualized with Alexa Fluor 488–conjugated antibody. The colocalization of TROY (red) with PDZ-RhoGEF (green) appears as a yellow color in the merged image. Cells were counterstained with DAPI (blue) (bars = 10 μm). (G) 293 cells were co-transfected with AU1-tagged TROY, Myc-tagged PRG, and HA-tagged Pyk2, and 24 hours later, cells were lysed and immunoprecipitated with goat anti-Myc or goat anti-AU1 antibodies or goat IgG. Immunoprecipitates or WCL were immunoblotted (IB) with the indicated antibodies. (H) Left panel, 293 cells were transfected with HA-tagged LARG and/or FLAG-tagged Pyk2. Twenty-four hours later, the cells were lysed and immunoprecipitated with anti-FLAG antibody or mouse IgG. Immunoprecipitates or WCL were IB with anti-FLAG or anti-HA antibodies. Right panel, 293 cells were co-transfected with Myc-tagged PRG and FLAG-tagged WT Pyk2 or kinase-deficient (KD) Pyk2 for 24 hours. Cells were lysed and immunoprecipitated with anti-Myc antibody. Immunoprecipitates or WCL were IB with the indicated antibodies.", "figure_related_sentences": "To determine possible mechanisms through which TROY induces GBM cell invasion, we performed immunoprecipitation of TROY from T98G glioma cells overexpressing TROY and analyzed the precipitates with MALDI-TOF and MS/MS to identify proteins that are capable of interacting with TROY and potentially mediating TROY signaling [13]. Several proteins were identified in the TROY immunoprecipitates, among which PDZ-RhoGEF was of particular interest because it has previously been reported to be involved in cellular motility [30,31]. To confirm the interaction between TROY and PDZ-RhoGEF, 293 cells co-transfected with HA-tagged TROY and Myc-tagged PDZ-RhoGEF were immunoprecipitated with an anti-Myc antibody, and the precipitates were immunoblotted with anti-HA and anti-Myc antibodies. Immunoblotting demonstrated that HA-tagged TROY co-immunoprecipitated with Myc-tagged PDZ-RhoGEF, refuting an interaction between TROY and PDZ-RhoGEF (Figure 1A). Endogenous PDZ-RhoGEF was found to co-immunoprecipitate with endogenous TROY in T98G glioma cells as well as primary GBM patient-derived xenografts GBM10 and GBM43 cells (Figure 1, B-D). The expression pattern of endogenous TROY and TROY interactants in the different cell lines is shown in Supplementary Figure 1. To explore the specificity of the interaction between TROY and PDZ-RhoGEF, we examined whether TROY could interact with LARG, a closely related GEF belonging to the same RhoGEF subfamily as PDZ-RhoGEF. 293 cells were co-transfected with HA-tagged LARG and/or Myc-tagged TROY. Immunoprecipitation of the transfected cell lysates with an anti-Myc antibody followed by immunoblotting of the precipitates with the anti-HA antibody showed that LARG was not present in the TROY-Myc immunoprecipitates, suggesting a specific interaction of TROY with PDZ-RhoGEF (Figure 1E). To further confirm the interaction, we examined the colocalization of TROY and PDZ-RhoGEF by immunofluorescence analysis. T98G, GBM10, and GBM43 cells were stained with anti-TROY and anti–PDZ-RhoGEF antibodies and examined by confocal microscopy (Figure 1F). Consistent with previous results [13], TROY staining was predominately near the cell periphery and enriched in lamellipodia, and the merged images contradicted colocalization of TROY and PDZ-RhoGEF.", "inconsistent_part": "", "tampered_sentences": ["None"], "golden_sentences": ["None"], "metadata": {"all_images_paths": ["text_image_inconsistency/trend/2010130827_TII_02/figure/2010130827_TII_02_0.png"], "tampered": false, "paper_ids": ["2010003807"], "panel_ids": ["None"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000027/panel/2000000027_6_1/2000000027_6_1_38.png", "question_id": "duplication_retract_1", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [5, 6, 8, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000027/panel/2000000027_6_1/2000000027_6_1_38.png", "retract/2000000027/panel/2000000027_6_1/2000000027_6_1_16.png"], "tampered": true, "paper_ids": ["2000000027", "2000000027"], "panel_ids": ["2000000027_6_1_38", "2000000027_6_1_16"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000027/panel/2000000027_6_1/2000000027_6_1_40.png", "question_id": "duplication_retract_2", "fraud_type": "duplication", "fraud_sub_types": ["rotated"], "ground_truth": ["C"], "mask_indices": [5, 6, 8, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000027/panel/2000000027_6_1/2000000027_6_1_40.png", "retract/2000000027/panel/2000000027_6_1/2000000027_6_1_16.png"], "tampered": true, "paper_ids": ["2000000027", "2000000027"], "panel_ids": ["2000000027_6_1_40", "2000000027_6_1_16"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000027/panel/2000000027_6_1/2000000027_6_1_18.png", "question_id": "duplication_retract_3", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [7], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000027/panel/2000000027_6_1/2000000027_6_1_18.png", "retract/2000000027/panel/2000000027_6_1/2000000027_6_1_17.png"], "tampered": true, "paper_ids": ["2000000027", "2000000027"], "panel_ids": ["2000000027_6_1_18", "2000000027_6_1_17"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000027/panel/2000000027_6_1/2000000027_6_1_37.png", "question_id": "duplication_retract_4", "fraud_type": "duplication", "fraud_sub_types": ["rotated"], "ground_truth": ["C"], "mask_indices": [2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000027/panel/2000000027_6_1/2000000027_6_1_37.png", "retract/2000000027/panel/2000000027_6_1/2000000027_6_1_18.png"], "tampered": true, "paper_ids": ["2000000027", "2000000027"], "panel_ids": ["2000000027_6_1_37", "2000000027_6_1_18"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000027/panel/2000000027_6_1/2000000027_6_1_37.png", "question_id": "duplication_retract_5", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000027/panel/2000000027_6_1/2000000027_6_1_37.png", "retract/2000000027/panel/2000000027_6_1/2000000027_6_1_35.png"], "tampered": true, "paper_ids": ["2000000027", "2000000027"], "panel_ids": ["2000000027_6_1_37", "2000000027_6_1_35"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000027/panel/2000000027_6_1/2000000027_6_1_18.png", "question_id": "duplication_retract_6", "fraud_type": "duplication", "fraud_sub_types": ["rotated"], "ground_truth": ["C"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000027/panel/2000000027_6_1/2000000027_6_1_18.png", "retract/2000000027/panel/2000000027_6_1/2000000027_6_1_35.png"], "tampered": true, "paper_ids": ["2000000027", "2000000027"], "panel_ids": ["2000000027_6_1_18", "2000000027_6_1_35"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000027/panel/2000000027_6_1/2000000027_6_1_40.png", "question_id": "duplication_retract_7", "fraud_type": "duplication", "fraud_sub_types": ["rotated"], "ground_truth": ["C"], "mask_indices": [1, 2, 4, 5, 7, 8], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000027/panel/2000000027_6_1/2000000027_6_1_40.png", "retract/2000000027/panel/2000000027_6_1/2000000027_6_1_38.png"], "tampered": true, "paper_ids": ["2000000027", "2000000027"], "panel_ids": ["2000000027_6_1_40", "2000000027_6_1_38"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000028/panel/2000000028_6_1/2000000028_6_1_36.png", "question_id": "duplication_retract_8", "fraud_type": "duplication", "fraud_sub_types": ["scaling"], "ground_truth": ["B"], "mask_indices": [1, 2, 3, 4, 5, 6, 8, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000028/panel/2000000028_6_1/2000000028_6_1_36.png", "retract/2000000028/panel/2000000028_6_1/2000000028_6_1_21.png"], "tampered": true, "paper_ids": ["2000000028", "2000000028"], "panel_ids": ["2000000028_6_1_36", "2000000028_6_1_21"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000029/panel/2000000029_6_1/2000000029_6_1_4.png", "question_id": "duplication_retract_9", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000029/panel/2000000029_6_1/2000000029_6_1_4.png", "retract/2000000029/panel/2000000029_5_1/2000000029_5_1_3.png"], "tampered": true, "paper_ids": ["2000000029", "2000000029"], "panel_ids": ["2000000029_6_1_4", "2000000029_5_1_3"], "figure_ids": ["None"], "scenario": "Chart"}} {"file_name": "retract/2000000029/panel/2000000029_5_1/2000000029_5_1_5.png", "question_id": "duplication_retract_10", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [7], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000029/panel/2000000029_5_1/2000000029_5_1_5.png", "retract/2000000029/panel/2000000029_5_1/2000000029_5_1_4.png"], "tampered": true, "paper_ids": ["2000000029", "2000000029"], "panel_ids": ["2000000029_5_1_5", "2000000029_5_1_4"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000029/panel/2000000029_5_1/2000000029_5_1_5.png", "question_id": "duplication_retract_11", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [7], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000029/panel/2000000029_5_1/2000000029_5_1_5.png", "retract/2000000029/panel/2000000029_6_1/2000000029_6_1_5.png"], "tampered": true, "paper_ids": ["2000000029", "2000000029"], "panel_ids": ["2000000029_5_1_5", "2000000029_6_1_5"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000029/panel/2000000029_6_1/2000000029_6_1_4.png", "question_id": "duplication_retract_12", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [4, 5, 7, 8], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000029/panel/2000000029_6_1/2000000029_6_1_4.png", "retract/2000000029/panel/2000000029_8_1/2000000029_8_1_8.png"], "tampered": true, "paper_ids": ["2000000029", "2000000029"], "panel_ids": ["2000000029_6_1_4", "2000000029_8_1_8"], "figure_ids": ["None"], "scenario": "Chart"}} {"file_name": "retract/2000000029/panel/2000000029_5_1/2000000029_5_1_5.png", "question_id": "duplication_retract_13", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [4, 