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Immunoregulatory cytokine interleukin-10 ( IL-10 ) is elevated in sera from patients with systemic lupus erythematosus ( SLE ) correlating with disease activity . The established association of IL10 with SLE and other autoimmune diseases led us to fine map causal variant ( s ) and to explore underlying mechanisms . We ...	Systemic lupus erythematosus ( SLE ) , a debilitating autoimmune disease characterized by the production of pathogenic autoantibodies , has a strong genetic basis . Variants of the IL10 gene , which encodes cytokine interleukin-10 ( IL-10 ) with known function of promoting B cell hyperactivity and autoantibody producti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Preferential Binding to Elk-1 by SLE-Associated IL10 Risk Allele Upregulates IL10 Expression
Tungiasis or jigger infestation is a parasitic disease caused by the female sand flea Tunga penetrans . Secondary infection of the lesions caused by this flea is common in endemic communities . This study sought to shed light on the bacterial pathogens causing secondary infections in tungiasis lesions and their suscept...	Secondary bacterial infection of tungiaisis lesions is a threat to jigger infested patients . Once the flea penetrates the skin , it leaves an opening on the skin through which it lays eggs , defecates and breathes throughout it’s life cycle on the host . At the same time , it feeds on the host’s blood hence a direct c...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "bacteriology", "antimicrobials", "gram", "positive", "bacteria", "gram", "negative", "bacteria", "invertebrates", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "drugs", "microbiology", "animals", "staphylococcus", "au...	2017	Secondary bacterial infections and antibiotic resistance among tungiasis patients in Western, Kenya
Diarrheal diseases are among the most frequent causes of morbidity and mortality in children worldwide , especially in resource-poor areas . This case-control study assessed the associations between gastrointestinal infections and diarrhea in children from rural Ghana . Stool samples were collected from 548 children wi...	Gastrointestinal infections are frequent in many low-income countries . However , their role in diarrheal diseases is still under discussion . Many epidemiological studies focus on individuals with diarrheal symptoms only , ignoring the fact that infections may progress asymptomatically as well . In order to identify i...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Gastrointestinal Infections and Diarrheal Disease in Ghanaian Infants and Children: An Outpatient Case-Control Study
Histones package DNA and regulate epigenetic states . For the latter , probably the most important histone is H3 . Mammals have three near-identical H3 isoforms: canonical H3 . 1 and H3 . 2 , and the replication-independent variant H3 . 3 . This variant can accumulate in slowly dividing somatic cells , replacing canoni...	Histones package DNA and regulate chromosome activity . Histone H3 is particularly important in this regard . The H3 . 3 isoform is unique , among H3 histones , in being able to incorporate into chromosomes independent of DNA replication . Thus , in slowly- or non-dividing somatic cells , H3 . 3 histone can take on the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Contribution of the Two Genes Encoding Histone Variant H3.3 to Viability and Fertility in Mice
We propose a top-down approach to the symptoms of schizophrenia based on a statistical dynamical framework . We show that a reduced depth in the basins of attraction of cortical attractor states destabilizes the activity at the network level due to the constant statistical fluctuations caused by the stochastic spiking ...	One of the hallmarks of schizophrenia is the complexity and heterogeneity of the illness . We propose that part of the reason for the inconsistent symptoms may be a reduced signal-to-noise ratio and increased statistical fluctuations in different cortical brain networks . The novelty of the approach described here is t...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "spiking", "dynamics", "schizophrenia", "attractor", "networks", "neuroscience", "homo", "(human)", "neuronal", "networks" ]	2007	A Dynamical Systems Hypothesis of Schizophrenia
In trypanosomatids , gene expression is regulated mainly by post-transcriptional mechanisms , which affect mRNA processing , translation and degradation . Currently , our understanding of factors that regulate either mRNA stability or translation is rather limited . We know that often , the regulators are proteins that...	Survival and adaptation of trypanosomatids to new surroundings requires activation of specific gene networks . This is mainly achieved by post-transcriptional mechanisms , and proteins that bind to specific mRNAs , and influence degradation or translation , are known to be important . However , only few such proteins h...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "cell", "biology", "biology", "and", "life", "sciences", "proteomics", "microbiology", "molecular", "cell", "biology" ]	2014	A Genome-Wide Tethering Screen Reveals Novel Potential Post-Transcriptional Regulators in Trypanosoma brucei
Deciphering the architecture of the tRNA pool is a prime challenge in translation research , as tRNAs govern the efficiency and accuracy of the process . Towards this challenge , we created a systematic tRNA deletion library in Saccharomyces cerevisiae , aimed at dissecting the specific contribution of each tRNA gene t...	Transfer RNAs are an important component of the translation machinery . Despite extensive biochemical investigations , a systems-level investigation of tRNAs' functional roles in physiology , and genetic interactions among them , is lacking . We created a comprehensive tRNA deletion library in yeast and assessed the es...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "rna", "cellular", "stress", "responses", "model", "organisms", "molecular", "cell", "biology", "rna", "processing", "nucleic", "acids", "gene", "regulation", "genetics", "gene", "expression", "molecular", "genetics", "population", "genetics", "b...	2014	A Comprehensive tRNA Deletion Library Unravels the Genetic Architecture of the tRNA Pool
In humans and rodents , stress promotes habit-based behaviors that can interfere with action–outcome decision-making . Further , developmental stressor exposure confers long-term habit biases across rodent–primate species . Despite these homologies , mechanisms remain unclear . We first report that exposure to the prim...	Stress can impair the ability of individuals to select actions based on their consequences , promoting instead the acquisition of habits—automatic behaviors that are insensitive to action–outcome relationships . Stress in adolescence can have particularly long-lasting consequences , affecting behavior and mood regulati...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "swimming", "medicine", "and", "health", "sciences", "brain", "vertebrates", "mice", "neuroscience", "habits", "mammals", "animals", "biological", "locomotion", "animal", "behavior", "zoology", "neuronal", "dendrites", "animal", "cells", "behavior", "neostriatum", "amyg...	2017	Regulation of actions and habits by ventral hippocampal trkB and adolescent corticosteroid exposure
Yaws is endemic in Ghana . The World Health Organization ( WHO ) has launched a new global eradication campaign based on total community mass treatment with azithromycin . Achieving high coverage of mass treatment will be fundamental to the success of this new strategy; coverage is dependent , in part , on appropriate ...	Yaws , a bacterial skin infection , is endemic in Ghana . WHO has launched a campaign to eradicate yaws based on community mass treatment with the antibiotic azithromycin . Community perceptions of disease are an important contributor to participation in mass treatment interventions . This study used questionnaires to ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "dermatology", "medicine", "and", "health", "sciences", "demography", "tropical", "diseases", "geographical", "locations", "health", "care", "treponematoses", "bacterial", "diseases", "health", "care", "providers", "skin", "infections", "global", "health", "neglected", ...	2017	Knowledge, attitudes and practices towards yaws and yaws-like skin disease in Ghana
The Eastern North American monarch butterfly , Danaus plexippus , is famous for its spectacular seasonal long-distance migration . In recent years , it has also emerged as a novel system to study how animal circadian clocks keep track of time and regulate ecologically relevant daily rhythmic activities and seasonal beh...	With a rich biology that includes a clock-regulated migratory behavior and a circadian clock possessing mammalian clock orthologues , the monarch butterfly is an unconventional system with broad appeal to study circadian and seasonal rhythms . While clockwork mechanisms and rhythmic behavioral outputs have been studied...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "carbohydrate", "metabolism", "invertebrates", "gene", "regulation", "glucose", "metabolism", "animals", "dna", "transcription", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "experimental", "organism", "systems", "chronobiology", "molecular", "bio...	2019	Genome-wide discovery of the daily transcriptome, DNA regulatory elements and transcription factor occupancy in the monarch butterfly brain
Oral cholera vaccines are primarily recommended by the World Health Organization for cholera control in endemic countries . However , the number of cholera vaccines currently produced is very limited and examples of OCV use in endemic countries , and especially in urban settings , are scarce . A vaccination campaign wa...	The oral cholera vaccine , Shanchol , has already been shown as an effective tool in controlling a cholera outbreak . The limited amount of doses , concurrently with the logistic constraints associated with a targeted vaccination campaign are serious difficulties to tackle in order to organize a vaccination campaign in...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "clinical", "research", "design", "population", "dynamics", "immunology", "tropical", "diseases", "census", "vaccines", "preventive", "medicine", "bacterial", "diseases", "research", "design", "global", "health", "neglected", "tr...	2018	Highly targeted cholera vaccination campaigns in urban setting are feasible: The experience in Kalemie, Democratic Republic of Congo
Candida albicans is the most common cause of hematogenously disseminated and oropharyngeal candidiasis . Both of these diseases are characterized by fungal invasion of host cells . Previously , we have found that C . albicans hyphae invade endothelial cells and oral epithelial cells in vitro by inducing their own endoc...	The fungus Candida albicans is usually a harmless colonizer of human mucosal surfaces . In the mouth , it can cause oropharyngeal candidiasis , also called thrush . In hospitalized and immunocompromised patients , C . albicans can enter the blood stream and be carried throughout the body to cause a disseminated infecti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "infectious", "diseases", "cell", "biology", "yeast", "and", "fungi", "microbiology" ]	2007	Als3 Is a Candida albicans Invasin That Binds to Cadherins and Induces Endocytosis by Host Cells
