Split (3)

train · 24.8k rows

headings list	keywords list	title stringlengths 20 281	id stringlengths 20 20	toc stringlengths 57 522 ⌀	sections list	abstract list	summary list	year stringclasses 13 values
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "primates", "oncology", "mammals", "computational biology", "homo (human)", "genetics and genomics" ]	Integration of Genome and Chromatin Structure with Gene Expression Profiles To Predict c-MYC Recognition Site Binding and Function	journal.pcbi.0030063	null	[ [ "MYC plays a critical role in regulating cell proliferation , growth , apoptosis , and differentiation .", "Human malignancies are often associated with aberration of the c-MYC gene [1–3] .", "The diversity of its functions has been attributed to c-MYC's ability to activate or repress the transcriptio...	[ "The MYC genes encode nuclear sequence specific–binding DNA-binding proteins that are pleiotropic regulators of cellular function , and the c-MYC proto-oncogene is deregulated and/or mutated in most human cancers .", "Experimental studies of MYC binding to the genome are not fully consistent .", "While many c-M...	[ "c-MYC is an important proto-oncogene that controls the expression of many other genes , and MYC regulation is deranged in many cancers .", "Identifying c-MYC target genes is one of the key steps to understand both the biological role and molecular mechanism of c-MYC action .", "Defining the complete list of c-...	2007
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "physics/interdisciplinary physics", "cell biology/cell signaling", "cell biology/cell growth and division", "biophysics/theory and simulation", "computational biology/molecular dynamics", "computer science/numerical analysis and theoretical computing", "computational biology", "chemical biology", "...	Regulation of Signal Duration and the Statistical Dynamics of Kinase Activation by Scaffold Proteins	journal.pcbi.1000099	null	[ [ "In the context of signal transduction , cells integrate signals derived from membrane proximal events and convert them into the appropriate cell decision .", "Within the complex networks that integrate these signals lies a highly conserved motif involving the sequential activation of multiple protein kin...	[ "Scaffolding proteins that direct the assembly of multiple kinases into a spatially localized signaling complex are often essential for the maintenance of an appropriate biological response .", "Although scaffolds are widely believed to have dramatic effects on the dynamics of signal propagation , the mechanisms ...	[ "Signal transduction is the science of cellular communication .", "Cells detect signals from their environment and use them to make decisions such as whether or when to proliferate .", "Tight regulation of signal transduction is required for all healthy cells , and aberrant signaling leads to countless diseases...	2008
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biophysics/biomacromolecule-ligand interactions", "biochemistry/biomacromolecule-ligand interactions", "biochemistry/drug discovery" ]	FINDSITELHM: A Threading-Based Approach to Ligand Homology Modeling	journal.pcbi.1000405	null	[ [ "Ligand virtual screen is widely used in rational drug discovery [1] , [2] .", "The first stage of", "structure-based ligand screening is the prediction of the binding mode adopted by", "the small molecule complexed to its target receptor protein; a variety of algorithms", "have been developed...	[ "Ligand virtual screening is a widely used tool to assist in new pharmaceutical", "discovery .", "In practice , virtual screening approaches have a number of", "limitations , and the development of new methodologies is required .", "Previously ,", "we showed that remotely related proteins identified by th...	[ "As an integral part of drug development , high-throughput virtual screening is a", "widely used tool that could in principle significantly reduce the cost and time", "to discovery of new pharmaceuticals .", "In practice , virtual screening algorithms", "suffer from a number of limitations .", "The high s...	2009
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "systems biology", "developmental neuroscience", "theoretical biology", "neural homeostasis", "computational neuroscience", "sensory systems", "biology", "neuroscience" ]	Sparse Coding Models Can Exhibit Decreasing Sparseness while Learning Sparse Codes for Natural Images	journal.pcbi.1003182	null	[ [ "A central question in systems neuroscience is whether optimization principles can account for the architecture and physiology of the nervous system .", "One candidate principle is sparse coding ( SC ) , which posits that neurons encode input stimuli efficiently: stimuli should be encoded with maximum fid...	[ "The sparse coding hypothesis has enjoyed much success in predicting response properties of simple cells in primary visual cortex ( V1 ) based solely on the statistics of natural scenes .", "In typical sparse coding models , model neuron activities and receptive fields are optimized to accurately represent input ...	[ "The popular sparse coding theory posits that the receptive fields of visual cortical neurons maximize the efficiency of the neural representation of natural images .", "Models implementing this idea typically minimize a combination of the error in reconstructing natural images from neural activities , and the av...	2013
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "microbial evolution", "virology", "population genetics", "biology", "microbiology", "evolutionary biology" ]	Variation in RNA Virus Mutation Rates across Host Cells	journal.ppat.1003855	null	[ [ "RNA viruses show extremely high genetic variability and rapid evolution , ultimately due to their elevated rates of spontaneous mutation , which range from 10−6 to 10−4 substitutions per nucleotide per round of copying ( s/n/r ) .", "However , mutation rate estimates vary considerably , even for the same...	[ "It is well established that RNA viruses exhibit higher rates of spontaneous mutation than DNA viruses and microorganisms .", "However , their mutation rates vary amply , from 10−6 to 10−4 substitutions per nucleotide per round of copying ( s/n/r ) and the causes of this variability remain poorly understood .", ...	[ "RNA viruses show high rates of spontaneous mutation , a feature that profoundly influences viral evolution , disease emergence , the appearance of drug resistances , and vaccine efficacy .", "However , RNA virus mutation rates vary substantially and the factors determining this variability remain poorly understo...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "dengue virus", "children", "medicine and health sciences", "body fluids", "pathology and laboratory medicine", "pathogens", "microbiology", "pediatrics", "viruses", "age groups", "research design", "adults", "rna viruses", "signs and symptoms", "cohort studies", "pediatric infections"...	Incidence of Dengue Virus Infection in Adults and Children in a Prospective Longitudinal Cohort in the Philippines	journal.pntd.0004337	null	[ [ "Dengue virus ( DENV ) is the leading cause of vector-borne viral disease globally with an estimated 390 million infections and 96 million symptomatic cases occurring annually [1] .", "Ecologic and demographic changes are thought to be major contributing factors to the emergence of dengue over the past fe...	[ "The mean age of dengue has been increasing in some but not all countries .", "We sought to determine the incidence of dengue virus ( DENV ) infection in adults and children in a prospective cohort study in the Philippines where dengue is hyperendemic .", "A prospective cohort of subjects ≥6 months old in Cebu ...	[ "The average age of dengue has been increasing in some but not all dengue endemic countries .", "To investigate the age pattern of dengue in people of all ages ≥6 months old , a prospective community-based cohort study was undertaken in Cebu City , Philippines where dengue virus has been circulating for many deca...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "biochemistry", "infectious diseases", "zoonoses", "hantavirus", "coagulation factors", "proteins", "virology", "biology", "microbiology", "viral diseases" ]	Endothelial Cell Permeability during Hantavirus Infection Involves Factor XII-Dependent Increased Activation of the Kallikrein-Kinin System	journal.ppat.1003470	null	[ [ "The Bunyaviridae family encompasses viruses that cause numerous hemorrhagic fever diseases in humans .", "The genus Hantavirus includes Old World and New World viral lineages .", "Old World hantaviruses are widespread throughout Asia and Europe and are associated with the clinical syndrome , hemorrha...	[ "Hemorrhagic fever with renal syndrome ( HFRS ) and hantavirus pulmonary syndrome ( HPS ) are diseases caused by hantavirus infections and are characterized by vascular leakage due to alterations of the endothelial barrier .", "Hantavirus-infected endothelial cells ( EC ) display no overt cytopathology; consequen...	[ "Primary manifestations of disease due to hantavirus infections include systemic vascular leakage and hypotension for which the underlying mechanism is not known .", "A particularly perplexing finding is that the vascular endothelium remains intact during hantavirus infection and with no apparent cytopathic effec...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "dengue virus", "invertebrates", "medicine and health sciences", "air travel", "pathology and laboratory medicine", "china", "pathogens", "geographical locations", "microbiology", "social sciences", "human mobility", "animals", "viruses", "rna viruses", "insect vectors", "human geograp...	Seasonal and interannual risks of dengue introduction from South-East Asia into China, 2005-2015	journal.pntd.0006743	null	[ [ "The substantial growth and reach of human travel in recent decades has contributed to the global spread of infectious diseases [1–4] .", "In particular , air travel has allowed human hosts or carriers of pathogens to move long distances within the incubation period of infections [5] , such as the viruses...	[ "Due to worldwide increased human mobility , air-transportation data and mathematical models have been widely used to measure risks of global dispersal of pathogens .", "However , the seasonal and interannual risks of pathogens importation and onward transmission from endemic countries have rarely been quantified...	[ "Given the global expanding distribution of Aedes mosquitoes , dengue has established itself throughout the world’s tropical and subtropical regions in both endemic and epidemic transmission cycles , causing significant morbidity and mortality .", "Moreover , the rise of air travel over the past century has resul...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases", "hiv infections", "medicine and health sciences", "clinical immunology", "aids", "immune deficiency", "biology and life sciences", "immunology", "viral diseases" ]	CD4 Depletion in SIV-Infected Macaques Results in Macrophage and Microglia Infection with Rapid Turnover of Infected Cells	journal.ppat.1004467	null	[ [ "The interaction between HIV and CD4+ T-cells is complex , and may result in contrasting effects with respect to virus replication .", "On the one hand , CD4+ T-cells have a beneficial role as mediators of antiviral immune responses , both directly and by providing help for HIV-specific CD8+ T-cells and B...	[ "In rhesus macaques ( RMs ) , experimental depletion of CD4+ T-cells prior to SIV infection results in higher viremia and emergence of CD4-independent SIV-envelopes .", "In this study we used the rhesus recombinant anti-CD4 antibody CD4R1 to deplete RM CD4+ T-cells prior to SIVmac251 infection and investigate the...	[ "CD4+ T-cells are both mediators of antiviral immune response and critical targets for HIV replication .", "We have previously shown that experimental depletion of CD4+ T-cells prior to SIV infection in rhesus macaques results in higher viremia and the emergence of CD4-independent SIV-envelopes .", "The finding...	2014
[ "Introduction", "Design and implementation", "Results", "Availability and future directions" ]	[ "graphical user interfaces", "engineering and technology", "protein expression", "human factors engineering", "stem cells", "molecular biology techniques", "research and analysis methods", "computer and information sciences", "cell potency", "imaging techniques", "animal cells", "man-computer ...	Context-explorer: Analysis of spatially organized protein expression in high-throughput screens	journal.pcbi.1006384	null	[ [ "Emerging pieces of evidence stress the importance of a cell’s local microenvironment as a regulator of cellular phenotype and gene expression heterogeneity within cell populations .", "Microenvironmental parameters such as mechanical forces , cell to cell contact and endogenous signaling , all vary betwe...	[ "A growing body of evidence highlights the importance of the cellular microenvironment as a regulator of phenotypic and functional cellular responses to perturbations .", "We have previously developed cell patterning techniques to control population context parameters , and here we demonstrate context-explorer ( ...	[ "Cell behavior is influenced by cues that cells receive from their surrounding environment such as signals secreted from other cells and cell-to-cell contact .", "These factors are spatially heterogeneous and cells at different positions within a colony will experience varying degrees of influence from such envir...	2019
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "pathology and laboratory medicine", "togaviruses", "chikungunya infection", "pathogens", "tropical diseases", "microbiology", "geographical locations", "animals", "alphaviruses", "viruses", "developmental biology", "chikungunya virus", "r...	Evidence of vertical transmission of Zika virus in field-collected eggs of Aedes aegypti in the Brazilian Amazon	journal.pntd.0006594	null	[ [ "The arboviruses transmitted by mosquitoes of the genus Aedes , like chikungunya virus ( CHIKV ) , dengue virus ( DENV ) , Zika virus ( ZIKV ) , and yellow fever virus ( YFV ) have reached threatening numbers in the last years , with a huge impact on public health systems in several countries throughout the w...	[ "Arboviruses are viruses transmitted to humans and other animals by the bite of hematophagous arthropods .", "Infections caused by chikungunya virus ( CHIKV ) , dengue virus ( DENV ) , Zika virus ( ZIKV ) , and the deadlier yellow fever virus ( YFV ) are current public health problems in several countries , mainl...	[ "The control of the vast majority of arbovirus infections relies on entomological measures to reduce mosquito infestation .", "Therefore , this study analyzed the use of ovitraps for arboviral surveillance in a mid-size city of the Amazonas state , Brazil .", "We found one larva pool infected with chikungunya v...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "clinical research design" ]	Cost-Effectiveness Analysis of Three Leprosy Case Detection Methods in Northern Nigeria	journal.pntd.0001818	null	[ [ "Leprosy is a communicable disease caused by a bacillus , Mycobacterium Leprae , which can lead to permanent disability among sufferers with significant psychosocial and economic burden .", "The disease causes skin lesions and nerve damages which progress to deformities of the eyes , hands and feet [1]–[2...	[ "Despite several leprosy control measures in Nigeria , child proportion and disability grade 2 cases remain high while new cases have not significantly reduced , suggesting continuous spread of the disease .", "Hence , there is the need to review detection methods to enhance identification of early cases for effe...	[ "Reported increases in child proportions and disability grade 2 cases in Nigeria suggest that leprosy disease is still spreading in the country .", "This indicates the need to review case finding strategies to improve case detection for effective control of the disease .", "It was necessary that available metho...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics", "biology", "microbiology", "molecular cell biology", "genetics and genomics" ]	The Min System and Nucleoid Occlusion Are Not Required for Identifying the Division Site in Bacillus subtilis but Ensure Its Efficient Utilization	journal.pgen.1002561	null	[ [ "Mechanisms that regulate cell division in time and space are of fundamental importance to biology because they ensure equal partitioning of DNA into newborn cells .", "Failure to do so can lead to cell death .", "The earliest observable event in cell division in rod-shaped bacteria such as Escherichi...	