5, 7, 8], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000029/panel/2000000029_5_1/2000000029_5_1_5.png", "retract/2000000029/panel/2000000029_8_1/2000000029_8_1_10.png"], "tampered": true, "paper_ids": ["2000000029", "2000000029"], "panel_ids": ["2000000029_5_1_5", "2000000029_8_1_10"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000029/panel/2000000029_5_1/2000000029_5_1_5.png", "question_id": "duplication_retract_14", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [4, 5, 7, 8], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000029/panel/2000000029_5_1/2000000029_5_1_5.png", "retract/2000000029/panel/2000000029_8_1/2000000029_8_1_11.png"], "tampered": true, "paper_ids": ["2000000029", "2000000029"], "panel_ids": ["2000000029_5_1_5", "2000000029_8_1_11"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000029/panel/2000000029_5_1/2000000029_5_1_5.png", "question_id": "duplication_retract_15", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [4, 5, 7, 8], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000029/panel/2000000029_5_1/2000000029_5_1_5.png", "retract/2000000029/panel/2000000029_8_1/2000000029_8_1_12.png"], "tampered": true, "paper_ids": ["2000000029", "2000000029"], "panel_ids": ["2000000029_5_1_5", "2000000029_8_1_12"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000033/panel/2000000033_2_1/2000000033_2_1_8.png", "question_id": "duplication_retract_16", "fraud_type": "duplication", "fraud_sub_types": ["scaling"], "ground_truth": ["B"], "mask_indices": [1, 2, 4, 5, 7, 8], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000033/panel/2000000033_2_1/2000000033_2_1_8.png", "retract/2000000033/panel/2000000033_2_1/2000000033_2_1_7.png"], "tampered": true, "paper_ids": ["2000000033", "2000000033"], "panel_ids": ["2000000033_2_1_8", "2000000033_2_1_7"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000033/panel/2000000033_2_1/2000000033_2_1_38.png", "question_id": "duplication_retract_17", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000033/panel/2000000033_2_1/2000000033_2_1_38.png", "retract/2000000033/panel/2000000033_2_1/2000000033_2_1_35.png"], "tampered": true, "paper_ids": ["2000000033", "2000000033"], "panel_ids": ["2000000033_2_1_38", "2000000033_2_1_35"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000034/panel/2000000034_7_1/2000000034_7_1_5.png", "question_id": "duplication_retract_18", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [3], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000034/panel/2000000034_7_1/2000000034_7_1_5.png", "retract/2000000034/panel/2000000034_7_1/2000000034_7_1_2.png"], "tampered": true, "paper_ids": ["2000000034", "2000000034"], "panel_ids": ["2000000034_7_1_5", "2000000034_7_1_2"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000034/panel/2000000034_7_1/2000000034_7_1_9.png", "question_id": "duplication_retract_19", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [5, 6], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000034/panel/2000000034_7_1/2000000034_7_1_9.png", "retract/2000000034/panel/2000000034_7_1/2000000034_7_1_8.png"], "tampered": true, "paper_ids": ["2000000034", "2000000034"], "panel_ids": ["2000000034_7_1_9", "2000000034_7_1_8"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000037/panel/2000000037_5_1/2000000037_5_1_21.png", "question_id": "duplication_retract_20", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000037/panel/2000000037_5_1/2000000037_5_1_21.png", "retract/2000000037/panel/2000000037_4_1/2000000037_4_1_2.png"], "tampered": true, "paper_ids": ["2000000037", "2000000037"], "panel_ids": ["2000000037_5_1_21", "2000000037_4_1_2"], "figure_ids": ["None"], "scenario": "Micrograph"}} {"file_name": "retract/2000000037/panel/2000000037_5_1/2000000037_5_1_16.png", "question_id": "duplication_retract_21", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 3], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000037/panel/2000000037_5_1/2000000037_5_1_16.png", "retract/2000000037/panel/2000000037_4_1/2000000037_4_1_8.png"], "tampered": true, "paper_ids": ["2000000037", "2000000037"], "panel_ids": ["2000000037_5_1_16", "2000000037_4_1_8"], "figure_ids": ["None"], "scenario": "Micrograph"}} {"file_name": "retract/2000000037/panel/2000000037_11_1/2000000037_11_1_26.png", "question_id": "duplication_retract_22", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 3, 4, 5, 6], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000037/panel/2000000037_11_1/2000000037_11_1_26.png", "retract/2000000037/panel/2000000037_11_1/2000000037_11_1_21.png"], "tampered": true, "paper_ids": ["2000000037", "2000000037"], "panel_ids": ["2000000037_11_1_26", "2000000037_11_1_21"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000037/panel/2000000037_11_1/2000000037_11_1_26.png", "question_id": "duplication_retract_23", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 3, 4, 5, 6], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000037/panel/2000000037_11_1/2000000037_11_1_26.png", "retract/2000000037/panel/2000000037_11_1/2000000037_11_1_22.png"], "tampered": true, "paper_ids": ["2000000037", "2000000037"], "panel_ids": ["2000000037_11_1_26", "2000000037_11_1_22"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000037/panel/2000000037_11_1/2000000037_11_1_27.png", "question_id": "duplication_retract_24", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [3, 6, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000037/panel/2000000037_11_1/2000000037_11_1_27.png", "retract/2000000037/panel/2000000037_11_1/2000000037_11_1_23.png"], "tampered": true, "paper_ids": ["2000000037", "2000000037"], "panel_ids": ["2000000037_11_1_27", "2000000037_11_1_23"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000038/panel/2000000038_5_1/2000000038_5_1_10.png", "question_id": "duplication_retract_25", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000038/panel/2000000038_5_1/2000000038_5_1_10.png", "retract/2000000038/panel/2000000038_5_1/2000000038_5_1_7.png"], "tampered": true, "paper_ids": ["2000000038", "2000000038"], "panel_ids": ["2000000038_5_1_10", "2000000038_5_1_7"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000038/panel/2000000038_5_1/2000000038_5_1_10.png", "question_id": "duplication_retract_26", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000038/panel/2000000038_5_1/2000000038_5_1_10.png", "retract/2000000038/panel/2000000038_5_1/2000000038_5_1_11.png"], "tampered": true, "paper_ids": ["2000000038", "2000000038"], "panel_ids": ["2000000038_5_1_10", "2000000038_5_1_11"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000039/panel/2000000039_30_1/2000000039_30_1_3.png", "question_id": "duplication_retract_27", "fraud_type": "duplication", "fraud_sub_types": ["scaling"], "ground_truth": ["B"], "mask_indices": [7], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000039/panel/2000000039_30_1/2000000039_30_1_3.png", "retract/2000000039/panel/2000000039_28_1/2000000039_28_1_9.png"], "tampered": true, "paper_ids": ["2000000039", "2000000039"], "panel_ids": ["2000000039_30_1_3", "2000000039_28_1_9"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000039/panel/2000000039_30_1/2000000039_30_1_5.png", "question_id": "duplication_retract_28", "fraud_type": "duplication", "fraud_sub_types": ["scaling"], "ground_truth": ["B"], "mask_indices": [1, 2, 3, 4, 5, 6], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000039/panel/2000000039_30_1/2000000039_30_1_5.png", "retract/2000000039/panel/2000000039_28_1/2000000039_28_1_15.png"], "tampered": true, "paper_ids": ["2000000039", "2000000039"], "panel_ids": ["2000000039_30_1_5", "2000000039_28_1_15"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000001/panel/2000000001_9_1/2000000001_9_1_3.png", "question_id": "duplication_retract_29", "fraud_type": "duplication", "fraud_sub_types": ["parameter-modified"], "ground_truth": ["E"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000001/panel/2000000001_9_1/2000000001_9_1_3.png", "retract/2000000001/panel/2000000001_9_1/2000000001_9_1_3.png"], "tampered": true, "paper_ids": ["2000000001", "2000000001"], "panel_ids": ["2000000001_9_1_7", "2000000001_9_1_3"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000041/panel/2000000041_4_1/2000000041_4_1_20.png", "question_id": "duplication_retract_30", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000041/panel/2000000041_4_1/2000000041_4_1_20.png", "retract/2000000041/panel/2000000041_4_1/2000000041_4_1_19.png"], "tampered": true, "paper_ids": ["2000000041", "2000000041"], "panel_ids": ["2000000041_4_1_20", "2000000041_4_1_19"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000041/panel/2000000041_4_1/2000000041_4_1_24.png", "question_id": "duplication_retract_31", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [4], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000041/panel/2000000041_4_1/2000000041_4_1_24.png", "retract/2000000041/panel/2000000041_4_1/2000000041_4_1_23.png"], "tampered": true, "paper_ids": ["2000000041", "2000000041"], "panel_ids": ["2000000041_4_1_24", "2000000041_4_1_23"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000041/panel/2000000041_5_2/2000000041_5_2_20.png", "question_id": "duplication_retract_32", "fraud_type": "duplication", "fraud_sub_types": ["flipped"], "ground_truth": ["D"], "mask_indices": [6], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000041/panel/2000000041_5_2/2000000041_5_2_20.png", "retract/2000000041/panel/2000000041_5_2/2000000041_5_2_19.png"], "tampered": true, "paper_ids": ["2000000041", "2000000041"], "panel_ids": ["2000000041_5_2_20", "2000000041_5_2_19"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000043/panel/2000000043_4_1/2000000043_4_1_18.png", "question_id": "duplication_retract_33", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000043/panel/2000000043_4_1/2000000043_4_1_18.png", "retract/2000000043/panel/2000000043_4_1/2000000043_4_1_17.png"], "tampered": true, "paper_ids": ["2000000043", "2000000043"], "panel_ids": ["2000000043_4_1_18", "2000000043_4_1_17"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000018/panel/2000000018_5_1/2000000018_5_1_21.png", "question_id": "duplication_retract_34", "fraud_type": "duplication", "fraud_sub_types": ["parameter-modified"], "ground_truth": ["E"], "mask_indices": [1, 