Hepatitis C virus ( HCV ) is present in the host with multiple variants generated by its error prone RNA-dependent RNA polymerase . Little is known about the initial viral diversification and the viral life cycle processes that influence diversity . We studied the diversification of HCV during acute infection in 17 pla...	Hepatitis C virus ( HCV ) is a RNA virus that infects over 170 million people across the world . It leads to a chronic infection in the majority of people who are infected ( >70% ) . Most people only discover that they are infected long after initial infection . Thus , it is difficult to study the very early events in ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "hepatitis", "c", "medicine", "infectious", "diseases", "infectious", "hepatitis", "hepatitis", "gastroenterology", "and", "hepatology", "viral", "diseases", "infectious", "disease", "modeling", "liver", "diseases" ]	2012	Quantifying the Diversification of Hepatitis C Virus (HCV) during Primary Infection: Estimates of the In Vivo Mutation Rate
Why gene order is conserved over long evolutionary timespans remains elusive . A common interpretation is that gene order conservation might reflect the existence of functional constraints that are important for organismal performance . Alteration of the integrity of genomic regions , and therefore of those constraints...	Eukaryotic genomes have been reshaped by chromosomal rearrangements during evolution . However , the comparison of distantly related species has uncovered unusually large genomic regions with conserved gene organization . A widely accepted explanation is that , in those regions , there exist genes with joint and/or int...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genomics", "genetics", "molecular", "genetics", "biology", "evolutionary", "biology", "genetics", "and", "genomics" ]	2012	Evaluation of the Role of Functional Constraints on the Integrity of an Ultraconserved Region in the Genus Drosophila
Dengue virus ( DENV ) is an extraordinary health burden on global scale , but still lacks effective vaccine . The Philippines is endemic for dengue fever , but massive employment of insecticides favored the development of resistance mutations in its major vector , Aedes aegypti . Alternative vector control strategies c...	Dengue fever threatens the health of millions in the tropics and its causative agent , dengue virus , is mainly transmitted by the mosquito Aedes aegypti . To control the spread of the virus , insecticides have been abundantly used but Ae . aegypti has developed a genetic resistance to them . Currently , alternative me...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Human-Mediated Marine Dispersal Influences the Population Structure of Aedes aegypti in the Philippine Archipelago
Indoor residual spraying ( IRS ) of DDT is used to control visceral leishmaniasis ( VL ) in India . However , the quality of spraying is severely compromised by a lack of affordable field assays to monitor target doses of insecticide . Our aim was to develop a simple DDT insecticide quantification kit ( IQK ) for monit...	Visceral leishmaniasis ( VL ) is a major parasitic disease on the Indian Subcontinent , with 85% of the disease incidence in India . DDT is being used to control the sandfly vector of VL , but the quality of indoor residual spraying ( IRS ) is not routinely assessed due to a lack of practical assays . Here we have deve...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2016	Development of a Simple Dipstick Assay for Operational Monitoring of DDT
Systemic lupus erythematosus is a complex and potentially fatal autoimmune disease , characterized by autoantibody production and multi-organ damage . By a genome-wide association study ( 320 patients and 1 , 500 controls ) and subsequent replication altogether involving a total of 3 , 300 Asian SLE patients from Hong ...	In this study , we first conducted a genome-wide association study in a Hong Kong Chinese population , followed by replication in three other cohorts from Mainland China and a cohort from Thailand , which totaled 3 , 300 Asian patients and 4 , 200 ethnically and geographically matched controls . We identified novel var...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "genetics", "and", "genomics/gene", "discovery", "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/genetics", "of", "the", "immune", "system", "genetics", "and", "genomics/complex", "traits", "rheumatolo...	2010	Genome-Wide Association Study in Asian Populations Identifies Variants in ETS1 and WDFY4 Associated with Systemic Lupus Erythematosus
High resolution structures of antibody-antigen complexes are useful for analyzing the binding interface and to make rational choices for antibody engineering . When a crystallographic structure of a complex is unavailable , the structure must be predicted using computational tools . In this work , we illustrate a novel...	Antibodies are proteins that are key elements of the immune system and increasingly used as drugs . Antibodies bind tightly and specifically to antigens to block their activity or to mark them for destruction . Three-dimensional structures of the antibody-antigen complexes are useful for understanding their mechanism a...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "immunology/antigen", "processing", "and", "recognition", "biophysics/protein", "folding", "biochemistry/protein", "folding", "biophysics/theory", "and", "simulation", "pharmacology/drug", "development", "molecular", "biology/bioinformatics", "biophysics/biomacromolecule-ligand", "in...	2010	SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models
Efficient acquisition of extracellular nutrients is essential for bacterial pathogenesis , however the identities and mechanisms for transport of many of these substrates remain unclear . Here , we investigate the predicted iron-binding transporter AfuABC and its role in bacterial pathogenesis in vivo . By crystallogra...	Essentially all Gram-negative pathogens are reliant on specific transport machineries termed binding protein-dependent transporters ( BPDTs ) to transport solutes such as amino acids , sugars and metal ions across their membranes . In this study we investigated AfuABC , a predicted iron-transporting BPDT found in many ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Active Transport of Phosphorylated Carbohydrates Promotes Intestinal Colonization and Transmission of a Bacterial Pathogen
Transforming growth factor ( TGF ) -β inhibits hepatitis B virus ( HBV ) replication although the intracellular effectors involved are not determined . Here , we report that reduction of HBV transcripts by TGF-β is dependent on AID expression , which significantly decreases both HBV transcripts and viral DNA , resultin...	HBV is one of the causative factors of hepatocellular carcinoma . Recent studies have shown that the members of the APOBEC deaminase family are antiviral factors that suppress the replication of viruses , such as HIV-1 and HBV . APOBEC3G suppresses viral replication by either hypermutation of nascent DNA or inhibition ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	TGF-β Suppression of HBV RNA through AID-Dependent Recruitment of an RNA Exosome Complex
Many Gram-negative bacterial pathogens express contact-dependent growth inhibition ( CDI ) systems that promote cell-cell interaction . CDI+ bacteria express surface CdiA effector proteins , which transfer their C-terminal toxin domains into susceptible target cells upon binding to specific receptors . CDI+ cells also ...	Bacterial pathogens often live in crowded communities where cells reside in close contact with one another . Many of these bacteria possess contact-dependent growth inhibition ( CDI ) systems , which allow cells to touch and inhibit each other using toxic CdiA proteins . CDI+ bacteria also produce immunity proteins tha...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "complement", "system", "medicine", "and", "health", "sciences", "toxins", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "toxicology", "toxic", "agents", "plasmid", "constructio...	2016	CdiA Effectors from Uropathogenic Escherichia coli Use Heterotrimeric Osmoporins as Receptors to Recognize Target Bacteria
The balance of quiescence and cell division is critical for tissue homeostasis and organismal health . Serum stimulation of fibroblasts is well studied as a classic model of entry into the cell division cycle , but the induction of cellular quiescence , such as by serum deprivation ( SD ) , is much less understood . He...	Cells constantly sense their environment to decide whether to divide . Many genes that control the entry into cell division are known , and their excessive activation may cause cancer . In contrast , the way that cells cease to divide was thought to be a passive process , where signals for cell division gradually decay...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "cell", "biology", "genetics", "and", "genomics", "homo", "(human)", "computational", "biology" ]	2007	A Transcriptional Program Mediating Entry into Cellular Quiescence
HIV-1-containing internal compartments are readily detected in images of thin sections from infected cells using conventional transmission electron microscopy , but the origin , connectivity , and 3D distribution of these compartments has remained controversial . Here , we report the 3D distribution of viruses in HIV-1...	Current treatment regimens for HIV-infected individuals are not capable of eradicating HIV infection , even though combinations of highly potent antiviral drugs are used . Indeed , drug regimens must be periodically altered as the virus resurges from a persistent reservoir . Macrophages , which serve as “search-and-des...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "virology/vaccines", "virology/virion", "structure,", "assembly,", "and", "egress", "cell", "biology/membranes", "and", "sorting", "infectious", "diseases/hiv", "infection", "and", "aids", "infectious", "diseases/viral", "infections" ]	2009	Ion-Abrasion Scanning Electron Microscopy Reveals Surface-Connected Tubular Conduits in HIV-Infected Macrophages
After many years of neglect , schistosomiasis control is going to scale . The strategy of choice is preventive chemotherapy , that is the repeated large-scale administration of praziquantel ( a safe and highly efficacious drug ) to at-risk populations . The frequency of praziquantel administration is based on endemicit...	More than 200 million people are affected by the snailborne disease schistosomiasis . The main strategy to control schistosomiasis is to regularly treat school-aged children with the drug praziquantel . The frequency of praziquantel treatment depends on the average prevalence of schistosomiasis , which can be defined a...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "epidemiology", "biology", "population", "biology", "spatial", "epidemiology" ]	2012	Determining Treatment Needs at Different Spatial Scales Using Geostatistical Model-Based Risk Estimates of Schistosomiasis
The origins of crop diseases are linked to domestication of plants . Most crops were domesticated centuries – even millennia – ago , thus limiting opportunity to understand the concomitant emergence of disease . Kiwifruit ( Actinidia spp . ) is an exception: domestication began in the 1930s with outbreaks of canker dis...	Despite considerable scientific advances in plant protection during the last century , agricultural crops remain vulnerable to infection by pathogens . The intensive cultivation particularly of clonally propagated crop plants increases the potential for the emergence and rapid spread of new diseases . Pseudomonas syrin...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "evolutionary", "ecology", "genome", "evolution", "comparative", "genomics", "biology", "genomics", "evolutionary", "biology", "genomic", "evolution", "evolutionary", "genetics" ]	2013	Genomic Analysis of the Kiwifruit Pathogen Pseudomonas syringae pv. actinidiae Provides Insight into the Origins of an Emergent Plant Disease