[ "Precise temporal and spatial control of cell division is essential for progeny survival .", "The current general view is that precise positioning of the division site at midcell in rod-shaped bacteria is a result of the combined action of the Min system and nucleoid ( chromosome ) occlusion .", "Both systems p...	[ "How organisms regulate biological processes so that they occur at the correct place within the cell is a fundamental question in research .", "Spatial regulation of cell division is vital to ensure equal partitioning of DNA into newborn cells .", "Correct positioning of the division site at the cell centre in ...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "neuroscience/behavioral neuroscience", "neuroscience/sensory systems", "computational biology/computational neuroscience", "evolutionary biology/animal behavior", "computational biology/systems biology" ]	The Morphology of the Rat Vibrissal Array: A Model for Quantifying Spatiotemporal Patterns of Whisker-Object Contact	journal.pcbi.1001120	null	[ [ "Animals use movements to acquire and refine incoming sensory data as they explore and navigate the environment .", "This means that – except under rare conditions most often found in the laboratory – sensing is an active process , constrained and shaped by the biomechanics of the muscles and by the mater...	[ "In all sensory modalities , the data acquired by the nervous system is shaped by the biomechanics , material properties , and the morphology of the peripheral sensory organs .", "The rat vibrissal ( whisker ) system is one of the premier models in neuroscience to study the relationship between physical embodimen...	[ "Animals move in order to sense the world .", "Sensing is thus an active process , constrained by muscle biomechanics and by the material , shape , and structure of the sensing organs .", "The rat vibrissal system provides an ideal model to examine how the physical embodiment of a sensory array shapes the sensi...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "cell physiology", "carbohydrate metabolism", "medicine and health sciences", "applied mathematics", "enzymology", "cell metabolism", "simulation and modeling", "algorithms", "mathematics", "genome analysis", "enzyme metabolism", "pharmacology", "drug metabolism", "enzyme chemistry", "re...	Increasing consensus of context-specific metabolic models by integrating data-inferred cell functions	journal.pcbi.1006867	null	[ [ "Genome-scale metabolic models ( GeMs ) have been widely used for model-guided analysis of large omics datasets , since they provide cellular context to these data by establishing a mechanistic link from genotype to phenotype .", "GeMs include all reactions in an organism .", "Since not all enzymes ar...	[ "Genome-scale metabolic models provide a valuable context for analyzing data from diverse high-throughput experimental techniques .", "Models can quantify the activities of diverse pathways and cellular functions .", "Since some metabolic reactions are only catalyzed in specific environments , several algorithm...	[ "Genome-scale models of human metabolism have facilitated numerous exciting discoveries regarding human physiology and therapeutics .", "The accuracy of results from such studies requires that models capture the tissue or cell-type specific metabolism .", "In hopes to obtain accurate models , several algorithms...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "embryology", "organism development", "gene expression", "genetics", "organogenesis", "biology", "anatomy and physiology", "evolutionary biology", "pattern formation", "evolutionary developmental biology" ]	A Combination of Activation and Repression by a Colinear Hox Code Controls Forelimb-Restricted Expression of Tbx5 and Reveals Hox Protein Specificity	journal.pgen.1004245	null	[ [ "Forelimbs and hindlimbs are derivatives of the lateral plate mesoderm ( LPM ) that arise at fixed positions along the vertebrate body axis .", "Limb formation is initiated by limb induction signals from axial tissues [1] .", "The presumptive limb-forming regions initially express two T-box genes prio...	[ "Tight control over gene expression is essential for precision in embryonic development and acquisition of the regulatory elements responsible is the predominant driver for evolution of new structures .", "Tbx5 and Tbx4 , two genes expressed in forelimb and hindlimb-forming regions respectively , play crucial rol...	[ "The acquisition of limbs during vertebrate evolution was a very successful innovation that enabled this group of species to diversify and colonise land .", "It has become clear recently that the primary driver behind the evolution of new structures , such as limbs , is the acquisition of novel regulatory element...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "mycology", "model organisms", "fungal evolution", "microbial evolution", "microbial pathogens", "yeast and fungal models", "biology", "microbiology", "yeast" ]	Genetic and Genomic Architecture of the Evolution of Resistance to Antifungal Drug Combinations	journal.pgen.1003390	null	[ [ "The evolution of drug resistance is a ubiquitous phenomenon that has a profound impact on human health .", "With the widespread deployment of antimicrobial agents in both clinical and environmental settings , the rate at which resistance evolves in pathogen populations far outpaces the rate at which new ...	[ "The evolution of drug resistance in fungal pathogens compromises the efficacy of the limited number of antifungal drugs .", "Drug combinations have emerged as a powerful strategy to enhance antifungal efficacy and abrogate drug resistance , but the impact on the evolution of drug resistance remains largely unexp...	[ "Fungal infections are a leading cause of mortality worldwide and are difficult to treat due to the limited number of antifungal drugs , whose effectiveness is compromised by the emergence of drug resistance .", "A powerful strategy to combat drug resistance is combination therapy .", "Inhibiting the molecular ...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics and genomics/chromosome biology" ]	Csm4-Dependent Telomere Movement on Nuclear Envelope Promotes Meiotic Recombination	journal.pgen.1000196	null	[ [ "Meiotic recombination promotes the faithful segregation of homologous chromosomes at meiosis I ( MI ) by creating physical linkages between the homologs [1] , [2] .", "Recombination produces two types of products: crossovers ( COs ) and non-crossovers ( NCOs ) .", "Only COs mature into exchanges betw...	[ "During meiotic prophase , chromosomes display rapid movement , and their telomeres attach to the nuclear envelope and cluster to form a “chromosomal bouquet . ”", "Little is known about the roles of the chromosome movement and telomere clustering in this phase .", "In budding yeast , telomere clustering is pro...	[ "Meiosis is a specialized cell division that produces haploid gametes .", "Homologous recombination plays a pivotal role in the segregation of homologous chromosomes during meiosis I by creating physical linkages between the chromosomes .", "Drastic reorganization of chromosomes in the nucleus is a prominent fe...	2008
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "invertebrates", "dengue virus", "medicine and health sciences", "pathology and laboratory medicine", "engineering and technology", "transportation", "pathogens", "geographical locations", "microbiology", "social sciences", "human mobility", "animals", "transportation infrastructure", "roa...	The introduction of dengue follows transportation infrastructure changes in the state of Acre, Brazil: A network-based analysis	journal.pntd.0006070	null	[ [ "The successful invasion of a parasite into a new place is the result of the interaction between two players: the invading species and the invaded community .", "In the context of dengue , the invaded community is composed of two main species: human hosts and mosquitoes of the species Ae .", "aegypti ...	[ "Human mobility , presence and passive transportation of Aedes aegypti mosquito , and environmental characteristics are a group of factors which contribute to the success of dengue spread and establishment .", "To understand this process , we assess data from dengue national and municipal basins regarding populat...	[ "The present ecological study is aimed at characterizing introduction and spread of dengue in the state of Acre , located in Brazil’s north region .", "We use sociodemographic and entomological data from the year 2000 , when the first case was registered in Acre , up to 2015 , when it was already endemic in most ...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "evolutionary biology/evolutionary ecology", "evolutionary biology/evolutionary and comparative genetics", "genetics and genomics/complex traits" ]	Speeding Up Microevolution: The Effects of Increasing Temperature on Selection and Genetic Variance in a Wild Bird Population	journal.pbio.1000585	The authors show that environmental variation may lead to a positive association between the annual strength of selection and expression of genetic variance in a wild bird population, which can speed up microevolution and have important consequences for how fast natural populations adapt to environmental changes.	[ [ "Predicting an evolutionary response to selection in a phenotypic trait requires knowledge of the strength of selection acting on the trait and its genetic basis .", "Although it has long been recognized that the strength , and direction , of selection may vary with environmental conditions ( e . g . , [1...	[ "The amount of genetic variance underlying a phenotypic trait and the strength of selection acting on that trait are two key parameters that determine any evolutionary response to selection .", "Despite substantial evidence that , in natural populations , both parameters may vary across environmental conditions ,...	[ "The speed of evolutionary change in a phenotypic trait is determined by two key components: the amount of genetic variance underlying the trait and the strength of selection acting on it .", "Many studies have shown that both selection and expression of genetic variance may depend on the environmental conditions...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "immune cells", "vesicles", "pathology and laboratory medicine", "enzyme-linked immunoassays", "hepacivirus", "antigen-presenting cells", "pathogens", "immunology", "biological cultures", "microbiology", "hepatoma cells", "viruses", "animal models", "dendr...	Hepatitis C Virus Stimulates Murine CD8α-Like Dendritic Cells to Produce Type I Interferon in a TRIF-Dependent Manner	journal.ppat.1005736	null	[ [ "Hepatitis C virus ( HCV ) infection constitutes a major global health problem since more than 140 million people suffer from chronic sequelae of the infection [1] .", "Once infected , approximately 80% of the individuals are not able to clear the pathogen and develop a chronic infection that often is ass...	[ "Hepatitis C virus ( HCV ) induces interferon ( IFN ) stimulated genes in the liver despite of distinct innate immune evasion mechanisms , suggesting that beyond HCV infected cells other cell types contribute to innate immune activation .", "Upon coculture with HCV replicating cells , human CD141+ myeloid dendrit...	[ "HCV is an RNA virus that , following exposure , in most cases establishes chronic infection .", "The virus has evolved numerous immune evasion strategies , including direct interference with interferon production .", "Nevertheless , HCV infection activates interferon-stimulated genes in the liver , implying th...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "circuit models", "auditory system", "central nervous system", "synapses", "computational neuroscience", "biology", "sensory systems", "neuroscience", "neurophysiology" ]	Coexistence of Lateral and Co-Tuned Inhibitory Configurations in Cortical Networks	journal.pcbi.1002161	null	[ [ "The firing properties and receptive fields of neurons in sensory cortex are heterogeneous and can vary both quantitatively and qualitatively with changing stimuli .", "The diverse responses are well exemplified in the primary auditory cortex ( A1 ) , where firing ranges from phasic ( only at stimulus ons...	[ "The responses of neurons in sensory cortex depend on the summation of excitatory and inhibitory synaptic inputs .", "How the excitatory and inhibitory inputs scale with stimulus depends on the network architecture , which ranges from the lateral inhibitory configuration where excitatory inputs are more narrowly ...	[ "The cerebral cortex contains a network of electrically active cells ( neurons ) interconnected by synapses , which may be excitatory ( tending to increase activity ) or inhibitory .", "Network activity , i . e . , the ensemble of activity patterns of the individual cells , is driven by input from the sense organ...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "computational neuroscience", "biology", "sensory systems", "neuroscience" ]	Computing with Neural Synchrony	journal.pcbi.1002561	null	[ [ "Neuronal synchronization is ubiquitous in the nervous system [1] , [2] .", "In the retina , neighboring cells are often synchronized at a fine timescale [3] , [4] , and relative spike timing carries information about visual stimuli [5] .", "Visual and somatosensory stimulation also elicits synchroniz...	[ "Neurons communicate primarily with spikes , but most theories of neural computation are based on firing rates .", "Yet , many experimental observations suggest that the temporal coordination of spikes plays a role in sensory processing .", "Among potential spike-based codes , synchrony appears as a good candid...	[ "How does the brain compute ?", "Traditional theories of neural computation describe the operating function of neurons in terms of average firing rates , with the timing of spikes bearing little information .", "However , numerous studies have shown that spike timing can convey information and that neurons are ...	2012
[ "Introduction", "Materials and Methods", "Results and Discussion" ]	[ "biology", "computational biology", "microbiology", "biophysics", "macromolecular structure analysis" ]	Biochemical, Mutational and In Silico Structural Evidence for a Functional Dimeric Form of the Ornithine Decarboxylase from Entamoeba histolytica	journal.pntd.0001559	null	[ [ "Amoebiasis is an infectious disease caused by single-celled parasitic protozoan Entamoeba histolytica .", "Parasitic amoeba infects liver and intestine , which may cause mild diarrhea and serious dysentery with bloody and mucoid stool .", "If untreated , the parasite can cause life-threatening hemorr...	[ "Entamoeba histolytica is responsible for causing amoebiasis .", "Polyamine biosynthesis pathway enzymes are potential drug targets in parasitic protozoan diseases .", "The first and rate-limiting step of this pathway is catalyzed by ornithine decarboxylase ( ODC ) .", "ODC enzyme functions as an obligate dim...	[ "E . histolytica genome sequence divulged the existence of ornithine decarboxylase enzyme that performs the first-rate limiting catalytic step of polyamine biosynthetic pathway .", "ODC enzyme is a potent therapeutic target in many eukaryotic disease causing pathogens .", "DFMO , a potent substrate analogue inh...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Prioritising Infectious Disease Mapping	journal.pntd.0003756	null	[ [ "Maps provide an essential evidence-base to support progress towards global health commitments [1] .", "For example , they provide important baseline estimates of disease limits [2–7] , transmission [8–10] and clinical burden [11–14]; underpin surveillance systems and outbreak tracking [15 , 16]; help tar...	[ "Increasing volumes of data and computational capacity afford unprecedented opportunities to scale up infectious disease ( ID ) mapping for public health uses .", "Whilst a large number of IDs show global spatial variation , comprehensive knowledge of these geographic patterns is poor .", "Here we use an object...	[ "Maps have long been used to not only visualise , but also to inform infectious disease control efforts , identify and predict areas of greatest risk of specific diseases , and better understand the epidemiology of disease over various spatial scales .", "In spite of the utilities of such outputs , globally compr...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "bacteriology", "sequencing techniques", "cell cycle and cell division", "cell processes", "microbiology", "cloning", "genome sequencing", "genetic elements", "bacterial genetics", "molecular biology techniques", "microbial genetics", "microbial genomics", "research and analysis methods", ...	