2, 3, 4, 5, 6], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000018/panel/2000000018_5_1/2000000018_5_1_21.png", "retract/2000000018/panel/2000000018_5_1/2000000018_5_1_20.png"], "tampered": true, "paper_ids": ["2000000018", "2000000018"], "panel_ids": ["2000000018_5_1_21", "2000000018_5_1_20"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000043/panel/2000000043_6_1/2000000043_6_1_13.png", "question_id": "duplication_retract_35", "fraud_type": "duplication", "fraud_sub_types": ["rotated"], "ground_truth": ["C"], "mask_indices": [4, 5, 6], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000043/panel/2000000043_6_1/2000000043_6_1_13.png", "retract/2000000043/panel/2000000043_6_1/2000000043_6_1_14.png"], "tampered": true, "paper_ids": ["2000000043", "2000000043"], "panel_ids": ["2000000043_6_1_13", "2000000043_6_1_14"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000044/panel/2000000044_8_1/2000000044_8_1_12.png", "question_id": "duplication_retract_36", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [4, 5, 6], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000044/panel/2000000044_8_1/2000000044_8_1_12.png", "retract/2000000044/panel/2000000044_8_1/2000000044_8_1_11.png"], "tampered": true, "paper_ids": ["2000000044", "2000000044"], "panel_ids": ["2000000044_8_1_12", "2000000044_8_1_11"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000044/panel/2000000044_8_1/2000000044_8_1_12.png", "question_id": "duplication_retract_37", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [2, 3, 5, 6, 8, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000044/panel/2000000044_8_1/2000000044_8_1_12.png", "retract/2000000044/panel/2000000044_8_1/2000000044_8_1_11.png"], "tampered": true, "paper_ids": ["2000000044", "2000000044"], "panel_ids": ["2000000044_8_1_12", "2000000044_8_1_11"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000045/panel/2000000045_6_1/2000000045_6_1_24.png", "question_id": "duplication_retract_38", "fraud_type": "duplication", "fraud_sub_types": ["flipped"], "ground_truth": ["D"], "mask_indices": [1, 2, 4, 5, 7, 8], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000045/panel/2000000045_6_1/2000000045_6_1_24.png", "retract/2000000045/panel/2000000045_5_1/2000000045_5_1_6.png"], "tampered": true, "paper_ids": ["2000000045", "2000000045"], "panel_ids": ["2000000045_6_1_24", "2000000045_5_1_6"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000045/panel/2000000045_8_1/2000000045_8_1_18.png", "question_id": "duplication_retract_39", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [4, 5, 6], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000045/panel/2000000045_8_1/2000000045_8_1_18.png", "retract/2000000045/panel/2000000045_8_1/2000000045_8_1_15.png"], "tampered": true, "paper_ids": ["2000000045", "2000000045"], "panel_ids": ["2000000045_8_1_18", "2000000045_8_1_15"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000046/panel/2000000046_24_1/2000000046_24_1_13.png", "question_id": "duplication_retract_40", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000046/panel/2000000046_24_1/2000000046_24_1_13.png", "retract/2000000046/panel/2000000046_24_1/2000000046_24_1_1.png"], "tampered": true, "paper_ids": ["2000000046", "2000000046"], "panel_ids": ["2000000046_24_1_13", "2000000046_24_1_1"], "figure_ids": ["None"], "scenario": "Micrograph"}} {"file_name": "retract/2000000046/panel/2000000046_24_1/2000000046_24_1_16.png", "question_id": "duplication_retract_41", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 3], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000046/panel/2000000046_24_1/2000000046_24_1_16.png", "retract/2000000046/panel/2000000046_24_1/2000000046_24_1_12.png"], "tampered": true, "paper_ids": ["2000000046", "2000000046"], "panel_ids": ["2000000046_24_1_16", "2000000046_24_1_12"], "figure_ids": ["None"], "scenario": "Micrograph"}} {"file_name": "retract/2000000046/panel/2000000046_24_1/2000000046_24_1_18.png", "question_id": "duplication_retract_42", "fraud_type": "duplication", "fraud_sub_types": ["rotated"], "ground_truth": ["C"], "mask_indices": [6, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000046/panel/2000000046_24_1/2000000046_24_1_18.png", "retract/2000000046/panel/2000000046_24_1/2000000046_24_1_18.png"], "tampered": true, "paper_ids": ["2000000046", "2000000046"], "panel_ids": ["2000000046_24_1_18", "2000000046_24_1_18"], "figure_ids": ["None"], "scenario": "Micrograph"}} {"file_name": "retract/2000000046/panel/2000000046_25_1/2000000046_25_1_17.png", "question_id": "duplication_retract_43", "fraud_type": "duplication", "fraud_sub_types": ["rotated"], "ground_truth": ["C"], "mask_indices": [1, 2, 4, 5], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000046/panel/2000000046_25_1/2000000046_25_1_17.png", "retract/2000000046/panel/2000000046_25_1/2000000046_25_1_17.png"], "tampered": true, "paper_ids": ["2000000046", "2000000046"], "panel_ids": ["2000000046_25_1_17", "2000000046_25_1_17"], "figure_ids": ["None"], "scenario": "Micrograph"}} {"file_name": "retract/2000000047/panel/2000000047_7_1/2000000047_7_1_1.png", "question_id": "duplication_retract_44", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 4, 5, 7, 8], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000047/panel/2000000047_7_1/2000000047_7_1_1.png", "retract/2000000047/panel/2000000047_3_2/2000000047_3_2_1.png"], "tampered": true, "paper_ids": ["2000000047", "2000000047"], "panel_ids": ["2000000047_7_1_1", "2000000047_3_2_1"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000048/panel/2000000048_7_1/2000000048_7_1_6.png", "question_id": "duplication_retract_45", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 4, 5, 7, 8], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000048/panel/2000000048_7_1/2000000048_7_1_6.png", "retract/2000000048/panel/2000000048_7_1/2000000048_7_1_1.png"], "tampered": true, "paper_ids": ["2000000048", "2000000048"], "panel_ids": ["2000000048_7_1_6", "2000000048_7_1_1"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000048/panel/2000000048_7_1/2000000048_7_1_1.png", "question_id": "duplication_retract_46", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [4, 5, 7, 8], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000048/panel/2000000048_7_1/2000000048_7_1_1.png", "retract/2000000048/panel/2000000048_7_1/2000000048_7_1_5.png"], "tampered": true, "paper_ids": ["2000000048", "2000000048"], "panel_ids": ["2000000048_7_1_1", "2000000048_7_1_5"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000049/panel/2000000049_5_1/2000000049_5_1_18.png", "question_id": "duplication_retract_47", "fraud_type": "duplication", "fraud_sub_types": ["parameter-modified"], "ground_truth": ["E"], "mask_indices": [4, 5, 6], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000049/panel/2000000049_5_1/2000000049_5_1_18.png", "retract/2000000049/panel/2000000049_5_1/2000000049_5_1_13.png"], "tampered": true, "paper_ids": ["2000000049", "2000000049"], "panel_ids": ["2000000049_5_1_18", "2000000049_5_1_13"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000049/panel/2000000049_5_1/2000000049_5_1_22.png", "question_id": "duplication_retract_48", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000049/panel/2000000049_5_1/2000000049_5_1_22.png", "retract/2000000049/panel/2000000049_5_1/2000000049_5_1_21.png"], "tampered": true, "paper_ids": ["2000000049", "2000000049"], "panel_ids": ["2000000049_5_1_22", "2000000049_5_1_21"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000049/panel/2000000049_5_1/2000000049_5_1_34.png", "question_id": "duplication_retract_49", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000049/panel/2000000049_5_1/2000000049_5_1_34.png", "retract/2000000049/panel/2000000049_5_1/2000000049_5_1_25.png"], "tampered": true, "paper_ids": ["2000000049", "2000000049"], "panel_ids": ["2000000049_5_1_34", "2000000049_5_1_25"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000049/panel/2000000049_5_1/2000000049_5_1_49.png", "question_id": "duplication_retract_50", "fraud_type": "duplication", "fraud_sub_types": ["parameter-modified"], "ground_truth": ["E"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000049/panel/2000000049_5_1/2000000049_5_1_49.png", "retract/2000000049/panel/2000000049_5_1/2000000049_5_1_43.png"], "tampered": true, "paper_ids": ["2000000049", "2000000049"], "panel_ids": ["2000000049_5_1_49", "2000000049_5_1_43"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000050/panel/2000000050_8_1/2000000050_8_1_7.png", "question_id": "duplication_retract_51", "fraud_type": "duplication", "fraud_sub_types": ["rotated"], "ground_truth": ["C"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000050/panel/2000000050_8_1/2000000050_8_1_7.png", "retract/2000000050/panel/2000000050_8_1/2000000050_8_1_5.png"], "tampered": true, "paper_ids": ["2000000050", "2000000050"], "panel_ids": ["2000000050_8_1_7", "2000000050_8_1_5"], "figure_ids": ["None"], "scenario": "Physical