Plasmodium sporozoites , the causative agent of malaria , are injected into their vertebrate host through the bite of an infected Anopheles mosquito , homing to the liver where they invade hepatocytes to proliferate and develop into merozoites that , upon reaching the bloodstream , give rise to the clinical phase of in...	During a mammalian malaria infection , Plasmodium sporozoites injected by an infected mosquito travel to the liver where they invade hepatocytes and multiply into thousands of new parasites . These newly formed merozoites are then released into the bloodstream where they infect red blood cells and cause the symptoms of...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "microbiology/parasitology", "cell", "biology/cell", "signaling" ]	2008	Kinome-Wide RNAi Screen Implicates at Least 5 Host Hepatocyte Kinases in Plasmodium Sporozoite Infection
Although numerous quantitative trait loci ( QTL ) influencing disease-related phenotypes have been detected through gene mapping and positional cloning , identification of the individual gene ( s ) and molecular pathways leading to those phenotypes is often elusive . One way to improve understanding of genetic architec...	Although numerous quantitative trait loci ( QTL ) influencing disease-related phenotypes have been detected through gene mapping and positional cloning , identifying individual genes and their potential roles in molecular pathways leading to disease remains a challenge . In this study , we include transcriptional and m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/complex", "traits", "genetics", "and", "genomics/bioinformatics", "genetics", "and", "genomics/disease", "models", "diabetes", "and", "endocrinology/obesity"...	2008	Genetic Networks of Liver Metabolism Revealed by Integration of Metabolic and Transcriptional Profiling
When mitochondrial respiration or ubiquinone production is inhibited in Caenorhabditis elegans , behavioral rates are slowed and lifespan is extended . Here , we show that these perturbations increase the expression of cell-protective and metabolic genes and the abundance of mitochondrial DNA . This response is similar...	Mitochondrial respiration generates energy in the form of adenosine triphospate ( ATP ) , a molecule that powers many cellular processes . When respiration is inhibited in C . elegans , rates of behavior and growth are slowed and , interestingly , lifespan is extended . In this study , we investigated the mechanism of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/gene", "function", "genetics", "and", "genomics/gene", "expression" ]	2009	A Regulated Response to Impaired Respiration Slows Behavioral Rates and Increases Lifespan in Caenorhabditis elegans
Relationships between spiking-neuron and rate-based approaches to the dynamics of neural assemblies are explored by analyzing a model system that can be treated by both methods , with the rate-based method further averaged over multiple neurons to give a neural-field approach . The system consists of a chain of neurons...	We develop and demonstrate a model that allows us to examine how the predictions of spiking and rate-based models of neurons and their interactions are related . First , the behavior of a chain of neurons is explored by simulating each spiking neuron and spike-mediated interactions between neurons individually . Second...	[ "Abstract", "Introduction", "Models", "Results", "Discussion" ]	[ "physics", "statistical", "mechanics", "biophysic", "al", "simulations", "computational", "neuroscience", "neural", "networks", "biophysics", "simulations", "biophysics", "theory", "biology", "computational", "biology", "biophysics", "neuroscience" ]	2012	Complementarity of Spike- and Rate-Based Dynamics of Neural Systems
The fitness landscape captures the relationship between genotype and evolutionary fitness and is a pervasive metaphor used to describe the possible evolutionary trajectories of adaptation . However , little is known about the actual shape of fitness landscapes , including whether valleys of low fitness create local fit...	How organisms adapt to their environment is of central importance in biology , but the molecular underpinnings of adaptation are difficult to discover . Fitness landscapes illustrate possible steps adaptive evolution can take to increase the evolutionary fitness of individuals within a population , and the shape of the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "evolution", "evolutionary", "selection", "epistasis", "genome", "sequencing", "biology", "adaptation", "natural", "selection", "heredity", "genetics", "genomics", "evolutionary", "biology", "genomic", "evolution", "evolutionary", "processes", "genetics", "and", ...	2011	Reciprocal Sign Epistasis between Frequently Experimentally Evolved Adaptive Mutations Causes a Rugged Fitness Landscape
Auxin underlies many processes in plant development and physiology , and this makes it of prime importance to understand its movements through plant tissues . In stems and coleoptiles , classic experiments showed that the peak region of a pulse of radio-labelled auxin moves at a roughly constant velocity down a stem or...	Auxin is one of the most important signalling molecules in plants . It is a key player in the development of veins and plant organs , and in responses that the plant makes to light and gravity . Yet we have a rather limited understanding of how auxin moves around plant tissues . I show here that a classic experiment , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Models" ]	[]	2015	The Shape of an Auxin Pulse, and What It Tells Us about the Transport Mechanism
The mosquito Aedes aegypti was recently transinfected with a life-shortening strain of the endosymbiont Wolbachia pipientis ( wMelPop ) as the first step in developing a biocontrol strategy for dengue virus transmission . In addition to life-shortening , the wMelPop-infected mosquitoes also exhibit increased daytime ac...	The primary mosquito vector of dengue virus , Aedes aegypti , has recently been artificially infected with a symbiotic bacterium called Wolbachia pipientis . This bacterium occurs naturally inside the cells of ∼66% of insect species . The Wolbachia used to infect A . aegypti shortens the insect's lifespan . Because onl...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "ecology/behavioral", "ecology" ]	2009	Wolbachia Infection Reduces Blood-Feeding Success in the Dengue Fever Mosquito, Aedes aegypti
RNA interference ( RNAi ) -related pathways target viruses and transposable element ( TE ) transcripts in plants , fungi , and ecdysozoans ( nematodes and arthropods ) , giving protection against infection and transmission . In each case , this produces abundant TE and virus-derived 20-30nt small RNAs , which provide a...	The presence of abundant virus-derived small RNAs in infected plants , fungi , nematodes , and arthropods suggests that Dicer-dependent antiviral RNAi is an ancient and conserved defence . Using metagenomic sequencing from wild-caught organisms we find that antiviral RNAi is variable across animals . We identify a dist...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "sequencing", "techniques", "invertebrates", "rna", "interference", "vertebrates", "animals", "mammals", "dogs", "viruses", "rna", "viruses", "epigenetics", "molecular", "biology", "techniques", "rna", "sequencing", "echinoderms", "starfish", "plants", "research", "and", ...	2018	Metagenomic sequencing suggests a diversity of RNA interference-like responses to viruses across multicellular eukaryotes
Bovine tuberculosis ( BTB ) is an endemic zoonosis in Morocco caused by Mycobacterium bovis , which infects many domestic animals and is transmitted to humans through consumption of raw milk or from contact with infected animals . The prevalence of BTB in Moroccan cattle is estimated at 18% , and 33% at the individual ...	Tuberculosis is a disease of humans and animals which mainly affects the lungs but can also manifest in other organs . A variety of tuberculosis bacteria cause the disease and are usually transmitted through air , i . e . inhalation of aerosols . Bovine tuberculosis ( BTB ) occurs predominantly among domestic cattle , ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion", "and", "conclusions", "Model", "properties" ]	[ "death", "rates", "livestock", "morocco", "medicine", "and", "health", "sciences", "ruminants", "demography", "geographical", "locations", "tropical", "diseases", "vertebrates", "animals", "mammals", "animal", "slaughter", "bacterial", "diseases", "animal", "management", ...	2017	Transmission dynamics and elimination potential of zoonotic tuberculosis in morocco
Erns is an essential virion glycoprotein with RNase activity that suppresses host cellular innate immune responses upon being partially secreted from the infected cells . Its unusual C-terminus plays multiple roles , as the amphiphilic helix acts as a membrane anchor , as a signal peptidase cleavage site , and as a ret...	The Erns protein ( envelope protein , RNase , secreted ) of pestiviruses represents one of the most fascinating proteins in virology . Erns is not only an essential structural component of the virus particle but also an unspecific RNase . The latter activity is dispensable for pestivirus replication but represents a vi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "chemistry", "veterinary", "science", "biology" ]	2014	Structure of the Membrane Anchor of Pestivirus Glycoprotein Erns, a Long Tilted Amphipathic Helix
The unique ability of intrinsically disordered proteins ( IDPs ) to fold upon binding to partner molecules makes them functionally well-suited for cellular communication networks . For example , the folding-binding of different IDP sequences onto the same surface of an ordered protein provides a mechanism for signaling...	A substantial fraction of our proteins are believed to be partly or completely disordered , meaning that they contain regions that lack a stable folded structure under typical physiological conditions . This is a feature which plays a key role in their functions . For example , it allows them to have many structurally ...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "biophysic", "al", "simulations", "protein", "folding", "biology", "computational", "biology", "biophysics", "simulations", "biophysics" ]	2012	Binding of Two Intrinsically Disordered Peptides to a Multi-Specific Protein: A Combined Monte Carlo and Molecular Dynamics Study
Meiotic recombination is a major factor of genome evolution , deeply characterized in only a few model species , notably the yeast Saccharomyces cerevisiae . Consequently , little is known about variations of its properties across species . In this respect , we explored the recombination landscape of Lachancea kluyveri...	Meiotic recombination promotes accurate chromosome segregation and genetic diversity . To date , the mechanisms and rules lying behind recombination were dissected using model organisms such as the budding yeast Saccharomyces cerevisiae . To assess the conservation and variation of this process over a broad evolutionar...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Conclusion", "Materials", "and", "methods" ]	[ "fungal", "spores", "meiosis", "cell", "cycle", "and", "cell", "division", "cell", "processes", "fungi", "model", "organisms", "fungal", "evolution", "experimental", "organism", "systems", "dna", "fungal", "reproduction", "homologous", "recombination", "saccharomyces", ...	2017	Variation of the meiotic recombination landscape and properties over a broad evolutionary distance in yeasts
The Southeast Asian liver fluke ( Opisthorchis viverrini ) chronically infects and affects tens of millions of people in regions of Asia , leading to chronic illness and , importantly , inducing malignant cancer ( = cholangiocarcinoma ) . In spite of this , little is known , at the molecular level , about the parasite ...	Opistorchis viverrini is an important and neglected parasite affecting ∼9 million people in South-east Asia . The parasite has a complex life-cycle which involves an intermediate phase in cyprinoid fishes . Consumption of raw or under-cooked fish infected with the metacercarial ( larval ) stage of O . viverreni results...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "genome", "expression", "analysis", "parasitic", "diseases", "parasitology", "dna", "transcription", "neglected", "tropical", "diseases", "zoology", "infectious", "diseases", "gene", "expression", "biology", "helminthology", "opisthorchiasis", "genetics", "genom...	2012	Molecular Changes in Opisthorchis viverrini (Southeast Asian Liver Fluke) during the Transition from the Juvenile to the Adult Stage
