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Accurately modeling the DNA sequence preferences of transcription factors ( TFs ) , and using these models to predict in vivo genomic binding sites for TFs , are key pieces in deciphering the regulatory code . These efforts have been frustrated by the limited availability and accuracy of TF binding site motifs , usuall...	Transcription factors ( TFs ) are proteins that bind sites in the non-coding DNA and regulate the expression of targeted genes . Being able to predict the genome-wide binding locations of TFs is an important step in deciphering gene regulatory networks . Historically , there was very limited experimental data on the DN...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mathematics/statistics", "computational", "biology/comparative", "sequence", "analysis", "computational", "biology/transcriptional", "regulation", "computational", "biology" ]	2010	High Resolution Models of Transcription Factor-DNA Affinities Improve In Vitro and In Vivo Binding Predictions
Virulence of the most deadly malaria parasite Plasmodium falciparum is linked to the variant surface antigen PfEMP1 , which is encoded by about 60 var genes per parasite genome . Although the expression of particular variants has been associated with different clinical outcomes , little is known about var gene expressi...	Parasites of the species Plasmodium falciparum , which are responsible for the most severe forms of malaria , escape from the human immune response by antigenic variation . A repertoire of 60 var genes codes for a broad range of different variant antigens presented on the surface of infected erythrocytes . These antige...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "parasite", "groups", "body", "fluids", "pathology", "and", "laboratory", "medicine", "parasite", "replication", "plasmodium", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "apicomplexa...	2016	Mosquito Passage Dramatically Changes var Gene Expression in Controlled Human Plasmodium falciparum Infections
Proteorhodopsins are globally abundant photoproteins found in bacteria in the photic zone of the ocean . Although their function as proton pumps with energy-yielding potential has been demonstrated , the ecological role of proteorhodopsins remains largely unexplored . Here , we report the presence and function of prote...	It is estimated that marine microscopic algae—phytoplankton—are responsible for half of the Earth's photosynthesis . As much as half of the surface ocean bacteria have proteorhodopsins , which are membrane proteins that allow harvesting of energy from sunlight , implying a potentially significant role of non–chlorophyl...	[ "Abstract", "Introduction", "Results/Discussion", "Material", "and", "Methods" ]	[ "marine", "and", "aquatic", "sciences/microbiology", "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "biochemistry/membrane", "proteins", "and", "energy", "transduction" ]	2010	Proteorhodopsin Phototrophy Promotes Survival of Marine Bacteria during Starvation
Triatoma dimidiata is one of the most significant vectors of Chagas disease in Central America and Colombia , and , as in most species , its pattern of genetic variation within and among populations is strongly affected by its phylogeographic history . A putative origin from Central America has been proposed for Colomb...	The Chagas disease vector Triatoma dimidiata is one of the most important vectors in America , owing to its wide genetic and epidemiological heterogeneity . Colombian T . dimidiata populations occupy eclectic sylvatic ecotopes , but have also been found in dwellings infected with Trypanosoma cruzi , and therefore it is...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "haplotypes", "genetic", "polymorphism", "effective", "population", "size", "molecular", "systematics", "population", "genetics", "biology", "evolutionary", "biology", "evolutionary", "systematics", "evolutionary", "genetics" ]	2014	Molecular Evidence of Demographic Expansion of the Chagas Disease Vector Triatoma dimidiata (Hemiptera, Reduviidae, Triatominae) in Colombia
The plasticity of the human nervous system allows us to acquire an open-ended repository of sensorimotor skills in adulthood , such as the mastery of tools , musical instruments or sports . How novel sensorimotor skills are learned from scratch is yet largely unknown . In particular , the so-called inverse mapping from...	Even in adulthood , humans can learn to master new motor skills with unfamiliar mappings between desired goals or sensations and corresponding movements , such as playing tennis or musical instruments . To master a new skill involves the resolution of motor redundancy; that is a selection from many possible movements t...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "learning", "medicine", "and", "health", "sciences", "ellipses", "engineering", "and", "technology", "statistics", "social", "sciences", "geometry", "neuroscience", "learning", "and", "memory", "multivariate", "analysis", "age", "groups", "adults", "cognitive", "psychol...	2019	Goal-related feedback guides motor exploration and redundancy resolution in human motor skill acquisition
Different strains and species of the soil phytopathogen Agrobacterium possess the ability to transfer and integrate a segment of DNA ( T-DNA ) into the genome of their eukaryotic hosts , which is mainly mediated by a set of virulence ( vir ) genes located on the bacterial Ti-plasmid that also contains the T-DNA . To da...	Since the discovery of gene transfer from Agrobacterium to host plants in the late 1970s , this bacterial pathogen has been widely used in research and biotechnology to generate transgenic plants . Agrobacterium’s infection process relies on a set of virulence proteins that mediate the transfer of a segment of its own ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "plant", "anatomy", "microbiology", "plant", "science", "rhizobium", "genetically", "modified", "plants", "plant", "genomics", "molecular", "biology", "techniques", "plants", "bacteria", "genetic", "engineering", "agrobacteria", "research", "and", "analys...	2016	A Functional Bacterium-to-Plant DNA Transfer Machinery of Rhizobium etli
C-to-U editing of transcripts in plant organelles is carried out by small ( <400 kD ) protein complexes called editosomes . Recognition of the proper C target for editing is mediated by pentatricopeptide repeat ( PPR ) containing proteins that recognize cis-elements . Members of two additional gene families , the RIP/M...	Transcripts encoding chloroplast and mitochondrial proteins of flowering plants are profoundly affected by RNA editing . In Arabidopsis , over 600 genomically-encoded Cs are modified to Us in organelle transcripts , altering the encoded amino acids and creating stop and start codons . Pentatricopeptide proteins are kno...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[]	2015	A Zinc Finger Motif-Containing Protein Is Essential for Chloroplast RNA Editing
The immunocytes that regulate papillomavirus infection and lesion development in humans and animals remain largely undefined . We found that immunocompetent mice with varying H-2 haplotypes displayed asymptomatic skin infection that produced L1 when challenged with 6×1010 MusPV1 virions , the recently identified domest...	Infection with papillomaviruses can cause benign warts ( papillomas ) on skin and mucosae of humans and animals but also malignancies , especially anogenital carcinomas and , in genetically predisposed or immunocompromised individuals , cutaneous squamous cell cancers . Control and clearance of these viruses are though...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "dermatology", "infectious", "diseases", "medicine", "and", "health", "sciences", "biology", "and", "life", "sciences", "immunology", "microbiology" ]	2014	Strain-Specific Properties and T Cells Regulate the Susceptibility to Papilloma Induction by Mus musculus Papillomavirus 1
To understand the regulation of tissue-specific gene expression , the GTEx Consortium generated RNA-seq expression data for more than thirty distinct human tissues . This data provides an opportunity for deriving shared and tissue specific gene regulatory networks on the basis of co-expression between genes . However ,...	Cells in different tissues perform very different functions with the same DNA . This requires tissue-specific gene expression and regulation; understanding this tissue-specificity is often instrumental to understanding complex diseases . Here , we use tissue-specific gene expression data to learn tissue-specific gene r...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Sharing and Specificity of Co-expression Networks across 35 Human Tissues
Hookworm infection is considered one of the most important poverty-promoting neglected tropical diseases , infecting 576 to 740 million people worldwide , especially in the tropics and subtropics . These blood-feeding nematodes have a remarkable ability to downmodulate the host immune response , protecting themselves f...	The hookworm infection is characterized by the long-term survival of the parasite and the concomitant modulation of the host immunity . Among several mechanisms that may account for the suppression of T cell response , we here described the presence and role of T regulatory cells ( also known as Tregs ) in the human ho...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "immunity", "immunology", "biology", "microbiology", "zoology", "parasitology" ]	2011	Induction of CD4+CD25+FOXP3+ Regulatory T Cells during Human Hookworm Infection Modulates Antigen-Mediated Lymphocyte Proliferation
Filamentous fungi that thrive on plant biomass are the major producers of hydrolytic enzymes used to decompose lignocellulose for biofuel production . Although induction of cellulases is regulated at the transcriptional level , how filamentous fungi sense and signal carbon-limited conditions to coordinate cell metaboli...	Many filamentous fungi that grow on plant biomass are capable of producing lignocellulase enzymes to break down plant cell walls into utilizable sugars , thus holding great potential in reducing the cost of the next-generation biofuels . Cellulase production is subject to induction by the presence of plant biomass comp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "applied", "microbiology", "biochemistry", "enzymes", "biology", "and", "life", "sciences", "enzymology", "microbiology" ]	2014	VIB1, a Link between Glucose Signaling and Carbon Catabolite Repression, Is Essential for Plant Cell Wall Degradation by Neurospora crassa
Although much effort has been directed at dissecting the mechanisms of central tolerance , the role of thymic stromal cells remains elusive . In order to further characterize this event , we developed a mouse model restricting LacZ to thymic stromal cotransporter ( TSCOT ) -expressing thymic stromal cells ( TDLacZ ) . ...	T cells play critical roles in the immune response . While developing in the thymus ( from whence T cells and their precursors , thymocytes , derive their name ) , thymocytes are selected for the ability to recognize harmful antigen ( positive selection ) , while those that respond to antigens present in their own body...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "cell", "biology", "immunology" ]	2008	TSCOT + Thymic Epithelial Cell-Mediated Sensitive CD4 Tolerance by Direct Presentation
The piwi-interacting RNAs ( piRNA ) are small RNAs that target selfish transposable elements ( TEs ) in many animal genomes . Until now , piRNAs’ role in TE population dynamics has only been discussed in the context of their suppression of TE transposition , which alone is not sufficient to account for the skewed frequ...	The piwi-interacting RNAs ( piRNAs ) are small RNAs that can suppress the expression of selfish transposable elements ( TEs ) in many animal genomes . One mechanism by which piRNAs silence TEs is through the formation of heterochromatin , which is condensed chromatin and generally associated with repressed gene express...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Role of piRNA-Mediated Epigenetic Silencing in the Population Dynamics of Transposable Elements in Drosophila melanogaster