Object"}} {"file_name": "retract/2000000050/panel/2000000050_8_1/2000000050_8_1_15.png", "question_id": "duplication_retract_52", "fraud_type": "duplication", "fraud_sub_types": ["scaling", "rotated"], "ground_truth": ["B", "C"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000050/panel/2000000050_8_1/2000000050_8_1_15.png", "retract/2000000050/panel/2000000050_8_1/2000000050_8_1_5.png"], "tampered": true, "paper_ids": ["2000000050", "2000000050"], "panel_ids": ["2000000050_8_1_15", "2000000050_8_1_5"], "figure_ids": ["None"], "scenario": "Physical Object"}} {"file_name": "retract/2000000050/panel/2000000050_8_1/2000000050_8_1_5.png", "question_id": "duplication_retract_53", "fraud_type": "duplication", "fraud_sub_types": ["rotated"], "ground_truth": ["C"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000050/panel/2000000050_8_1/2000000050_8_1_5.png", "retract/2000000050/panel/2000000050_8_1/2000000050_8_1_15.png"], "tampered": true, "paper_ids": ["2000000050", "2000000050"], "panel_ids": ["2000000050_8_1_5", "2000000050_8_1_15"], "figure_ids": ["None"], "scenario": "Physical Object"}} {"file_name": "retract/2000000051/panel/2000000051_9_1/2000000051_9_1_1.png", "question_id": "duplication_retract_54", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000051/panel/2000000051_9_1/2000000051_9_1_1.png", "retract/2000000051/panel/2000000051_9_1/2000000051_9_1_1.png"], "tampered": true, "paper_ids": ["2000000051", "2000000051"], "panel_ids": ["2000000051_9_1_1", "2000000051_9_1_1"], "figure_ids": ["None"], "scenario": "Medical Imaging"}} {"file_name": "retract/2000000051/panel/2000000051_9_1/2000000051_9_1_1.png", "question_id": "duplication_retract_55", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000051/panel/2000000051_9_1/2000000051_9_1_1.png", "retract/2000000051/panel/2000000051_9_1/2000000051_9_1_3.png"], "tampered": true, "paper_ids": ["2000000051", "2000000051"], "panel_ids": ["2000000051_9_1_1", "2000000051_9_1_3"], "figure_ids": ["None"], "scenario": "Medical Imaging"}} {"file_name": "retract/2000000051/panel/2000000051_9_1/2000000051_9_1_27.png", "question_id": "duplication_retract_56", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000051/panel/2000000051_9_1/2000000051_9_1_27.png", "retract/2000000051/panel/2000000051_9_1/2000000051_9_1_13.png"], "tampered": true, "paper_ids": ["2000000051", "2000000051"], "panel_ids": ["2000000051_9_1_27", "2000000051_9_1_13"], "figure_ids": ["None"], "scenario": "Medical Imaging"}} {"file_name": "retract/2000000051/panel/2000000051_9_1/2000000051_9_1_78.png", "question_id": "duplication_retract_57", "fraud_type": "duplication", "fraud_sub_types": ["scaling", "rotated"], "ground_truth": ["B", "C"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000051/panel/2000000051_9_1/2000000051_9_1_78.png", "retract/2000000051/panel/2000000051_9_1/2000000051_9_1_77.png"], "tampered": true, "paper_ids": ["2000000051", "2000000051"], "panel_ids": ["2000000051_9_1_78", "2000000051_9_1_77"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000040/panel/2000000040_8_2/2000000040_8_2_18.png", "question_id": "duplication_retract_58", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 4, 5, 7, 8], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000040/panel/2000000040_8_2/2000000040_8_2_18.png", "retract/2000000040/panel/2000000040_8_2/2000000040_8_2_21.png"], "tampered": true, "paper_ids": ["2000000040", "2000000040"], "panel_ids": ["2000000040_8_2_18", "2000000040_8_2_21"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000052/panel/2000000052_20_1/2000000052_20_1_5.png", "question_id": "duplication_retract_59", "fraud_type": "duplication", "fraud_sub_types": ["parameter-modified"], "ground_truth": ["E"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000052/panel/2000000052_20_1/2000000052_20_1_5.png", "retract/2000000052/panel/2000000052_20_1/2000000052_20_1_1.png"], "tampered": true, "paper_ids": ["2000000052", "2000000052"], "panel_ids": ["2000000052_20_1_5", "2000000052_20_1_1"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000052/panel/2000000052_21_1/2000000052_21_1_4.png", "question_id": "duplication_retract_60", "fraud_type": "duplication", "fraud_sub_types": ["rotated"], "ground_truth": ["C"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000052/panel/2000000052_21_1/2000000052_21_1_4.png", "retract/2000000052/panel/2000000052_21_1/2000000052_21_1_3.png"], "tampered": true, "paper_ids": ["2000000052", "2000000052"], "panel_ids": ["2000000052_21_1_4", "2000000052_21_1_3"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000061/panel/2000000061_2_1/2000000061_2_1_6.png", "question_id": "duplication_retract_61", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000061/panel/2000000061_2_1/2000000061_2_1_6.png", "retract/2000000061/panel/2000000061_2_1/2000000061_2_1_3.png"], "tampered": true, "paper_ids": ["2000000061", "2000000061"], "panel_ids": ["2000000061_2_1_6", "2000000061_2_1_3"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000040/panel/2000000040_3_1/2000000040_3_1_24.png", "question_id": "duplication_retract_62", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [3, 6, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000040/panel/2000000040_3_1/2000000040_3_1_24.png", "retract/2000000040/panel/2000000040_3_1/2000000040_3_1_22.png"], "tampered": true, "paper_ids": ["2000000040", "2000000040"], "panel_ids": ["2000000040_3_1_24", "2000000040_3_1_22"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000063/panel/2000000063_3_1/2000000063_3_1_38.png", "question_id": "duplication_retract_63", "fraud_type": "duplication", "fraud_sub_types": ["rotated"], "ground_truth": ["C"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000063/panel/2000000063_3_1/2000000063_3_1_38.png", "retract/2000000063/panel/2000000063_3_1/2000000063_3_1_35.png"], "tampered": true, "paper_ids": ["2000000063", "2000000063"], "panel_ids": ["2000000063_3_1_38", "2000000063_3_1_35"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000064/panel/2000000064_6_1/2000000064_6_1_8.png", "question_id": "duplication_retract_64", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [2, 3, 5, 6, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000064/panel/2000000064_6_1/2000000064_6_1_8.png", "retract/2000000064/panel/2000000064_5_1/2000000064_5_1_6.png"], "tampered": true, "paper_ids": ["2000000064", "2000000064"], "panel_ids": ["2000000064_6_1_8", "2000000064_5_1_6"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000064/panel/2000000064_6_2/2000000064_6_2_14.png", "question_id": "duplication_retract_65", "fraud_type": "duplication", "fraud_sub_types": ["flipped"], "ground_truth": ["D"], "mask_indices": [2, 3, 5, 6, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000064/panel/2000000064_6_2/2000000064_6_2_14.png", "retract/2000000064/panel/2000000064_6_2/2000000064_6_2_3.png"], "tampered": true, "paper_ids": ["2000000064", "2000000064"], "panel_ids": ["2000000064_6_2_14", "2000000064_6_2_3"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000064/panel/2000000064_6_2/2000000064_6_2_3.png", "question_id": "duplication_retract_66", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [2, 3, 5, 6, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000064/panel/2000000064_6_2/2000000064_6_2_3.png", "retract/2000000064/panel/2000000064_6_2/2000000064_6_2_14.png"], "tampered": true, "paper_ids": ["2000000064", "2000000064"], "panel_ids": ["2000000064_6_2_3", "2000000064_6_2_14"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000066/panel/2000000066_7_1/2000000066_7_1_5.png", "question_id": "duplication_retract_67", "fraud_type": "duplication", "fraud_sub_types": ["flipped"], "ground_truth": ["D"], "mask_indices": [1, 2, 4, 5, 7, 8], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000066/panel/2000000066_7_1/2000000066_7_1_5.png", "retract/2000000066/panel/2000000066_7_1/2000000066_7_1_4.png"], "tampered": true, "paper_ids": ["2000000066", "2000000066"], "panel_ids": ["2000000066_7_1_5", "2000000066_7_1_4"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000066/panel/2000000066_7_1/2000000066_7_1_4.png", "question_id": "duplication_retract_68", "fraud_type": "duplication", "fraud_sub_types": ["flipped"], "ground_truth": ["D"], "mask_indices": [2, 3, 5, 6, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000066/panel/2000000066_7_1/2000000066_7_1_4.png", "retract/2000000066/panel/2000000066_7_1/2000000066_7_1_5.png"], "tampered": true, "paper_ids": ["2000000066", "2000000066"], "panel_ids": ["2000000066_7_1_4", "2000000066_7_1_5"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000067/panel/2000000067_5_1/2000000067_5_1_5.png", "question_id": "duplication_retract_69", "fraud_type": "duplication", "fraud_sub_types": ["direct", "rotated"], "ground_truth": ["A", "C"], "mask_indices": [4, 5, 6, 8], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000067/panel/2000000067_5_1/2000000067_5_1_5.png", "retract/2000000067/panel/2000000067_5_1/2000000067_5_1_1.png"], "tampered": true, "paper_ids": ["2000000067", "2000000067"], "panel_ids": ["2000000067_5_1_5", "2000000067_5_1_1"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000067/panel/2000000067_5_1/2000000067_5_1_9.png", "question_id": "duplication_retract_70", "fraud_type": "duplication", "fraud_sub_types": ["direct", "rotated"], "ground_truth": ["A", "C"], "mask_indices": [4, 