G protein coupled receptors ( GPCRs ) allow for the transmission of signals across biological membranes . For a number of GPCRs , this signaling was shown to be coupled to prior dimerization of the receptor . The chemokine receptor type 4 ( CXCR4 ) was reported before to form dimers and their functionality was shown to...	The G protein coupled C-X-C chemokine receptor type 4 ( CXCR4 ) is a transmembrane receptor that plays an essential role in the human immune system . However , overexpression of CXCR4 has been shown to lead to metastasis of breast and lung cancer cells . Furthermore , the HI-Virus infects T-cells through binding to CXC...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "dimers", "(chemical", "physics)", "crystal", "structure", "condensed", "matter", "physics", "crystals", "membrane", "receptor", "signaling", "materials", "science", "crystallography", "g", "protein", "coupled", "receptors", "materials", "by", "structure", "physical", "...	2016	Dynamic Cholesterol-Conditioned Dimerization of the G Protein Coupled Chemokine Receptor Type 4
Our understanding of the wiring map of the brain , known as the connectome , has increased greatly in the last decade , mostly due to technological advancements in neuroimaging techniques and improvements in computational tools to interpret the vast amount of available data . Despite this , with the exception of the C ...	Tract tracing is a highly accurate procedure for identifying animal brain connectivity . However , the technique is labor intensive and requires the sacrifice of animal subjects . In our work , we describe a computational method that is able to predict the presence or absence of unobserved connections , without having ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "diagnostic", "radiology", "tractography", "nervous", "system", "brain", "vertebrates", "neuroscience", "animals", "mammals", "magnetic", "resonance", "imaging", "primates", "brain", "morphometry", "brain", "mapping", "neuroimaging...	2017	The missing link: Predicting connectomes from noisy and partially observed tract tracing data
Dengue , chikungunya , and Zika virus epidemics transmitted by Aedes aegypti mosquitoes have recently ( re ) emerged and spread throughout the Americas , Southeast Asia , the Pacific Islands , and elsewhere . Understanding how environmental conditions affect epidemic dynamics is critical for predicting and responding t...	Mosquito-borne viruses like dengue , Zika , and chikungunya have recently caused large epidemics that are partly driven by temperature . Using a mathematical model built from laboratory experimental data for Aedes aegypti mosquitoes and dengue virus , we examine the impact of variation in seasonal temperature regimes o...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "china", "immunology", "geographical", "locations", "animals", "seasons", "insect", "vectors", "infectious", "diseases", "south", "america", "aedes", "aegypti", "disease", "vectors", "brazil", "insects", "arthrop...	2018	Seasonal temperature variation influences climate suitability for dengue, chikungunya, and Zika transmission
Human genome-wide association studies have linked single nucleotide polymorphisms ( SNPs ) on chromosome 9p21 . 3 near the INK4/ARF ( CDKN2a/b ) locus with susceptibility to atherosclerotic vascular disease ( ASVD ) . Although this locus encodes three well-characterized tumor suppressors , p16INK4a , p15INK4b , and ARF...	Unbiased studies of the human genome have identified strong genetic determinants of atherosclerotic vascular disease ( ASVD ) on chromosome 9p21 . 3 . This region of the genome does not encode genes previously linked to ASVD , but does contain the INK4/ARF tumor suppressor locus . Products of the INK4/ARF locus regulat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/rna", "splicing", "genetics", "and", "genomics/cancer", "genetics", "cell", "biology/gene", "expression", "cardiovascular", "disorders/peripheral", "vascular", "disease" ]	2010	Expression of Linear and Novel Circular Forms of an INK4/ARF-Associated Non-Coding RNA Correlates with Atherosclerosis Risk
A family of hydrophilic acylated surface ( HASP ) proteins , containing extensive and variant amino acid repeats , is expressed at the plasma membrane in infective extracellular ( metacyclic ) and intracellular ( amastigote ) stages of Old World Leishmania species . While HASPs are antigenic in the host and can induce ...	Single-celled Leishmania parasites , transmitted by sand flies , infect humans and other mammals in many tropical and sub-tropical regions , giving rise to a spectrum of diseases called the leishmaniases . Species of parasite within the Leishmania genus can be divided into two groups ( referred to as sub-genera ) that ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "genetics", "and", "genomics/genomics", "molecular", "biology", "cell", "biology/gene", "expression", "infectious", "diseases/protozoal", "infections" ]	2010	Leishmania-Specific Surface Antigens Show Sub-Genus Sequence Variation and Immune Recognition
To ascertain the clinical features and visual outcome of toxoplasma retinochoroiditis in a large series of cases . Two hundred and thirty subjects diagnosed with active toxoplasma retinochoroiditis were prospectively followed for periods ranging from 269 to 1976 days . All patients presented with active retinochoroidit...	Ocular toxoplasmosis affects millions of people worldwide and is a cause of severe vision loss . Prospective studies on the disease are rare and require long and expensive follow-ups . A network of intricate host and parasite factors can influence its evolution and its treatment is still subject of discussion and contr...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "toxoplasma", "gondii", "social", "sciences", "parasitic", "diseases", "neuroscience", "parasitic", "protozoans", "protozoans", "signs", "and", "symptoms", "toxoplasma", "pharmaceutics"...	2016	Toxoplasmic Retinochoroiditis: Clinical Characteristics and Visual Outcome in a Prospective Study
Productive infection by herpesviruses involve the disabling of host-cell intrinsic defenses by viral encoded tegument proteins . Epstein-Barr Virus ( EBV ) typically establishes a non-productive , latent infection and it remains unclear how it confronts the host-cell intrinsic defenses that restrict viral gene expressi...	Persistent infection by Epstein-Barr virus ( EBV ) is associated with a variety of diseases , including lymphoid and epithelial tumors . Despite a wealth of information on the mechanism of viral persistence , relatively little is known about the early steps of EBV infection and viral gene activation . Host cells active...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biology" ]	2011	EBV Tegument Protein BNRF1 Disrupts DAXX-ATRX to Activate Viral Early Gene Transcription
Electrical activity plays a pivotal role in glucose-stimulated insulin secretion from pancreatic -cells . Recent findings have shown that the electrophysiological characteristics of human -cells differ from their rodent counterparts . We show that the electrophysiological responses in human -cells to a range of ion cha...	Insulin is a glucose-lowering hormone secreted from the pancreatic -cells in response to raised plasma glucose levels , and it is now well-established that defective insulin secretion plays a pivotal role in the development of diabetes . The -cells are electrically active , and use electrical activity to transduce an i...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "insulin", "endocrine", "system", "biology", "anatomy", "and", "physiology", "electrophysiology", "computational", "biology", "endocrine", "physiology" ]	2014	Mathematical Modeling of Heterogeneous Electrophysiological Responses in Human β-Cells
Herpes simplex virus type 2 ( HSV-2 ) glycoprotein D ( gD2 ) subunit antigen is included in many preclinical candidate vaccines . The rationale for including gD2 is to produce antibodies that block crucial gD2 epitopes involved in virus entry and cell-to-cell spread . HSV-2 gD2 was the only antigen in the Herpevac Tria...	Herpes simplex virus type 2 ( HSV-2 ) glycoprotein D ( gD2 ) mediates virus entry and cell-to-cell spread . We hypothesized that an effective gD2 vaccine needs to block these activities . Neutralizing titers , which assess blocking virus entry , correlated with protection against HSV-2 genital lesions in gD2-immunized ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "enzyme-linked", "immunoassays", "viral", "transmission", "and", "infection", "engineering", "and", "technology", "immunology", "microbiology", "vertebrates", "animals", "mammals", "animal", "models", "vacci...	2018	Vaccine-induced antibodies to herpes simplex virus glycoprotein D epitopes involved in virus entry and cell-to-cell spread correlate with protection against genital disease in guinea pigs
Accurate genome duplication underlies genetic homeostasis . Metazoan Mdm2 binding protein ( MTBP ) forms a main regulatory platform for origin firing together with Treslin/TICRR and TopBP1 ( Topoisomerase II binding protein 1 ( TopBP1 ) –interacting replication stimulating protein/TopBP1-interacting checkpoint and repl...	Efficient and well-regulated DNA replication origin firing is central to ensure complete and accurate genome duplication before cell division . We here use bioinformatics and cultured human cells to understand the role of the essential origin firing factor Mdm2 binding protein ( MTBP ) . We prove that MTBP is orthologo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "binding", "cell", "physiology", "molecular", "probe", "techniques", "gene", "regulation", "cell", "cycle", "and", "cell", "division", "cell", "processes", "immunoblotting", "green", "fluorescent", "protein", "dna-binding", "proteins", "luminescent", "proteins",...	2019	The Cdk8/19-cyclin C transcription regulator functions in genome replication through metazoan Sld7
Ergosterol is an important constituent of fungal membranes . Azoles inhibit ergosterol biosynthesis , although the cellular basis for their antifungal activity is not understood . We used multiple approaches to demonstrate a critical requirement for ergosterol in vacuolar H+-ATPase function , which is known to be essen...	Systemic fungal infections impose a significant threat to public health and therapeutic options to treat these diseases remain limited . Azoles represent the largest category of anti-fungal drugs and repress fungal growth by inhibiting biosynthesis of ergosterol , an important constituent of fungal membranes . Despite ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "pharmacology", "microbiology/medical", "microbiology", "biochemistry/membrane", "proteins", "and", "energy", "transduction", "infectious", "diseases/antimicrobials", "and", "drug", "resistance" ]	2010	Requirement for Ergosterol in V-ATPase Function Underlies Antifungal Activity of Azole Drugs
Group A Streptococcus ( GAS ) is deleterious pathogenic bacteria whose interaction with blood vessels leads to life-threatening bacteremia . Although xenophagy , a special form of autophagy , eliminates invading GAS in epithelial cells , we found that GAS could survive and multiply in endothelial cells . Endothelial ce...	Autophagy is an intracellular bulk degradation system to survive within starved condition , which is one of the most common threats limiting organism’s expansion . By the system , cells digest their own cytoplasmic compartments that are sequestered by double membrane structure called autophagosome . It is also utilized...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "death", "medicine", "and", "health", "sciences", "autophagic", "cell", "death", "neurochemistry", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "endothelial", "cells", "pathogens", "cell", "processes", "microbiology", "neuroscience", "salm...	2017	Endothelial cells are intrinsically defective in xenophagy of Streptococcus pyogenes