Memory T cell inflation is a process in which a subset of cytomegalovirus ( CMV ) specific CD8 T cells continuously expands mainly during latent infection and establishes a large and stable population of effector memory cells in peripheral tissues . Here we set out to identify in vivo parameters that promote and limit ...	Cytomegalovirus induces a lifelong infection in the majority of the world's population , due to the ability of the virus to establish latency . Upon CMV infection , large numbers of effector memory T cells are induced in peripheral tissues , a process that is termed memory inflation . As inflationary T cells are highly...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "reproductive", "system", "immune", "cells", "immune", "physiology", "body", "fluids", "spleen", "immunology", "microbiology", "cytotoxic", "t", "cells", "research", "and", "analysis", "methods", "specimen", ...	2019	Early primed KLRG1- CMV-specific T cells determine the size of the inflationary T cell pool
Exit from mitosis in budding yeast is triggered by activation of the key mitotic phosphatase Cdc14 . At anaphase onset , the protease separase and Zds1 promote the downregulation of PP2ACdc55 phosphatase , which facilitates Cdk1-dependent phosphorylation of Net1 and provides the first wave of Cdc14 activity . Once Cdk1...	Cell cycle studies over the years have tried to elucidate the molecular mechanisms behind cell division , one of the most highly regulated of all cell processes , which ensures life in all organisms . Protein phosphorylation emerged as a key regulatory mechanism in the cell cycle . The highly conserved family of cyclin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Dual Regulation of the Mitotic Exit Network (MEN) by PP2A-Cdc55 Phosphatase
Aging and longevity are complex traits influenced by genetic and environmental factors . To identify quantitative trait loci ( QTLs ) that control replicative lifespan , we employed an outbred Saccharomyces cerevisiae model , generated by crossing a vineyard and a laboratory strain . The predominant QTL mapped to the r...	Although many aging regulators have been discovered , we are still uncovering how each contributes to the basic biology underlying cell lifespan and how certain longevity-promoting regimens , such as calorie restriction , manipulate the aging process across species . Since many cellular aging processes between human ce...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "population", "genetics", "quantitative", "traits", "anatomy", "and", "physiology", "microbiology", "physiological", "processes", "model", "organisms", "dna", "replication", "dna", "genetic", "polymorphism", "biology", "molecular", ...	2013	A Natural Polymorphism in rDNA Replication Origins Links Origin Activation with Calorie Restriction and Lifespan
Day-length is important for regulating the transition to reproductive development ( flowering ) in plants . In the model plant Arabidopsis thaliana , the transcription factor CONSTANS ( CO ) promotes expression of the florigen FLOWERING LOCUS T ( FT ) , constituting a key flowering pathway under long-day photoperiods ....	The photoperiodic flowering in Arabidopsis requires the key regulator CO and its target gene FT . However , how CO regulates FT expression in the context of chromatin remains largely obscure . In this work , we present Arabidopsis MRG1/2 as novel chromatin effectors directly involved in the CO-FT photoperiodic flowerin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "plant", "science", "plant", "growth", "and", "development", "genetics", "plant", "genetics", "epigenetics", "biology", "and", "life", "sciences", "histone", "modification" ]	2014	Regulation of Arabidopsis Flowering by the Histone Mark Readers MRG1/2 via Interaction with CONSTANS to Modulate FT Expression
The protozoan parasite Giardia intestinalis and the pathogenic bacterium Helicobacter pylori are well known for their high prevalences in human hosts worldwide . The prevalence of both organisms is known to peak in densely populated , low resource settings and children are infected early in life . Different Giardia gen...	G . intestinalis and H . pylori are known to infect the gastrointestinal tract of humans early in life and to be very prevalent in endemic areas throughout life . H . pylori colonizes the gastric mucosa and may give rise to peptic ulcers , chronic gastritis and gastric cancer whereas Giardia causes diarrhea , bloating ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "gastrointestinal", "infections" ]	2012	Common Coinfections of Giardia intestinalis and Helicobacter pylori in Non-Symptomatic Ugandan Children
Cell entry by non-enveloped viruses requires translocation into the cytosol of a macromolecular complex—for double-strand RNA viruses , a complete subviral particle . We have used live-cell fluorescence imaging to follow rotavirus entry and penetration into the cytosol of its ∼700 Å inner capsid particle ( “double-laye...	Non-enveloped viruses ( viruses lacking a lipid-bilayer membrane ) require local disruption of a cellular membrane to gain access to the cell interior and thereby initiate infection . Most double-strand RNA viruses have an outer protein layer that mediates this entry step and an inner-capsid particle that transcribes t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "cell", "biology", "virology", "biology", "and", "life", "sciences", "microbiology", "molecular", "cell", "biology" ]	2014	Structural Correlates of Rotavirus Cell Entry
The relationship between mosquito vectors and lymphatic filariasis ( LF ) parasites can result in a range of transmission outcomes . Anophelines are generally characterized as poor vectors due to an inability to support development at low densities . However , it is important to understand the potential for transmissio...	Lymphatic filariasis ( LF ) elimination requires interrupting transmission of microfilaria ( mf ) from humans to mosquitoes for 5–7 years , the average life span of adult worms . Current mf prevalence thresholds , below which transmission cannot be sustained , are unknown . Anopheline-transmitted LF is thought to be ea...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2013	Mosquito-Parasite Interactions Can Shape Filariasis Transmission Dynamics and Impact Elimination Programs
Most mutations that compromise meiotic recombination or synapsis in mouse spermatocytes result in arrest and apoptosis at the pachytene stage of the first meiotic prophase . Two main mechanisms are thought to trigger arrest: one independent of the double-strand breaks ( DSBs ) that initiate meiotic recombination , and ...	Meiosis is the specialized cell division by which haploid cells are produced . As germ cells enter the first meiotic prophase , programmed double-stranded breaks ( DSBs ) are formed throughout the genome . Repair of these DSBs by homologous recombination is crucial for proper segregation of homologous chromosomes at th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The ATM Signaling Cascade Promotes Recombination-Dependent Pachytene Arrest in Mouse Spermatocytes
Kupffer cells ( KCs ) are widely considered important contributors to liver injury during viral hepatitis due to their pro-inflammatory activity . Herein we utilized hepatitis B virus ( HBV ) -replication competent transgenic mice and wild-type mice infected with a hepatotropic adenovirus to demonstrate that KCs do not...	Kupffer cells ( KCs ) , the resident macrophages of the liver , are considered important contributors to liver injury during viral hepatitis due to their pro-inflammatory activity . Herein we utilized two different mouse models of viral hepatitis ( where liver damage is triggered , as during viral hepatitis in humans ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "immune", "cells", "immunity", "to", "infections", "immunology", "microbiology", "liver", "diseases", "adaptive", "immunity", "infectious", "hepatitis", "hepatitis", "gastroenterology", "and", "hepatology", "infectious", "diseases", "t", "cells", "biology", ...	2011	Kupffer Cells Hasten Resolution of Liver Immunopathology in Mouse Models of Viral Hepatitis
Mosquito-borne diseases continue to remain major threats to human and animal health and impediments to socioeconomic development . Increasing mosquito resistance to chemical insecticides is a great public health concern , and new strategies/technologies are necessary to develop the next-generation of vector control too...	There is an urgent need for new interventions and novel insecticides to control mosquito vectors of human disease agents . Nanoparticle-based strategies have been explored extensively as means to deliver a molecule of interest for medical applications ( e . g . , antigens , drugs , nucleic acids , etc . ) to particular...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Biodistribution and Toxicity Studies of PRINT Hydrogel Nanoparticles in Mosquito Larvae and Cells
Both aging and chronic inflammation produce complex structural and biochemical alterations to the lung known to impact work of breathing . Mice deficient in surfactant protein D ( Sftpd ) develop progressive age-related lung pathology characterized by tissue destruction/remodeling , accumulation of foamy macrophages an...	Aging and chronic inflammation produce complex changes to the structure of the lung including accumulation of cells and debris , thinning and destruction of air sacs , altered airway size and increased tendency for airway collapse . As these structural changes are observed concurrently , their individual contributions ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "immunology", "vertebrates", "mice", "animals", "mammals", "simulation", "and", "modeling", "histology", "signs", "and", "symptoms", "materials", "science", "surfactants", "elastin", ...	2017	Histologic and biochemical alterations predict pulmonary mechanical dysfunction in aging mice with chronic lung inflammation
The aim of this study was to compare the safety and immunogenicity between purified vero cell rabies vaccine ( PVRV ) and purified chick embryo cell vaccine ( PCECV ) in patients with WHO category II animal exposure , especially in different age groups . In one-year clinical observation after vaccination with PVRV or P...	Nowadays , many approved vaccines with different components ( such as purified vero cell rabies vaccine [PVRV] , purified chick embryo cell vaccine [PCECV] , and Human diploid cell vaccine [HDCV] ) and many regimens with different vaccination schedules ( Zagreb , Essen ) are being used in the world . Thus , we compared...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biology", "and", "life", "sciences", "viral", "vaccines", "microbiology", "virology" ]	2014	Comparison of Safety and Immunogenicity of PVRV and PCECV Immunized in Patients with WHO Category II Animal Exposure: A Study Based on Different Age Groups
ClinicalTrials . gov Clinical Trial NCT00594880 Infection with Human Immunodeficiency Virus ( HIV ) results in widespread inflammation in infected individuals with key changes in the immune system that have important clinical implications . Untreated HIV disease is characterized by high levels of systemic and tissue-lo...	Though the advent of antiretroviral therapy ( ART ) has significantly improved the lives of individuals infected with the Human Immunodeficiency Virus ( HIV ) , those on therapy still suffer from an enhanced risk of morbidities and mortalities that is caused , at least in part by , overactivation of the immune system ....	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "hiv", "infections", "organoids", "medicine", "and", "health", "sciences", "innate", "immune", "system", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "biopsy", "pathogens", "biological", "cultures", "immunology", "microbiology", "su...	2018	A20 upregulation during treated HIV disease is associated with intestinal epithelial cell recovery and function
The distribution of transposable elements ( TEs ) in a genome reflects a balance between insertion rate and selection against new insertions . Understanding the distribution of TEs therefore provides insights into the forces shaping the organization of genomes . Past research has shown that TEs tend to accumulate in ge...	Transposable elements ( TEs ) are parasitic DNA segments that can move within a host genome . These selfish mobile elements are present in virtually all eukaryote species and can contribute significantly to their DNA . TEs multiply by copying themselves within the genome . Depending on where they land , new copies can ...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "arthropods", "eukaryotes", "evolutionary", "biology", "drosophila", "animals", "genetics", "and", "genomics", "insects" ]	2007	Genome Organization and Gene Expression Shape the Transposable Element Distribution in the Drosophila melanogaster Euchromatin
