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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", "Methods" ]	[ "genome-wide association studies", "applied mathematics", "variant genotypes", "population genetics", "alleles", "genetic mapping", "simulation and modeling", "algorithms", "probability distribution", "mathematics", "statistics (mathematics)", "test statistics", "genome analysis", "populat...	Bias Characterization in Probabilistic Genotype Data and Improved Signal Detection with Multiple Imputation	journal.pgen.1006091	null	[ [ "Genome-wide association studies ( GWAS ) have become a primary tool to elucidate the correlations between SNP genotypes and complex phenotypes in large cohorts .", "Association studies initially assumed the existence of genotype calls: for each sample at each assayed variant , either reference allele hom...	[ "Missing data are an unavoidable component of modern statistical genetics .", "Different array or sequencing technologies cover different single nucleotide polymorphisms ( SNPs ) , leading to a complicated mosaic pattern of missingness where both individual genotypes and entire SNPs are sporadically absent .", ...	[ "Genetic research has been focused at analysis of datapoints that are assumed to be deterministically known .", "However , the majority of current , high throughput data is only probabilistically known , and proper methods for handing such uncertain genotypes are limited .", "Here , we build on existing theory ...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics and genomics/comparative genomics", "computational biology/transcriptional regulation", "computational biology/evolutionary modeling", "evolutionary biology/pattern formation", "genetics and genomics/bioinformatics", "genetics and genomics/population genetics" ]	Evolution of Regulatory Sequences in 12 Drosophila Species	journal.pgen.1000330	null	[ [ "Gene regulation is well recognized as a major determinant of how an organism functions [1] , and is also gaining recognition as an important evolutionary substrate [2] , [3] .", "Transcription control is one of the most common forms of gene regulation , and is known to be implemented through regulatory s...	[ "Characterization of the evolutionary constraints acting on cis-regulatory sequences is crucial to comparative genomics and provides key insights on the evolution of organismal diversity .", "We study the relationships among orthologous cis-regulatory modules ( CRMs ) in 12 Drosophila species , especially with re...	[ "The spatial–temporal expression pattern of a gene , which is crucial to its function , is controlled by cis-regulatory DNA sequences .", "Forming the basic units of regulatory sequences are transcription factor binding sites , often organized into larger modules that determine gene expression in response to comb...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "death rates", "medicine and health sciences", "melioidosis", "population dynamics", "geographical locations", "diabetes mellitus", "bacterial diseases", "age groups", "endocrine disorders", "population biology", "public and occupational health", "infectious diseases", "endocrinology", "me...	Modelling population dynamics and seasonal movement to assess and predict the burden of melioidosis	journal.pntd.0007380	null	[ [ "Melioidosis is an infection caused by the Gram-negative bacillus Burkholderia pseudomallei , which exhibits marked seasonality in most settings where it is endemic , including Southeast Asia and Northern Australia [1] .", "Melioidosis is a communicable disease that is usually transmitted via contaminated...	[ "Melioidosis is an infectious disease that is transmitted mainly through contact with contaminated soil or water , and exhibits marked seasonality in most settings , including Southeast Asia .", "In this study , we used mathematical modelling to examine the impacts of such demographic changes on melioidosis incid...	[ "Melioidosis is an infectious disease caused by the Gram-negative bacillus Burkholderia pseudomallei , which exhibits marked seasonality in most settings where it occurs , such as Southeast Asia and Northern Australia .", "Most of the population at risk of contracting melioidosis lives in rural areas; particularl...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "genetics", "biology and life sciences", "genomics", "evolutionary biology", "clinical genetics" ]	Pseudoautosomal Region 1 Length Polymorphism in the Human Population	journal.pgen.1004578	null	[ [ "The human sex chromosomes originate from an ancestral homologous chromosome pair .", "During mammalian evolution , these chromosomes lost homology due to progressive degradation of the Y chromosome .", "The decay of the Y chromosome started with the introduction of sex determination factors , which i...	[ "The human sex chromosomes differ in sequence , except for the pseudoautosomal regions ( PAR ) at the terminus of the short and the long arms , denoted as PAR1 and PAR2 .", "The boundary between PAR1 and the unique X and Y sequences was established during the divergence of the great apes .", "During a copy numb...	[ "The human sex chromosomes differ in sequence , except for homologous sequences at both ends , termed the pseudoautosomal regions ( PAR1 and PAR2 ) .", "PAR enables the pairing of chromosomes Y and X during meiosis .", "The PARs are located at the termini of respectively the short and long arms of chromosomes X...	2014