DNA Replication Control Is Linked to Genomic Positioning of Control Regions in Escherichia coli	journal.pgen.1006286	null	[ [ "The circular chromosome of Escherichia coli is replicated bidirectionally from a single origin , oriC .", "The DnaA protein is responsible for replication initiation [1] .", "DnaA belongs to the AAA+ ( ATPases Associated with diverse Activities ) proteins and can bind both ATP and ADP with similar hi...	[ "Chromosome replication in Escherichia coli is in part controlled by three non-coding genomic sequences , DARS1 , DARS2 , and datA that modulate the activity of the initiator protein DnaA .", "The relative distance from oriC to the non-coding regions are conserved among E . coli species , despite large variations...	[ "Replication of the E . coli chromosome is the central event in the cell cycle , with the control of replication enforced at the level of initiation .", "DnaA is the key protein responsible for initiation at the origin of replication ( oriC ) , and is active in this when bound to ATP and inactive when bound to AD...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[]	Distinct DNA-binding surfaces in the ATPase and linker domains of MutLγ determine its substrate specificities and exert separable functions in meiotic recombination and mismatch repair	journal.pgen.1006722	null	[ [ "During meiosis , cells undergo DNA recombination to form crossovers between homologous pairs of chromosomes ( homologs ) .", "Crossovers promote accurate segregation of homologs at the first meiotic division and increase genetic diversity by breaking up linkage groups [1] .", "Recombination is initia...	[ "Mlh1-Mlh3 ( MutLγ ) is a mismatch repair factor with a central role in formation of meiotic crossovers , presumably through resolution of double Holliday junctions .", "MutLγ has DNA-binding , nuclease , and ATPase activities , but how these relate to one another and to in vivo functions are unclear .", "Here ...	[ "Sexual reproduction involves the fusion of two gametes that each contain half of the DNA from each parent .", "These gametes are generated through a specialized cellular division called meiosis .", "During meiosis , the cell faces the challenge of identifying the appropriate pairs of chromosomes that need to b...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "diabetes mellitus", "type 2 diabetes", "metabolic disorders", "medicine and health sciences" ]	Possible Role of Interleukin-1β in Type 2 Diabetes Onset and Implications for Anti-inflammatory Therapy Strategies	journal.pcbi.1003798	null	[ [ "Despite more than 350 million patients worldwide and the concomitant expensive socioeconomic burden , the pathogenesis of type 2 diabetes ( T2D ) is not yet completely understood .", "T2D is a progressive disease .", "The most important physiological components of T2D are insulin resistance , which i...	[ "Increasing evidence of a role of chronic inflammation in type 2 diabetes progression has led to the development of therapies targeting the immune system .", "We develop a model of interleukin-1β dynamics in order to explain principles of disease onset .", "The parameters in the model are derived from in vitro ...	[ "Insulin resistance and relative insulin deficiency are two hallmarks of type 2 diabetes .", "While insulin resistance is always present in the early phase , it is β-cell failure that determines the pace of the disease onset .", "Increasing evidence that the immune system is activated and plays an important rol...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "systems biology", "biochemistry", "plant science", "mathematics", "plant biology", "applied mathematics", "biology", "computational biology", "genetics and genomics" ]	Functional Analysis of Metabolic Channeling and Regulation in Lignin Biosynthesis: A Computational Approach	journal.pcbi.1002769	null	[ [ "Lignin is a phenolic heteropolymer in the secondary cell walls of vascular plants .", "It is derived mainly from three hydroxycinnamyl alcohol monomers , namely p-coumaryl , coniferyl , and sinapyl alcohols , which , when incorporated into the lignin polymer , give rise to p-hydroxyphenyl ( H ) , guaiacy...	[ "Lignin is a polymer in secondary cell walls of plants that is known to have negative impacts on forage digestibility , pulping efficiency , and sugar release from cellulosic biomass .", "While targeted modifications of different lignin biosynthetic enzymes have permitted the generation of transgenic plants with ...	[ "The organization of cooperating enzymes into complexes is a pervasive feature of metabolism .", "In particular , this phenomenon has been shown to participate in the regulation of flux through the networks of both primary and secondary metabolism in plants .", "It remains a challenging task to unravel the orga...	2012
[ "Introduction", "Results and discussion", "Methods" ]	[ "functional genomics", "genome evolution", "statistics", "metabolic networks", "operons", "regression analysis", "genomic databases", "mathematics", "metabolites", "network analysis", "genome analysis", "dna", "research and analysis methods", "computer and information sciences", "prokary...	Metabolic adaptations underlying genome flexibility in prokaryotes	journal.pgen.1007763	null	[ [ "Prokaryotes exhibit remarkable genome flexibility , with strains from the same species often containing dramatically different gene content [1–4] .", "Intraspecific differences in gene content are often characterized by a “core” genome ( genes common to all strains ) and “accessory” genome ( genes found ...	[ "Even across genomes of the same species , prokaryotes exhibit remarkable flexibility in gene content .", "We do not know whether this flexible or “accessory” content is mostly neutral or adaptive , largely due to the lack of explicit analyses of accessory gene function .", "Here , across 96 diverse prokaryotic...	[ "Recent and rapid advancements in genome sequencing technologies have revealed key insights into the world of bacteria and archaea .", "One puzzling aspect uncovered by these studies is the following: genomes of the same species can often look very different .", "Specifically , some “core” genes are maintained ...	2018
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "developmental biology", "ecology", "caenorhabditis", "evolutionary biology", "genetics and genomics" ]	A Caenorhabditis elegans Wild Type Defies the Temperature–Size Rule Owing to a Single Nucleotide Polymorphism in tra-3	journal.pgen.0030034	null	[ [ "For many decades biologists have been intrigued by the relation between body size and temperature .", "It was discovered that ectotherms—animals that maintain their body temperature by absorbing heat from the surrounding environment such as fish and all invertebrates—reproduce later at a larger size when...	[ "Ectotherms rely for their body heat on surrounding temperatures .", "A key question in biology is why most ectotherms mature at a larger size at lower temperatures , a phenomenon known as the temperature–size rule .", "Since temperature affects virtually all processes in a living organism , current theories to...	[ "Biologists are fascinated by variation in body size , which is hardly surprising , considering that the range of body sizes spans orders of magnitude from bacteria to blue whales .", "Even within species , body sizes can vary dramatically .", "This intraspecies variation is intriguing because it suggests stron...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "protein kinase signaling cascade", "signal transduction", "molecular cell biology", "immune physiology", "cytokines", "physiology", "biology", "anatomy and physiology", "signaling cascades" ]	Protein Kinase Activity of Phosphoinositide 3-Kinase Regulates Cytokine-Dependent Cell Survival	journal.pbio.1001515	The protein kinase activity of PI3K phosphorylates specific serine residues in growth factor receptors to promote cell survival; these events are constitutively activated in some leukemias.	[ [ "A key mechanism by which growth factors and cytokines promote cell survival is via the phosphoinositide 3-kinase ( PI3K ) pathway and constitutive PI3K signaling is known to promote autonomous cell survival and transformation [1] .", "The recruitment and activation of class 1A isoforms of PI3K ( p110α , ...	[ "The dual specificity protein/lipid kinase , phosphoinositide 3-kinase ( PI3K ) , promotes growth factor-mediated cell survival and is frequently deregulated in cancer .", "However , in contrast to canonical lipid-kinase functions , the role of PI3K protein kinase activity in regulating cell survival is unknown ....	[ "The ability of cells to survive in the absence of proliferation ( cell division ) , differentiation ( cell maturation ) or activation allows tissues to maintain cell populations that are poised for rapid responses to damage , infections , or other physiological demands .", "While this “survival-only” response is...	2013
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "cell biology", "protein translation", "fungal genetics", "gene expression", "genetics", "translation termination", "biology and life sciences", "peroxisomes", "cellular structures and organelles" ]	Ribosomal Readthrough at a Short UGA Stop Codon Context Triggers Dual Localization of Metabolic Enzymes in Fungi and Animals	journal.pgen.1004685	null	[ [ "Although translation of mRNA usually occurs with high fidelity , different recoding mechanisms exist that alter the amino acid sequence of the resulting polypeptide [1] , [2] .", "Programmed ribosomal frameshifting and stop codon readthrough are commonly used to maximize genomic coding capacity in viruse...	[ "Translation of mRNA into a polypeptide chain is a highly accurate process .", "Many prokaryotic and eukaryotic viruses , however , use leaky termination of translation to optimize their coding capacity .", "Although growing evidence indicates the occurrence of ribosomal readthrough also in higher organisms , a...	[ "Eukaryotic organisms use various strategies to generate protein isoforms with different function or intracellular localization from a single gene .", "While differential splicing of mRNA is the most common mechanism to expand the number of encoded proteins , translational readthrough of stop codons is an alterna...	2014
[ "Introduction", "Results", "Discussion", "Experimental Procedures" ]	[ "phosphorylation", "rna interference", "enzyme-linked immunoassays", "chemical compounds", "organic compounds", "immunoprecipitation", "basic amino acids", "amino acids", "epigenetics", "immunologic techniques", "cellular structures and organelles", "research and analysis methods", "lipids",...	PI(4)P Promotes Phosphorylation and Conformational Change of Smoothened through Interaction with Its C-terminal Tail	journal.pbio.1002375	The signaling molecule Hedgehog promotes the production and release of the specific phospholipid PI(4)P, which directly interacts with Smoothened, activating it via phosphorylation and accumulation in the cilia.	[ [ "The Hedgehog ( Hh ) signaling pathway plays important roles in both embryonic development and adult tissue homeostasis [1–3] .", "In Drosophila , the Hh signal is transduced through a receptor system at the plasma membrane , which includes the receptor complex Patched-Interference Hh ( Ptc-Ihog ) and the...	[ "In Hedgehog ( Hh ) signaling , binding of Hh to the Patched-Interference Hh ( Ptc-Ihog ) receptor complex relieves Ptc inhibition on Smoothened ( Smo ) .", "A longstanding question is how Ptc inhibits Smo and how such inhibition is relieved by Hh stimulation .", "In this study , we found that Hh elevates produ...	[ "The Hedgehog ( Hh ) signaling pathway plays important roles in both embryonic development and adult tissue homeostasis .", "A critical step in Hh signal transduction is the inhibition of Smoothened ( Smo ) , an atypical G protein-coupled receptor ( GPCR ) , by the Hh receptor Patched ( Ptc ) .", "It is a longs...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "mechanisms of signal transduction", "signaling networks", "membrane receptor signaling", "growth factors", "signaling pathways", "biophysics simulations", "biochemistry simulations", "proteins", "biology", "biophysics", "systems biology", "biochemistry", "biochemical simulations", "signal...	Model-Based Analysis of HER Activation in Cells Co-Expressing EGFR, HER2 and HER3	journal.pcbi.1003201	null	[ [ "The HER family ( Human Epidermal growth factor Receptor , also known as the ErbB family ) of cell surface receptors plays critical roles in normal cell physiology , development , and cancer pathophysiology [1] , [2] , [3] , [4] .", "The family consists of the four closely related transmembrane receptor t...	[ "The HER/ErbB family of receptor tyrosine kinases drives critical responses in normal physiology and cancer , and the expression levels of the various HER receptors are critical determinants of clinical outcomes .", "HER activation is driven by the formation of various dimer complexes between members of this rece...	[ "A family of cell surface molecules called the HER receptor family plays important roles in normal physiology and cancer .", "This family has four members , HER1-4 .", "These receptors convert signals received from the extracellular environment into cell decisions such as growth and survival – a process termed ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	SPOC1-Mediated Antiviral Host Cell Response Is Antagonized Early in Human Adenovirus Type 5 Infection	journal.ppat.1003775	null	[ [ "DNA viruses require nuclear transport of their genomes to productively infect the host cell and initiate efficient replication .", "Simultaneously , introduction of viral nucleic acids into the host cell nucleus triggers danger signals , and activates DDR ( DNA damage response ) prior to cell cycle arres...	[ "Little is known about immediate phases after viral infection and how an incoming viral genome complex counteracts host cell defenses , before the start of viral gene expression .", "Adenovirus ( Ad ) serves as an ideal model , since entry and onset of gene expression are rapid and highly efficient , and mechanis...	[ "Viruses have acquired functions that target and modulate host cell signaling and diverse regulatory cascades , leading to efficient viral propagation .", "During the course of productive infection , Ad gene products manipulate destruction pathways to prevent viral clearance or cell death prior to viral genome am...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/microbial evolution and genomics", "cell biology", "microbiology", "evolutionary biology", "molecular biology" ]	Allelic Exchange of Pheromones and Their Receptors Reprograms Sexual Identity in Cryptococcus neoformans	journal.pgen.1000860	null	[ [ "One of the most important processes that occurs in cells is the specification of cell type , and it is by this process that cells adopt the genetic state that governs their subsequent behaviors .", "One mechanism of cell type-specification is the expression of genes encoded only in a given cell type .", ...	[ "Cell type specification is a fundamental process that all cells must carry out to ensure appropriate behaviors in response to environmental stimuli .", "In fungi , cell identity is critical for defining “sexes” known as mating types and is controlled by components of mating type ( MAT ) loci .", "MAT–encoded g...	[ "All organisms that undergo sexual reproduction carry out specific mechanisms to establish different sexes .", "In fungi , sexual identity is typically determined by components housed within specialized regions of chromosomes known as mating-type ( MAT ) loci .", "MAT–encoded genes function to define sexes via ...	2010