Consideration of previous successes and failures is essential to mastering a motor skill . Much of what we know about how humans and animals learn from such reinforcement feedback comes from experiments that involve sampling from a small number of discrete actions . Yet , it is less understood how we learn through rein...	In recent years it has been shown that reinforcement feedback may also subserve our ability to acquire new motor skills . Here we address how the reinforcement gradient influences motor learning . We found that a steeper gradient increased both the rate and likelihood of learning . Moreover , while many mainstream theo...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "learning", "medicine", "and", "health", "sciences", "exponential", "functions", "social", "sciences", "neuroscience", "learning", "and", "memory", "simulation", "and", "modeling", "cognitive", "psychology", "mathematics", "probability", "distribution", "body", "limbs", ...	2019	The gradient of the reinforcement landscape influences sensorimotor learning
Rates of evolution span orders of magnitude among RNA viruses with important implications for viral transmission and emergence . Although the tempo of viral evolution is often ascribed to viral features such as mutation rates and transmission mode , these factors alone cannot explain variation among closely related vir...	Rapid evolution of RNA viruses is intimately linked to their success in overcoming the defenses of their hosts . Several studies have shown that rates of viral evolution can vary dramatically among distantly related viral families . Variability in the speed of evolution among closely related viruses has received less a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "types", "viral", "classification", "microbiology", "rabies", "rna", "viruses", "veterinary", "science", "emergence", "veterinary", "diseases", "zoonotic", "diseases", "biology", "behavioral", "ecology", "wildlife", "ecology", "virology", "evolutionary", "biolog...	2012	Rates of Viral Evolution Are Linked to Host Geography in Bat Rabies
Elite suppressors ( ES ) are a rare subset of HIV-1–infected individuals who are able to maintain HIV-1 viral loads below the limit of detection by ultra-sensitive clinical assays in the absence of antiretroviral therapy . Mechanism ( s ) responsible for this elite control are poorly understood but likely involve both ...	The majority of HIV-1–infected individuals experience high plasma viral loads and CD4+ T cells loss in the absence of antiretroviral therapy . However , a very rare and important subset of individuals termed elite suppressors is able to maintain HIV-1 plasma viral loads below the limit of viral detection in the absence...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "virology/mechanisms", "of", "resistance", "and", "susceptibility,", "including", "host", "genetics", "infectious", "diseases/hiv", "infection", "and", "aids", "virology/immunodeficiency", "viruses" ]	2009	Elite Suppressor–Derived HIV-1 Envelope Glycoproteins Exhibit Reduced Entry Efficiency and Kinetics
Toxoplasma gondii infects up to one third of the world's population . A key to the success of T . gondii as a parasite is its ability to persist for the life of its host as bradyzoites within tissue cysts . The glycosylated cyst wall is the key structural feature that facilitates persistence and oral transmission of th...	Toxoplasma gondii causes severe encephalitis in immune compromised hosts after reactivation of brain cysts that persist for the life span of the host . The biological mechanisms of bradyzoite persistence within cysts are not fully understood . The glycosylated cyst wall is thought to play a crucial role in survival of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	The Toxoplasma gondii Cyst Wall Protein CST1 Is Critical for Cyst Wall Integrity and Promotes Bradyzoite Persistence
Human respiratory syncytial virus ( HRSV ) and , to a lesser extent , human metapneumovirus ( HMPV ) and human parainfluenza virus type 3 ( HPIV3 ) , can re-infect symptomatically throughout life without significant antigenic change , suggestive of incomplete or short-lived immunity . In contrast , re-infection by infl...	The respiratory viruses human respiratory syncytial virus ( HRSV ) and , to a lesser extent , human metapneumovirus virus ( HMPV ) and human parainfluenza virus ( HPIV3 ) , can re-infect humans throughout life without significant antigenic change , suggesting that immunity to these viruses is incomplete . In contrast ,...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immune", "cells", "rna", "viruses", "immunity", "virology", "immune", "activation", "antigen-presenting", "cells", "immunity", "to", "infections", "immunology", "biology", "microbiology", "viral", "classification" ]	2011	Low CCR7-Mediated Migration of Human Monocyte Derived Dendritic Cells in Response to Human Respiratory Syncytial Virus and Human Metapneumovirus
Trypanosoma cruzi , the etiological agent of Chagas' disease , is an early divergent eukaryote in which control of gene expression relies mainly in post-transcriptional mechanisms . Transcription levels are globally up and down regulated during the transition between proliferating and non-proliferating life-cycle stage...	Infection with Trypanosoma cruzi produces a condition known as Chagas disease which affects at least 17 million people . Adenylate kinases , so called myokinases , are involved in a wide variety of processes , mainly related to their role in nucleotide interconversion and energy management . Recently , nuclear isoforms...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Discussion" ]	[ "cellular", "structures", "enzymes", "microbiology", "parastic", "protozoans", "nucleolus", "metabolic", "pathways", "biology", "biochemistry", "rna", "trypanosoma", "rna", "processing", "cell", "biology", "nucleic", "acids", "protozoology", "molecular", "cell", "biology"...	2013	Molecular and Functional Characterization of a Trypanosoma cruzi Nuclear Adenylate Kinase Isoform
Functional effects of different mutations are known to combine to the total effect in highly nontrivial ways . For the trait under evolutionary selection ( ‘fitness’ ) , measured values over all possible combinations of a set of mutations yield a fitness landscape that determines which mutational states can be reached ...	Fitness landscapes describe the fitness of related genotypes in a given environment , and can be used to identify which mutational steps lead towards higher fitness under particular evolutionary scenarios . The structure of a fitness landscape results from the way mutations interact in determining fitness , and can be ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "population", "genetics", "microbiology", "epistasis", "mutation", "fungi", "population", "biology", "mycology", "evolutionary", "modeling", "biology", "evolutionary", "theory", "adaptation", "heredity", "genetics", "computational", "biology", "evolutionary", "biology", "ev...	2011	Evolutionary Accessibility of Mutational Pathways
Gastrointestinal side effects are among the most common classes of adverse reactions associated with orally absorbed drugs . These effects decrease patient compliance with the treatment and induce undesirable physiological effects . The prediction of drug action on the gut wall based on in vitro data solely can improve...	The gut wall is the first barrier that encounters orally absorbed drugs , and it substantially modulates the bioavailability of drugs and supports several classes of side effects . We developed context-specific metabolic models of the enterocyte constrained by drug-induced gene expression and trained a machine learning...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "artificial", "intelligence", "genome", "analysis", "pharmacology", "molecular", "biology", "techniques", "drug", "metabolism", "digestive", "system", "research", "and", "analysis", "methods", "cell", "labeling", "computer", "and...	2019	Predicting gastrointestinal drug effects using contextualized metabolic models
Japan has been free from rabies since the 1950s . However , during the early 1900s several large-scale epidemics spread throughout the country . Here we investigate the dynamics of these epidemics between 1914 and 1933 in Osaka Prefecture , using archival data including newspapers . The association between dog rabies c...	Rabies is a lethal zoonosis mostly transmitted through bites by dogs infected with rabies virus . Japan has been free from rabies since the 1950s . However , there were several large-scale epidemics before its elimination . These past epidemics occurred both before and after dog rabies vaccine became available . Moreov...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "animal", "types", "medicine", "and", "health", "sciences", "infectious", "disease", "epidemiology", "japan", "immunology", "tropical", "diseases", "geographical", "locations", "vertebrates", "pets", "and", "companion", "animals", "dogs", "animals", "mammals", "preventi...	2017	The rise and fall of rabies in Japan: A quantitative history of rabies epidemics in Osaka Prefecture, 1914–1933
Human cytomegalovirus ( HCMV ) infections of healthy individuals are mostly unnoticed and result in viral latency . However , HCMV can also cause devastating disease , e . g . , upon reactivation in immunocompromised patients . Yet , little is known about human immune cell sensing of DNA-encoded HCMV . Recent studies i...	Human cytomegalovirus ( HCMV ) has been shown to induce type I interferon ( IFN-I ) responses in myeloid cells such as plasmacytoid dendritic cells ( pDC ) . Although these cells were reported to sense the viral DNA genome in a Toll-like receptor ( TLR ) -dependent manner , previous studies showed that individuals disp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "pathogens", "immunology", "microbiology", "cytomegalovirus", "infection", "viruses", "bone", "marrow", "cells", "non-coding...	2016	cGAS Senses Human Cytomegalovirus and Induces Type I Interferon Responses in Human Monocyte-Derived Cells
In 1997 , the World Health Assembly adopted Resolution 50 . 29 , committing to the elimination of lymphatic filariasis ( LF ) as a public health problem , subsequently targeted for 2020 . The initial estimates were that 1 . 2 billion people were at-risk for LF infection globally . Now , 13 years after the Global Progra...	Lymphatic filariasis ( LF ) is a widespread neglected tropical disease most frequently recognized as elephantiasis that is caused by parasitic worms and spread by mosquitoes . To overcome this public health problem , the World Health Organization created the Global Programme to Eliminate Lymphatic Filariasis ( GPELF ) ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "helminth", "infections", "medicine", "and", "health", "sciences", "filariasis", "neglected", "tropical", "diseases", "tropical", "diseases", "parasitic", "diseases", "lymphatic", "filariasis" ]	2014	Assessing Progress in Reducing the At-Risk Population after 13 Years of the Global Programme to Eliminate Lymphatic Filariasis
Organism cells proliferate and die to build , maintain , renew and repair it . The cellular history of an organism up to any point in time can be captured by a cell lineage tree in which vertices represent all organism cells , past and present , and directed edges represent progeny relations among them . The root repre...	The history of an organism's cells , from a single cell until any particular moment in time , can be captured by a cell lineage tree . Many fundamental open questions in biology and medicine , such as which cells give rise to metastases , whether oocytes and beta cells renew , and what is the role of stem cells in brai...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Comparing Algorithms That Reconstruct Cell Lineage Trees Utilizing Information on Microsatellite Mutations