[ "Introduction", "Results and Discussion", "Materials and Methods" ]	[ "biochemistry/chemical biology of the cell", "biophysics/biomacromolecule-ligand interactions", "biophysics/membrane proteins and energy transduction", "chemical biology/macromolecular chemistry", "biochemistry/membrane proteins and energy transduction" ]	Voltage-Dependent Gating in a “Voltage Sensor-Less” Ion Channel	journal.pbio.1000315	An unusual mechanism of ion channel regulation generates voltage-dependent gating in the absence of a canonical voltage-sensing domain.	[ [ "While the entire complement of ion channels in a given cell contributes to the membrane voltage , only a subset ( the voltage-gated cation channel family ) responds significantly to changes in membrane voltage , and the molecular mechanisms underlying their voltage dependence remain the subject of considerab...	[ "The voltage sensitivity of voltage-gated cation channels is primarily attributed to conformational changes of a four transmembrane segment voltage-sensing domain , conserved across many levels of biological complexity .", "We have identified a remarkable point mutation that confers significant voltage dependence...	[ "Ion channels are proteins that regulate the transfer of ions across the cell membrane .", "The ions travel via a pore formed by the different subunits that constitute the channels , and this pore can be gated by changes in the electrical field across cell membranes .", "The canonical mechanism underlying volta...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	LINE-1 Mediated Insertion into Poc1a (Protein of Centriole 1 A) Causes Growth Insufficiency and Male Infertility in Mice	journal.pgen.1005569	null	[ [ "Normal adult stature in humans is achieved primarily through regulation of long bone growth , which occurs through endochondral ossification [1 , 2] .", "This process begins with the differentiation of mesenchymal stem cells into chondrocytes in regions of the body where skeletal elements will eventually...	[ "Skeletal dysplasias are a common , genetically heterogeneous cause of short stature that can result from disruptions in many cellular processes .", "We report the identification of the lesion responsible for skeletal dysplasia and male infertility in the spontaneous , recessive mouse mutant chagun .", "We dete...	[ "Severe short stature in humans has many causes including defects in skeletal and hormonal growth regulation .", "Primordial dwarfisms are congenital growth defects that involve mutations in genes for DNA repair , DNA replication , splicing of U12 introns , and centrosome dynamics .", "We discovered that the sp...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "viral envelope", "viral entry", "viral transmission and infection", "virology", "biology and life sciences", "microbiology", "viral structure" ]	Functional Fluorescent Protein Insertions in Herpes Simplex Virus gB Report on gB Conformation before and after Execution of Membrane Fusion	journal.ppat.1004373	null	[ [ "Herpes simplex virus infections are common , with severe disease striking some individuals while others are asymptomatic .", "Herpes simplex virus type 1 ( HSV-1 ) afflicts roughly 70% of individuals within the United States [1] , while HSV-2 afflicts approximately 16% [2] .", "Infection is chronic ,...	[ "Entry of herpes simplex virus ( HSV ) into a target cell requires complex interactions and conformational changes by viral glycoproteins gD , gH/gL , and gB .", "During viral entry , gB transitions from a prefusion to a postfusion conformation , driving fusion of the viral envelope with the host cell membrane ."...	[ "Viral fusion proteins undergo complicated conformational changes in order to fuse viral and host membranes during viral entry .", "Conformational changes between prefusion and postfusion states also allow the virus to hide critical regions of the fusion machinery from the immune system .", "The structure of he...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "heme", "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "hela cells", "oxidative stress", "pathogens", "immunology", "biological cultures", "microbiology", "retroviruses", "viruses", "rna viruses", "cell cultures", "research and analy...	HTLV-1 basic leucine zipper factor protects cells from oxidative stress by upregulating expression of Heme Oxygenase I	journal.ppat.1007922	null	[ [ "The accumulation of reactive oxygen ( ROS ) and nitrogen species ( RNS ) is known to induce damage to cellular structures , including genetic material .", "Oxidative DNA damage can result in cell cycle arrest , the induction of replicative senescence , and initiation of apoptosis [1] .", "To avoid th...	[ "Adult T-cell Leukemia ( ATL ) is a lymphoproliferative disease of CD4+ T-cells infected with Human T-cell Leukemia Virus type I ( HTLV-1 ) .", "With the exception of allogeneic hematopoietic stem cell transplantation , there are no effective treatments to cure ATL , and ATL cells often acquire resistance to conv...	[ "Human T-cell Leukemia Virus type I ( HTLV-1 ) infection causes a fatal form of leukemia known as Adult T-cell Leukemia ( ATL ) .", "Given that most current anti-cancer drugs fail to eradicate the leukemic cells in ATL patients , novel treatment strategies are required .", "One approach is to target functions o...