The pyrabactin resistance 1 ( PYR1 ) /PYR1-like ( PYL ) /regulatory component of abscisic acid ( ABA ) response ( RCAR ) proteins comprise a well characterized family of ABA receptors . Recent investigations have revealed two subsets of these receptors that , in the absence of ABA , either form inactive homodimers ( PY...	Protein pyrabactin resistance 1 ( PYR1 ) belongs to a group of PYR1-like ( PYL ) proteins that regulate plant development and responses to conditions of drought and salinity . Recent studies have reported characterization of their molecular structures as well as elucidation of important aspects of their function; highl...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "biomacromolecule-ligand", "interactions", "physics", "statistical", "mechanics", "protein", "folding", "macromolecular", "assemblies", "biophysics", "theory", "chemistry", "biology", "computational", "chemistry", "biophysics", "simulations", "biophysics" ]	2013	Molecular Mechanisms in the Activation of Abscisic Acid Receptor PYR1
ARFI elastrography has been used as a noninvasive method to assess the severity of liver fibrosis in viral hepatitis , although with few studies in schistosomiasis mansoni . We aimed to evaluate the performance of point shear wave elastography ( pSWE ) for predicting significant periportal fibrosis ( PPF ) in schistoso...	In the developing world , over 207 million people are infected with parasitic Schistosoma worms . Among the species of Schistosoma that infect humans Schistosoma mansoni is one of the most common causes of illness . Here , we investigated the performance of point shear wave elastography ( pSWE ) for predicting signific...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "medicine", "and", "health", "sciences", "diagnostic", "radiology", "ultrasound", "imaging", "helminths", "tropical", "diseases", "fibrosis", "parasitic", "diseases", "animals", "liver", "diseases", "developmental", ...	2018	Liver ultrasound elastography for the evaluation of periportal fibrosis in schistosomiasis mansoni: A cross-sectional study
It is widely believed that the modular organization of cellular function is reflected in a modular structure of molecular networks . A common view is that a “module” in a network is a cohesively linked group of nodes , densely connected internally and sparsely interacting with the rest of the network . Many algorithms ...	Cellular function is widely believed to be organized in a modular fashion . On all scales and at all levels of complexity , relatively independent sub-units perform relatively independent sub-tasks . This functional modularity must be reflected in the topology of molecular networks . But how a functional module should ...	[ "Abstract", "Discussion" ]	[ "computational", "biology/systems", "biology" ]	2010	Protein Interaction Networks—More Than Mere Modules
The cytotoxin-associated gene ( Cag ) pathogenicity island is a strain-specific constituent of Helicobacter pylori ( H . pylori ) that augments cancer risk . CagA translocates into the cytoplasm where it stimulates cell signaling through the interaction with tyrosine kinase c-Met receptor , leading cellular proliferati...	Chronic gastric inflammation , typically caused by Helicobacter pylori ( H . pylori ) , is the most consistent lesion leading to cancer . During a well-choreographed interaction between H . pylori and the host , the progression from chronic inflammation to cancer involves gastric epithelial changes with evidence of hyp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	CD44 Plays a Functional Role in Helicobacter pylori-induced Epithelial Cell Proliferation
The separation of the optic neuroepithelium into future retina and retinal pigment epithelium ( RPE ) is a critical event in early eye development in vertebrates . Here we show in mice that the transcription factor PAX6 , well-known for its retina-promoting activity , also plays a crucial role in early pigment epitheli...	The retinal pigment epithelium or RPE in the back of the eye is critical for the normal function of the retina , and its abnormalities can lead to retinal disorders such as adult-onset macular degeneration . Insights into the pathogenesis of such disorders , and potential therapies , may come from using RPE cells gener...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "genetics", "biology", "molecular", "cell", "biology", "neuroscience", "genetics", "and", "genomics" ]	2012	A Regulatory Loop Involving PAX6, MITF, and WNT Signaling Controls Retinal Pigment Epithelium Development
RNA polyadenylation ( pA ) is one of the major steps in regulation of gene expression at the posttranscriptional level . In this report , a genome landscape of pA sites of viral transcripts in B lymphocytes with Kaposi sarcoma-associated herpesvirus ( KSHV ) infection was constructed using a modified PA-seq strategy . ...	A genome-wide polyadenylation landscape in the expression of human herpesviruses has not been reported . In this study , we provide the first genome landscape of viral RNA polyadenylation sites in B cells from KSHV latent to lytic infection by using a modified PA-seq protocol and selectively validated by 3′ RACE . We f...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	A Viral Genome Landscape of RNA Polyadenylation from KSHV Latent to Lytic Infection
Asymptomatic persons infected with the parasites causing visceral leishmaniasis ( VL ) usually outnumber clinically apparent cases by a ratio of 4–10 to 1 . We assessed the risk of progression from infection to disease as a function of DAT and rK39 serological titers . We used available data on four cohorts from villag...	To study the association between positive serology for VL among asymptomatic persons and progression to disease , we analyzed combined data from two different cohort studies in which over 32 , 000 subjects were enrolled . All subjects were screened for presence of antibodies to L . donovani with DAT and rK39 . After an...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "epidemiology" ]	2014	Strong Association between Serological Status and Probability of Progression to Clinical Visceral Leishmaniasis in Prospective Cohort Studies in India and Nepal
It has been reported that feeding mice resveratrol activates AMPK and SIRT1 in skeletal muscle leading to deacetylation and activation of PGC-1α , increased mitochondrial biogenesis , and improved running endurance . This study was done to further evaluate the effects of resveratrol , SIRT1 , and PGC-1α deacetylation o...	Studies on cultured muscle cells have shown that treatment with resveratrol , a chemical famously found in the skin of red grapes , stimulates the manufacture of new mitochondria . This has been attributed to the activation of the deacetylase SIRT1 either directly by resveratrol or indirectly via the activation of AMP-...	[ "Abstract", "Introduction", "Results", "Discussion", "Experimental", "Procedures" ]	[ "biology" ]	2013	Effects of Resveratrol and SIRT1 on PGC-1α Activity and Mitochondrial Biogenesis: A Reevaluation
Ebola virus ( EBOV ) caused more than 11 , 000 deaths during the 2013–2016 epidemic in West Africa without approved vaccines or immunotherapeutics . Despite its high lethality in some individuals , EBOV infection can produce little to no symptoms in others . A better understanding of the immune responses in individuals...	The 2013–2016 West African Ebola virus ( EBOV ) outbreak is the largest on record with over 28 , 000 reported symptomatic cases and more than 11 , 000 deaths . We developed a simple and inexpensive modified anthrax toxin-based ELISPOT assay to detect and characterize the T cell responses elicited by prior exposure to E...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "cell", "physiology", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "cells", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "viruses", "filoviruses", ...	2018	A modified anthrax toxin-based enzyme-linked immunospot assay reveals robust T cell responses in symptomatic and asymptomatic Ebola virus exposed individuals
Leishmania parasites have evolved sophisticated mechanisms to subvert macrophage immune responses by altering the host cell signal transduction machinery , including inhibition of JAK/STAT signalling and other transcription factors such as AP-1 , CREB and NF-κB . AP-1 regulates pro-inflammatory cytokines , chemokines a...	Leishmaniasis is a tropical disease affecting more than 12 million people around the world . The disease is caused by the Leishmania parasites that are transmitted to the mammalian host by a sandfly vector when it takes a blood meal . The parasites are able to survive and multiply inside of cells that comprise the prim...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/immune", "response", "immunology/innate", "immunity", "microbiology/parasitology", "infectious", "diseases/protozoal", "infections", "immunology/immunity", "to", "infections" ]	2010	Leishmania-Induced Inactivation of the Macrophage Transcription Factor AP-1 Is Mediated by the Parasite Metalloprotease GP63
Conventional and regulatory T cells develop in the thymus where they are exposed to samples of self-peptide MHC ( pMHC ) ligands . This probabilistic process selects for cells within a range of responsiveness that allows the detection of foreign antigen without excessive responses to self . Regulatory T cells are thoug...	T cells develop in the thymus , where they are vetted – they must respond weakly to self-antigens , but not so strongly as to risk causing autoimmunity . This selection process involves developing T cells being exposed to a large sample of self-peptides presented on specialised cells in the thymus , and deciding to die...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "immunology", "biology", "computational", "biology" ]	2013	Models of Self-Peptide Sampling by Developing T Cells Identify Candidate Mechanisms of Thymic Selection
In early 2015 , a ZIKA Virus ( ZIKV ) infection outbreak was recognized in northeast Brazil , where concerns over its possible links with infant microcephaly have been discussed . Providing a causal link between ZIKV infection and birth defects is still a challenge . MicroRNAs ( miRNAs ) are small noncoding RNAs ( sncR...	The potential interaction between ZIKA Virus ( ZIKV ) infection and infant brain defects still has no explanatory mechanism . The mechanism of action for several other viruses have been described , and are often related to the control or production of sncRNA ( small noncoding RNA ) molecules , which regulate the expres...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "medicine", "and", "health", "sciences", "microcephaly", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "pathogens", "microbiology", "database", "searching", "human", "genomics", "viruses", "developmental", "biology", "micrornas", "rna", "viruses", ...	2016	ZIKV – CDB: A Collaborative Database to Guide Research Linking SncRNAs and ZIKA Virus Disease Symptoms
In the infectious stage of Trypanosoma brucei , an important parasite of humans and livestock , the mitochondrial ( mt ) membrane potential ( Δψm ) is uniquely maintained by the ATP hydrolytic activity and subsequent proton pumping of the essential FoF1-ATPase . Intriguingly , this multiprotein complex contains several...	The presence of the FoF1-ATP synthase in every aerobic organism suggests that evolution has settled on a basic blueprint for the complex rotary motor capable of synthesizing life’s universal energy currency—ATP . However , compared to yeast and mammalian models of the FoF1-ATP synthase , several recent studies have rep...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	ATPaseTb2, a Unique Membrane-bound FoF1-ATPase Component, Is Essential in Bloodstream and Dyskinetoplastic Trypanosomes