Schistosoma mansoni exists in a complex environmental milieu that may select for significant evolutionary changes in this species . In Kenya , the sympatric distribution of S . mansoni with S . rodhaini potentially influences the epidemiology , ecology , and evolutionary biology of both species , because they infect th...	One of the world's most prevalent neglected diseases is schistosomiasis , which infects approximately 200 million people worldwide . Schistosoma mansoni is transmitted to humans by skin penetration by free-living larvae that develop in freshwater snails . The origin of this species is East Africa , where it coexists wi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "evolutionary", "biology", "infectious", "diseases/helminth", "infections", "ecology" ]	2008	Interactions between Natural Populations of Human and Rodent Schistosomes in the Lake Victoria Region of Kenya: A Molecular Epidemiological Approach
Despite the global distribution and public health consequences of Taenia tapeworms , the life cycles of taeniids infecting wildlife hosts remain largely undescribed . The larval stage of Taenia serialis commonly parasitizes rodents and lagomorphs , but has been reported in a wide range of hosts that includes geladas ( ...	Although tapeworm parasites of the genus Taenia are globally distributed and inflict enormous socioeconomic and health costs on their hosts , which include humans , little is known about taeniid tapeworms that infect wildlife . This gap in knowledge prevents an assessment of the potential for these parasites to infect ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "animal", "types", "medicine", "and", "health", "sciences", "body", "fluids", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "vertebrates", "parasitic", "diseases", "animals", "mammals", "urine", "primates", "veterinary", "diagnostics", "...	2017	Identifying wildlife reservoirs of neglected taeniid tapeworms: Non-invasive diagnosis of endemic Taenia serialis infection in a wild primate population
Interferons ( IFNs ) target macrophages to regulate inflammation and resistance to microbial infections . The type II IFN ( IFNγ ) acts on a cell surface receptor ( IFNGR ) to promote gene expression that enhance macrophage inflammatory and anti-microbial activity . Type I IFNs can dampen macrophage responsiveness to I...	Interferon ( IFN ) γ promotes host resistance to invasive bacterial infections , but type I IFNs suppress macrophage activation and increase susceptibility to L . monocytogenes and other pathogenic bacteria . IFNγ promotes resistance by potently activating macrophages to become pro-inflammatory and antimicrobial . Type...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "spleen", "pathogens", "immunology", "microbiology", "bone", "marrow", "cells", "animal", "models", "model", "organisms"...	2017	Down regulation of macrophage IFNGR1 exacerbates systemic L. monocytogenes infection
Rabies is a neglected zoonotic disease that causes an estimated 60 , 000 human deaths annually . The main burden lies on developing countries in Asia and Africa , where surveillance and disease detection is hampered by absence of adequate laboratory facilities and/or the difficulties of submitting samples from remote a...	Despite being preventable with adequate biologicals , rabies still causes an estimated 60 , 000 human deaths annually . The main burden lies on developing countries in Asia and Africa , where dog rabies surveillance is hampered by laboratory confirmation of disease due to a number of reasons , including laboratory infr...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "reverse", "transcriptase-polymerase", "chain", "reaction", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "tropical", "diseases", "microbiology", "vertebrates", "rna", "extraction", "animals", "mammals", "dogs", "virus...	2016	Evaluation of Six Commercially Available Rapid Immunochromatographic Tests for the Diagnosis of Rabies in Brain Material
Dengue hemorrhagic fever ( DHF ) and dengue shock syndrome ( DSS ) are severe disease manifestations that can occur following sequential infection with different dengue virus serotypes ( DENV1-4 ) . At present , there are no licensed therapies to treat DENV-induced disease . DHF and DSS are thought to be mediated by se...	Dengue hemorrhagic fever ( DHF ) and dengue shock syndrome ( DSS ) are severe disease manifestations following secondary heterotypic dengue virus ( DENV ) infections . DENV infects almost 400 million people annually and there are currently no licensed therapies to treat DENV-induced disease . DHF and DSS are mediated b...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "dengue", "virus", "medicine", "and", "health", "sciences", "immune", "physiology", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "pathogens", "epitope", "mapping", "immunology", "tropical", "diseases", "microbiology", "alternative", "spli...	2017	Dengue virus specific IgY provides protection following lethal dengue virus challenge and is neutralizing in the absence of inducing antibody dependent enhancement
We previously reported a multigene family of monodomain Kunitz proteins from Echinococcus granulosus ( EgKU-1-EgKU-8 ) , and provided evidence that some EgKUs are secreted by larval worms to the host interface . In addition , functional studies and homology modeling suggested that , similar to monodomain Kunitz familie...	Parasite secretions are key players at host-parasite interfaces: parasite establishment and persistence rely , to a great extent , on interactions between these molecules and their host counterparts . We present the functional characterization of a multigene family of secreted Kunitz proteins from the cestode Echinococ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "chemical", "compounds", "pathology", "and", "laboratory", "medicine", "enzymes", "enzymology", "neuroscience", "organic", "compounds", "serine", "proteases", "physiological", "processes", "serine", "amino", "acids", "enzyme", "i...	2017	Functional diversity of secreted cestode Kunitz proteins: Inhibition of serine peptidases and blockade of cation channels
Noroviruses are important human pathogens responsible for most cases of viral epidemic gastroenteritis worldwide . Murine norovirus-1 ( MNV-1 ) is one of several murine noroviruses isolated from research mouse facilities and has been used as a model of human norovirus infection . MNV-1 infection has been shown to requi...	Gastroenteritis is a common disease in both developed and developing countries . The two main causes of this affliction are bacteria and viruses . The primary viruses implicated in gastroenteritis have been shown to be noroviruses , which include Norwalk virus , notorious for numerous recent outbreaks on cruise ships ....	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/viral", "infections", "immunology/immunity", "to", "infections", "immunology/innate", "immunity" ]	2008	MDA-5 Recognition of a Murine Norovirus
In higher eukaryotes , messenger RNAs ( mRNAs ) are exported from the nucleus to the cytoplasm via factors deposited near the 5′ end of the transcript during splicing . The signal sequence coding region ( SSCR ) can support an alternative mRNA export ( ALREX ) pathway that does not require splicing . However , most SSC...	The function and evolution of introns have been topics of great interest since introns were discovered in the 1970s . Introns that interrupt protein-coding regions have the most obvious potential to affect coding sequences and their evolution , and they have therefore been studied most intensively . However , about one...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/sequence", "motif", "analysis", "genetics", "and", "genomics/functional", "genomics", "molecular", "biology/bioinformatics", "molecular", "biology/mrna", "transport", "and", "localization", "computational", "biology/genomics", "genetics", "and", "genom...	2011	Genome Analysis Reveals Interplay between 5′UTR Introns and Nuclear mRNA Export for Secretory and Mitochondrial Genes
Dengue is one of the most important arboviral diseases caused by infection of four serotypes of dengue virus ( DEN ) . We found that activation of interferon regulatory factor 3 ( IRF3 ) triggered by viral infection and by foreign DNA and RNA stimulation was blocked by DEN-encoded NS2B3 through a protease-dependent mec...	The pathogenesis of severe dengue diseases remains unclear , but magnitude of dengue virus ( DEN ) replication is believed to be one of the major determining factors . Thus , revealing how DEN evades the host defense mechanism such as type I interferon ( IFN ) system is important for better understanding this devastati...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "immunology", "biology", "microbiology" ]	2012	Dengue Virus Targets the Adaptor Protein MITA to Subvert Host Innate Immunity
Stress-induced changes of gene expression are crucial for survival of eukaryotic cells . Regulation at the level of translation provides the necessary plasticity for immediate changes of cellular activities and protein levels . In this study , we demonstrate that exposure to oxidative stress results in a quick repressi...	Adequate reprogramming of metabolic activities by environmental stress or suboptimal growth conditions is crucial for cell survival . Cells employ a remarkable diversity of processes to maintain its homeostasis at all levels of gene expression , including chromatin remodeling , mRNA expression and degradation , transla...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Reversible and Rapid Transfer-RNA Deactivation as a Mechanism of Translational Repression in Stress
Poxviruses encode a large variety of proteins that mimic , block or enhance host cell signaling pathways on their own benefit . It has been reported that mitogen-activated protein kinases ( MAPKs ) are specifically upregulated during vaccinia virus ( VACV ) infection . Here , we have evaluated the role of the MAPK nega...	Phosphorylation is a post-translational modification that is highly conserved throughout the animal kingdom . Viruses have evolved to acquire their own kinases and phosphatases and to be able to modulate host phosphorylation mechanisms on their benefit . DUSP1 is an early induced gene that belongs to the superfamily of...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2013	Involvement of the Cellular Phosphatase DUSP1 in Vaccinia Virus Infection
Sex determination is remarkably dynamic; many taxa display shifts in the location of sex-determining loci or the evolution of entirely new sex-determining systems . Predominant theories for why we observe such transitions generally conclude that novel sex-determining systems are favoured by selection if they equalise t...	Systems of sex determination are strikingly diverse and labile in many clades . This poses the question: what drives transitions between sex-determining systems ? Here , we use models to derive conditions under which new sex-determining systems spread . Prevailing views suggest that new sex-determining systems are favo...	[ "Abstract", "Introduction", "Results", "Discussion", "Conclusion" ]	[ "medicine", "and", "health", "sciences", "genetic", "diseases", "alleles", "genetic", "mapping", "developmental", "biology", "population", "biology", "morphogenesis", "autosomal", "recessive", "diseases", "inherited", "metabolic", "disorders", "glycogen", "storage", "dise...	2018	Haploid selection, sex ratio bias, and transitions between sex-determining systems
A central question in neuroscience is to understand how noisy firing patterns are used to transmit information . Because neural spiking is noisy , spiking patterns are often quantified via pairwise correlations , or the probability that two cells will spike coincidentally , above and beyond their baseline firing rate ....	A central question in neuroscience is to understand how noisy firing patterns are used to transmit information . We quantify spiking patterns by using pairwise correlations , or the probability that two cells will spike coincidentally , above and beyond their baseline firing rate . One observation frequently made in ex...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "action", "potentials", "medicine", "and", "health", "sciences", "neural", "networks", "membrane", "potential", "electrophysiology", "neuroscience", "mathematics", "statistics", "(mathematics)", "network", "analysis", "computational", "neuroscience", "coding", "mechanisms", ...	2017	When do correlations increase with firing rates in recurrent networks?