5, 6, 8], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000067/panel/2000000067_5_1/2000000067_5_1_9.png", "retract/2000000067/panel/2000000067_5_1/2000000067_5_1_5.png"], "tampered": true, "paper_ids": ["2000000067", "2000000067"], "panel_ids": ["2000000067_5_1_9", "2000000067_5_1_5"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000067/panel/2000000067_5_1/2000000067_5_1_1.png", "question_id": "duplication_retract_71", "fraud_type": "duplication", "fraud_sub_types": ["direct", "rotated"], "ground_truth": ["A", "C"], "mask_indices": [4, 5, 6], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000067/panel/2000000067_5_1/2000000067_5_1_1.png", "retract/2000000067/panel/2000000067_5_1/2000000067_5_1_9.png"], "tampered": true, "paper_ids": ["2000000067", "2000000067"], "panel_ids": ["2000000067_5_1_1", "2000000067_5_1_9"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000067/panel/2000000067_6_1/2000000067_6_1_5.png", "question_id": "duplication_retract_72", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000067/panel/2000000067_6_1/2000000067_6_1_5.png", "retract/2000000067/panel/2000000067_6_1/2000000067_6_1_1.png"], "tampered": true, "paper_ids": ["2000000067", "2000000067"], "panel_ids": ["2000000067_6_1_5", "2000000067_6_1_1"], "figure_ids": ["None"], "scenario": "Chart"}} {"file_name": "retract/2000000067/panel/2000000067_6_1/2000000067_6_1_6.png", "question_id": "duplication_retract_73", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000067/panel/2000000067_6_1/2000000067_6_1_6.png", "retract/2000000067/panel/2000000067_6_1/2000000067_6_1_2.png"], "tampered": true, "paper_ids": ["2000000067", "2000000067"], "panel_ids": ["2000000067_6_1_6", "2000000067_6_1_2"], "figure_ids": ["None"], "scenario": "Chart"}} {"file_name": "retract/2000000067/panel/2000000067_6_1/2000000067_6_1_7.png", "question_id": "duplication_retract_74", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000067/panel/2000000067_6_1/2000000067_6_1_7.png", "retract/2000000067/panel/2000000067_6_1/2000000067_6_1_3.png"], "tampered": true, "paper_ids": ["2000000067", "2000000067"], "panel_ids": ["2000000067_6_1_7", "2000000067_6_1_3"], "figure_ids": ["None"], "scenario": "Chart"}} {"file_name": "retract/2000000067/panel/2000000067_6_1/2000000067_6_1_8.png", "question_id": "duplication_retract_75", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000067/panel/2000000067_6_1/2000000067_6_1_8.png", "retract/2000000067/panel/2000000067_6_1/2000000067_6_1_4.png"], "tampered": true, "paper_ids": ["2000000067", "2000000067"], "panel_ids": ["2000000067_6_1_8", "2000000067_6_1_4"], "figure_ids": ["None"], "scenario": "Chart"}} {"file_name": "retract/2000000067/panel/2000000067_6_1/2000000067_6_1_1.png", "question_id": "duplication_retract_76", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000067/panel/2000000067_6_1/2000000067_6_1_1.png", "retract/2000000067/panel/2000000067_6_1/2000000067_6_1_5.png"], "tampered": true, "paper_ids": ["2000000067", "2000000067"], "panel_ids": ["2000000067_6_1_1", "2000000067_6_1_5"], "figure_ids": ["None"], "scenario": "Chart"}} {"file_name": "retract/2000000067/panel/2000000067_6_1/2000000067_6_1_2.png", "question_id": "duplication_retract_77", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000067/panel/2000000067_6_1/2000000067_6_1_2.png", "retract/2000000067/panel/2000000067_6_1/2000000067_6_1_6.png"], "tampered": true, "paper_ids": ["2000000067", "2000000067"], "panel_ids": ["2000000067_6_1_2", "2000000067_6_1_6"], "figure_ids": ["None"], "scenario": "Chart"}} {"file_name": "retract/2000000067/panel/2000000067_6_1/2000000067_6_1_3.png", "question_id": "duplication_retract_78", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000067/panel/2000000067_6_1/2000000067_6_1_3.png", "retract/2000000067/panel/2000000067_6_1/2000000067_6_1_7.png"], "tampered": true, "paper_ids": ["2000000067", "2000000067"], "panel_ids": ["2000000067_6_1_3", "2000000067_6_1_7"], "figure_ids": ["None"], "scenario": "Chart"}} {"file_name": "retract/2000000067/panel/2000000067_6_1/2000000067_6_1_4.png", "question_id": "duplication_retract_79", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000067/panel/2000000067_6_1/2000000067_6_1_4.png", "retract/2000000067/panel/2000000067_6_1/2000000067_6_1_8.png"], "tampered": true, "paper_ids": ["2000000067", "2000000067"], "panel_ids": ["2000000067_6_1_4", "2000000067_6_1_8"], "figure_ids": ["None"], "scenario": "Chart"}} {"file_name": "retract/2000000067/panel/2000000067_7_1/2000000067_7_1_6.png", "question_id": "duplication_retract_80", "fraud_type": "duplication", "fraud_sub_types": ["scaling"], "ground_truth": ["B"], "mask_indices": [1, 2, 3, 4, 5, 6], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000067/panel/2000000067_7_1/2000000067_7_1_6.png", "retract/2000000067/panel/2000000067_7_1/2000000067_7_1_1.png"], "tampered": true, "paper_ids": ["2000000067", "2000000067"], "panel_ids": ["2000000067_7_1_6", "2000000067_7_1_1"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000067/panel/2000000067_7_1/2000000067_7_1_11.png", "question_id": "duplication_retract_81", "fraud_type": "duplication", "fraud_sub_types": ["rotated"], "ground_truth": ["C"], "mask_indices": [7, 8], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000067/panel/2000000067_7_1/2000000067_7_1_11.png", "retract/2000000067/panel/2000000067_7_1/2000000067_7_1_6.png"], "tampered": true, "paper_ids": ["2000000067", "2000000067"], "panel_ids": ["2000000067_7_1_11", "2000000067_7_1_6"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000067/panel/2000000067_7_1/2000000067_7_1_6.png", "question_id": "duplication_retract_82", "fraud_type": "duplication", "fraud_sub_types": ["direct", "rotated"], "ground_truth": ["A", "C"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000067/panel/2000000067_7_1/2000000067_7_1_6.png", "retract/2000000067/panel/2000000067_7_1/2000000067_7_1_11.png"], "tampered": true, "paper_ids": ["2000000067", "2000000067"], "panel_ids": ["2000000067_7_1_6", "2000000067_7_1_11"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000067/panel/2000000067_8_1/2000000067_8_1_2.png", "question_id": "duplication_retract_83", "fraud_type": "duplication", "fraud_sub_types": ["rotated"], "ground_truth": ["C"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000067/panel/2000000067_8_1/2000000067_8_1_2.png", "retract/2000000067/panel/2000000067_8_1/2000000067_8_1_1.png"], "tampered": true, "paper_ids": ["2000000067", "2000000067"], "panel_ids": ["2000000067_8_1_2", "2000000067_8_1_1"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000067/panel/2000000067_8_1/2000000067_8_1_1.png", "question_id": "duplication_retract_84", "fraud_type": "duplication", "fraud_sub_types": ["rotated"], "ground_truth": ["C"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000067/panel/2000000067_8_1/2000000067_8_1_1.png", "retract/2000000067/panel/2000000067_8_1/2000000067_8_1_2.png"], "tampered": true, "paper_ids": ["2000000067", "2000000067"], "panel_ids": ["2000000067_8_1_1", "2000000067_8_1_2"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000067/panel/2000000067_8_1/2000000067_8_1_7.png", "question_id": "duplication_retract_85", "fraud_type": "duplication", "fraud_sub_types": ["rotated"], "ground_truth": ["C"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000067/panel/2000000067_8_1/2000000067_8_1_7.png", "retract/2000000067/panel/2000000067_8_1/2000000067_8_1_6.png"], "tampered": true, "paper_ids": ["2000000067", "2000000067"], "panel_ids": ["2000000067_8_1_7", "2000000067_8_1_6"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000067/panel/2000000067_8_1/2000000067_8_1_6.png", "question_id": "duplication_retract_86", "fraud_type": "duplication", "fraud_sub_types": ["rotated"], "ground_truth": ["C"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000067/panel/2000000067_8_1/2000000067_8_1_6.png", "retract/2000000067/panel/2000000067_8_1/2000000067_8_1_7.png"], "tampered": true, "paper_ids": ["2000000067", "2000000067"], "panel_ids": ["2000000067_8_1_6", "2000000067_8_1_7"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000015/panel/2000000015_3_1/2000000015_3_1_6.png", "question_id": "duplication_retract_87", "fraud_type": "duplication", "fraud_sub_types": ["scaling"], "ground_truth": ["B"], "mask_indices": [4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000015/panel/2000000015_3_1/2000000015_3_1_6.png", "retract/2000000015/panel/2000000015_3_1/2000000015_3_1_5.png"], "tampered": true, "paper_ids": ["2000000015", "2000000015"], "panel_ids": ["2000000015_3_1_6", "2000000015_3_1_5"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000016/panel/2000000016_6_3/2000000016_6_3_3.png", "question_id": "duplication_retract_88", "fraud_type": "duplication", "fraud_sub_types": ["parameter-modified"], "ground_truth": ["E"], "mask_indices": [4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000016/panel/2000000016_6_3/2000000016_6_3_3.png", "retract/2000000016/panel/2000000016_6_2/2000000016_6_2_2.png"], "tampered": true, "paper_ids": ["2000000016", "2000000016"], "panel_ids": ["2000000016_6_3_3", "2000000016_6_2_2"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000018/panel/2000000018_5_1/2000000018_5_1_15.png", "question_id": "duplication_retract_89", "fraud_type": "duplication", "fraud_sub_types": ["parameter-modified"], "ground_truth": ["E"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000018/panel/2000000018_5_1/2000000018_5_1_15.png", "retract/2000000018/panel/2000000018_5_1/2000000018_5_1_5.png"], "tampered": true, "paper_ids": ["2000000018", "2000000018"], "panel_ids": ["2000000018_5_1_15", "2000000018_5_1_5"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000018/panel/2000000018_5_1/2000000018_5_1_9.png", "question_id": "duplication_retract_90", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000018/panel/2000000018_5_1/2000000018_5_1_9.png", "retract/2000000018/panel/2000000018_5_1/2000000018_5_1_8.png"], "tampered": true, "paper_ids": ["2000000018", "2000000018"], "panel_ids": ["2000000018_5_1_9", "2000000018_5_1_8"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000018/panel/2000000018_5_1/2000000018_5_1_13.png", "question_id": "duplication_retract_91", "fraud_type": "duplication", "fraud_sub_types": ["flipped"], "ground_truth": ["D"], "mask_indices": [2, 