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "genome-wide association studies", "medicine and health sciences", "diabetic endocrinology", "gene regulation", "cell cycle and cell division", "cell processes", "hormones", "endocrine physiology", "genome analysis", "mammalian genomics", "insulin", "endocrinology", "gene expression", "gen...	The Transcription Factor Nfatc2 Regulates β-Cell Proliferation and Genes Associated with Type 2 Diabetes in Mouse and Human Islets	journal.pgen.1006466	null	[ [ "Human genome-wide association studies ( GWAS ) have identified genetic variation at >130 loci that is associated with various traits linked to the development of T2D .", "The vast majority of the T2D-associated SNPs occur in intergenic or intronic regions , implying that they are involved in gene regulat...	[ "Human genome-wide association studies ( GWAS ) have shown that genetic variation at >130 gene loci is associated with type 2 diabetes ( T2D ) .", "We asked if the expression of the candidate T2D-associated genes within these loci is regulated by a common locus in pancreatic islets .", "Using an obese F2 mouse ...	[ "Genome-wide association studies ( GWAS ) and linkage studies provide a powerful way to establish a causal connection between a gene locus and a physiological or pathophysiological phenotype .", "We wondered if candidate genes associated with type 2 diabetes in human populations , in addition to being causal for ...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "plant science", "infectious disease epidemiology", "epidemiology", "plant pathology", "biology and life sciences" ]	Burden of Disease Measured by Disability-Adjusted Life Years and a Disease Forecasting Time Series Model of Scrub Typhus in Laiwu, China	journal.pntd.0003420	null	[ [ "Scrub typhus , also known as tsutsugamushi disease , is a zoonosis transmitted by chigger bites ( larval trombiculid mites ) and infection with Orientia tsutsugamushi ( O . tsutsugamushi ) , a Gram-negative obligate intracellular bacterium .", "Globally , scrub typhus is distributed widely in the Pacific...	[ "Laiwu District is recognized as a hyper-endemic region for scrub typhus in Shandong Province , but the seriousness of this problem has been neglected in public health circles .", "A disability-adjusted life years ( DALYs ) approach was adopted to measure the burden of scrub typhus in Laiwu , China during the per...	[ "Scrub typhus , also known as tsutsugamushi disease , is a zoonosis transmitted by chigger bites ( larval trombiculid mites ) and the pathogen Orientia tsutsugamushi ( O . tsutsugamushi ) , a Gram-negative obligate intracellular bacterium .", "It is distributed widely in the Pacific regions of Asia , and the isla...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Burden of Mycobacterium ulcerans Disease (Buruli Ulcer) and the Underreporting Ratio in the Territory of Songololo, Democratic Republic of Congo	journal.pntd.0002563	null	[ [ "Cutaneous infection by Mycobacterium ulcerans , also known as Buruli ulcer ( BU ) , represents the third most common mycobacterial disease in the world after tuberculosis and leprosy [1] .", "In Africa , children under 15 years old have the highest incidence , but healthy persons of all ages , races , an...	[ "Cutaneous infection by Mycobacterium ulcerans , also known as Buruli ulcer ( BU ) , represents the third most common mycobacterial disease in the world after tuberculosis and leprosy .", "Data on the burden of BU disease in the Democratic Republic of Congo are scanty .", "This study aimed to estimate the preva...	[ "Buruli ulcer ( BU ) is a necrotizing bacterial infection of skin , subcutaneous tissue and bone , caused by an environmental pathogen , Mycobacterium ulcerans .", "BU is considered as one of the Neglected Tropical Diseases with a poorly known global prevalence , and mainly affects remote rural African communitie...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "taxonomy", "medicine and health sciences", "body fluids", "pathology and laboratory medicine", "pathogens", "immunology", "microbiology", "hepatitis b virus", "liver diseases", "viruses", "preventive medicine", "phylogenetics", "data management", "phylogenetic analysis", "gastroenterolo...	Hepatitis B and hepatitis D virus infections in the Central African Republic, twenty-five years after a fulminant hepatitis outbreak, indicate continuing spread in asymptomatic young adults	journal.pntd.0006377	null	[ [ "Hepatitis B virus ( HBV ) infection can be prevented by vaccination , which can obviate progression of chronic liver disease to cirrhosis , liver failure and hepatocellular carcinoma .", "However , owing to limited access to vaccination during the past 30 years in resource-poor countries , more than 2 bi...	[ "Hepatitis delta virus ( HDV ) increases morbidity in Hepatitis B virus ( HBV ) -infected patients .", "In the mid-eighties , an outbreak of HDV fulminant hepatitis ( FH ) in the Central African Republic ( CAR ) killed 88% of patients hospitalized in Bangui .", "We evaluated infections with HBV and HDV among st...	[ "In the Central African Republic ( CAR ) , due to 20 years of conflict , the health system has been disorganized .", "This could contribute to maintenance of high transmission levels of Hepatitis B Virus ( HBV ) and its satellite Hepatitis Delta Virus ( HDV ) .", "This work studies the evolution of both infecti...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "health education and awareness", "health services research", "tropical diseases", "geographical locations", "vertebrates", "animals", "health care", "reptiles", "myanmar", "rural areas", "neglected tropical diseases", "snakebite", "geography", "snakes", ...	Snakebite incidence in two townships in Mandalay Division, Myanmar	journal.pntd.0006643	null	[ [ "Snakebite is a major global health issue .", "The estimated global annual incidence is about 5 million snakebites resulting in between 81 , 000 and 138 , 000 deaths [1] .", "In 1998 , Chippaux [2] estimated the incidence as high as 5 . 4 million bites and in 2000 , White [3] suggested more than 150 ,...	[ "The global incidence of snakebite is estimated at more than 2 . 5 million cases annually , with greater than 100 , 000 deaths .", "Historically , Myanmar has one of the highest incidences of venomous snakebites .", "In order to improve the health outcomes of snakebite patients in Myanmar , access to accurate s...	[ "Snakebite is a major health issue affecting large numbers of people , particularly in tropical developing countries .", "Myanmar has one of the highest incidences of venomous snakebite in the world .", "Considering changes in demography , development , agricultural practices , knowledge about prevention and pr...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "oncology", "statistical models", "medicine and health sciences", "mathematics", "statistics (mathematics)", "basic cancer research", "biology and life sciences", "physical sciences", "computational biology", "evolutionary biology", "genomics statistics", "evolutionary processes" ]	Identification of Constrained Cancer Driver Genes Based on Mutation Timing	journal.pcbi.1004027	null	[ [ "Carcinogenesis is an evolutionary process driven by the accumulation of advantageous mutations in single cells and the subsequent outgrowth of those cells due to clonal expansion .", "Mutations in certain genes are present in a large fraction of cancers , such as TP53 mutations; others exhibit high mutat...	[ "Cancer drivers are genomic alterations that provide cells containing them with a selective advantage over their local competitors , whereas neutral passengers do not change the somatic fitness of cells .", "Cancer-driving mutations are usually discriminated from passenger mutations by their higher degree of recu...	[ "Cancer genome sequencing projects result in vast amounts of cancer mutation data .", "However , our understanding of which mutations are driving tumor growth and which are selectively neutral is lagging behind .", "Functional interactions among mutations can result in mutational dependencies , and these mutati...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Transmission of Leishmania donovani in the Hills of Eastern Nepal, an Outbreak Investigation in Okhaldhunga and Bhojpur Districts	journal.pntd.0003966	null	[ [ "Visceral Leishmaniasis ( VL ) is a vector-borne parasitic disease that is fatal if left untreated .", "With an estimated 162 , 000 to 313 , 000 new cases per year in northeast India , Nepal and Bangladesh , VL poses a public health problem in the Indian subcontinent ( ISC ) [1] .", "In this region , ...	[ "In the Indian subcontinent , Visceral leishmaniasis is endemic in a geographical area coinciding with the Lower Gangetic Plain , at low altitude .", "VL occurring in residents of hill districts is therefore often considered the result of Leishmania donovani infection during travel .", "Early 2014 we conducted ...	[ "Visceral leishmaniasis is a neglected but deadly disease occurring in north-eastern India , the south-eastern lowland of Nepal , and the Ganges delta in Bangladesh; all part of the Lower Gangetic plains .", "Districts at higher altitude , such as those situated in the foothills of the Himalaya in Nepal , are con...	2015
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "genome sequencing", "genome complexity", "genome evolution", "microbial evolution", "biology", "genomics", "comparative genomics", "microbiology", "genetics and genomics" ]	Azospirillum Genomes Reveal Transition of Bacteria from Aquatic to Terrestrial Environments	journal.pgen.1002430	null	[ [ "Fossil records indicate that life appeared in marine environments ∼3 . 5–3 . 8 billion years ago ( Gyr ) [1] and transitioned to terrestrial ecosystems ∼2 . 6 Gyr [2] .", "The lack of fossil records for bacteria makes it difficult to assess the timing of their transition to terrestrial environments; howe...	[ "Fossil records indicate that life appeared in marine environments ∼3 . 5 billion years ago ( Gyr ) and transitioned to terrestrial ecosystems nearly 2 . 5 Gyr .", "Sequence analysis suggests that “hydrobacteria” and “terrabacteria” might have diverged as early as 3 Gyr .", "Bacteria of the genus Azospirillum a...	[ "Genome sequencing and analysis of plant-associated beneficial soil bacteria Azospirillum spp .", "reveals that these organisms transitioned from aquatic to terrestrial environments significantly later than the suggested major Precambrian divergence of aquatic and terrestrial bacteria .", "Separation of Azospir...	2011
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "genetics", "biology", "genomics", "evolutionary biology", "genetics and genomics" ]	Genetic Architecture of Highly Complex Chemical Resistance Traits across Four Yeast Strains	journal.pgen.1002570	null	[ [ "Most traits of agricultural , evolutionary , and medical significance are genetically complex , involving multiple genes that interact with one another and the environment [1] .", "Despite decades of effort , our understanding of how such traits are specified at the genetic level remains incomplete [2] ....	[ "Many questions about the genetic basis of complex traits remain unanswered .", "This is in part due to the low statistical power of traditional genetic mapping studies .", "We used a statistically powerful approach , extreme QTL mapping ( X-QTL ) , to identify the genetic basis of resistance to 13 chemicals in...	[ "Most heritable traits of agricultural , evolutionary , and medical significance are specified by multiple genetic loci .", "Despite decades of research , we have only a limited understanding of the genetic basis of such complex traits .", "Studies in model organisms have the potential to provide fundamental in...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "mathematics", "physiology", "dog", "computational biology", "homo (human)", "cardiovascular disorders" ]	From Inverse Problems in Mathematical Physiology to Quantitative Differential Diagnoses	journal.pcbi.0030204	null	[ [ "The potential of computer-based , algorithmic support for medical decision making in data-rich environments , and in particular in the context of evidence-based practice , was recognized early on and has been pursued extensively [3 , 7–11] .", "Few of these efforts , which mostly have consisted of rule-b...	[ "The improved capacity to acquire quantitative data in a clinical setting has generally failed to improve outcomes in acutely ill patients , suggesting a need for advances in computer-supported data interpretation and decision making .", "In particular , the application of mathematical models of experimentally el...	[ "Although quantitative physiology has developed numerous mathematical descriptions of components of the human body , their application in clinical medicine has been limited to a few mostly primitive and physiologically inaccurate models .", "One reason for this is that the inverse problem of identifying unknown m...	2007
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "vaccination", "infectious diseases", "immune cells", "clinical immunology", "immunity", "immunology", "biology", "computational biology", "microbiology" ]	Degenerate T-cell Recognition of Peptides on MHC Molecules Creates Large Holes in the T-cell Repertoire	journal.pcbi.1002412	null	[ [ "The recognition of peptide-MHC-I complexes ( pMHC ) by the T-cell receptor ( TCR ) is required for effector T-cells to kill an infected cell .", "Although some MHC-I molecules have a preference to present pathogen-derived peptides [1] , pMHC are formed with both self and nonself peptides .", "Therefo...	[ "The cellular immune system screens peptides presented by host cells on MHC molecules to assess if the cells are infected .", "In this study we examined whether the presented peptides contain enough information for a proper self/nonself assessment by comparing the presented human ( self ) and bacterial or viral (...	[ "Human cells sample short peptides from endogenous proteins , and present them to the immune system via HLA class I molecules on the cell surface .", "T-cells scan the presented peptides and need to discriminate foreign ( nonself ) peptides from human ( self ) peptides .", "We show that this is a difficult task...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "agriculture", "biology" ]	Polycomb Group Gene OsFIE2 Regulates Rice (Oryza sativa) Seed Development and Grain Filling via a Mechanism Distinct from Arabidopsis	journal.pgen.1003322	null	[ [ "Rice ( Oryza sativa ) serves as the staple food for over half of the world's population .", "The main body of rice grain is endosperm , which is consumed as food .", "Endosperm stores energy primarily in the form of starch , storage proteins , and lipids .", "As in other angiosperms , rice seed d...	[ "Cereal endosperm represents 60% of the calories consumed by human beings worldwide .", "In addition , cereals also serve as the primary feedstock for livestock .", "However , the regulatory mechanism of cereal endosperm and seed development is largely unknown .", "Polycomb complex has been shown to play a ke...	[ "Rice is the staple food for over half of the world's population and an important feedstock for livestock .", "The rice grain is mainly endosperm tissue .", "The regulatory mechanism of rice endosperm development is still largely unknown thus far .", "Understanding the underlying mechanism will lead to crop y...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "haplotypes", "social sciences", "archaeology", "gene pool", "genetic polymorphism", "physical anthropology", "paleontology", "genetics", "biology and life sciences", "population genetics", "gene flow", "population biology", "evolutionary biology", "anthropology", "paleoanthropology", ...	Ancient DNA Analysis of 8000 B.C. Near Eastern Farmers Supports an Early Neolithic Pioneer Maritime Colonization of Mainland Europe through Cyprus and the Aegean Islands	journal.pgen.1004401	null	[ [ "The term “Neolithic” refers to the profound cultural and technical changes that accompanied the transition from a hunter-gatherer subsistence economy to an agro-pastoral producing system [1] .", "The first Neolithic societies originated 12 to 10 thousand years ago in a region of the Near East traditional...	[ "The genetic impact associated to the Neolithic spread in Europe has been widely debated over the last 20 years .", "Within this context , ancient DNA studies have provided a more reliable picture by directly analyzing the protagonist populations at different regions in Europe .", "However , the lack of availab...	[ "Since the original human expansions out of Africa 200 , 000 years ago , different prehistoric and historic migration events have taken place in Europe .", "Considering that the movement of the people implies a consequent movement of their genes , it is possible to estimate the impact of these migrations through ...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "biofilms", "blood cells", "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "chemical compounds", "oxides", "pathogens", "immunology", "microbiology", "animal models", "developmental biology", "fungi", "model organisms", "experimental organism systems"...	Candida albicans FRE8 encodes a member of the NADPH oxidase family that produces a burst of ROS during fungal morphogenesis	journal.ppat.1006763	null	[ [ "Reactive oxygen species ( ROS ) including superoxide anion and hydrogen peroxide play diverse roles in biology .", "ROS can inflict severe oxidative damage to cellular components , but when carefully controlled , ROS can also be used to combat infection and act in cell signaling processes .", "A well...	[ "Until recently , NADPH oxidase ( NOX ) enzymes were thought to be a property of multicellularity , where the reactive oxygen species ( ROS ) produced by NOX acts in signaling processes or in attacking invading microbes through oxidative damage .", "We demonstrate here that the unicellular yeast and opportunistic...	