Purpureocillium lilacinum of Ophiocordycipitaceae is one of the most promising and commercialized agents for controlling plant parasitic nematodes , as well as other insects and plant pathogens . However , how the fungus functions at the molecular level remains unknown . Here , we sequenced two isolates ( PLBJ-1 and PL...	Purpureocillium lilacinum , a well-known bio-control agent against various plant pathogens in agriculture , can produce antibiotic leucinostatins—peptaibiotic with extensive biological activities , including antimalarial , antiviral , antibacterial , antifungal , and antitumor activities , as well as phytotoxic . We ha...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "fungal", "genetics", "computational", "biology", "parasitic", "diseases", "nematode", "infections", "fungi", "plant", "science", "phylogenetic", "analysis", "genome", "analysis", "plant", "pathology", "molecular", "biology", "te...	2016	Biosynthesis of Antibiotic Leucinostatins in Bio-control Fungus Purpureocillium lilacinum and Their Inhibition on Phytophthora Revealed by Genome Mining
The persistence of a spatially structured population is determined by the rate of dispersal among habitat patches . If the local dynamic at the subpopulation level is extinction-prone , the system viability is maximal at intermediate connectivity where recolonization is allowed , but full synchronization that enables c...	No one can produce all his needs by himself . Personal autarky poses a serious danger of collapse in cases of illness , drought , etc . Trade reduces the impact of local catastrophes , thus increasing economic stability . However , the recent series of econo-crises revealed that globalization induces coherence among ma...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "ecology/conservation", "and", "restoration", "ecology", "ecology/community", "ecology", "and", "biodiversity", "ecology/spatial", "and", "landscape", "ecology", "ecology/theoretical", "ecology", "ecology/population", "ecology", "ecology/ecosystem", "ecology" ]	2010	Optimizing Metapopulation Sustainability through a Checkerboard Strategy
Local field potentials ( LFPs ) are widely used to study the function of local networks in the brain . They are also closely correlated with the blood-oxygen-level-dependent signal , the predominant contrast mechanism in functional magnetic resonance imaging . We developed a new laminar cortex model ( LCM ) to simulate...	Local field potentials ( LFPs ) are low-frequency fluctuations of the electric fields produced by the brain . They have been widely studied to understand brain function and activity . LFPs reflect the activity of neurons within a few square millimeters of the cerebral cortex , an area containing more than 10 , 000 neur...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "circuit", "models", "computational", "neuroscience", "biology", "computational", "biology", "sensory", "systems", "neuroscience" ]	2012	The Laminar Cortex Model: A New Continuum Cortex Model Incorporating Laminar Architecture
Bacterial cyclic glucans are glucose polymers that concentrate within the periplasm of alpha-proteobacteria . These molecules are necessary to maintain the homeostasis of the cell envelope by contributing to the osmolarity of Gram negative bacteria . Here , we demonstrate that Brucella β 1 , 2 cyclic glucans are potent...	Vaccination is one of the key strategies to fight against infectious diseases though numerous diseases remain without appropriate vaccines . The challenge is to generate potent vaccines capable of inducing long-lasting immunity in humans . Successful vaccines include adjuvants that enhance and appropriately skew the im...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "humoral", "immunity", "immune", "cells", "cytokines", "immune", "activation", "antigen-presenting", "cells", "immunity", "to", "infections", "immunology", "microbiology", "host-pathogen", "interaction", "adaptive", "immunity", "immunomodulation", "bacterial", "pathogens", ...	2012	Brucella β 1,2 Cyclic Glucan Is an Activator of Human and Mouse Dendritic Cells
Outer membrane vesicles are nano-sized microvesicles shed from the outer membrane of Gram-negative bacteria and play important roles in immune priming and disease pathogenesis . However , our current mechanistic understanding of vesicle-host cell interactions is limited by a lack of methods to study the rapid kinetics ...	All Gram negative species of bacteria , including those that cause significant disease , release small vesicles from their cell membrane . These vesicles deliver toxins and other virulence factors to host cells during infection . Current methods for studying host cell entry are limited due to the nanometer size and rap...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "vesicles", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "hela", "cells", "enzymes", "pathogens", "cell", "processes", "biological", "cultures", "microbiology"...	2017	Lipopolysaccharide structure impacts the entry kinetics of bacterial outer membrane vesicles into host cells
Understanding the mechanisms that generate complex host-parasite interactions , and how they contribute to variation between and within hosts , is important for predicting risk of infection and transmission , and for developing more effective interventions based on parasite properties . We used the T . retortaeformis (...	Host-parasite interactions frequently lead to complex dynamics of infection that can be difficult to explain when parasite data are not accurate or complete , which is often the case in natural systems . We used the helminth-rabbit study case and developed a state-space mathematical model to capture the variation in in...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "helminths", "vertebrates", "rabbits", "parasitic", "diseases", "animals", "mammals", "animal", "models", "physiological", "processes", "developmental", "biology", "experimental", "organism", "systems", "population",...	2018	Changes in parasite traits, rather than intensity, affect the dynamics of infection under external perturbation
HIV controllers are rare individuals who spontaneously control HIV replication in the absence of antiretroviral treatment . Emerging evidence indicates that HIV control is mediated through very active cellular immune responses , though how such responses can persist over time without immune exhaustion is not yet unders...	HIV infection , if left untreated , leads to the progressive disruption of the immune system , the destruction of the CD4+ T cell population , and the occurrence of multiple opportunistic infections . However , a small fraction of HIV-infected individuals ( less than 1% ) avoid these deleterious effects by spontaneousl...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/antigen", "processing", "and", "recognition", "virology/immunodeficiency", "viruses", "infectious", "diseases/hiv", "infection", "and", "aids", "immunology/immunity", "to", "infections", "virology/host", "antiviral", "responses" ]	2010	HIV Controller CD4+ T Cells Respond to Minimal Amounts of Gag Antigen Due to High TCR Avidity
The retinal pigment epithelium ( RPE ) is a specialized monolayer of pigmented cells within the eye that is critical for maintaining visual system function . Diseases affecting the RPE have dire consequences for vision , and the most prevalent of these is atrophic ( dry ) age-related macular degeneration ( AMD ) , whic...	Diseases resulting in retinal pigment epithelium ( RPE ) degeneration are among the leading causes of blindness worldwide , and no therapy exists that can replace RPE or restore lost vision . One intriguing possibility is the development of therapies focused on stimulating endogenous RPE regeneration . For this to be p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "death", "neurobiology", "of", "disease", "and", "regeneration", "medicine", "and", "health", "sciences", "fish", "cell", "processes", "ocular", "anatomy", "social", "sciences", "vertebrates", "neuroscience", "animals", "cell", "differentiation", "animal", "mo...	2019	Regeneration of the zebrafish retinal pigment epithelium after widespread genetic ablation
The orphan , atypical response regulators BldM and WhiI each play critical roles in Streptomyces differentiation . BldM is required for the formation of aerial hyphae , and WhiI is required for the differentiation of these reproductive structures into mature spores . To gain insight into BldM function , we defined the ...	Two-component signal transduction systems are a primary means of regulating gene expression in bacteria . Recognizing the diversity of mechanisms associated with these systems is therefore critical to understanding the full signaling potential of bacterial cells . We have analyzed the behavior of two orphan , atypical ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "signal", "transduction", "transcriptional", "signaling", "transcription", "activators", "cell", "biology", "proteins", "mechanisms", "of", "signal", "transduction", "transcription", "factors", "gene", "expression", "genetics", "regulatory", "proteins", "bio...	2014	Response Regulator Heterodimer Formation Controls a Key Stage in Streptomyces Development
Schistosoma flatworm parasites cause schistosomiasis , a chronic and debilitating disease of poverty in developing countries . Praziquantel is employed for treatment and disease control . However , its efficacy spectrum is incomplete ( less active or inactive against immature stages of the parasite ) and there is a con...	Just one drug is available to treat schistosomiasis , a parasitic disease that affects hundreds of millions of people in developing countries . In the search for new drugs and drug targets , therefore , we have been interested in the schistosome version of human polo-like kinase ( huPLK ) 1 , an enzyme with critical fu...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2016	Structure-Bioactivity Relationship for Benzimidazole Thiophene Inhibitors of Polo-Like Kinase 1 (PLK1), a Potential Drug Target in Schistosoma mansoni
Extrachromosomal DNA amplification is frequent in the protozoan parasite Leishmania selected for drug resistance . The extrachromosomal amplified DNA is either circular or linear , and is formed at the level of direct or inverted homologous repeated sequences that abound in the Leishmania genome . The RAD51 recombinase...	Extrachromosomal DNA amplification is frequent in the human protozoan parasite Leishmania when challenged with drug or other stressful conditions . DNA amplicons , either circular or linear , are formed by recombination between direct or inverted repeats spread throughout the genome of the parasite . The recombinase RA...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "medicine", "and", "health", "sciences", "biology", "and", "life", "sciences", "tropical", "diseases", "parasitic", "diseases", "parasitology" ]	2014	Formation of Linear Amplicons with Inverted Duplications in Leishmania Requires the MRE11 Nuclease
Relative contribution of these infections on anemia in pregnancy is not certain . While measures to protect pregnant women against malaria have been scaling up , interventions against helminthes have received much less attention . In this study , we determine the relative impact of helminthes and malaria on maternal an...	International guidelines recommend routine prevention and treatments which are safe and effective during pregnancy to reduce hookworm , malaria and other infections among pregnant women living in geographic areas where these infections are prevalent . Despite their effectiveness , programs to address common infections ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "hookworm", "infection", "parasitic", "diseases", "helminth", "infection" ]	2014	The Association of Parasitic Infections in Pregnancy and Maternal and Fetal Anemia: A Cohort Study in Coastal Kenya