Brucellosis and coxiellosis are known to be endemic in ruminant populations throughout Afghanistan , but information about their prevalence and factors that affect prevalence in householders and livestock under diverse husbandry systems and pastoral settings is sparse . We conducted a cross-sectional survey to investig...	Our study alerted authorities to a hitherto unrecognised high prevalence of C . burnetii infections , acted as a catalyst for the introduction of a national vaccination programme for protection of sheep and goats from brucellosis using Rev1 vaccine , demonstrated the benefits of a coordinated approach and fostered a be...	[ "Abstract", "Introduction", "Methods", "Discussion" ]	[]	2015	Brucellosis and Coxiella burnetii Infection in Householders and Their Animals in Secure Villages in Herat Province, Afghanistan: A Cross-Sectional Study
Most diversity in animals and plants results from the modification of already existing structures . Many organ systems , for example , are permanently modified during evolution to create developmental and morphological diversity , but little is known about the evolution of the underlying developmental mechanisms . The ...	Diversity of biological form in animals can be generated by the modification of already existing developmental and morphological structures . One major challenge in evolutionary biology is to identify the molecular and genetic changes associated with such morphological modifications . A decade ago , the theory of devel...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2011	Antagonism of LIN-17/Frizzled and LIN-18/Ryk in Nematode Vulva Induction Reveals Evolutionary Alterations in Core Developmental Pathways
Hsp70 chaperones are well known for their important functions in maintaining protein homeostasis during thermal stress conditions . In many bacteria the Hsp70 homolog DnaK is also required for growth in the absence of stress . The molecular reasons underlying Hsp70 essentiality remain in most cases unclear . Here , we ...	Molecular chaperones of the Hsp70 family belong to the most conserved cellular machineries throughout the tree of life . These proteins play key roles in maintaining protein homeostasis , especially under heat stress conditions . In diverse bacteria the Hsp70 homolog DnaK is essential for growth even in the absence of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cellular", "stress", "responses", "caulobacter", "enzymes", "cell", "processes", "enzymology", "mutation", "prokaryotic", "models", "dna", "replication", "experimental", "organism", "systems", "gene", "types", "dna", "molecular", "biology", "techniques", "bacteria", "r...	2017	An essential regulatory function of the DnaK chaperone dictates the decision between proliferation and maintenance in Caulobacter crescentus
Integrating large-scale functional genomic data has significantly accelerated our understanding of gene functions . However , no algorithm has been developed to differentiate functions for isoforms of the same gene using high-throughput genomic data . This is because standard supervised learning requires ‘ground-truth’...	In mammalian genomes , a single gene can be alternatively spliced into multiple isoforms which greatly increase the functional diversity of the genome . In the human , more than 95% of multi-exon genes undergo alternative splicing . It is hard to computationally differentiate the functions for the splice isoforms of th...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	Systematically Differentiating Functions for Alternatively Spliced Isoforms through Integrating RNA-seq Data
Hierarchical organization—the recursive composition of sub-modules—is ubiquitous in biological networks , including neural , metabolic , ecological , and genetic regulatory networks , and in human-made systems , such as large organizations and the Internet . To date , most research on hierarchy in networks has been lim...	Hierarchy is a ubiquitous organizing principle in biology , and a key reason evolution produces complex , evolvable organisms , yet its origins are poorly understood . Here we demonstrate for the first time that hierarchy evolves as a result of the costs of network connections . We confirm a previous finding that conne...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetic", "networks", "neural", "networks", "engineering", "and", "technology", "neuroscience", "logic", "circuits", "network", "analysis", "genome", "analysis", "computer", "and", "information", "sciences", "animal", "cells", "evolutionary", "genetics", "cellular", "n...	2016	The Evolutionary Origins of Hierarchy
Plasmodium parasites invade and multiply inside red blood cells ( RBC ) . Through a cycle of maturation , asexual replication , rupture and release of multiple infective merozoites , parasitised RBC ( pRBC ) can reach very high numbers in vivo , a process that correlates with disease severity in humans and experimental...	Malaria occurs when Plasmodium parasites replicate inside red blood cells , with the number of parasitised cells ( pRBC ) correlating with disease severity . Antibodies are highly effective at controlling pRBC numbers in the bloodstream , and yet we know very little about how they function in vivo . Human in vitro stud...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "serum", "complement", "system", "medicine", "and", "health", "sciences", "parasite", "groups", "immune", "physiology", "body", "fluids", "immunology", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "parasitemia", "animal", "models", "apico...	2019	Plasmodium-specific antibodies block in vivo parasite growth without clearing infected red blood cells
Aiming at the design of an allosteric modulator of the neonatal Fc receptor ( FcRn ) –Immunoglobulin G ( IgG ) interaction , we developed a new methodology including NMR fragment screening , X-ray crystallography , and magic-angle-spinning ( MAS ) NMR at 100 kHz after sedimentation , exploiting very fast spinning of th...	In drug design , a detailed characterization of structural changes induced by drug binding is useful for further optimizing lead compounds . In many cases , structural alterations are distant from the compound binding site , potentially acting through allosteric effects . These allosteric effects are often difficult to...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "biotechnology", "medicine", "and", "health", "sciences", "methods", "and", "resources", "crystal", "structure", "chemical", "compounds", "small", "molecules", "nmr", "spectroscopy", "immunology", "condensed", "matter", "physics", "organic", "compounds", "crystals", "ma...	2018	Insight into small molecule binding to the neonatal Fc receptor by X-ray crystallography and 100 kHz magic-angle-spinning NMR
Successful behavior requires selection and preferred processing of relevant sensory information . The cortical representation of relevant sensory information has been related to neuronal oscillations in the gamma frequency band . Pain is of invariably high behavioral relevance and , thus , nociceptive stimuli receive p...	Pain is a highly subjective sensation of inherent behavioral importance and is therefore expected to receive enhanced processing in relevant brain regions . We show that painful stimuli induce high-frequency oscillations in the electrical activity of the human primary somatosensory cortex . Amplitudes of these pain-ind...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience", "homo", "(human)" ]	2007	Gamma Oscillations in Human Primary Somatosensory Cortex Reflect Pain Perception
The phenotype of any organism on earth is , in large part , the consequence of interplay between numerous gene products encoded in the genome , and such interplay between gene products affects the evolutionary fate of the genome itself through the resulting phenotype . In this regard , contemporary genomes can be used ...	Genes in organisms have a number of interactions with one another in their biological contexts . For example , proteins produced from one gene may interact with other proteins produced from another gene to perform together a particular biological task , and such pairs of cooperative genes may often reside together in t...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "physics", "biochemistry", "protein", "interactions", "theoretical", "biology", "interdisciplinary", "physics", "molecular", "biology", "biophysics", "theory", "synthetic", "biology", "biology", "computational", "biology", "metabolic", "networks", "biophysics", "proteomics" ]	2011	Genetic Co-Occurrence Network across Sequenced Microbes
The world is rapidly becoming urban with the global population living in cities projected to double by 2050 . This increase in urbanization poses new challenges for the spread and control of communicable diseases such as malaria . In particular , urban environments create highly heterogeneous socio-economic and environ...	Urbanization and environmental change are the main driving forces of ecological and social change around the globe , specifically in developing countries and for human health . Cities in developing countries exhibit rapid and unplanned urbanization which creates heterogeneous environmental and socio-economic conditions...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "parasite", "groups", "plasmodium", "atmospheric", "science", "tropical", "diseases", "geographical", "locations", "india", "parasitic", "diseases", "parasitic", "protozoans", "parasit...	2016	Population Density, Climate Variables and Poverty Synergistically Structure Spatial Risk in Urban Malaria in India
Investigation of macromolecular structure and dynamics is fundamental to understanding how macromolecules carry out their functions in the cell . Significant advances have been made toward this end in silico , with a growing number of computational methods proposed yearly to study and simulate various aspects of macrom...	This paper provides an overview of recent advancements in computational methods for modeling macromolecular structure and dynamics . The focus is on methods aimed at providing efficient representations of macromolecular structure spaces for the purpose of characterizing equilibrium dynamics . The overview is meant to p...	[ "Abstract", "Introduction", "Recent", "Applications", "Made", "Possible", "by", "Hardware", "and", "Algorithmic", "Advancements", "Categorization", "by", "Algorithmic", "Frameworks", "Conclusions" ]	[ "applied", "mathematics", "simulation", "and", "modeling", "algorithms", "review", "mathematics", "protein", "structure", "prediction", "protein", "structure", "macromolecules", "thermodynamics", "research", "and", "analysis", "methods", "polymer", "chemistry", "proteins", ...	2016	Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics
Human T-cell leukemia virus type 1 ( HTLV-1 ) is the etiological agent of adult T-cell leukemia/lymphoma ( ATLL ) , an aggressive malignant proliferation of activated CD4+ T lymphocytes . The viral Tax oncoprotein is critically involved in both HTLV-1-replication and T-cell proliferation , a prerequisite to the develop...	The viral Tax oncoprotein is a critical contributor to the development of adult T-cell leukemia/lymphoma , an aggressive malignant proliferation of T lymphocytes . Tax contains a PDZ domain-binding motif ( PBM ) that favors the interaction with several cellular PDZ proteins . Here , we compare the in vivo involvement o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "cell", "physiology", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "body", "fluids", "spleen", "pathogens", "293t", "cells", "immunology", "biological", "cultures", ...	2018	PDZ domain-binding motif of Tax sustains T-cell proliferation in HTLV-1-infected humanized mice