3, 5, 6, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000018/panel/2000000018_5_1/2000000018_5_1_13.png", "retract/2000000018/panel/2000000018_5_1/2000000018_5_1_9.png"], "tampered": true, "paper_ids": ["2000000018", "2000000018"], "panel_ids": ["2000000018_5_1_13", "2000000018_5_1_9"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000018/panel/2000000018_5_1/2000000018_5_1_9.png", "question_id": "duplication_retract_92", "fraud_type": "duplication", "fraud_sub_types": ["flipped"], "ground_truth": ["D"], "mask_indices": [2, 3, 5, 6, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000018/panel/2000000018_5_1/2000000018_5_1_9.png", "retract/2000000018/panel/2000000018_5_1/2000000018_5_1_13.png"], "tampered": true, "paper_ids": ["2000000018", "2000000018"], "panel_ids": ["2000000018_5_1_9", "2000000018_5_1_13"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000018/panel/2000000018_5_1/2000000018_5_1_20.png", "question_id": "duplication_retract_93", "fraud_type": "duplication", "fraud_sub_types": ["parameter-modified"], "ground_truth": ["E"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000018/panel/2000000018_5_1/2000000018_5_1_20.png", "retract/2000000018/panel/2000000018_5_1/2000000018_5_1_16.png"], "tampered": true, "paper_ids": ["2000000018", "2000000018"], "panel_ids": ["2000000018_5_1_20", "2000000018_5_1_16"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000018/panel/2000000018_5_1/2000000018_5_1_16.png", "question_id": "duplication_retract_94", "fraud_type": "duplication", "fraud_sub_types": ["parameter-modified"], "ground_truth": ["E"], "mask_indices": [2, 3], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000018/panel/2000000018_5_1/2000000018_5_1_16.png", "retract/2000000018/panel/2000000018_5_1/2000000018_5_1_21.png"], "tampered": true, "paper_ids": ["2000000018", "2000000018"], "panel_ids": ["2000000018_5_1_16", "2000000018_5_1_21"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000018/panel/2000000018_5_1/2000000018_5_1_23.png", "question_id": "duplication_retract_95", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [3, 6, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000018/panel/2000000018_5_1/2000000018_5_1_23.png", "retract/2000000018/panel/2000000018_5_1/2000000018_5_1_22.png"], "tampered": true, "paper_ids": ["2000000018", "2000000018"], "panel_ids": ["2000000018_5_1_23", "2000000018_5_1_22"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000018/panel/2000000018_5_1/2000000018_5_1_26.png", "question_id": "duplication_retract_96", "fraud_type": "duplication", "fraud_sub_types": ["parameter-modified"], "ground_truth": ["E"], "mask_indices": [4, 5, 6], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000018/panel/2000000018_5_1/2000000018_5_1_26.png", "retract/2000000018/panel/2000000018_5_1/2000000018_5_1_23.png"], "tampered": true, "paper_ids": ["2000000018", "2000000018"], "panel_ids": ["2000000018_5_1_26", "2000000018_5_1_23"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000018/panel/2000000018_5_1/2000000018_5_1_23.png", "question_id": "duplication_retract_97", "fraud_type": "duplication", "fraud_sub_types": ["parameter-modified"], "ground_truth": ["E"], "mask_indices": [2, 3], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000018/panel/2000000018_5_1/2000000018_5_1_23.png", "retract/2000000018/panel/2000000018_5_1/2000000018_5_1_26.png"], "tampered": true, "paper_ids": ["2000000018", "2000000018"], "panel_ids": ["2000000018_5_1_23", "2000000018_5_1_26"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000019/panel/2000000019_5_2/2000000019_5_2_8.png", "question_id": "duplication_retract_98", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000019/panel/2000000019_5_2/2000000019_5_2_8.png", "retract/2000000019/panel/2000000019_5_1/2000000019_5_1_2.png"], "tampered": true, "paper_ids": ["2000000019", "2000000019"], "panel_ids": ["2000000019_5_2_8", "2000000019_5_1_2"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000019/panel/2000000019_5_2/2000000019_5_2_17.png", "question_id": "duplication_retract_99", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000019/panel/2000000019_5_2/2000000019_5_2_17.png", "retract/2000000019/panel/2000000019_5_2/2000000019_5_2_9.png"], "tampered": true, "paper_ids": ["2000000019", "2000000019"], "panel_ids": ["2000000019_5_2_17", "2000000019_5_2_9"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000022/panel/2000000022_8_1/2000000022_8_1_16.png", "question_id": "duplication_retract_100", "fraud_type": "duplication", "fraud_sub_types": ["flipped"], "ground_truth": ["D"], "mask_indices": [4, 5, 7, 8], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000022/panel/2000000022_8_1/2000000022_8_1_16.png", "retract/2000000022/panel/2000000022_8_1/2000000022_8_1_7.png"], "tampered": true, "paper_ids": ["2000000022", "2000000022"], "panel_ids": ["2000000022_8_1_16", "2000000022_8_1_7"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000022/panel/2000000022_8_1/2000000022_8_1_10.png", "question_id": "duplication_retract_101", "fraud_type": "duplication", "fraud_sub_types": ["flipped"], "ground_truth": ["D"], "mask_indices": [4, 5], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000022/panel/2000000022_8_1/2000000022_8_1_10.png", "retract/2000000022/panel/2000000022_8_1/2000000022_8_1_9.png"], "tampered": true, "paper_ids": ["2000000022", "2000000022"], "panel_ids": ["2000000022_8_1_10", "2000000022_8_1_9"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000023/panel/2000000023_5_1/2000000023_5_1_3.png", "question_id": "duplication_retract_102", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [7], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000023/panel/2000000023_5_1/2000000023_5_1_3.png", "retract/2000000023/panel/2000000023_5_1/2000000023_5_1_2.png"], "tampered": true, "paper_ids": ["2000000023", "2000000023"], "panel_ids": ["2000000023_5_1_3", "2000000023_5_1_2"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000023/panel/2000000023_5_1/2000000023_5_1_2.png", "question_id": "duplication_retract_103", "fraud_type": "duplication", "fraud_sub_types": ["rotated"], "ground_truth": ["C"], "mask_indices": [1, 4, 7], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000023/panel/2000000023_5_1/2000000023_5_1_2.png", "retract/2000000023/panel/2000000023_5_1/2000000023_5_1_3.png"], "tampered": true, "paper_ids": ["2000000023", "2000000023"], "panel_ids": ["2000000023_5_1_2", "2000000023_5_1_3"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000023/panel/2000000023_5_1/2000000023_5_1_3.png", "question_id": "duplication_retract_104", "fraud_type": "duplication", "fraud_sub_types": ["rotated"], "ground_truth": ["C"], "mask_indices": [1, 2, 4, 5, 7, 8], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000023/panel/2000000023_5_1/2000000023_5_1_3.png", "retract/2000000023/panel/2000000023_5_1/2000000023_5_1_4.png"], "tampered": true, "paper_ids": ["2000000023", "2000000023"], "panel_ids": ["2000000023_5_1_3", "2000000023_5_1_4"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000023/panel/2000000023_5_1/2000000023_5_1_4.png", "question_id": "duplication_retract_105", "fraud_type": "duplication", "fraud_sub_types": ["rotated"], "ground_truth": ["C"], "mask_indices": [5, 6, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000023/panel/2000000023_5_1/2000000023_5_1_4.png", "retract/2000000023/panel/2000000023_5_1/2000000023_5_1_5.png"], "tampered": true, "paper_ids": ["2000000023", "2000000023"], "panel_ids": ["2000000023_5_1_4", "2000000023_5_1_5"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000023/panel/2000000023_5_1/2000000023_5_1_9.png", "question_id": "duplication_retract_106", "fraud_type": "duplication", "fraud_sub_types": ["rotated"], "ground_truth": ["C"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000023/panel/2000000023_5_1/2000000023_5_1_9.png", "retract/2000000023/panel/2000000023_5_1/2000000023_5_1_7.png"], "tampered": true, "paper_ids": ["2000000023", "2000000023"], "panel_ids": ["2000000023_5_1_9", "2000000023_5_1_7"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000035/panel/2000000035_4_1/2000000035_4_1_1.png", "question_id": "duplication_retract_107", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 4, 5, 7, 8], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000035/panel/2000000035_4_1/2000000035_4_1_1.png"], "tampered": true, "paper_ids": ["2000000035"], "panel_ids": ["2000000035_4_1_1"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000035/panel/2000000035_4_1/2000000035_4_1_2.png", "question_id": "duplication_retract_108", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 3, 4, 6, 7, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000035/panel/2000000035_4_1/2000000035_4_1_2.png"], "tampered": true, "paper_ids": ["2000000035"], "panel_ids": ["2000000035_4_1_2"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000037/panel/2000000037_10_1/2000000037_10_1_5.png", "question_id": "duplication_retract_109", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000037/panel/2000000037_10_1/2000000037_10_1_5.png"], "tampered": true, "paper_ids": ["2000000037"], "panel_ids": ["2000000037_10_1_5"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000037/panel/2000000037_10_1/2000000037_10_1_7.png", "question_id": "duplication_retract_110", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [2, 3, 5, 6], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000037/panel/2000000037_10_1/2000000037_10_1_7.png"], "tampered": true, "paper_ids": ["2000000037"], "panel_ids": ["2000000037_10_1_7"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000037/panel/2000000037_10_1/2000000037_10_1_13.png", "question_id": "duplication_retract_111", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 4, 5, 7, 8], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000037/panel/2000000037_10_1/2000000037_10_1_13.png"], "tampered": true, "paper_ids": ["2000000037"], "panel_ids": ["2000000037_10_1_13"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000037/panel/2000000037_10_1/2000000037_10_1_14.png", "question_id": "duplication_retract_112", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 4, 5, 7, 8], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000037/panel/2000000037_10_1/2000000037_10_1_14.png"], "tampered": true, "paper_ids": ["2000000037"], "panel_ids": ["2000000037_10_1_14"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000037/panel/2000000037_10_1/2000000037_10_1_15.png", "question_id": "duplication_retract_113", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [4, 5], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000037/panel/2000000037_10_1/2000000037_10_1_15.png"], "tampered": true, "paper_ids": ["2000000037"], "panel_ids": ["2000000037_10_1_15"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000037/panel/2000000037_10_1/2000000037_10_1_21.png", "question_id": "duplication_retract_114", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [4, 5], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000037/panel/2000000037_10_1/2000000037_10_1_21.png"], "tampered": true, "paper_ids": ["2000000037"], "panel_ids": ["2000000037_10_1_21"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000046/panel/2000000046_24_1/2000000046_24_1_9.png", "question_id": "duplication_retract_115", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [2, 5, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000046/panel/2000000046_24_1/2000000046_24_1_9.png"], "tampered": true, "paper_ids": ["2000000046"], "panel_ids": ["2000000046_24_1_9"], "figure_ids": ["None"], "scenario": "Micrograph"}} {"file_name": "retract/2000000043/panel/2000000043_4_1/2000000043_4_1_8.png", "question_id": "duplication_retract_116", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 3, 4, 6, 7, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000043/panel/2000000043_4_1/2000000043_4_1_8.png"], "tampered": true, "paper_ids": ["2000000043"], "panel_ids": ["2000000043_4_1_8"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000039/panel/2000000039_30_1/2000000039_30_1_8.png", "question_id": "duplication_retract_117", "fraud_type": "duplication", "fraud_sub_types": ["rotated"], "ground_truth": ["C"], "mask_indices": [7], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000039/panel/2000000039_30_1/2000000039_30_1_8.png"], "tampered": true, "paper_ids": ["2000000039"], "panel_ids": ["2000000039_30_1_8"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000046/panel/2000000046_24_1/2000000046_24_1_5.png", "question_id": "duplication_retract_118", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [5, 6, 8], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000046/panel/2000000046_24_1/2000000046_24_1_5.png"], "tampered": true, "paper_ids": ["2000000046"], "panel_ids": ["2000000046_24_1_5"], "figure_ids": ["None"], "scenario": "Micrograph"}} {"file_name": "retract/2000000060/panel/2000000060_8_1/2000000060_8_1_12.png", "question_id": "duplication_retract_119", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [2, 3, 5, 6, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000060/panel/2000000060_8_1/2000000060_8_1_12.png"], "tampered": true, "paper_ids": ["2000000060"], "panel_ids": ["2000000060_8_1_12"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000061/panel/2000000061_2_1/2000000061_2_1_6.png", "question_id": "duplication_retract_120", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000061/panel/2000000061_2_1/2000000061_2_1_6.png"], "tampered": true, "paper_ids": ["2000000061"], "panel_ids": ["2000000061_2_1_6"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000063/panel/2000000063_3_1/2000000063_3_1_38.png", "question_id": "duplication_retract_121", "fraud_type": "duplication", "fraud_sub_types": ["rotated"], "ground_truth": ["C"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000063/panel/2000000063_3_1/2000000063_3_1_38.png"], "tampered": true, "paper_ids": ["2000000063"], "panel_ids": ["2000000063_3_1_38"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000064/panel/2000000064_6_2/2000000064_6_2_9.png", "question_id": "duplication_retract_122", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 3, 4, 6, 7, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000064/panel/2000000064_6_2/2000000064_6_2_9.png"], "tampered": true, "paper_ids": ["2000000064"], "panel_ids": ["2000000064_6_2_9"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000067/panel/2000000067_8_1/2000000067_8_1_4.png", "question_id": "duplication_retract_123", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000067/panel/2000000067_8_1/2000000067_8_1_4.png"], "tampered": true, "paper_ids": ["2000000067"], "panel_ids": ["2000000067_8_1_4"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000067/panel/2000000067_8_1/2000000067_8_1_5.png", "question_id": "duplication_retract_124", "fraud_type": "duplication", "fraud_sub_types": ["direct"], "ground_truth": ["A"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000067/panel/2000000067_8_1/2000000067_8_1_5.png"], "tampered": true, "paper_ids": ["2000000067"], "panel_ids": ["2000000067_8_1_5"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000032/panel/2000000032_8_2/2000000032_8_2_1.png", "question_id": "forgery_retract_1", "fraud_type": "forgery", "fraud_sub_types": [""], "ground_truth": ["A"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000032/panel/2000000032_8_2/2000000032_8_2_1.png"], "tampered": true, "paper_ids": ["2000000032"], "panel_ids": ["2000000032_8_2_1"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000058/panel/2000000058_4_1/2000000058_4_1_1.png", "question_id": "forgery_retract_2", "fraud_type": "forgery", "fraud_sub_types": [""], "ground_truth": ["A"], "mask_indices": [1, 4, 7], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000058/panel/2000000058_4_1/2000000058_4_1_1.png"], "tampered": true, "paper_ids": ["2000000058"], "panel_ids": ["2000000058_4_1_1"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000058/panel/2000000058_4_1/2000000058_4_1_4.png", "question_id": "forgery_retract_3", "fraud_type": "forgery", "fraud_sub_types": [""], "ground_truth": ["A"], "mask_indices": [2, 5, 8], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000058/panel/2000000058_4_1/2000000058_4_1_4.png"], "tampered": true, "paper_ids": ["2000000058"], "panel_ids": ["2000000058_4_1_4"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000058/panel/2000000058_4_1/2000000058_4_1_5.png", "question_id": "forgery_retract_4", "fraud_type": "forgery", "fraud_sub_types": [""], "ground_truth": ["A"], "mask_indices": [1, 4, 7], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000058/panel/2000000058_4_1/2000000058_4_1_5.png"], "tampered": true, "paper_ids": ["2000000058"], "panel_ids": ["2000000058_4_1_5"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000058/panel/2000000058_4_2/2000000058_4_2_3.png", "question_id": "forgery_retract_5", "fraud_type": "forgery", "fraud_sub_types": [""], "ground_truth": ["A"], "mask_indices": [1, 4, 7], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000058/panel/2000000058_4_2/2000000058_4_2_3.png"], "tampered": true, "paper_ids": ["2000000058"], "panel_ids": ["2000000058_4_2_3"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000058/panel/2000000058_4_2/2000000058_4_2_10.png", "question_id": "forgery_retract_6", "fraud_type": "forgery", "fraud_sub_types": [""], "ground_truth": ["A"], "mask_indices": [1, 2, 4, 5, 8], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000058/panel/2000000058_4_2/2000000058_4_2_10.png"], "tampered": true, "paper_ids": ["2000000058"], "panel_ids": ["2000000058_4_2_10"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000058/panel/2000000058_5_1/2000000058_5_1_4.png", "question_id": "forgery_retract_7", "fraud_type": "forgery", "fraud_sub_types": [""], "ground_truth": ["A"], "mask_indices": [1, 4, 7], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000058/panel/2000000058_5_1/2000000058_5_1_4.png"], "tampered": true, "paper_ids": ["2000000058"], "panel_ids": ["2000000058_5_1_4"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000058/panel/2000000058_5_1/2000000058_5_1_6.png", "question_id": "forgery_retract_8", "fraud_type": "forgery", "fraud_sub_types": [""], "ground_truth": ["A"], "mask_indices": [2, 5, 8], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000058/panel/2000000058_5_1/2000000058_5_1_6.png"], "tampered": true, "paper_ids": ["2000000058"], "panel_ids": ["2000000058_5_1_6"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000058/panel/2000000058_5_1/2000000058_5_1_7.png", "question_id": "forgery_retract_9", "fraud_type": "forgery", "fraud_sub_types": [""], "ground_truth": ["A"], "mask_indices": [1, 2, 4, 5, 7, 8], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000058/panel/2000000058_5_1/2000000058_5_1_7.png"], "tampered": true, "paper_ids": ["2000000058"], "panel_ids": ["2000000058_5_1_7"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000059/panel/2000000059_8_1/2000000059_8_1_2.png", "question_id": "forgery_retract_10", "fraud_type": "forgery", "fraud_sub_types": [""], "ground_truth": ["A"], "mask_indices": [2, 5, 8], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000059/panel/2000000059_8_1/2000000059_8_1_2.png"], "tampered": true, "paper_ids": ["2000000059"], "panel_ids": ["2000000059_8_1_2"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000066/panel/2000000066_6_1/2000000066_6_1_9.png", "question_id": "forgery_retract_11", "fraud_type": "forgery", "fraud_sub_types": [""], "ground_truth": ["A"], "mask_indices": [1, 2, 4, 5, 7, 8], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000066/panel/2000000066_6_1/2000000066_6_1_9.png"], "tampered": true, "paper_ids": ["2000000066"], "panel_ids": ["2000000066_6_1_9"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000031/panel/2000000031_5_1/2000000031_5_1_1.png", "question_id": "forgery_retract_12", "fraud_type": "forgery", "fraud_sub_types": ["copy-move"], "ground_truth": ["B"], "mask_indices": [6], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000031/panel/2000000031_5_1/2000000031_5_1_1.png"], "tampered": true, "paper_ids": ["2000000031"], "panel_ids": ["2000000031_5_1_1"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000031/panel/2000000031_5_1/2000000031_5_1_2.png", "question_id": "forgery_retract_13", "fraud_type": "forgery", "fraud_sub_types": ["copy-move"], "ground_truth": ["B"], "mask_indices": [3, 6], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000031/panel/2000000031_5_1/2000000031_5_1_2.png"], "tampered": true, "paper_ids": ["2000000031"], "panel_ids": ["2000000031_5_1_2"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000031/panel/2000000031_8_1/2000000031_8_1_1.png", "question_id": "forgery_retract_14", "fraud_type": "forgery", "fraud_sub_types": ["copy-move"], "ground_truth": ["B"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000031/panel/2000000031_8_1/2000000031_8_1_1.png"], "tampered": true, "paper_ids": ["2000000031"], "panel_ids": ["2000000031_8_1_1"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000031/panel/2000000031_8_1/2000000031_8_1_3.png", "question_id": "forgery_retract_15", "fraud_type": "forgery", "fraud_sub_types": ["copy-move"], "ground_truth": ["B"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000031/panel/2000000031_8_1/2000000031_8_1_3.png"], "tampered": true, "paper_ids": ["2000000031"], "panel_ids": ["2000000031_8_1_3"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000031/panel/2000000031_10_1/2000000031_10_1_10.png", "question_id": "forgery_retract_16", "fraud_type": "forgery", "fraud_sub_types": ["copy-move"], "ground_truth": ["B"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000031/panel/2000000031_10_1/2000000031_10_1_10.png"], "tampered": true, "paper_ids": ["2000000031"], "panel_ids": ["2000000031_10_1_10"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000032/panel/2000000032_8_2/2000000032_8_2_1.png", "question_id": "forgery_retract_17", "fraud_type": "forgery", "fraud_sub_types": ["copy-move"], "ground_truth": ["B"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000032/panel/2000000032_8_2/2000000032_8_2_1.png"], "tampered": true, "paper_ids": ["2000000032"], "panel_ids": ["2000000032_8_2_1"], "figure_ids": ["None"], "scenario": "Stained Micrograph"}} {"file_name": "retract/2000000034/panel/2000000034_7_1/2000000034_7_1_4.png", "question_id": "forgery_retract_18", "fraud_type": "forgery", "fraud_sub_types": ["copy-move"], "ground_truth": ["B"], "mask_indices": [4], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000034/panel/2000000034_7_1/2000000034_7_1_4.png"], "tampered": true, "paper_ids": ["2000000034"], "panel_ids": ["2000000034_7_1_4"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000034/panel/2000000034_7_1/2000000034_7_1_9.png", "question_id": "forgery_retract_19", "fraud_type": "forgery", "fraud_sub_types": ["copy-move"], "ground_truth": ["B"], "mask_indices": [4, 5, 6], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000034/panel/2000000034_7_1/2000000034_7_1_9.png"], "tampered": true, "paper_ids": ["2000000034"], "panel_ids": ["2000000034_7_1_9"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000006/panel/2000000006_6_1/2000000006_6_1_1.png", "question_id": "forgery_retract_20", "fraud_type": "forgery", "fraud_sub_types": ["copy-move"], "ground_truth": ["B"], "mask_indices": [4, 5, 6], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000006/panel/2000000006_6_1/2000000006_6_1_1.png"], "tampered": true, "paper_ids": ["2000000006"], "panel_ids": ["2000000006_6_1_1"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000006/panel/2000000006_6_1/2000000006_6_1_3.png", "question_id": "forgery_retract_21", "fraud_type": "forgery", "fraud_sub_types": ["copy-move"], "ground_truth": ["B"], "mask_indices": [5, 6], "mask_caption": "The image was divided ino a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row,left\nBlock 2=first row, center\nBlock 3 =first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6= second row, right\nBlock 7= third row, left\nBlock 8= third row, center\nBlock 9= third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000006/panel/2000000006_6_1/2000000006_6_1_3.png"], "tampered": true, "paper_ids": ["2000000006"], "panel_ids": ["2000000006_6_1_3"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000064/panel/2000000064_5_1/2000000064_5_1_6.png", "question_id": "forgery_retract_22", "fraud_type": "forgery", "fraud_sub_types": ["copy-move"], "ground_truth": ["B"], "mask_indices": [2, 3, 5, 6, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000064/panel/2000000064_5_1/2000000064_5_1_6.png"], "tampered": true, "paper_ids": ["2000000064"], "panel_ids": ["2000000064_5_1_6"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000066/panel/2000000066_5_1/2000000066_5_1_7.png", "question_id": "forgery_retract_23", "fraud_type": "forgery", "fraud_sub_types": ["copy-move"], "ground_truth": ["B"], "mask_indices": [1, 3, 4, 6, 7, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000066/panel/2000000066_5_1/2000000066_5_1_7.png"], "tampered": true, "paper_ids": ["2000000066"], "panel_ids": ["2000000066_5_1_7"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000066/panel/2000000066_6_1/2000000066_6_1_7.png", "question_id": "forgery_retract_24", "fraud_type": "forgery", "fraud_sub_types": ["copy-move"], "ground_truth": ["B"], "mask_indices": [2, 5, 8], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000066/panel/2000000066_6_1/2000000066_6_1_7.png"], "tampered": true, "paper_ids": ["2000000066"], "panel_ids": ["2000000066_6_1_7"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000014/panel/2000000014_5_1/2000000014_5_1_7.png", "question_id": "forgery_retract_25", "fraud_type": "forgery", "fraud_sub_types": ["copy-move"], "ground_truth": ["B"], "mask_indices": [4, 5, 6], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000014/panel/2000000014_5_1/2000000014_5_1_7.png"], "tampered": true, "paper_ids": ["2000000014"], "panel_ids": ["2000000014_5_1_7"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000014/panel/2000000014_5_1/2000000014_5_1_8.png", "question_id": "forgery_retract_26", "fraud_type": "forgery", "fraud_sub_types": ["copy-move"], "ground_truth": ["B"], "mask_indices": [4, 5, 6], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000014/panel/2000000014_5_1/2000000014_5_1_8.png"], "tampered": true, "paper_ids": ["2000000014"], "panel_ids": ["2000000014_5_1_8"], "figure_ids": ["None"], "scenario": "Others"}} {"file_name": "retract/2000000021/panel/2000000021_3_2/2000000021_3_2_1.png", "question_id": "forgery_retract_27", "fraud_type": "forgery", "fraud_sub_types": ["copy-move"], "ground_truth": ["B"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000021/panel/2000000021_3_2/2000000021_3_2_1.png"], "tampered": true, "paper_ids": ["2000000021"], "panel_ids": ["2000000021_3_2_1"], "figure_ids": ["None"], "scenario": "Micrograph"}} {"file_name": "retract/2000000021/panel/2000000021_3_3/2000000021_3_3_1.png", "question_id": "forgery_retract_28", "fraud_type": "forgery", "fraud_sub_types": ["copy-move"], "ground_truth": ["B"], "mask_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9], "mask_caption": "The image was divided into a 3-row by 3-column equal-area grid, resulting in 9 blocks.\nThe numbering goes left to right, top to bottom:\nBlock 1 = first row, left\nBlock 2 = first row, center\nBlock 3 = first row, right\nBlock 4 = second row, left\nBlock 5 = second row, center\nBlock 6 = second row, right\nBlock 7 = third row, left\nBlock 8 = third row, center\nBlock 9 = third row, right", "mask_path": "", "figure_caption": "", "figure_related_sentences": "", "inconsistent_part": "", "tampered_sentences": [""], "golden_sentences": [""], "metadata": {"all_images_paths": ["retract/2000000021/panel/2000000021_3_3/2000000021_3_3_1.png"], "tampered": true, "paper_ids": ["2000000021"], "panel_ids": ["2000000021_3_3_1"], "figure_ids": ["None"], "scenario": "Micrograph"}}