The composition of the gut microbiome in industrialized populations differs from those living traditional lifestyles . However , it has been difficult to separate the contributions of human genetic and geographic factors from lifestyle . Whether shifts away from the foraging lifestyle that characterize much of humanity...	Although much of humanity’s history has been spent foraging in the forests , the advent of agriculture approximately 10 , 000 years ago and industrialization approximately 250 years ago mark major shifts in human lifestyle . Several studies have investigated the effect of industrialization on the human gut microbiome—a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "water", "resources", "gut", "bacteria", "microbiome", "surface", "water", "microbiology", "social", "sciences", "diet", "ethnicities", "animal", "behavior", "nutrition", "zoology", ...	2018	Gut microbiome transition across a lifestyle gradient in Himalaya
Maintenance of cellular size is a fundamental systems level process that requires balancing of cell growth with proliferation . This is achieved via the cell division cycle , which is driven by the sequential accumulation and destruction of cyclins . The regulatory network around these cyclins , particularly in G1 , ha...	The size between different organisms ranges considerably , yet , the size of the individuals and even the same types of cells within the individuals are remarkably constant . Cell size emerges from the balance between how fast the cell grows and the frequency with which it divides . This system level coordination of gr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Bud-Localization of CLB2 mRNA Can Constitute a Growth Rate Dependent Daughter Sizer
Blood flukes ( Schistosoma spp . ) are parasites that can survive for years or decades in the vasculature of permissive mammalian hosts , including humans . Proteolytic enzymes ( proteases ) are crucial for successful parasitism , including aspects of invasion , maturation and reproduction . Most attention has focused ...	Schistosomes are blood flukes that live in the blood system and cause chronic and debilitating infection in hundreds of millions of people . Proteolytic enzymes ( proteases ) produced by the parasite allow it to survive and reproduce . We focused on understanding the repertoire of trypsin- and chymotrypsin-like Schisto...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biochemistry", "hydrolases", "enzymes", "biology", "and", "life", "sciences", "enzymology", "microbiology", "parasitology" ]	2014	Trypsin- and Chymotrypsin-Like Serine Proteases in Schistosoma mansoni – ‘The Undiscovered Country’
Leprosy elimination defined as a registered prevalence rate of less than 1 case per 10 , 000 persons was achieved in Kenya at the national level in 1989 . However , there are still pockets of leprosy in some counties where late diagnosis and consequent physical disability persist . The epidemiology of leprosy in Kenya ...	Leprosy is a chronic bacterial disease that mainly affects the nerves . If untreated , it may cause progressive and permanent damage to the skin , nerves , limbs , and eyes leading to physical disability . Through use of a combination of drugs , Kenya was able to declare the disease as eliminated in the year 1989 . How...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "statistics", "tropical", "diseases", "geographical", "locations", "health", "care", "bacterial", "diseases", "chi", "square", "tests", "mathematics", "aquatic", "environments", "bod...	2019	The spatial epidemiology of leprosy in Kenya: A retrospective study
The life long relationship between herpes simplex virus and its host hinges on the ability of the virus to aggressively replicate in epithelial cells at the site of infection and transport into the nervous system through axons innervating the infection site . Interaction between the virus and the sensory neuron represe...	Herpes simplex virus remains a significant human pathogen associated with extensive acute and chronic disease in humans worldwide . The virus invades the peripheral and central nervous systems where it replicates but also establishes life-long latent infections in neurons . Two distinct viral transcriptional programs s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "microbiology", "neuroscience", "protein", "expression", "eye", "diseases", "molecular", "biology", "techniques", "mammalian", "genomics", "eyes", "research", "and", "analysis", "methods", "animal", "cells", "biological", "tissue...	2016	De Novo Herpes Simplex Virus VP16 Expression Gates a Dynamic Programmatic Transition and Sets the Latent/Lytic Balance during Acute Infection in Trigeminal Ganglia
More than 100 years after Grigg’s influential analysis of species’ borders , the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity . The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to...	The flow of genetic diversity across environments has conflicting effects . On the beneficial side , it increases the genetic variation that is necessary for adaptation and counters the loss of genetic diversity due to genetic drift . However , it may also swamp adaptation to local conditions . This interplay is crucia...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "population", "metrics", "genetic", "load", "heredity", "genetics", "biology", "and", "life", "sciences", "population", "genetics", "population", "biology", "evolutionary", "adaptation", "evolutionary", "biology", "gene", "flow", "evolutionary", "processes", "genetic", ...	2018	Is the sky the limit? On the expansion threshold of a species’ range
Periplasmic binding proteins ( PBPs ) in association with ABC transporters select and import a wide variety of ligands into bacterial cytoplasm . They can also take up toxic molecules , as observed in the case of the phytopathogen Agrobacterium tumefaciens strain C58 . This organism contains a PBP called AccA that medi...	We succeeded in understanding how the periplasmic protein AccA from the pathogen A . tumefaciens can bind both the plant compound agrocinopine and the antibiotic agrocin 84 . Whereas agrocinopine acts as a nutrient and regulatory signal in A . tumefaciens , agrocin 84 is lethal once degraded by the enzyme AccF into a t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	A Pyranose-2-Phosphate Motif Is Responsible for Both Antibiotic Import and Quorum-Sensing Regulation in Agrobacterium tumefaciens
Quiescent CD4+ T cells restrict human immunodeficiency virus type 1 ( HIV-1 ) infection at early steps of virus replication . Low levels of both deoxyribonucleotide triphosphates ( dNTPs ) and the biosynthetic enzymes required for their de novo synthesis provide one barrier to infection . CD4+ T cell activation induces...	Replication of all human viruses depends on building blocks derived from the metabolic pathways of the infected host cell . The production of progeny virions requires synthesis of viral nucleic acids from deoxyribonucleotide triphosphates ( dNTPs ) . HIV-1 infection in resting T cells is limited , at least in part , be...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Phospholipase D1 Couples CD4+ T Cell Activation to c-Myc-Dependent Deoxyribonucleotide Pool Expansion and HIV-1 Replication
Robust methods for identifying patterns of expression in genome-wide data are important for generating hypotheses regarding gene function . To this end , several analytic methods have been developed for detecting periodic patterns . We improve one such method , JTK_CYCLE , by explicitly calculating the null distributio...	Much biomedical research focuses on how the expression of genes changes over time . Many genes’ activities vary periodically . For example , circadian rhythms repeat daily with the light-dark cycle . Understanding how such rhythms couple to biological processes requires statistical methods that can identify cycling tim...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Improved Statistical Methods Enable Greater Sensitivity in Rhythm Detection for Genome-Wide Data
Arenaviruses are one of the largest families of human hemorrhagic fever viruses and are known to infect both mammals and snakes . Arenaviruses package a large ( L ) and small ( S ) genome segment in their virions . For segmented RNA viruses like these , novel genotypes can be generated through mutation , recombination ...	The facility with which viruses evolve underlies many of the problems they cause . Virus evolution is the reason we need a new flu vaccine each year . It’s how HIV and other viruses develop drug resistance . And it enables viruses to occasionally jump from animals to humans and cause new diseases . It is therefore impo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Widespread Recombination, Reassortment, and Transmission of Unbalanced Compound Viral Genotypes in Natural Arenavirus Infections
Amyloids are ordered protein aggregates that are typically associated with neurodegenerative diseases and cognitive impairment . By contrast , the amyloid-like state of the neuronal RNA binding protein Orb2 in Drosophila was recently implicated in memory consolidation , but it remains unclear what features of this func...	Amyloids are ordered protein aggregates typically associated with neurodegenerative diseases , such as Alzheimer disease and Parkinson disease , which usually result in cognitive impairment . However , the amyloid state of the neuronal RNA binding protein Orb2 shows a quite opposite behaviour: instead of impairment , i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "microinjection", "enzymes", "enzymology", "neuroscience", "learning", "and", "memory", "animals", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "immunoprecipitation", "materials", "science", "cognition", "memory", "molecular", "bi...	2016	Molecular Basis of Orb2 Amyloidogenesis and Blockade of Memory Consolidation
Small RNAs called PIWI -interacting RNAs ( piRNAs ) are essential for transposon control and fertility in animals . Primary processing is the small RNA biogenesis pathway that uses long single-stranded RNA precursors to generate millions of individual piRNAs , but the molecular mechanisms that identify a transcript as ...	PIWI-interacting RNAs ( piRNAs ) are 24–30 nucleotide ( nt ) small RNAs that are exclusively expressed in animal germlines and are essential for suppression of transposable elements or ‘jumping genes’ . Millions of piRNAs are produced from single-stranded transcripts that arise from large RNA polymerase II transcriptio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "reproductive", "system", "enzymes", "annealing", "(genetics)", "enzymology", "precursor", "cells", "animals", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "immunoprecipitation", "rna", "...	2017	Recruitment of Armitage and Yb to a transcript triggers its phased processing into primary piRNAs in Drosophila ovaries