[ "We demonstrate here that the opportunistic human fungal pathogen Candida albicans uses a NADPH oxidase enzyme ( NOX ) and reactive oxygen species ( ROS ) to control morphogenesis in an animal host .", "C . albicans was not previously known to express NOX enzymes as these were thought to be a property of multicel...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Dual Expression Profile of Type VI Secretion System Immunity Genes Protects Pandemic Vibrio cholerae	journal.ppat.1003752	null	[ [ "Vibrio cholerae is the etiological agent of the diarrheal disease cholera .", "This pathogen utilizes a wide array of virulence factors during host infection including the well-characterized cholera toxin ( CT ) and toxin-coregulated pilus ( TCP ) .", "In addition , V . cholerae possesses numerous ot...	[ "The Vibrio cholerae type VI secretion system ( T6SS ) assembles as a molecular syringe that injects toxic protein effectors into both eukaryotic and prokaryotic cells .", "We previously reported that the V . cholerae O37 serogroup strain V52 maintains a constitutively active T6SS to kill other Gram-negative bact...	[ "Vibrio cholerae is the causative agent of the diarrheal disease cholera .", "This bacterium uses the type VI secretion system ( T6SS ) to kill other bacteria and host cells .", "The T6SS is a molecular syringe that Gram-negative bacteria use to inject toxic effectors into target cells in a contact-dependent ma...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell physiology", "ecology and environmental sciences", "chemical compounds", "electron donors", "oxygen", "cell metabolism", "sulfur", "oxygen metabolism", "sulfides", "ecological metrics", "chemistry", "oxidation", "biochemistry", "biomass", "cell biology", "ecology", "biology and...	Multiscale analysis of autotroph-heterotroph interactions in a high-temperature microbial community	journal.pcbi.1006431	null	[ [ "Microorganisms are the largest component of the biosphere and drive biogeochemical cycles through metabolic activity [1] .", "Microorganisms commonly exist in biofilms or mats that contain numerous microenvironments due to the interplay between convection- , diffusion- , and chemical concentration gradie...	[ "Interactions among microbial community members can lead to emergent properties , such as enhanced productivity , stability , and robustness .", "Iron-oxide mats in acidic ( pH 2–4 ) , high-temperature ( > 65 °C ) springs of Yellowstone National Park contain relatively simple microbial communities and are well-ch...	[ "Microbial communities often display emergent properties , such as enhanced productivity , stability , and robustness , compared to their component populations in isolation .", "However , determining the governing principles of these emergent properties can be elusive due to the complexities of interpreting and i...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "evolutionary biology", "genetics and genomics" ]	Evolution of a New Function by Degenerative Mutation in Cephalochordate Steroid Receptors	journal.pgen.1000191	null	[ [ "All major models of duplicate gene evolution to date assume that the two genes' products do not interact with each other physically or functionally .", "Mutations in one copy therefore have no effect on the functions of the other .", "In the classic model [7] , [11] , having two copies of a gene is p...	[ "Gene duplication is the predominant mechanism for the evolution of new genes .", "Major existing models of this process assume that duplicate genes are redundant; degenerative mutations in one copy can therefore accumulate close to neutrally , usually leading to loss from the genome .", "When gene products dim...	[ "Most genes evolved by duplication of more ancient genes .", "Under existing models of this process , mutations that compromise one copy have no effect on the other; as long as one copy remains intact , such “degenerative” mutations are shielded from selection .", "Because degenerative mutations are common , mo...	2008
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "eye infections", "public and occupational health", "bacterial diseases", "infectious diseases", "medicine and health sciences", "global health", "ophthalmology", "neglected tropical diseases", "tropical diseases", "trachoma" ]	Reliability of Trachoma Clinical Grading—Assessing Grading of Marginal Cases	journal.pntd.0002840	null	[ [ "The World Health Organization ( WHO ) recommends clinical examination of the upper tarsal conjunctiva of children for trachoma to determine when to start and stop mass antibiotic distributions , and when to declare elimination as a public health concern [1]–[4] .", "A considerable portion of the evidence...	[ "Clinical examination of trachoma is used to justify intervention in trachoma-endemic regions .", "Currently , field graders are certified by determining their concordance with experienced graders using the kappa statistic .", "Unfortunately , trachoma grading can be highly variable and there are cases where ev...	[ "Trachoma is the leading infectious cause of blindness and the World Health Organization plans to eliminate it as a public health concern worldwide by the year 2020 .", "This effort in large part involves mass oral antibiotic distributions to communities .", "A simplified trachoma grading scale is used to asses...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "protein interactions", "drugs and devices", "chemical biology", "biomechanics", "protein folding", "protein structure", "proteins", "chemistry", "biology", "recombinant proteins", "biophysics", "physics", "biochemistry", "protein chemistry" ]	Common Features at the Start of the Neurodegeneration Cascade	journal.pbio.1001335	A single-molecule study reveals that neurotoxic proteins share common structural features that may trigger neurodegeneration, thus identifying new targets for therapy and diagnosis.	[ [ "Amyloid-related neurodegenerative diseases are incurable disorders that are currently classified as conformational diseases ( a subset of the proteinopathies ) .", "These diseases are thought to be primarily caused by an unknown conformational change in specific proteins , termed “neurotoxic proteins” ( ...	[ "Amyloidogenic neurodegenerative diseases are incurable conditions with high social impact that are typically caused by specific , largely disordered proteins .", "However , the underlying molecular mechanism remains elusive to established techniques .", "A favored hypothesis postulates that a critical conforma...	[ "Neurodegenerative diseases like Alzheimer's or Parkinson's are currently incurable .", "They are caused by different proteins that , under certain circumstances , aggregate and become toxic as we grow older , but the molecular events underlying this process remain unclear .", "The lack of a well-defined struct...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "natural selection", "human genetics", "genetics", "population genetics", "biology", "evolutionary biology", "evolutionary processes", "genetics and genomics", "evolutionary genetics", "evolutionary theory" ]	Distinguishing between Selective Sweeps from Standing Variation and from a De Novo Mutation	journal.pgen.1003011	null	[ [ "Detection of selected regions has been a major goal in population genetics in recent years [9]–[13] .", "Rather than working with the full data , all of these studies simplified their data by using various statistics designed to detect the signal of selection ( see e . g . [12] , [14] ) .", "These st...	[ "An outstanding question in human genetics has been the degree to which adaptation occurs from standing genetic variation or from de novo mutations .", "Here , we combine several common statistics used to detect selection in an Approximate Bayesian Computation ( ABC ) framework , with the goal of discriminating b...	[ "Considerable effort has been devoted to detecting genes that are under natural selection , and hundreds of such genes have been identified in previous studies .", "Here , we present a method for extending these studies by inferring parameters , such as selection coefficients and the time when a selected variant ...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "model organisms", "neurological disorders", "neurology", "genetics", "biology", "neuroscience", "genetics and genomics" ]	Pathogenic Mechanism of the FIG4 Mutation Responsible for Charcot-Marie-Tooth Disease CMT4J	journal.pgen.1002104	null	[ [ "The lipid phosphatase FIG4/SAC3 is broadly expressed in eukaryotic cells from yeast to mammals .", "Mutations of FIG4 are responsible for Charcot-Marie-Tooth Disease type 4J ( OMIM 611228 ) , an atypical , autosomal recessive form of CMT with severe motor dysfunction and rapid progression [1] , [2] .", ...	[ "CMT4J is a severe form of Charcot-Marie-Tooth neuropathy caused by mutation of the phosphoinositide phosphatase FIG4/SAC3 .", "Affected individuals are compound heterozygotes carrying the missense allele FIG4-I41T in combination with a null allele .", "Analysis using the yeast two-hybrid system demonstrated th...	[ "Charcot-Marie-Tooth disease type 4J is a severe neurological disorder with childhood or adult onset and progression to loss of mobility and death .", "Patients inherit a mutation that changes amino acid residue 41 of the FIG4 protein from isoleucine to threonine .", "We report that this mutation destabilizes t...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "glycolipids", "animal models of disease", "endoplasmic reticulum", "cell processes", "enzymology", "biological cultures", "microbiology", "animal models", "model organisms", "cell cultures", "glycoproteins", "enzyme inhibitors", "cellular structures and organelles", "research and analysis...	Iminosugars Inhibit Dengue Virus Production via Inhibition of ER Alpha-Glucosidases—Not Glycolipid Processing Enzymes	journal.pntd.0004524	null	[ [ "Iminosugars are considered to be promising candidates for broad-spectrum antiviral activity because of their presumed mechanism of action as glycoprotein processing inhibitors [1] .", "1-Deoxynojirimycin ( DNJ ) iminosugar derivatives possess glucose stereochemistry and inhibit infectious virus productio...	[ "It has long been thought that iminosugar antiviral activity is a function of inhibition of endoplasmic reticulum-resident α-glucosidases , and on this basis , many iminosugars have been investigated as therapeutic agents for treatment of infection by a diverse spectrum of viruses , including dengue virus ( DENV ) ...	[ "Current treatment of dengue virus infection is supportive; however , iminosugars have been widely investigated as an antiviral strategy .", "The means by which these molecules are thought to exert their antiviral effects is through inhibition of host-resident glycoprotein processing enzymes , the endoplasmic ret...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "plant science", "plant biology", "biology" ]	Two-Component Elements Mediate Interactions between Cytokinin and Salicylic Acid in Plant Immunity	journal.pgen.1002448	null	[ [ "The first layer of active plant immunity begins with the recognition of microbial molecules , followed by activation of an effective defense response [1] .", "Non-adapted pathogens are halted by this defense response , whereas adapted pathogens are able to overcome these defense responses via deployment ...	[ "Recent studies have revealed an important role for hormones in plant immunity .", "We are now beginning to understand the contribution of crosstalk among different hormone signaling networks to the outcome of plant–pathogen interactions .", "Cytokinins are plant hormones that regulate development and responses...	[ "Plant hormones play an important role in many aspects of a plant's life cycle , from the regulation of development to responses to constantly changing environmental conditions .", "In the past decade , the importance of hormones in plant immunity against a variety of pathogens has been uncovered .", "In this m...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "rift valley fever virus", "pathology and laboratory medicine", "hela cells", "gene regulation", "pathogens", "enzymes", "biological cultures", "vector-borne diseases", "microbiology", "enzymology", "viruses", "rna viruses", "cell cultures", "microbial gen...	Protein Kinase R Degradation Is Essential for Rift Valley Fever Virus Infection and Is Regulated by SKP1-CUL1-F-box (SCF)FBXW11-NSs E3 Ligase	journal.ppat.1005437	null	[ [ "Activated double-stranded ( ds ) RNA-dependent protein kinase ( PKR or EIF2AK2 ) plays a vital role in antiviral defense primarily by inhibiting protein synthesis and augmenting interferon responses [1] .", "PKR is a serine/threonine kinase that is maintained as an inactive monomer and undergoes activati...	[ "Activated protein kinase R ( PKR ) plays a vital role in antiviral defense primarily by inhibiting protein synthesis and augmenting interferon responses .", "Many viral proteins have adopted unique strategies to counteract the deleterious effects of PKR .", "The NSs ( Non-structural s ) protein which is encode...	[ "Rift Valley fever ( RVF ) is a severe disease caused by infection with the Rift Valley fever virus ( RVFV ) that affects humans and livestock and occurs in large epidemics .", "Currently there are no FDA-approved drugs or vaccines to treat RVF .", "Many viruses have evolved unique strategies to overcome host i...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "chromatin immunoprecipitation", "biochemistry", "genomics", "proteins", "genome analysis", "transcription factors", "gene expression", "genetics", "gene regulation", "biology and life sciences", "dna-binding proteins", "computational biology" ]	Targeted H3R26 Deimination Specifically Facilitates Estrogen Receptor Binding by Modifying Nucleosome Structure	journal.pgen.1004613	null	[ [ "The nucleosome represents the fundamental unit of chromatin and consists of 147 bp of DNA wrapped ∼1 . 7 times around the histone octamer core particle [1] .", "The N-terminal tails of histones are disordered and reside outside of core nucleosome/DNA structure but they harbor amino acid residues that can...	[ "Transcription factor binding to DNA in vivo causes the recruitment of chromatin modifiers that can cause changes in chromatin structure , including the modification of histone tails .", "We previously showed that estrogen receptor ( ER ) target gene activation is facilitated by peptidylarginine deiminase 2 ( PAD...	[ "Transcription factors bind to DNA to activate and repress gene transcription .", "Many transcription factors , particularly nuclear receptors , associate with their cognate DNA element in a highly dynamic manner in vivo .", "Highly acetylated histone tails and DNase sensitive chromatin are amenable to the init...	2014
[ "Introduction", "Materials and methods", "Results and discussion" ]	[ "protein interactions", "condensed matter physics", "geometry", "cargo proteins", "plant science", "mathematics", "photosynthesis", "ribulose-1,5-bisphosphate carboxylase oxygenase", "thermodynamics", "proteins", "chemistry", "physics", "biochemistry", "stoichiometry", "plant biochemistr...	The role of the encapsulated cargo in microcompartment assembly	journal.pcbi.1006351	null	[ [ "While it has long been recognized that membrane-bound organelles organize the cytoplasm of eukaryotes , it is now evident that protein-based compartments play a similar role in many organisms .", "For example , bacterial microcompartments ( BMCs ) are icosahedral proteinaceous organelles that assemble ar...	[ "Bacterial microcompartments are large , roughly icosahedral shells that assemble around enzymes and reactants involved in certain metabolic pathways in bacteria .", "Motivated by microcompartment assembly , we use coarse-grained computational and theoretical modeling to study the factors that control the size an...	[ "Bacterial microcompartments are protein shells that encase enzymes and reactants to enable bacteria to perform vital reactions , such as breaking down chemicals for energy or converting the products of photosynthesis into sugars .", "Microcompartments are essential for many bacteria , including human pathogens ....	2018