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "mycology", "proteins", "biology", "microbiology" ]	A P-loop Mutation in Gα Subunits Prevents Transition to the Active State: Implications for G-protein Signaling in Fungal Pathogenesis	journal.ppat.1002553	null	[ [ "G protein-coupled receptors ( GPCRs ) convert extracellular signals to intracellular responses , primarily by stimulating guanine nucleotide exchange on heterotrimeric G-protein Gα subunits [1] .", "Upon receptor-stimulated exchange of GTP for GDP , Gα subunits undergo a conformational change , dominated...	[ "Heterotrimeric G-proteins are molecular switches integral to a panoply of different physiological responses that many organisms make to environmental cues .", "The switch from inactive to active Gαβγ heterotrimer relies on nucleotide cycling by the Gα subunit: exchange of GTP for GDP activates Gα , whereas its i...	[ "Heterotrimeric G-proteins function as molecular switches to convey cellular signals .", "When a G-protein coupled receptor encounters its ligand at the cellular membrane , it catalyzes guanine nucleotide exchange on the Gα subunit , resulting in a shift from an inactive to an active conformation .", "G-protein...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "mycobacterium leprae", "medicine and health sciences", "enzyme-linked immunoassays", "immunology", "tropical diseases", "biomarkers", "bacterial diseases", "neglected tropical diseases", "immunologic techniques", "bacteria", "research and analysis methods", "infectious diseases", "tuberculo...	Evaluation of antigen-specific immune responses for leprosy diagnosis in a hyperendemic area in China	journal.pntd.0006777	null	[ [ "Leprosy , a chronic disease caused by Mycobacteriumleprae ( M . leprae ) infection , has a wide range of clinical outcomes correlated with the host's immune response to the bacilli[1 , 2] .", "Current leprosy control strategies rely on diagnosing the disease as early as possible , followed by prompt trea...	[ "To evaluate antigen-specific immune responses for leprosy diagnosis in a hyperendemic area in China .", "Eighty-three leprosy patients and 161 non-leprosy controls were enrolled from Hani-yi Autonomous Prefecture of Honghe , Yunnan Province , China .", "Leprosy patients were divided into multibacillary ( MB , ...	[ "Although the implementation of World Health Organization ( WHO ) multidrug therapy ( MDT ) treatment has drastically reduced the number of registered leprosy cases , new case detection rates have stabilized over the last decade , and leprosy remains an important health problem in many regions .", "Antigen-specif...	2018
[ "Introduction", "Material and methods", "Results and discussion" ]	[ "group-specific staining", "medicine and health sciences", "animal diseases", "nervous system", "hematoxylin staining", "enzymes", "blood-brain barrier", "enzymology", "fluorophotometry", "animal prion diseases", "infectious disease control", "zoology", "research and analysis methods", "sp...	Prion pathogenesis is unaltered in a mouse strain with a permeable blood-brain barrier	journal.ppat.1007424	null	[ [ "Transmissible spongiform encephalopathies ( TSEs ) are progressive , invariably lethal neurodegenerative diseases which include Creutzfeldt–Jakob disease , kuru , fatal familial insomnia and Gerstmann–Sträussler–Scheinker syndrome in humans , scrapie in sheep , and bovine spongiform encephalopathy ( BSE ) in...	[ "Transmissible spongiform encephalopathies ( TSEs ) are caused by the prion , which consists essentially of PrPSc , an aggregated , conformationally modified form of the cellular prion protein ( PrPC ) .", "Although TSEs can be experimentally transmitted by intracerebral inoculation , most instances of infection ...	[ "Prion diseases or transmissible spongiform encephalopathies ( TSEs ) are incurable brain diseases caused by conformational changes in the endogenous prion protein .", "Prions can be transmitted through contaminated food , surgical instruments and blood .", "Transmission of prions has caused the kuru epidemic i...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "ecology and environmental sciences", "toxins", "pathology and laboratory medicine", "chemical compounds", "disaccharides", "cell cycle and cell division", "cell processes", "carbohydrates", "organic compounds", "toxicology", "toxic agents", "simulation and mo...	Lineage space and the propensity of bacterial cells to undergo growth transitions	journal.pcbi.1006380	null	[ [ "The process of cellular growth is both the distinguishing feature of living matter and central to the roles of regulatory networks from microbes to metazoa .", "Growth and division is also a primary source of phenotypic diversification .", "For instance , when a bacterial cell divides , and its cellu...	[ "The molecular makeup of the offspring of a dividing cell gradually becomes phenotypically decorrelated from the parent cell by noise and regulatory mechanisms that amplify phenotypic heterogeneity .", "Such regulatory mechanisms form networks that contain thresholds between phenotypes .", "Populations of cells...	