Genome-wide association study ( GWAS ) entails examining a large number of single nucleotide polymorphisms ( SNPs ) in a limited sample with hundreds of individuals , implying a variable selection problem in the high dimensional dataset . Although many single-locus GWAS approaches under polygenic background and populat...	Genome-wide association study is concerned with the associations between markers and traits of interest so as to identify all the significantly associated markers . In genome-wide association studies , hundreds of thousands of markers are genotyped for several hundreds of individuals . Usually , only a very minor subse...	[ "Abstract", "Introduction", "Results", "Discussion", "Conclusion", "Methods" ]	[ "genome-wide", "association", "studies", "applied", "mathematics", "brassica", "quantitative", "traits", "simulation", "and", "modeling", "algorithms", "model", "organisms", "mathematics", "statistics", "(mathematics)", "genome", "analysis", "experimental", "organism", "sys...	2017	Iterative sure independence screening EM-Bayesian LASSO algorithm for multi-locus genome-wide association studies
The current understanding of mammalian kidney development is largely based on mouse models . Recent landmark studies revealed pervasive differences in renal embryogenesis between mouse and human . The scarcity of detailed gene expression data in humans therefore hampers a thorough understanding of human kidney developm...	Regenerative medicine offers an exciting avenue to potential cures of kidney disease . However , a detailed knowledge of the structure and embryonic development of the kidney is crucial , both for stimulating regeneration in the body and for growing healthy kidney tissue in a dish . Most of such knowledge has been obta...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "kidney", "development", "marker", "genes", "precursor", "cells", "developmental", "biology", "organism", "development", "stem", "cells", "nephrons", "molecular", "biology", "techniques", "kidneys", "research", "and", "analysis",...	2019	Single-cell transcriptomics reveals gene expression dynamics of human fetal kidney development
Muscle contracts due to ATP-dependent interactions of myosin motors with thin filaments composed of the proteins actin , troponin , and tropomyosin . Contraction is initiated when calcium binds to troponin , which changes conformation and displaces tropomyosin , a filamentous protein that wraps around the actin filamen...	Despite decades of study , there is no clear connection between muscle contraction at the molecular and the macroscopic scale . For example , we cannot yet predict how a genetic defect in a muscle protein will result in a physiological change in the heart . This multi-scale understanding is difficult , in part , becaus...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Direct Measurements of Local Coupling between Myosin Molecules Are Consistent with a Model of Muscle Activation
Rubella virus ( RuV ) infection of pregnant women can cause fetal death , miscarriage , or severe fetal malformations , and remains a significant health problem in much of the underdeveloped world . RuV is a small enveloped RNA virus that infects target cells by receptor-mediated endocytosis and low pH-dependent membra...	Rubella virus ( RuV ) is a small enveloped RNA virus causing mild disease in children . However , infection of pregnant women can produce fetal death or congenital rubella syndrome , a constellation of severe birth defects including cataracts , hearing loss , heart disease and developmental delays . While vaccination h...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "medicine", "and", "health", "sciences", "viral", "transmission", "and", "infection", "virology", "biology", "and", "life", "sciences", "microbiology", "viral", "diseases", "viral", "structure", "rubella" ]	2014	Rubella Virus: First Calcium-Requiring Viral Fusion Protein
The diagnosis of Human African Trypanosomiasis relies mainly on the Card Agglutination Test for Trypanosomiasis ( CATT ) . While this test is successful , it is acknowledged that there may be room for improvement . Our aim was to develop a prototype lateral flow test based on the detection of antibodies to trypanosome ...	Human African Trypanosomiasis is caused by infection with Trypanosoma brucei gambiense or T . b . rhodesiense . Preliminary diagnosis of T . b . gambiense infection relies mainly on a Card Agglutination Test for Trypanosomiasis ( CATT ) , which has acknowledged limitations . New approaches are needed , first to identif...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "biochemistry", "infectious", "diseases", "diagnostic", "medicine", "immunology", "biology", "microbiology", "proteomics" ]	2013	Proteomic Selection of Immunodiagnostic Antigens for Human African Trypanosomiasis and Generation of a Prototype Lateral Flow Immunodiagnostic Device
Weight-loss interventions generally improve lipid profiles and reduce cardiovascular disease risk , but effects are variable and may depend on genetic factors . We performed a genetic association analysis of data from 2 , 993 participants in the Diabetes Prevention Program to test the hypotheses that a genetic risk sco...	The study included 2 , 993 participants from the Diabetes Prevention Program , a randomized clinical trial of intensive lifestyle intervention , metformin treatment , and placebo control . We examined associations between 32 gene variants that have been reproducibly associated with dyslipidemia and concentrations of li...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "diabetes", "mellitus", "type", "2", "drugs", "and", "devices", "endocrinology", "pharmacogenetics", "diabetic", "endocrinology", "pharmacology", "diabetes", "and", "endocrinology" ]	2012	Genetic Modulation of Lipid Profiles following Lifestyle Modification or Metformin Treatment: The Diabetes Prevention Program
Previous studies of repetitive elements ( REs ) have implicated a mechanistic role in generating new chimerical genes . Such examples are consistent with the classic model for exon shuffling , which relies on non-homologous recombination . However , recent data for chromosomal aberrations in model organisms suggest tha...	In numerous organisms , many new genes have been found to originate through dispersed gene duplication and exon/domain shuffling . What recombination mechanisms were involved in the duplication and the shuffling processes ? Lack of the intermediate products of recombination that share adequate sequence identity between...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology", "drosophila", "1" ]	2008	Repetitive Element-Mediated Recombination as a Mechanism for New Gene Origination in Drosophila
In Magnaporthe oryzae , the causal ascomycete of the devastating rice blast disease , the conidial germ tube tip must sense and respond to a wide array of requisite cues from the host in order to switch from polarized to isotropic growth , ultimately forming the dome-shaped infection cell known as the appressorium . Al...	Magnaporthe oryzae , a filamentous fungus , causes the devastating and economically important blast disease in rice and related species . It produces asexual spores , conidia , which can switch to a disease-causing mode of development in response to host and environmental cues . Activation of a highly conserved cell-si...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "plant", "science", "model", "organisms", "pest", "control", "genetics", "biology", "microbiology", "molecular", "cell", "biology", "agriculture" ]	2013	The Late Endosomal HOPS Complex Anchors Active G-Protein Signaling Essential for Pathogenesis in Magnaporthe oryzae
The innate immune system is essential for controlling viral infections , but several viruses have evolved strategies to escape innate immunity . RIG-I is a cytoplasmic viral RNA sensor that triggers the signal to induce type I interferon production in response to viral infection . RIG-I activation is regulated by the K...	The cytoplasmic viral RNA sensor RIG-I recognizes various types of pathogenic viruses and evokes innate immune responses , whereas several viruses have evolved strategies to escape the host innate immune responses . RIG-I triggers a signal to induce type I interferon and inflammatory cytokines . RIG-I activation is reg...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "signal", "transduction", "immunity", "mechanisms", "of", "signal", "transduction", "innate", "immunity", "immunology", "biology", "molecular", "cell", "biology" ]	2013	A Distinct Role of Riplet-Mediated K63-Linked Polyubiquitination of the RIG-I Repressor Domain in Human Antiviral Innate Immune Responses
Expression of co-inhibitory molecules is generally associated with T-cell dysfunction in chronic viral infections such as HIV or HCV . However , their relative contribution in the T-cell impairment remains unclear . In the present study , we have evaluated the impact of the expression of co-inhibitory molecules such as...	T-cell immune response is regulated by a variety of molecules known as co-inhibitory receptors . The over expression of co-inhibitory receptors has been observed in several chronic viral infections such as HIV disease , and is found to be associated with severe T-cell dysfunction . Recent studies have demonstrated that...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences", "immunology" ]	2014	CD160-Associated CD8 T-Cell Functional Impairment Is Independent of PD-1 Expression
Exhausted CD8+ T cell responses during chronic viral infections are defined by a complex expression pattern of inhibitory receptors . However , very little information is currently available about the coexpression patterns of these receptors on human virus-specific CD8+ T cells and their correlation with antiviral func...	About 170 million people are infected with hepatitis C virus ( HCV ) , which may cause severe liver disease and liver cancer . Upon acute infection , only about 30% of patients are able to eliminate the virus spontaneously while about 70% of patients develop chronic infection . It is known that a successful immune resp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/antigen", "processing", "and", "recognition", "gastroenterology", "and", "hepatology/hepatology", "immunology/immune", "response", "virology/immune", "evasion", "immunology/immunity", "to", "infections", "infectious", "diseases/gastrointestinal", "infections" ]	2010	Coexpression of PD-1, 2B4, CD160 and KLRG1 on Exhausted HCV-Specific CD8+ T Cells Is Linked to Antigen Recognition and T Cell Differentiation
Cytokinesis is powered by the contraction of actomyosin filaments within the newly assembled contractile ring . Microtubules are a spindle component that is essential for the induction of cytokinesis . This induction could use central spindle and/or astral microtubules to stimulate cortical contraction around the spind...	In animal cells , the last step of cell division , or cytokinesis , requires the action of a contractile ring—composed largely of actin and myosin filaments—that cleaves the cell in two . Before the cell divides , it first duplicates its genome and separates the chromosomes into the two newly forming daughter cells , a...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "biology" ]	2008	Redundant Mechanisms Recruit Actin into the Contractile Ring in Silkworm Spermatocytes
The bacterium Neisseria meningitidis is commonly found harmlessly colonising the mucosal surfaces of the human nasopharynx . Occasionally strains can invade host tissues causing septicaemia and meningitis , making the bacterium a major cause of morbidity and mortality in both the developed and developing world . The sp...	Human surface tissues , including the skin and gut lining , are host to many different species of bacteria . N . meningitidis is a species of bacteria that is only found in humans where it is able to colonise mucosal surfaces of the nasopharynx ( nose and throat ) . This association is normally harmless and at any one ...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "infectious", "diseases", "genetics", "and", "genomics", "microbiology", "eubacteria" ]	2007	Meningococcal Genetic Variation Mechanisms Viewed through Comparative Analysis of Serogroup C Strain FAM18