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "pathology and laboratory medicine", "statistics", "pathogens", "microbiology", "vertebrates", "social sciences", "animals", "simulation and modeling", "viruses", "animal behavior", "rna viruses", "mathematics", "network analysis", "infe...	A spatio-temporal individual-based network framework for West Nile virus in the USA: Spreading pattern of West Nile virus	journal.pcbi.1006875	null	[ [ "West Nile disease ( WND ) is a vector-borne zoonosis which may result from infection by West Nile virus ( WNV ) , a member of the family Flaviviridae , genus Flavivirus .", "This virus is the most common cause of arboviral disease in the United States [1] .", "From 1999 to 2017 , more than 48 thousan...	[ "West Nile virus ( WNV ) —a mosquito-borne arbovirus—entered the USA through New York City in 1999 and spread to the contiguous USA within three years while transitioning from epidemic outbreaks to endemic transmission .", "The virus is transmitted by vector competent mosquitoes and maintained in the avian popula...	[ "The underlying pattern of West Nile virus ( WNV ) geographic spread across the United States is not completely clear , which is a necessary step for continental or state level mitigation strategies to reduce WNV transmission .", "We report a network model that explains the geographic spread of WNV in the United ...	2019
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases", "immunology/immune response", "immunology/innate immunity", "infectious diseases/viral infections", "immunology/immunity to infections" ]	NK Cell–Like Behavior of Vα14i NK T Cells during MCMV Infection	journal.ppat.1000106	null	[ [ "The β-herpes murine cytomegalovirus ( MCMV ) is a well-characterized model of viral infection that results in a non-replicative , chronic infection of immune-competent animals [1] .", "MCMV is a cytopathic virus that is known to readily infect peritoneal macrophages , dendritic cells ( DC ) and hepatocyt...	[ "Immunity to the murine cytomegalovirus ( MCMV ) is critically dependent on the innate response for initial containment of viral replication , resolution of active infection , and proper induction of the adaptive phase of the anti-viral response .", "In contrast to NK cells , the Vα14 invariant natural killer T c...	[ "An efficient immune response to viral infection requires both innate and adaptive immune cells .", "Natural killer ( NK ) cells are a critical innate cellular component of the immune response to murine cytomegalovirus ( MCMV ) .", "Natural killer T ( NK T ) cells are non-classical T cells that have the potenti...	2008
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "biology", "microbiology" ]	Phase Variable O Antigen Biosynthetic Genes Control Expression of the Major Protective Antigen and Bacteriophage Receptor in Vibrio cholerae O1	journal.ppat.1002917	null	[ [ "Lipopolysaccharide ( LPS ) is a prominent constituent of the outer membrane of Gram-negative bacteria .", "The LPS molecule is divided into three components; lipid A , core oligosaccharide and O-specific polysaccharide ( or O antigen ) .", "The structure of the O antigen typically defines the serogro...	[ "The Vibrio cholerae lipopolysaccharide O1 antigen is a major target of bacteriophages and the human immune system and is of critical importance for vaccine design .", "We used an O1-specific lytic bacteriophage as a tool to probe the capacity of V . cholerae to alter its O1 antigen and identified a novel mechani...	[ "The O1 serogroup of Vibrio cholerae is the most common cause of the potentially fatal diarrheal disease cholera , which remains a significant global health burden worldwide .", "The O1 antigen is a constituent of the lipopolysaccharide portion of the outer membrane , and its location on the bacterial surface mak...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "velocity", "cognitive science", "medicine and health sciences", "classical mechanics", "reaction time", "vertebrates", "social sciences", "neuroscience", "animals", "mammals", "primates", "cognitive neuroscience", "vision", "eyes", "neuronal tuning", "sensory physiology", "monkeys",...	A Causal Role for the Cortical Frontal Eye Fields in Microsaccade Deployment	journal.pbio.1002531	Our eyes are constantly in motion. This study shows that the frontal eye fields (an area of the frontal cortex) contribute to the strategic deployment of microsaccades, which aid vision by precisely translating retinal images by a few photoreceptors.	[ [ "Microsaccades , which frequently occur during gaze fixation , translate retinal images by only a few photoreceptors .", "Despite their modest size , microsaccades strongly impact visual perception [1–5] and visually guided behavior [6–8] .", "Indeed , visual responses in a number of brain structures ...	[ "Microsaccades aid vision by helping to strategically sample visual scenes .", "Despite the importance of these small eye movements , no cortical area has ever been implicated in their generation .", "Here , we used unilateral and bilateral reversible inactivation of the frontal eye fields ( FEF ) to identify a...	[ "Microsaccades are small , fixational eye movements that precisely relocate the visual axis .", "Despite evidence that microsaccades can be strategically controlled in high-acuity visual tasks , impacting visual processing , and considerable knowledge about how microsaccades are generated by the oculomotor brains...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public health and epidemiology", "growth retardation", "social and behavioral sciences", "infectious disease epidemiology", "sociology", "pediatrics", "social epidemiology", "nutrition", "clinical epidemiology", "global health", "neglected tropical diseases", "epidemiological me...	Evaluation of the Health-related Quality of Life of Children in Schistosoma haematobium-endemic Communities in Kenya: A Cross-sectional Study	journal.pntd.0002106	null	[ [ "Schistosomiasis remains a public challenge globally with 93% of the estimated 237 million infections occurring in Africa [1] .", "Its transmission is mainly influenced by exposures to environmental factors ( contact with infested water , distance to infected water bodies ) , individual characteristics ( ...	[ "Schistosomiasis remains a global public health challenge , with 93% of the ∼237 million infections occurring in sub-Saharan Africa .", "Though rarely fatal , its recurring nature makes it a lifetime disorder with significant chronic health burdens .", "Much of its negative health impact is due to non-specific ...	[ "Because urogenital schistosomiasis is a multi-decadal chronic disease that begins in early childhood , and because it is a disease that may affect nearly everyone in endemic communities , its impact on personal health-related quality of life ( HrQoL ) has been difficult to gauge accurately .", "In order to provi...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "reverse transcriptase-polymerase chain reaction", "sequencing techniques", "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "split-decomposition method", "tropical diseases", "microbiology", "vertebrates", "animals", "mammals", "dogs", "viruses", "multiple...	A Pan-Lyssavirus Taqman Real-Time RT-PCR Assay for the Detection of Highly Variable Rabies virus and Other Lyssaviruses	journal.pntd.0005258	null	[ [ "Rabies is an acute progressive viral encephalitis characterized by central nervous system disorder that ultimately leads to death [1] .", "Rabies is the only disease considered to have nearly 100% mortality , and remains a major public health problem in Asia and Africa with 70 , 000 human deaths annually...	[ "Rabies , resulting from infection by Rabies virus ( RABV ) and related lyssaviruses , is one of the most deadly zoonotic diseases and is responsible for up to 70 , 000 estimated human deaths worldwide each year .", "Rapid and accurate laboratory diagnosis of rabies is essential for timely administration of post-...	[ "Rabies is a preventable disease–but is still responsible for approximately 70 , 000 human deaths worldwide each year .", "The majority of human deaths occur in Asia and Africa where there is a lack of diagnostic resources and expertise , making it difficult to develop effective prevention and control strategies ...	2017
[ "Introduction", "Materials and Methods", "Results/Discussion" ]	[ "evolutionary biology/human evolution", "infectious diseases/neglected tropical diseases", "microbiology/microbial evolution and genomics", "non-clinical medicine/history of medicine", "infectious diseases/sexually transmitted diseases", "molecular biology" ]	Syphilis at the Crossroad of Phylogenetics and Paleopathology	journal.pntd.0000575	null	[ [ "The widespread availability of effective antimicrobial therapy , in association with population screening , resulted in a considerable decline in the frequency of syphilis in the middle of the last century [1] .", "The mass campaigns around 1960 treated 46 out of 152 million people screened and , as a re...	[ "The origin of syphilis is still controversial .", "Different research avenues explore its fascinating history .", "Here we employed a new integrative approach , where paleopathology and molecular analyses are combined .", "As an exercise to test the validity of this approach we examined different hypotheses ...	[ "Syphilis is a reemerging disease burden .", "Although it has been studied for five centuries , its origin and spread is still controversial .", "Did it accompany the evolution of the genus Homo and does it date back to more than a million years or did it emerge only after Columbus's return to Europe ?", "Ini...	2010
[ "Introduction", "Results and discussion", "Methods" ]	[ "sequencing techniques", "parasite groups", "parasitic protozoans", "parasitology", "membrane proteins", "developmental biology", "apicomplexa", "molecular motors", "protozoans", "molecular biology techniques", "rna sequencing", "cellular structures and organelles", "motor proteins", "rese...	Comparative and functional genomics of the protozoan parasite Babesia divergens highlighting the invasion and egress processes	journal.pntd.0007680	null	[ [ "Babesiosis is a worldwide emerging infectious disease [1] caused by a protozoan parasite of the genus Babesia which is naturally transmitted by ixodid ticks and infects vertebrate erythrocytes .", "Parasite infection of natural hosts such as in cattle causes bovine babesiosis , resulting in high economic...	[ "Babesiosis is considered an emerging disease because its incidence has significantly increased in the last 30 years , providing evidence of the expanding range of this rare but potentially life-threatening zoonotic disease .", "Babesia divergens is a causative agent of babesiosis in humans and cattle in Europe ....	[ "Babesiosis has long been recognized as an economically important disease of cattle , but only in the last 40 years has Babesia been recognized as an important pathogen in humans .", "Babesiosis in humans is caused by one of several species ( B . microti , B . divergens , B . duncani and B . venatorum ) .", "Th...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cellular structures", "subcellular organelles", "molecular cell biology", "immune cells", "cell biology", "nk cells", "immunology", "biology", "cytoskeleton" ]	Natural Killer Cell Lytic Granule Secretion Occurs through a Pervasive Actin Network at the Immune Synapse	journal.pbio.1001151	Super-resolution imaging provides a new look at how the lytic granules in natural killer cells penetrate the filamentous actin network of the immunological synapse.	[ [ "Natural killer ( NK ) cells are lymphocytes of the innate immune system that function in clearance of tumor and virally infected cells [1] .", "Elimination of susceptible target cells is tightly regulated and follows ligation of germline-encoded activation receptors [2] .", "As NK cells do not requir...	[ "Accumulation of filamentous actin ( F-actin ) at the immunological synapse ( IS ) is a prerequisite for the cytotoxic function of natural killer ( NK ) cells .", "Subsequent to reorganization of the actin network , lytic granules polarize to the IS where their contents are secreted directly toward a target cell ...	[ "The immune system's natural killer cells eliminate diseased cells in the body .", "They do so by secreting toxic molecules directly towards the diseased cells , so causing their death .", "This process is essential for the host organism to defend itself against infectious diseases .", "The interface between ...	2011
[ "Introduction", "Results and discussion", "Materials and methods" ]	[ "b vitamins", "medicine and health sciences", "chemical compounds", "biotin", "metabolic processes", "parasitic protozoans", "organic compounds", "oxidative phosphorylation", "protozoans", "alkynes", "amino acids", "mitochondria", "energy-producing organelles", "bioenergetics", "pharmaco...	Photo-affinity labelling and biochemical analyses identify the target of trypanocidal simplified natural product analogues	journal.pntd.0005886	null	[ [ "Protozoan parasites of the Trypanosoma genus cause widespread disease and death across large regions of the developing world .", "In sub-Saharan Africa Trypanosoma brucei gambiense and T . b .", "rhodesiense are the causative agents of human African trypanosomiasis ( HAT , or African sleeping sicknes...	[ "Current drugs to treat African sleeping sickness are inadequate and new therapies are urgently required .", "As part of a medicinal chemistry programme based upon the simplification of acetogenin-type ether scaffolds , we previously reported the promising trypanocidal activity of compound 1 , a bis-tetrahydropyr...	[ "Millions of people are at risk of developing African sleeping sickness through infection with the parasite Trypanosoma brucei , which is fatal if untreated .", "Current therapies are antiquated and inadequate , requiring hospitalization to deliver them through complex regimens , thus new effective , cheap and ea...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "293t cells", "pathogens", "biological cultures", "microbiology", "vertebrates", "animals", "mammals", "genetic mapping", "plasmid construction", "retroviruses", "primates", "immunodeficiency viruses", "viruses", "rna...	Stably expressed APOBEC3H forms a barrier for cross-species transmission of simian immunodeficiency virus of chimpanzee to humans	journal.ppat.1006746	null	[ [ "Simian immunodeficiency virus ( SIV ) naturally infects many species of African Old-World monkeys , such as African green monkeys , mandrills and red-capped mangabey [1 , 2] .", "However , these viruses appear to be nonpathogenic in their natural hosts [2 , 3] .", "Chimpanzees ( cpz ) , which are the...	[ "APOBEC3s ( A3s ) are potent restriction factors of human immunodeficiency virus type 1/simian immunodeficiency viruses ( HIV-1/SIV ) , and can repress cross-species transmissions of lentiviruses .", "HIV-1 originated from a zoonotic infection of SIV of chimpanzee ( SIVcpz ) to humans .", "However , the impact ...	[ "Cellular cytidine deaminases of the APOBEC3 ( A3 ) family are potent restriction factors that are able to inhibit retroviruses , this A3 restriction is counteracted by lentivirus Vif proteins .", "Human APOBEC3H ( A3H ) represents the most evolutionarily divergent A3 gene; it includes seven haplotypes and severa...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "phosphorylation", "medicine and health sciences", "molecular probe techniques", "messenger rna", "cancers and neoplasms", "immunoblotting", "simulation and modeling", "oncology", "immunoprecipitation", "molecular biology techniques", "research and analysis methods", "proteins", "lung and in...	Identification of Cell Type-Specific Differences in Erythropoietin Receptor Signaling in Primary Erythroid and Lung Cancer Cells	journal.pcbi.1005049	null	[ [ "Lung carcinoma is one of the leading causes of cancer-related deaths worldwide .", "The main types of lung cancer are small-cell lung carcinoma ( SCLC ) and non-small-cell lung carcinoma ( NSCLC ) .", "NSCLC is the most frequent form with a prevalence of around 85% and can be classified in squamous-c...	[ "Lung cancer , with its most prevalent form non-small-cell lung carcinoma ( NSCLC ) , is one of the leading causes of cancer-related deaths worldwide , and is commonly treated with chemotherapeutic drugs such as cisplatin .", "Lung cancer patients frequently suffer from chemotherapy-induced anemia , which can be ...	[ "A major challenge in the development of therapeutic interventions is the selective inhibition of a signal transduction pathway in one cell type such as a cancer cell leaving the other cell type such as a healthy cell as unaffected as possible .", "Here , we propose a new approach that combines mathematical model...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "biochemistry", "eukaryotes", "molecular biology", "genetics and genomics" ]	Biosynthesis of Selenocysteine on Its tRNA in Eukaryotes	journal.pbio.0050004	Sec synthase, a conserved protein responsible for the biosynthesis of the rare 21st amino acid, selenocysteine, is identified in eukaryotes, and the underlying biochemical pathway is characterized.	