[ "One of the most important characteristics of a cell is whether it is growing .", "Actively growing cells can multiply exponentially .", "In the case of infections and cancer , growth causes problems for the host organism .", "On the other hand , cells that have stopped growing can allocate cellular resources...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "microbiology/innate immunity", "infectious diseases/bacterial infections", "microbiology/cellular microbiology and pathogenesis", "microbiology/medical microbiology", "infectious diseases/gastrointestinal infections" ]	A Rapid Change in Virulence Gene Expression during the Transition from the Intestinal Lumen into Tissue Promotes Systemic Dissemination of Salmonella	journal.ppat.1001060	null	[ [ "Epithelial barriers form a first line of defense against microbial invasion .", "However , the ability to cross this physical barrier does not automatically result in systemic dissemination of the invading microbe .", "For example , non-typhoidal Salmonella serotypes , such as Salmonella enterica ser...	[ "Bacterial pathogens causing systemic disease commonly evolve from organisms associated with localized infections but differ from their close relatives in their ability to overcome mucosal barriers by mechanisms that remain incompletely understood .", "Here we investigated whether acquisition of a regulatory gene...	[ "Some bacterial species contain pathogenic strains that are closely related genetically , but cause diseases that differ dramatically in their clinical presentation .", "One such species is Salmonella enterica , which contains non-typhoidal serotypes associated with a localized gastroenteritis and serotype Typhi ...	2010
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "plastic surgery and reconstructive techniques", "ears", "immunology", "parasitic diseases", "parasitic protozoans", "surgical and invasive medical procedures", "skin grafting", "protozoans", ...	Skin-resident CD4+ T cells protect against Leishmania major by recruiting and activating inflammatory monocytes	journal.ppat.1006349	null	[ [ "Tissue-resident memory T cells ( TRM ) are critical mediators of immunity against a number of different infections in a variety of different tissues [1–11] .", "Because they are typically located at barrier surfaces and therefore occupy the initial sites of infection , TRM cells are poised to provide rap...	[ "Tissue-resident memory T cells are required for establishing protective immunity against a variety of different pathogens , although the mechanisms mediating protection by CD4+ resident memory T cells are still being defined .", "In this study we addressed this issue with a population of protective skin-resident...	[ "Cutaneous leishmaniasis is a neglected tropical disease , causing significant worldwide morbidity .", "There is no vaccine for this infection , in part because of our limited understanding of the memory T cells that might contribute to immunity .", "We previously discovered that a population of skin-resident m...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular cell biology", "genetics", "cell biology", "biology and life sciences" ]	A Quality Control Mechanism Coordinates Meiotic Prophase Events to Promote Crossover Assurance	journal.pgen.1004291	null	[ [ "During sexual reproduction , meiotic chromosome segregation generates haploid gametes so that fertilization restores diploidy to the resulting embryo .", "Meiosis halves the DNA complement by segregating homologous chromosomes in one division and follows that reductional division with an equational divis...	[ "Meiotic chromosome segregation relies on homologous chromosomes being linked by at least one crossover , the obligate crossover .", "Homolog pairing , synapsis and meiosis specific DNA repair mechanisms are required for crossovers but how they are coordinated to promote the obligate crossover is not well underst...	[ "The production of sperm and eggs for sexual reproduction depends on meiosis .", "During this specialized cell division , homologous chromosomes are linked by at least one crossover recombination event , or chiasma , to promote their proper segregation .", "How events in meiotic prophase are coordinated to cont...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "psychology", "psychological adjustment", "behavior", "biology and life sciences", "social psychology", "social sciences", "evolutionary biology", "evolutionary emergence", "evolutionary processes" ]	Leadership in Moving Human Groups	journal.pcbi.1003541	null	[ [ "Schools of fish and flocks of birds move collectively towards a spatial goal [1] , [2] despite their large local group sizes and therefore reduced capacity for global or inter-individual communication across the group [3] , [4] .", "Behavioural modelling [5]–[7] and empirical research [8]–[10] have shown...	[ "How is movement of individuals coordinated as a group ?", "This is a fundamental question of social behaviour , encompassing phenomena such as bird flocking , fish schooling , and the innumerable activities in human groups that require people to synchronise their actions .", "We have developed an experimental ...	[ "Our article gives empirical evidence of group coordination mechanisms and basic rules of leadership that assist in leading a human group .", "Using a computer-based multi-client game that blocks explicit signals or other typical human information transfer , we offer a model of human group movement patterns appli...