Linear mixed effect models are powerful tools used to account for population structure in genome-wide association studies ( GWASs ) and estimate the genetic architecture of complex traits . However , fully-specified models are computationally demanding and common simplifications often lead to reduced power or biased in...	The goal of quantitative genetics is to characterize the relationship between genetic variation and variation in quantitative traits such as height , productivity , or disease susceptibility . A statistical method known as the linear mixed effect model has been critical to the development of quantitative genetics . Fir...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome-wide", "association", "studies", "statistics", "applied", "mathematics", "brassica", "random", "variables", "mathematical", "models", "covariance", "simulation", "and", "modeling", "algorithms", "model", "organisms", "mathematics", "test", "statistics", "genome", ...	2019	Fast and flexible linear mixed models for genome-wide genetics
The global prevalence of malaria has decreased over the past fifteen years , but similar gains have not been realized against Plasmodium vivax because this species is less responsive to conventional malaria control interventions aimed principally at P . falciparum . Approximately half of all malaria cases outside of Af...	Plasmodium vivax is the second most prevalent Plasmodium species amongst the five that can infect humans and cause malaria . The control and elimination of P . vivax is complicated by its specific biology , such as hard-to-detect low densities of blood-circulating parasites in infected individuals , the existence of pe...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "parasite", "groups", "medicine", "and", "health", "sciences", "body", "fluids", "plasmodium", "tropical", "diseases", "plasmodium", "falciparum", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "apicomplexa", "protozoans", "infectious", "disease", "co...	2017	Defining the next generation of Plasmodium vivax diagnostic tests for control and elimination: Target product profiles
Differentiation of hyphae into specialized infection structures , known as appressoria , is a common feature of plant pathogenic fungi that penetrate the plant cuticle . Appressorium formation in U . maydis is triggered by environmental signals but the molecular mechanism of this hyphal differentiation is largely unkno...	Pathogens exhibit various developmental stages during the process of infection and proliferation . The basidiomycete Ustilago maydis is a model organism for plant pathogenic fungi . On the plant surface U . maydis grows as a cell-cycle arrested filament . Growth of infectious hyphae involves regular formation of retrac...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "model", "organisms", "genetics", "biology", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2011	Septation of Infectious Hyphae Is Critical for Appressoria Formation and Virulence in the Smut Fungus Ustilago Maydis
Genetic generalised epilepsy ( GGE ) is the most common form of genetic epilepsy , accounting for 20% of all epilepsies . Genomic copy number variations ( CNVs ) constitute important genetic risk factors of common GGE syndromes . In our present genome-wide burden analysis , large ( ≥ 400 kb ) and rare ( < 1% ) autosoma...	Epilepsy affects about 4% of the general population during lifetime . The genetic generalised epilepsies ( GGEs ) represent the most common group of epilepsies with predominant genetic aetiology , accounting for 20% of all epilepsies . Despite their strong heritability , the genetic basis of the majority of patients wi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Burden Analysis of Rare Microdeletions Suggests a Strong Impact of Neurodevelopmental Genes in Genetic Generalised Epilepsies
African trypanosome procyclic forms multiply in the midgut of tsetse flies , and are routinely cultured at 27°C . Heat shocks of 37°C and above result in general inhibition of translation , and severe heat shock ( 41°C ) results in sequestration of mRNA in granules . The mRNAs that are bound by the zinc-finger protein ...	When trypanosomes are inside tsetse flies , they have to cope with temperature variations from below 20°C up to 37°C , due to diurnal variations and periodic intake of warm blood . In the laboratory , procyclic forms ( the form that multiplies in the midgut ) , are routinely cultured at 27°C . When procyclic forms are ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "sequencing", "techniques", "rna-binding", "proteins", "cellular", "stress", "responses", "medicine", "and", "health", "sciences", "messenger", "rna", "cell", "processes", "polyribosomes", "chaperone", "proteins", "sequence", "motif", "analysis", "molecular", "biology", ...	2016	Translation Regulation and RNA Granule Formation after Heat Shock of Procyclic Form Trypanosoma brucei: Many Heat-Induced mRNAs Are also Increased during Differentiation to Mammalian-Infective Forms
Lytic gammaherpesvirus ( GHV ) replication facilitates the establishment of lifelong latent infection , which places the infected host at risk for numerous cancers . As obligate intracellular parasites , GHVs must control and usurp cellular signaling pathways in order to successfully replicate , disseminate to stable l...	Systems-level evaluations of infection-related changes to host phosphoprotein networks are not currently available for any gammaherpesvirus ( GHV ) . Here we describe a quantitative phosphoproteomic analysis of productive GHV replication that demonstrates alterations in the phosphorylation status of more than 80% of ho...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Phosphoproteomic Analyses Reveal Signaling Pathways That Facilitate Lytic Gammaherpesvirus Replication
Chikungunya is an emerging public health problem in tropical and subtropical regions , due to ongoing transmission and its incapacitating acute disease phase , and chronic sequelae . The disease is responsible for a major impact on Health Related Quality of Life ( HRQoL ) , which may last several years . To our knowled...	Chikungunya is a disease caused by a virus , which is transmitted by mosquitoes . During the past years , major outbreaks of chikungunya have occurred in the Americas . Normally , chikungunya presents with an acute , fever-like disease . After acute disease , many people develop chronic disease manifestations , which a...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "physicians", "medical", "doctors", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "behavioral", "and", "social", "aspects", "of", "health", "medical", "personnel", "pathogens", "tropical...	2017	Health-related impact on quality of life and coping strategies for chikungunya: A qualitative study in Curaçao
The identification of functionally important residues is an important challenge for understanding the molecular mechanisms of proteins . Membrane protein transporters operate two-state allosteric conformational changes using functionally important cooperative residues that mediate long-range communication from the subs...	Major Facilitator Superfamily ( MFS ) transporters are one of the largest families of membrane protein transporters and are ubiquitous to all three kingdoms of life . Structural studies of MFS transporters have revealed that the members of this superfamily share structural homology; however , due to weak sequence simil...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/sequence", "motif", "analysis", "molecular", "biology/bioinformatics", "computational", "biology/macromolecular", "sequence", "analysis", "evolutionary", "biology/bioinformatics", "biophysics/membrane", "proteins", "and", "energy", "transduction" ]	2009	Integration of Evolutionary Features for the Identification of Functionally Important Residues in Major Facilitator Superfamily Transporters
The principal objective of this study was to assess a modeling approach to Lu . longipalpis distribution in an urban scenario , discriminating micro-scale landscape variables at microhabitat and macrohabitat scales and the presence from the abundance of the vector . For this objective , we studied vectors and domestic ...	Visceral leishmaniasis in America is caused by an unicellular organism , Leishmania infantum ( syn . chagasi ) that is transmitted by insects belonging to Diptera:Phlebotominae , Lutzomyia longipalpis being the principal vector in urban areas . Therefore , the prevention and control of this vector is a sound objective ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Lutzomyia longipalpis Presence and Abundance Distribution at Different Micro-spatial Scales in an Urban Scenario
The adipocyte-derived protein adiponectin is highly heritable and inversely associated with risk of type 2 diabetes mellitus ( T2D ) and coronary heart disease ( CHD ) . We meta-analyzed 3 genome-wide association studies for circulating adiponectin levels ( n = 8 , 531 ) and sought validation of the lead single nucleot...	Through a meta-analysis of genome-wide association studies of 14 , 733 individuals , we identified common base-pair variants in the genome which influence circulating adiponectin levels . Since adiponectin is an adipocyte-derived circulating protein which has been inversely associated with risk of obesity-related disea...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cardiovascular", "disorders/congenital", "heart", "disease", "diabetes", "and", "endocrinology/obesity", "genetics", "and", "genomics/genetics", "of", "disease", "diabetes", "and", "endocrinology/type", "2", "diabetes" ]	2009	A Genome-Wide Association Study Reveals Variants in ARL15 that Influence Adiponectin Levels
In many animal species , the sperm DNA is packaged with male germ line–specific chromosomal proteins , including protamines . At fertilization , these non-histone proteins are removed from the decondensing sperm nucleus and replaced with maternally provided histones to form the DNA replication competent male pronucleus...	Chromatin is composed of basic units called nucleosomes , in which DNA wraps around a core of histone proteins . HIRA is a histone chaperone that is specifically involved in the assembly of nucleosomes containing H3 . 3 , a universally conserved type of histone 3 . To understand the function of HIRA in vivo , the autho...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "drosophila", "genetics", "and", "genomics", "developmental", "biology", "molecular", "biology" ]	2007	The Essential Role of Drosophila HIRA for De Novo Assembly of Paternal Chromatin at Fertilization
Cytotoxic T lymphocytes ( CTL ) are a major factor in the control of HIV replication . CTL arise in acute infection , causing escape mutations to spread rapidly through the population of infected cells . As a result , the virus develops partial resistance to the immune response . The factors controlling the order of mu...	Like many viruses , HIV has evolved mechanisms to evade the host immune response . As early as a few weeks after infection is initiated , mutations appear in the viral genome that reduce the ability of cytotoxic T lymphocytes ( CTL ) to control virus replication . However , of the many mutations in the viral genome tha...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "population", "modeling", "evolutionary", "modeling", "biology", "and", "life", "sciences", "infectious", "disease", "modeling", "computational", "biology" ]	2014	The Route of HIV Escape from Immune Response Targeting Multiple Sites Is Determined by the Cost-Benefit Tradeoff of Escape Mutations