[ [ "Selenocysteine ( Sec ) is a selenium-containing amino acid that is cotranslationally inserted into protein and is recognized as the 21st amino acid in the genetic code [1–3] .", "Sec is incorporated into protein in all three lines of descent , eukaryota , archaea , and eubacteria , but unlike other amino...	[ "Selenocysteine ( Sec ) is cotranslationally inserted into protein in response to UGA codons and is the 21st amino acid in the genetic code .", "However , the means by which Sec is synthesized in eukaryotes is not known .", "Herein , comparative genomics and experimental analyses revealed that the mammalian Sec...	[ "Biosynthesis of the 20 canonical amino acids is well established in eukaryotes .", "However , many eukaryotes also have a rare selenium-containing amino acid , selenocysteine , which is the 21st amino acid in the genetic code .", "Selenium is essential for human health , and its health benefits , including pre...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "immune cells", "viral classification", "immunology", "host-pathogen interaction", "microbiology", "lymphoid organs", "retroviruses", "animal models", "immunodeficiency viruses", "model organisms", "animal models of infection", "infectious diseases", "viral immune evasion", "...	Electron Tomography of HIV-1 Infection in Gut-Associated Lymphoid Tissue	journal.ppat.1003899	null	[ [ "HIV-1 remains a significant public health concern with over 33 million people infected world-wide [1] .", "Most HIV-1 transmissions occur across an epithelial barrier , resulting in generation of a founder population within the mucosa , viral dissemination to lymphatic tissue , and exponential viral repl...	[ "Critical aspects of HIV-1 infection occur in mucosal tissues , particularly in the gut , which contains large numbers of HIV-1 target cells that are depleted early in infection .", "We used electron tomography ( ET ) to image HIV-1 in gut-associated lymphoid tissue ( GALT ) of HIV-1–infected humanized mice , the...	[ "HIV/AIDS remains a global public health problem with over 33 million people infected worldwide .", "High-resolution imaging of infected tissues by three-dimensional electron microscopy can reveal details of the structure of HIV-1 , the virus that causes AIDS , how it infects cells , and how and where the virus a...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "rna-binding proteins", "3' utr", "messenger rna", "rna extraction", "germ cells", "untranslated regions", "extraction techniques", "sperm", "research and analysis methods", "spermatids", "animal cells", "proteins", "gene expression", "biochemistry", "rna", "cell biology", "nucleic a...	Chromatoid Body Protein TDRD6 Supports Long 3’ UTR Triggered Nonsense Mediated mRNA Decay	journal.pgen.1005857	null	[ [ "During mammalian gametogenesis , substantial changes in chromosome structure and in gene expression profiles occur .", "Male germ cell transcription and transcriptomes have been studied quite extensively .", "Some transcriptome studies concern the whole testis , and thus represent combined somatic an...	[ "Chromatoid bodies ( CBs ) are spermiogenesis-specific organelles of largely unknown function .", "CBs harbor various RNA species , RNA-associated proteins and proteins of the tudor domain family like TDRD6 , which is required for a proper CB architecture .", "Proteome analysis of purified CBs revealed componen...	[ "Tudor-domain containing protein 6 ( TDRD6 ) is a central component of the chromatoid body ( CB ) in male germ cells .", "Chromatoid bodies , which are present in spermatids , contain RNA and protein , are not enclosed by membranes , and typically reside close to the nucleus .", "Without TDRD6 , a much distorte...	2016
[ "Introduction", "Results", "Discussion", "Methods", "Cluster distribution", "Correlation between bilayer surface curvature and the clustering of lipid molecules" ]	[ "cell physiology", "biochemistry", "lipids", "cell biology", "biology and life sciences", "computational biology", "molecular cell biology", "biophysics", "membrane trafficking", "biophysical simulations" ]	Lipid Clustering Correlates with Membrane Curvature as Revealed by Molecular Simulations of Complex Lipid Bilayers	journal.pcbi.1003911	null	[ [ "Our growing knowledge of lipid-lipid interactions [1] , [2] and of lipid involvement in the control of membrane protein function [3]–[8] highlights the importance of the complexity of composition , structure and dynamics of cell membranes .", "The large number of different lipid species in vivo has led t...	[ "Cell membranes are complex multicomponent systems , which are highly heterogeneous in the lipid distribution and composition .", "To date , most molecular simulations have focussed on relatively simple lipid compositions , helping to inform our understanding of in vitro experimental studies .", "Here we descri...	[ "Cell membranes play important roles in vivo both in shielding the cell interior from the surrounding environment and in cell function through lipid components of the membrane having roles in controlling protein function , cell signaling etc .", "We employ molecular dynamics simulations to explore the behavior of...	2014
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "drosophila melanogaster", "beauveria bassiana", "streptococcus pneumoniae", "immunology", "microbiology" ]	A Specific Primed Immune Response in Drosophila Is Dependent on Phagocytes	journal.ppat.0030026	null	[ [ "Immune responses are typically characterized as being either adaptive or innate .", "Adaptive immunity , which requires T and B cells , is specific , has memory , and is generally considered to be restricted to vertebrates .", "In contrast , the innate immune response is thought to act naïvely to eac...	[ "Drosophila melanogaster , like other invertebrates , relies solely on its innate immune response to fight invading microbes; by definition , innate immunity lacks adaptive characteristics .", "However , we show here that priming Drosophila with a sublethal dose of Streptococcus pneumoniae protects against an oth...	[ "Due to the common practice of vaccination and prominence of AIDS , people are already aware of the distinction between adaptive and innate immunity without realizing it .", "All organisms have an innate immune response , but only vertebrates possess T cells and the ability to produce antibodies .", "It has bee...	2007
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "dermatology", "infectious diseases", "drug therapy", "veterinary diseases", "zoonoses", "medicine and health sciences", "skin infections", "pharmaceutics", "population modeling", "leishmaniasis", "protozoan infections", "biology and life sciences", "tropical diseases", "infectious disease...	Direct Comparison of the Efficacy and Safety of Oral Treatments with Oleylphosphocholine (OlPC) and Miltefosine in a Mouse Model of L. major Cutaneous Leishmaniasis	journal.pntd.0003144	null	[ [ "Leishmaniasis describes a range of visceral and cutaneous disease forms caused by infection with protozoal parasites of the Leishmania genus , transmitted to humans by phlebotomine sandflies [1] , [2] .", "Cutaneous leishmaniasis ( CL ) is characterized by primary localized skin infections that sometimes...	[ "Cutaneous leishmaniasis ( CL ) represents a range of skin diseases caused by infection with Leishmania parasites and associated with tissue inflammation and skin ulceration .", "CL is clinically widespread in both the Old and New World but lacks treatments that are well tolerated , effective and inexpensive .", ...	[ "Cutaneous leishmaniasis ( CL ) is a vector-borne parasitic disease transmitted to humans by sandflies and characterized by local ulcerative skin lesions .", "The disease is linked to poverty in the Middle-East , North and East Africa , South-Central Asia and South America , with 0 . 7 to 1 . 2 million new annual...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "taxonomy", "invertebrates", "organismal evolution", "medicine and health sciences", "ecology and environmental sciences", "evolutionary biology", "biodiversity", "animals", "endocrine physiology", "developmental biology", "data management", "physiological parameters", "embryos", "imagos",...	The AmP project: Comparing species on the basis of dynamic energy budget parameters	journal.pcbi.1006100	null	[ [ "The role of biodiversity in ecosystem structure and functioning is central for conservation and environmental quality management , as well as biospherics and earth system studies .", "Biodiversity is not only about the number of species present , but also the number and nature of the different characteri...	[ "We developed new methods for parameter estimation-in-context and , with the help of 125 authors , built the AmP ( Add-my-Pet ) database of Dynamic Energy Budget ( DEB ) models , parameters and referenced underlying data for animals , where each species constitutes one database entry .", "The combination of DEB p...	[ "We discovered that parameters of Dynamic Energy Budget ( DEB ) models can be estimated from a set of simple data on animal life history aspects , growth and reproduction , if treated in combination .", "Apart from goodness-of-fit as an estimation criterion , relations with parameter values of other species are i...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine" ]	Climate-Based Models for Understanding and Forecasting Dengue Epidemics	journal.pntd.0001470	null	[ [ "Dengue viruses are the most important arthropod-borne viruses affecting humans .", "During the past century , the four serotypes ( DENV 1 - DENV 4 ) have spread to about a hundred countries in the tropical and subtropical world including Asia , Africa , the Americas and the Pacific .", "Each year , a...	[ "Dengue dynamics are driven by complex interactions between human-hosts , mosquito-vectors and viruses that are influenced by environmental and climatic factors .", "The objectives of this study were to analyze and model the relationships between climate , Aedes aegypti vectors and dengue outbreaks in Noumea ( Ne...	[ "Dengue fever is a major public health problem in the tropics and subtropics .", "Since no vaccine exists , understanding and predicting outbreaks remain of crucial interest .", "Climate influences the mosquito-vector biology and the viral transmission cycle .", "Its impact on dengue dynamics is of growing in...	2012
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "b vitamins", "parasite groups", "methods and resources", "chemical compounds", "biotin", "plasmodium", "endoplasmic reticulum", "cell processes", "green fluorescent protein", "organic compounds", "parasitic protozoans", "parasitology", "membrane proteins", "apicomplexa", "luminescent pr...	Integrative proteomics and bioinformatic prediction enable a high-confidence apicoplast proteome in malaria parasites	journal.pbio.2005895	null	[ [ "Identification of new antimalarial drug targets is urgently needed to address emerging resistance to all currently available therapies .", "However , nearly half of the Plasmodium falciparum genome encodes conserved proteins of unknown function [1] , obscuring critical pathways required for malaria patho...	[ "Malaria parasites ( Plasmodium spp . ) and related apicomplexan pathogens contain a nonphotosynthetic plastid called the apicoplast .", "Derived from an unusual secondary eukaryote–eukaryote endosymbiosis , the apicoplast is a fascinating organelle whose function and biogenesis rely on a complex amalgamation of ...	[ "Plasmodium parasites , which cause malaria , and related pathogens belonging to the phylum Apicomplexa contain a relict chloroplast called the apicoplast .", "During evolution , the apicoplast lost photosynthetic functions but retained critical metabolic pathways that are required for host cell infection .", "...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "face", "tropical diseases", "health care", "preventive medicine", "bacterial diseases", "health services administration and management", "eye diseases", "global health", "neglected tropical diseases", "sanitation", "public and occupational health", "infectiou...	Interventions to maximize facial cleanliness and achieve environmental improvement for trachoma elimination: A review of the grey literature	journal.pntd.0006178	null	[ [ "Behavior change reflects a process of modification and transformation .", "This process is complicated by an assortment of change antecedents , which are precursors that need to be addressed before behavior change and maintenance can occur .", "Antecedents include factors such as perceived risk of in...	[ "Efforts are underway to scale-up the facial cleanliness and environmental improvement ( F&E ) components of the World Health Organization’s SAFE strategy for elimination of trachoma as a public health problem .", "Improving understanding of the F&E intervention landscape could inform advancements prior to scale-...	[ "Trachoma is the world’s leading infectious cause of blindness .", "In light of a 2020 global target , the international trachoma community is intensifying its efforts to scale-up facial cleanliness and environmental improvement ( F&E ) components of the WHO-endorsed SAFE strategy for the elimination of trachoma ...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "phosphorylation", "plant anatomy", "rna interference", "gene regulation", "regulatory proteins", "brassica", "dna-binding proteins", "cereal crops", "plant science", "model organisms", "rice", "transcription factors", "crops", "epigenetics", "plants", "cellular structures and organell...	OVATE Family Protein 8 Positively Mediates Brassinosteroid Signaling through Interacting with the GSK3-like Kinase in Rice	journal.pgen.1006118	null	[ [ "OVATE gene was first cloned in tomato and demonstrated to encode a hydrophilic protein with putative bipartite nuclear localization signal , and a C-terminal domain of approximate 70 amino acids which is designated as the OVATE domain and conserved in tomato , Arabidopsis , and rice [1–3] .", "As a plant...	[ "OVATE gene was first identified as a key regulator of fruit shape in tomato .", "OVATE family proteins ( OFPs ) are characterized as plant-specific transcription factors and conserved in Arabidopsis , tomato , and rice .", "Roles of OFPs involved in plant development and growth are largely unknown .", "Brass...	[ "OVATE family proteins ( OFPs ) are characterized as plant-specific transcription factors and mainly function in affecting fruit shape , but the molecular mechanisms by which they function are largely unknown .", "Rice genome contains 31 OFPs , the roles of these OsOFPs involved in plant development and growth ar...	2016
[ "Introduction", "Results", "Discussion" ]	[ "infectious diseases/neglected tropical diseases", "computational biology/ecosystem modeling", "infectious diseases/viral infections", "virology/emerging viral diseases" ]	Risk Maps of Lassa Fever in West Africa	journal.pntd.0000388	null	[ [ "Lassa fever ( LF ) is a viral haemorrhagic fever the pathogenic agent of which is an arenavirus Lassa virus ( LASV ) first discovered in 1969 in Nigeria , in a missionary nurse living in Lassa , a village close to the border with Cameroon [1] .", "Lassa fever is widespread in West Africa , affecting 2 mi...	[ "Lassa fever is caused by a viral haemorrhagic arenavirus that affects two to three million people in West Africa , causing a mortality of between 5 , 000 and 10 , 000 each year .", "The natural reservoir of Lassa virus is the multi-mammate rat Mastomys natalensis , which lives in houses and surrounding fields ."...	[ "Previous studies on the eco-epidemiology of Lassa fever in Guinea , West Africa , have shown that the reservoir is two to three times more infected by Lassa virus in the rainy season than in the dry season .", "None of the intrinsic variables of the murine population , such as abundance or reproduction , was abl...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biophysics/macromolecular assemblies and machines", "cell biology/morphogenesis and cell biology", "biophysics/experimental biophysical methods", "cell biology/membranes and sorting", "cell biology/cytoskeleton" ]	Single Molecule Imaging Reveals Differences in Microtubule Track Selection Between Kinesin Motors	journal.pbio.1000216	Molecular motors differentially recognize and move cargo along discrete microtubule subpopulations in cells, resulting in preferential transport and targeting of subcellular cargoes.	[ [ "Understanding how cells generate intracellular structures and overall morphologies is one of the major goals of cell biology .", "For the cytoskeleton , strikingly different structures can be assembled from a set of highly conserved building blocks .", "For example , all microtubules are generated by...	[ "Cells generate diverse microtubule populations by polymerization of a common α/β-tubulin building block .", "How microtubule associated proteins translate microtubule heterogeneity into specific cellular functions is not clear .", "We evaluated the ability of kinesin motors involved in vesicle transport to rea...	[ "Eukaryotic cells assemble a variety of cytoskeletal structures from a set of highly conserved building blocks .", "For example , all microtubules are generated by the polymerization of a common α/β-tubulin subunit , yet cells can contain diverse , discrete populations of microtubule structures such as axonemes ,...	2009