Mounting evidence suggests that glycans , rather than merely serving as a “shield” , contribute critically to antigenicity of the HIV envelope ( Env ) glycoprotein , representing critical antigenic determinants for many broadly neutralizing antibodies ( bNAbs ) . While many studies have focused on defining the role of ...	Carbohydrates on the HIV Env glycoprotein , previously often considered as a “shield” permitting immune evasion , can themselves represent targets for broadly neutralizing antibody ( bNAb ) recognition . Efforts to define the impact of individual glycans on bNAb recognition have clearly illustrated the critical nature ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "machine", "learning", "algorithms", "medicine", "and", "health", "sciences", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "applied", "mathematics", "immunology", "microbiology", "retroviruses", "viruses", "immunodeficiency", "viruses",...	2018	Exploiting glycan topography for computational design of Env glycoprotein antigenicity
West Nile virions incorporate 180 envelope ( E ) proteins that orchestrate the process of virus entry and are the primary target of neutralizing antibodies . The E proteins of newly synthesized West Nile virus ( WNV ) are organized into trimeric spikes composed of pre-membrane ( prM ) and E protein heterodimers . Durin...	West Nile virus ( WNV ) virions incorporate 180 envelope ( E ) proteins that are the primary target of neutralizing antibodies . As newly formed WNV virions are released from infected cells , the E proteins undergo a significant organizational change associated with maturation into an infectious virus . However , this ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/vaccines", "infectious", "diseases/viral", "infections", "immunology/immune", "response", "virology/host", "antiviral", "responses" ]	2008	Maturation of West Nile Virus Modulates Sensitivity to Antibody-Mediated Neutralization
In plants , pollinator adaptation is considered to be a major driving force for floral diversification and speciation . However , the genetic basis of pollinator adaptation is poorly understood . The orchid genus Ophrys mimics its pollinators' mating signals and is pollinated by male insects during mating attempts . In...	In plants , the extraordinary floral diversity has been suggested to be a consequence of divergent adaptation . However , the genetic basis of this process is poorly understood . In this study , we take advantage of the high specificity of plant-pollinator interactions in the sexually deceptive orchid genus Ophrys . We...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "science", "plant", "evolution", "plant", "biology", "gene", "expression", "genetics", "plant", "genetics", "population", "genetics", "biology", "evolutionary", "biology", "plant", "ecology", "evolutionary", "genetics", "genetics", "and", "genomics", "plant-env...	2012	The Genetic Basis of Pollinator Adaptation in a Sexually Deceptive Orchid
Although the detection rate is decreasing , the proportion of new cases with WHO grade 2 disability ( G2D ) is increasing , creating concern among policy makers and the Brazilian government . This study aimed to identify spatial clustering of leprosy and classify high-risk areas in a major leprosy cluster using the Sat...	Brazil has still not achieved the goal of leprosy elimination established by the World Health Organization . The diagnosis and treatment of leprosy are available and the country is striving to fully integrate leprosy services into the existing general health services . Access to information , diagnosis and treatment wi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "disabilities", "tropical", "diseases", "geographical", "locations", "census", "geoinformatics", "health", "care", "bacterial", "diseases", "research", "design", "neglected", "tropical", "diseases", "spatial", "analysis", "research...	2017	Spatial clustering and local risk of leprosy in São Paulo, Brazil
Rates of evolution differ widely among proteins , but the causes and consequences of such differences remain under debate . With the advent of high-throughput functional genomics , it is now possible to rigorously assess the genomic correlates of protein evolutionary rate . However , dissecting the correlations among e...	Proteins encoded within a given genome are known to evolve at drastically different rates . Through recent large-scale studies , researchers have measured a wide variety of properties for all proteins in yeast . We are interested to know how these properties relate to one another and to what extent they explain evoluti...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/comparative", "sequence", "analysis", "computational", "biology/evolutionary", "modeling", "molecular", "biology/bioinformatics", "computational", "biology/macromolecular", "sequence", "analysis", "evolutionary", "biology/bioinformatics", "genetics", "and", ...	2009	Integrated Assessment of Genomic Correlates of Protein Evolutionary Rate
As increasingly more genomes are sequenced , the vast majority of proteins may only be annotated computationally , given experimental investigation is extremely costly . This highlights the need for computational methods to determine protein functions quickly and reliably . We believe dividing a protein family into sub...	The knowledge of protein functions is central for understanding life at a molecular level and has huge biochemical and pharmaceutical implications . However , despite best research efforts , a substantial and ever-increasing number of proteins predicted by genome sequencing projects still lack functional annotations . ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "sequencing", "techniques", "dehydration", "(medicine)", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "enzymes", "enzymology", "serine", "proteases", "signs", "and", "symptoms", "protein", "structure", "lyases", "molecular", "bi...	2016	Isofunctional Protein Subfamily Detection Using Data Integration and Spectral Clustering
One of the striking features of evolution is the appearance of novel structures in organisms . Recently , Kirschner and Gerhart have integrated discoveries in evolution , genetics , and developmental biology to form a theory of facilitated variation ( FV ) . The key observation is that organisms are designed such that ...	One of the striking features of evolution is the appearance of novel structures in organisms . The origin of the ability to generate novelty is one of the main mysteries in evolutionary theory . The molecular mechanisms that enhance the evolution of novelty were recently integrated by Kirschner and Gerhart in their the...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/evolutionary", "modeling", "evolutionary", "biology/bioinformatics" ]	2008	Facilitated Variation: How Evolution Learns from Past Environments To Generalize to New Environments
The budding yeast Saccharomyces cerevisiae alters its gene expression profile in response to a change in nutrient availability . The PHO system is a well-studied case in the transcriptional regulation responding to nutritional changes in which a set of genes ( PHO genes ) is expressed to activate inorganic phosphate ( ...	How does a microorganism adapt to changes in its environment ? Phosphate metabolism in the budding yeast Saccharomyces cerevisiae serves as a model for investigating mechanisms involved in physiological adaptation . The nutrient inorganic phosphate ( Pi ) is essential for building nucleic acids and phospholipids; when ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology", "molecular", "biology", "genetics", "and", "genomics" ]	2008	Nutrient-Regulated Antisense and Intragenic RNAs Modulate a Signal Transduction Pathway in Yeast
Schistosomiasis , a neglected global pandemic , may be curtailed by blocking transmission of the parasite via its intermediate hosts , aquatic snails . Elucidating the genetic basis of snail-schistosome interaction is a key to this strategy . Here we map a natural parasite-resistance polymorphism from a Caribbean popul...	Schistosomes are water-borne blood-flukes that are transmitted by snail vectors . They infect over 200 million people in more than 70 countries and cause severe and chronic disability . Snails naturally vary in resistance to this parasite even within species , so bolstering snail resistance in the wild would block tran...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Hyperdiverse Gene Cluster in Snail Host Conveys Resistance to Human Schistosome Parasites
Plasmacytoid and conventional dendritic cells ( pDCs and cDCs ) arise from monocyte and dendritic progenitors ( MDPs ) and common dendritic progenitors ( CDPs ) through gene expression changes that remain partially understood . Here we show that the Ikaros transcription factor is required for DC development at multiple...	Dendritic cells ( DCs ) are an important component of the immune system , and exist as two major subtypes: conventional DCs ( cDCs ) which present antigen via major histocompatibility class II molecules , and plasmacytoid DCs ( pDCs ) which act mainly as producers of type-I interferon in response to viral infections . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "b", "vitamins", "chemical", "compounds", "biotin", "gene", "regulation", "organic", "compounds", "notch", "signaling", "cell", "differentiation", "developmental", "biology", "regulator", "genes", "genome", "analysis", "gene", "types", "genomics", "gene", "expression", ...	2018	Ikaros cooperates with Notch activation and antagonizes TGFβ signaling to promote pDC development
From early dinosaurs with as many as nine wrist bones , modern birds evolved to develop only four ossifications . Their identity is uncertain , with different labels used in palaeontology and developmental biology . We examined embryos of several species and studied chicken embryos in detail through a new technique all...	When birds diverged from nonavian dinosaurs , one of the key adaptations for flight involved a remodelling of the bones of the wrist . However , the correspondence between bird and dinosaur wrist bones is controversial . To identify the bones in the bird wrist , data can be drawn from two radically different sources: (...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "paleontology", "biology", "and", "life", "sciences", "evolutionary", "biology", "zoology" ]	2014	New Developmental Evidence Clarifies the Evolution of Wrist Bones in the Dinosaur–Bird Transition
Gene regulatory networks are a crucial aspect of systems biology in describing molecular mechanisms of the cell . Various computational models rely on random gene selection to infer such networks from microarray data . While incorporation of prior knowledge into data analysis has been deemed important , in practice , i...	We have developed a methodology that combines standard computational analysis of gene expression data with knowledge in the literature to identify pathways of gene and protein interactions . We extract the knowledge from PubMed citations using a tool ( SemRep ) that identifies specific relationships between genes or pr...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "computer", "and", "information", "sciences", "natural", "language", "processing", "network", "analysis", "regulatory", "networks", "biology", "and", "life", "sciences", "information", "technology", "computational", "biology" ]	2014	Augmenting Microarray Data with Literature-Based Knowledge to Enhance Gene Regulatory Network Inference

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