Human cystic echinococcosis ( CE ) , caused by the larval stage of Echinococcus granulosus , with the liver as the most frequently affected organ , is known to be highly endemic in Tibetan communities of northwest Sichuan Province . Antiparasitic treatment with albendazole remains the primary choice for the great major...	Cystic echinococcosis is a serious public health problem in Tibetan communities of northwest Sichuan Province , China . Antiparasitic treatment with albendazole remains the only choice in most cases , due to the poor socio-economy and inadequate hospital facilities in this area . A post-treatment follow-up study was ca...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "diagnostic", "radiology", "clinical", "research", "design", "drugs", "and", "devices", "immunology", "parasitic", "diseases", "pharmacodynamics", "neglected", "tropical", "diseases", "pharmacology", "radiology", "ult...	2011	Post-Treatment Follow-Up Study of Abdominal Cystic Echinococcosis in Tibetan Communities of Northwest Sichuan Province, China
Strongyloidiasis is a much-neglected but sometimes fatal soil born helminthiasis . The causing agent , the small intestinal parasitic nematode Strongyloides stercoralis can reproduce sexually through the indirect/heterogonic life cycle , or asexually through the auto-infective or the direct/homogonic life cycles . Usua...	The vast majority of multicellular organisms reproduce sexually . Sexual reproduction is believed to be advantageous because meiotic recombination separates beneficial and deleterious mutations and generates new , possibly better allele combinations . However , sexual reproduction comes at a cost . Beneficial allele co...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "taxonomy", "invertebrates", "heterozygosity", "helminths", "hookworms", "animals", "genetic", "mapping", "parasitology", "necator", "americanus", "developmental", "biology", "phylogenetics", "data", "management", "phylogenetic", "analysis", "strongyloides", "stercoralis", "r...	2019	Characterization of a non-sexual population of Strongyloides stercoralis with hybrid 18S rDNA haplotypes in Guangxi, Southern China
A central issue in developmental biology is to uncover the mechanisms by which stem cells maintain their capacity to regenerate , yet at the same time produce daughter cells that differentiate and attain their ultimate fate as a functional part of a tissue or an organ . In this paper we propose that , during developmen...	The emergence of tumors results from altered cell differentiation and proliferation during organ and tissue development . Understanding how such altered or normal patterns are established is still a challenge . Molecular genetic approaches to understanding pattern formation have searched for key central genetic control...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "biology" ]	2013	Cell Patterns Emerge from Coupled Chemical and Physical Fields with Cell Proliferation Dynamics: The Arabidopsis thaliana Root as a Study System
Vaccination with plasmid DNA encoding Ag85A from M . bovis BCG can partially protect C57BL/6 mice against a subsequent footpad challenge with M . ulcerans . Unfortunately , this cross-reactive protection is insufficient to completely control the infection . Although genes encoding Ag85A from M . bovis BCG ( identical t...	Buruli ulcer ( BU ) is an infectious disease characterized by deep , ulcerating skin lesions , particularly on arms and legs , that are provoked by a toxin . BU is caused by a microbe belonging to the same family that also causes tuberculosis and leprosy . The disease is emerging as a serious health problem , especiall...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases" ]	2008	Improved Protective Efficacy of a Species-Specific DNA Vaccine Encoding Mycolyl-Transferase Ag85A from Mycobacterium ulcerans by Homologous Protein Boosting
Thermoanaerobic bacteria are of interest in cellulosic-biofuel production , due to their simultaneous pentose and hexose utilization ( co-utilization ) and thermophilic nature . In this study , we experimentally reconstructed the structure and dynamics of the first genome-wide carbon utilization network of thermoanaero...	Renewable liquid fuels derived from lignocellulosic biomass could alleviate global energy shortage and climate change . Cellulose and hemicellulose are the main components of lignocellulosic biomass . Therefore , the ability to simultaneously utilize pentose and hexose ( i . e . , co-utilization ) has been a crucial ch...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "biology", "microbiology", "genetics", "and", "genomics" ]	2011	The Thermoanaerobacter Glycobiome Reveals Mechanisms of Pentose and Hexose Co-Utilization in Bacteria
Advances in reporters for gene expression have made it possible to document and quantify expression patterns in 2D–4D . In contrast to microarrays , which provide data for many genes but averaged and/or at low resolution , images reveal the high spatial dynamics of gene expression . Developing computational methods to ...	High throughput image acquisition is a quickly increasing new source of data for problems in computational biology , such as phenotypic screens . Given the very diverse nature of imaging technology , samples , and biological questions , approaches are oftentimes very tailored and ad hoc to a specific data set . In part...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "expression", "analysis", "functional", "genomics", "dna", "transcription", "gene", "function", "developmental", "biology", "genome", "analysis", "tools", "embryology", "gene", "expression", "regulatory", "networks", "biology", "transcriptomes", "computer", "sci...	2011	Automatic Annotation of Spatial Expression Patterns via Sparse Bayesian Factor Models
Reevaluation of treatment guidelines for Old and New World leishmaniasis is urgently needed on a global basis because treatment failure is an increasing problem . Drug resistance is a fundamental determinant of treatment failure , although other factors also contribute to this phenomenon , including the global HIV/AIDS...	Chemotherapy is central to the control and management of leishmaniasis . Antimonials remain the primary drugs against different forms of leishmaniasis in several regions . However , resistance to antimony has necessitated the use of alternative medications , especially in the Indian subcontinent ( ISC ) . Compounds , n...	[ "Abstract", "Introduction", "TF", "beyond", "DR", "What", "do", "we", "mean", "by", "the", "term", "“drug", "resistance”?", "Molecular", "mechanisms", "of", "DR", "to", "antimonials", "Molecular", "epidemiology", "of", "DR", "in", "Molecular", "mechanisms", "of"...	[ "medicine", "and", "health", "sciences", "tropical", "diseases", "microbiology", "parasitic", "diseases", "parasitic", "protozoans", "review", "protozoans", "leishmania", "pharmaceutics", "antimony", "neglected", "tropical", "diseases", "pharmacology", "infectious", "diseas...	2017	Drug resistance and treatment failure in leishmaniasis: A 21st century challenge
MicroRNAs ( miRNAs ) regulate gene expression posttranscriptionally by interfering with a target mRNA's translation , stability , or both . We sought to dissect the respective contributions of translational inhibition and mRNA decay to microRNA regulation . We identified direct targets of a specific miRNA , miR-124 , b...	The human genome contains directions to regulate the timing and magnitude of expression of its thousands of genes . MicroRNAs are important regulatory RNAs that tune the expression levels of tens to hundreds of specific genes by pairing to complimentary stretches in the messenger RNAs from these genes , thereby reducin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/post-translational", "regulation", "of", "gene", "expression", "molecular", "biology/rna-protein", "interactions", "genetics", "and", "genomics", "molecular", "biology/translational", "regulation" ]	2009	Concordant Regulation of Translation and mRNA Abundance for Hundreds of Targets of a Human microRNA
During muscle development , myosin and actin containing filaments assemble into the highly organized sarcomeric structure critical for muscle function . Although sarcomerogenesis clearly involves the de novo formation of actin filaments , this process remained poorly understood . Here we show that mouse and Drosophila ...	Sarcomeres , the smallest contractile units of muscle , are formed by two major filament systems , the myosin containing thick and the actin containing thin filaments . Although it is well established that sarcomerogenesis involves the formation of novel actin filaments , so far it remained largely unclear how these fi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "biochemistry", "developmental", "biology", "cellular", "structures", "drosophila", "melanogaster", "model", "organisms", "molecular", "development", "macromolecular", "assemblies", "genetics", "molecular", "genetics", "cellular", "types", "biology", "mu...	2014	DAAM Is Required for Thin Filament Formation and Sarcomerogenesis during Muscle Development in Drosophila
Dengue , the predominant arthropod-borne viral disease affecting humans , is caused by one of four distinct serotypes ( DENV-1 , -2 , -3 or -4 ) . A literature analysis and review was undertaken to describe the molecular epidemiological trends in dengue disease and the knowledge generated in specific molecular topics i...	The wide distribution of the mosquito vector and the co-circulation of multiple dengue virus serotypes has led to increases in the incidence of dengue in the Americas , where it is a major public health concern . Identifying molecular epidemiological trends may help to identify the reasons for the re-emergence of dengu...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Discussion", "Conclusion" ]	[ "biogeography", "dengue", "virus", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "pathology", "and", "laboratory", "medicine", "infectious", "disease", "epidemiology", "pathogens", "population", "genetics", "geographical", "locati...	2017	Dengue in Latin America: Systematic Review of Molecular Epidemiological Trends
Estimates of current global rabies mortality range from 26 , 000 to 59 , 000 deaths per annum . Although pre-exposure prophylaxis using inactivated rabies virus vaccines ( IRVs ) is effective , it requires two to three doses and is regarded as being too expensive and impractical for inclusion in routine childhood immun...	Rabies was , after smallpox , the second human disease for which an efficacious vaccine was developed , by Pasteur in 1885 . Although it is eminently preventable , with highly efficacious vaccines available for both humans and animals , it still causes considerable mortality in low and middle-income countries . It is a...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "tropical", "diseases", "microbiology", "viruses", "vaccines", "preventive", "medicine", "rabies", "i...	2018	A simian-adenovirus-vectored rabies vaccine suitable for thermostabilisation and clinical development for low-cost single-dose pre-exposure prophylaxis
The bacterial flagellar motor can rotate either clockwise ( CW ) or counterclockwise ( CCW ) . Three flagellar proteins , FliG , FliM , and FliN , are required for rapid switching between the CW and CCW directions . Switching is achieved by a conformational change in FliG induced by the binding of a chemotaxis signalin...	The bacterial flagellum is a rotating organelle that governs cell motility . At the base of each flagellum is a motor powered by the electrochemical potential difference of specific ions across the cytoplasmic membrane . In response to environmental stimuli , rotation of the motor switches between counterclockwise and ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biophysics/macromolecular", "assemblies", "and", "machines", "microbiology", "biophysics" ]	2011	Structural Insight into the Rotational Switching Mechanism of the Bacterial Flagellar Motor

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