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "chemical compounds", "phosphates", "melioidosis", "immunology", "bacterial diseases", "lipid structure", "lipid analysis", "research and analysis methods", "infectious diseases", "lipids", "chemistry", "mass spectrometry", "molecular biology", "immune res...	Comprehensive analysis of clinical Burkholderia pseudomallei isolates demonstrates conservation of unique lipid A structure and TLR4-dependent innate immune activation	journal.pntd.0006287	null	[ [ "Burkholderia pseudomallei is a Gram-negative bacillus and the causative agent of melioidosis .", "This disease is endemic in Southeast Asia and northern Australia , with a mortality rate up to 40% in northeast Thailand and 20% in Australia [1 , 2] .", "The manifestations of disease vary from indolent...	[ "Burkholderia pseudomallei is an environmental bacterium that causes melioidosis , a major community-acquired infection in tropical regions .", "Melioidosis presents with a range of clinical symptoms , is often characterized by a robust inflammatory response , may relapse after treatment , and results in high mor...	[ "Melioidosis is a tropical infection caused by Burkholderia pseudomallei .", "Disease ranges from mild to lethal , and patients who die from melioidosis have greater inflammatory responses than survivors .", "Identifying variation in bacterial structures that alter the immune response is therefore important .",...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "yeast and fungi", "genetics and genomics", "saccharomyces" ]	A Multi-Step Pathway for the Establishment of Sister Chromatid Cohesion	journal.pgen.0030012	null	[ [ "Proper transmission of eukaryotic chromosomes during cell division requires DNA replication and three other DNA-dependent processes: recombination-dependent DNA repair , sister chromatid cohesion , and chromosome condensation .", "Each of these diverse processes requires protein complexes containing two ...	[ "The cohesion of sister chromatids is mediated by cohesin , a protein complex containing members of the structural maintenance of chromosome ( Smc ) family .", "How cohesins tether sister chromatids is not yet understood .", "Here , we mutate SMC1 , the gene encoding a cohesin subunit of budding yeast , by rand...	[ "Complexes containing members of the structural maintenance of chromosomes ( Smc ) family regulate higher order chromosome architecture in diverse aspects of DNA metabolism including chromosome condensation , sister chromatid cohesion , DNA repair , and global control of transcription .", "Smc complexes are thoug...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "developmental biology", "cell biology", "mus (mouse)", "neuroscience" ]	Rb-Mediated Neuronal Differentiation through Cell-Cycle–Independent Regulation of E2f3a	journal.pbio.0050179	The retinoblastoma protein (Rb), a tumor suppressor, promotes the differentiation of starburst amacrine cells in the retina by inhibiting the transcription factor E2f3a, whereas it suppresses retinal cell division and death by inhibiting E2f1.	[ [ "The simplicity of the retina makes it an ideal tissue to study neurogenesis .", "Its development proceeds through three overlapping steps starting with retinal progenitor cell ( RPC ) proliferation , followed by birth of post-mitotic retinal transition cells ( RTCs , also referred to as precursors ) , an...	[ "It has long been known that loss of the retinoblastoma protein ( Rb ) perturbs neural differentiation , but the underlying mechanism has never been solved .", "Rb absence impairs cell cycle exit and triggers death of some neurons , so differentiation defects may well be indirect .", "Indeed , we show that abno...	[ "The retinoblastoma protein ( Rb ) , an important tumor suppressor , blocks division and death by inhibiting the E2f transcription factor family .", "In contrast , Rb is thought to promote differentiation by potentiating tissue-specific transcription factors , although differentiation defects in Rb null cells cou...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "rna-binding proteins", "medicine and health sciences", "breast tumors", "protein interactions", "cancers and neoplasms", "basic cancer research", "oncology", "immunoprecipitation", "secondary lung tumors", "research and analysis methods", "proteins", "lung and intrathoracic tumors", "gene e...	Post-transcriptional Control of Tumor Cell Autonomous Metastatic Potential by CCR4-NOT Deadenylase CNOT7	journal.pgen.1005820	null	[ [ "Metastasis is a complex process in which tumor cells disseminate from the primary tumor site to form life-threatening lesions at distant sites .", "To successfully complete the metastatic process tumor cells must activate a series of molecular functions .", "These include motility and invasion to esc...	[ "Accumulating evidence supports the role of an aberrant transcriptome as a driver of metastatic potential .", "Deadenylation is a general regulatory node for post-transcriptional control by microRNAs and other determinants of RNA stability .", "Previously , we demonstrated that the CCR4-NOT scaffold component C...	[ "The majority of human cancer related death is due to the effects of metastasis , the process of cancer dissemination to and growth in distant organs .", "Primarily due to its complexity , the metastatic process remains incompletely understood .", "This complexity stems from the tumor cell’s dependence on multi...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "flow cytometry", "medicine and health sciences", "immune physiology", "crystal structure", "enzyme-linked immunoassays", "immunology", "condensed matter physics", "membrane fusion", "protein structure", "crystallography", "antibodies", "immunologic techniques", "cross reactivity", "cellul...	Engineering, Structure and Immunogenicity of the Human Metapneumovirus F Protein in the Postfusion Conformation	journal.ppat.1005859	null	[ [ "Human metapneumovirus ( hMPV ) was first isolated in 2001 from respiratory specimens collected from children with respiratory tract infections [1] .", "Sequence analysis was used to classify hMPV in the Metapneumovirus genus of the Pneumovirinae subfamily of paramyxoviruses .", "This subfamily also i...	[ "Human metapneumovirus ( hMPV ) is a paramyxovirus that is a common cause of bronchiolitis and pneumonia in children less than five years of age .", "The hMPV fusion ( F ) glycoprotein is the primary target of neutralizing antibodies and is thus a critical vaccine antigen .", "To facilitate structure-based vacc...	[ "Human metapneumovirus ( hMPV ) is a frequent cause of severe lower respiratory tract infections in very young children and a vaccine is not yet available .", "Protection against hMPV infection is afforded mainly by neutralizing antibodies directed against the fusion ( F ) glycoprotein .", "After iterative roun...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genome expression analysis", "mathematics", "statistics", "genetics", "biology", "genomics", "biostatistics", "gene networks", "genetics and genomics" ]	Variance of Gene Expression Identifies Altered Network Constraints in Neurological Disease	journal.pgen.1002207	null	[ [ "In studying biological systems , we tend to think of groups as being defined by specific , measurable parameters , and of the important differences between those groups as being defined by a significant average difference in those parameters .", "Much of the language we use in describing biological syste...	[ "Gene expression analysis has become a ubiquitous tool for studying a wide range of human diseases .", "In a typical analysis we compare distinct phenotypic groups and attempt to identify genes that are , on average , significantly different between them .", "Here we describe an innovative approach to the analy...	[ "Genes are a repository of information that provides the framework for cellular processes , with the flow of information from gene ( DNA ) to phenotype via an intermediate molecule—the messenger RNA .", "We understand that sequence variations in a gene may lead to phenotypic variations , but less well understood ...	2011
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "antimicrobials", "medicine and health sciences", "immune physiology", "pathology and laboratory medicine", "spleen", "melioidosis", "drugs", "immunology", "microbiology", "animal models", "bacterial diseases", "model organisms", "signs and symptoms", "antibacterials", "antibiotics", "...	Immune Modulation as an Effective Adjunct Post-exposure Therapeutic for B. pseudomallei	journal.pntd.0005065	null	[ [ "Melioidosis is a tropical and often fatal disease caused by the aerobic , Gram-negative facultative intracellular bacterium Burkholderia pseudomallei [1] .", "Traditional B . pseudomallei infection is associated with environmental exposures during the monsoon season in the tropics .", "It has also be...	[ "Melioidosis is caused by the facultative intracellular bacterium Burkholderia pseudomallei and is potentially fatal .", "Despite a growing global burden and high fatality rate , little is known about the disease .", "Recent studies demonstrate that cyclooxygenase-2 ( COX-2 ) inhibition is an effective post-exp...	[ "Burkholderia pseudomallei is the causative agent of melioidosis , a fatal tropical disease endemic in parts of Southwest Asia and Northern Australia .", "While it was once believed to be isolated to these areas , recent research indicates the global burden on melioidosis is growing .", "Furthermore , treatment...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "phosphorylation", "crystal structure", "chemical compounds", "enzymes", "condensed matter physics", "enzymology", "organic compounds", "basic amino acids", "protein structure", "amino acids", "crystallography", "solid state physics", "proteins", "protein kinases", "ubiquitination", "c...	Non-degradative Ubiquitination of Protein Kinases	journal.pcbi.1004898	null	[ [ "The best-characterized function of ubiquitin is as a marker for protein degradation .", "The 76-residue ubiquitin protein can be covalently attached at its C-terminus to a lysine side chain amine group or N-terminus of another protein .", "Typically , additional ubiquitin molecules are also attached ...	[ "Growing evidence supports other regulatory roles for protein ubiquitination in addition to serving as a tag for proteasomal degradation .", "In contrast to other common post-translational modifications , such as phosphorylation , little is known about how non-degradative ubiquitination modulates protein structur...	[ "Attachment of ubiquitin to another protein is typically used to mark the protein for degradation by the proteasome .", "However , recent studies show that many proteins are tagged with ubiquitin and not degraded .", "We hypothesized that ubiquitin can regulate the protein it is attached to by changing its stru...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology/effects of virus infection on host gene expression", "immunology/immunity to infections", "virology/new therapies, including antivirals and immunotherapy", "virology/host antiviral responses" ]	IL-10 Signaling Blockade Controls Murine West Nile Virus Infection	journal.ppat.1000610	null	[ [ "WNV has caused severe morbidity and mortality in both animals and humans since it first appeared in North America in 1999 .", "WNV is maintained in an enzootic cycle between mosquitoes and birds; but humans , horses and other mammals can be inadvertently infected by mosquitoes that carry the virus .", ...	[ "West Nile virus ( WNV ) , a mosquito-borne single-stranded RNA flavivirus , can cause significant human morbidity and mortality .", "Our data show that interleukin-10 ( IL-10 ) is dramatically elevated both in vitro and in vivo following WNV infection .", "Consistent with an etiologic role of IL-10 in WNV path...	[ "West Nile virus ( WNV ) , a mosquito-transmitted RNA virus , is a worldwide cause of severe human and animal infection .", "Mammalian host immune responses to WNV infection are not completely understood and a vaccine or specific therapy is unavailable for use in humans .", "In the present study , we investigat...	2009
[ "Introduction", "Results", "Discussion", "Models" ]	[ "cell physiology", "cell motility", "ellipses", "classical mechanics", "fluid mechanics", "cell cycle and cell division", "cell processes", "cadherins", "surface tension", "geometry", "cell polarity", "developmental biology", "mathematics", "materials science", "contractile proteins", ...	Dynamics of Cell Ensembles on Adhesive Micropatterns: Bridging the Gap between Single Cell Spreading and Collective Cell Migration	journal.pcbi.1004863	null	[ [ "Adhesive micropatterns ( MP ) determine the spatial distribution of the extracellular matrix ( ECM ) and therefore allow us to investigate and control cell shape , structure and function through experimental design .", "Over the last decade , they have emerged as an extremely versatile tool to investigat...	[ "The collective dynamics of multicellular systems arise from the interplay of a few fundamental elements: growth , division and apoptosis of single cells; their mechanical and adhesive interactions with neighboring cells and the extracellular matrix; and the tendency of polarized cells to move .", "Micropatterned...	[ "The collective dynamics of many cells is more than the sum of its parts .", "For example , large cell collectives often form streams , swirls or bridges that cannot be achieved by single cells .", "Yet the dynamic processes of single cells , especially their response to adhesive and mechanical cues , stays an ...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	The Herpes Simplex Virus Protein pUL31 Escorts Nucleocapsids to Sites of Nuclear Egress, a Process Coordinated by Its N-Terminal Domain	journal.ppat.1004957	null	[ [ "Morphogenesis of herpesviral capsids is an intricate process initiated in the infected nucleus [1] .", "A fragile procapsid is formed and packaged with one copy of the viral genome that is generated by cleavage of replicated concatameric DNA molecules .", "During this process , the rather spherical p...	[ "Progeny capsids of herpesviruses leave the nucleus by budding through the nuclear envelope .", "Two viral proteins , the membrane protein pUL34 and the nucleo-phosphoprotein pUL31 form the nuclear egress complex that is required for capsid egress out of the nucleus .", "All pUL31 orthologs are composed of a di...	[ "Herpesviral capsid assembly is initiated in the host nucleus .", "Due to size constraints , newly formed nucleocapsids are unable to leave the nucleus through the nuclear pore complex .", "Instead herpesviruses apply an evolutionarily conserved mechanism for nuclear export of capsids called nuclear egress .", ...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "sociology", "geographical locations", "social sciences", "health care", "ethnicities", "scale-free networks", "network analysis", "social networks", "nosocomial infections", "patients", "infectious diseases", "computer and information sciences", "hospitals"...	Spread of hospital-acquired infections: A comparison of healthcare networks	journal.pcbi.1005666	null	[ [ "The emergence and spread of multi-drug resistant organisms threatens healthcare systems worldwide . [1]", "This is particularly true concerning methicillin-resistant Staphylococcus aureus , vancomycin-resistant enterococci , and multi-resistant gram-negative bacteria such as carbapenemase-producing Enter...	[ "Hospital-acquired infections ( HAIs ) , including emerging multi-drug resistant organisms , threaten healthcare systems worldwide .", "Efficient containment measures of HAIs must mobilize the entire healthcare network .", "Thus , to best understand how to reduce the potential scale of HAI epidemic spread , we ...	[ "Hospital-acquired infections ( HAIs ) , including emerging multi-drug resistant organisms , threaten healthcare systems worldwide .", "Efficient containment measures of HAIs must mobilize the entire healthcare network .", "Thus , to best understand how to reduce the scale of potential HAI epidemic spread , we ...	2017

Subsets and Splits

No community queries yet

The top public SQL queries from the community will appear here once available.