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "neuroscience/behavioral neuroscience", "neuroscience/cognitive neuroscience", "neuroscience/neural homeostasis", "neuroscience/psychology", "neuroscience/theoretical neuroscience" ]	A Neural Computational Model of Incentive Salience	journal.pcbi.1000437	null	[ [ "Incentive salience is essentially a Pavlovian motivational response: it takes Pavlovian associations as its learned input .", "Potential differences between cached valence and motivation values for Pavlovian cues have been previously noted by computational modelers and learning theorists [14] , [18]–[22]...	[ "Incentive salience is a motivational property with ‘magnet-like’ qualities .", "When attributed to reward-predicting stimuli ( cues ) , incentive salience triggers a pulse of ‘wanting’ and an individual is pulled toward the cues and reward .", "A key computational question is how incentive salience is generate...	[ "Reward cues are potent triggers of desires , ranging from normal appetites to compulsive addictions .", "Food cues may trigger a sudden desire to eat before lunch , and drug cues may trigger even a ‘recovered addict’ to relapse again into drug taking .", "But learned cues are not constant in their motivating p...	2009
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "developmental biology", "developmental biology/morphogenesis and cell biology", "cell biology/cell signaling", "physiology/pattern formation", "developmental biology/organogenesis", "cell biology/gene expression" ]	Identification of Mechanosensitive Genes during Embryonic Bone Formation	journal.pcbi.1000250	null	[ [ "It is widely accepted that there is a relationship between the morphology of skeletal", "structures and the mechanical forces acting upon them .", "Such a relationship begins in", "the embryo where the importance of muscle for normal bone formation has been clearly", "demonstrated [1] , [2]; ...	[ "Although it is known that mechanical forces are needed for normal bone", "development , the current understanding of how biophysical stimuli are", "interpreted by and integrated with genetic regulatory mechanisms is limited .", "Mechanical forces are thought to be mediated in cells by", "“mechanosensitive”...	[ "While mechanical forces are known to be critical to adult bone maintenance and", "repair , the importance of mechanobiology in embryonic bone formation is less", "widely accepted .", "The influence of mechanical forces on cells is thought to be", "mediated by “mechanosensitive genes , ” genes which respond...	2008
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "antimicrobials", "medicine and health sciences", "drugs", "experimental design", "microbiology", "mathematical models", "simulation and modeling", "research design", "antibiotic resistance", "mathematics", "statistics (mathematics)", "antibiotics", "pharmacology", "research and analysis m...	Distinguishing Antimicrobial Models with Different Resistance Mechanisms via Population Pharmacodynamic Modeling	journal.pcbi.1004782	null	[ [ "Antimicrobial therapy greatly benefits from optimized antibiotic dosage regimens that are supported by pharmacokinetic ( PK ) and pharmacodynamic ( PD ) concepts .", "Traditionally , the minimum inhibitory concentration ( MIC ) has been the predominant measure of bacterial susceptibility to predict antib...	[ "Semi-mechanistic pharmacokinetic-pharmacodynamic ( PK-PD ) modeling is increasingly used for antimicrobial drug development and optimization of dosage regimens , but systematic simulation-estimation studies to distinguish between competing PD models are lacking .", "This study compared the ability of static and ...	[ "Mathematical models are increasingly used for analysis and interpretation of in vitro efficacy results of antimicrobial drugs .", "Various models are employed in the scientific literature and it seems that they are equally able to describe the observed data .", "The aim of the present study was to compare diff...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "genetics and genomics", "homo (human)" ]	Comparing the DNA Hypermethylome with Gene Mutations in Human Colorectal Cancer	journal.pgen.0030157	null	[ [ "It is now well established that loss of proper gene function in human cancer can occur through both genetic and epigenetic mechanisms [1 , 2] .", "The number of genes mutated in human tumor samples is being clarified .", "Recently , Sjöblom et al . [3] sequenced 13 , 023 genes in colorectal cancer ( ...	[ "We have developed a transcriptome-wide approach to identify genes affected by promoter CpG island DNA hypermethylation and transcriptional silencing in colorectal cancer .", "By screening cell lines and validating tumor-specific hypermethylation in a panel of primary human colorectal cancer samples , we estimate...	[ "Loss of gene expression in association with aberrant accumulation of 5-methylcytosine in gene promoter CpG islands is a common feature of human cancer .", "Here , we describe a method to discover these genes that permits identification of hundreds of novel candidate cancer genes in any cancer cell line .", "We...	2007
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "sequencing techniques", "biogeography", "ecology and environmental sciences", "medicine and health sciences", "population genetics", "vertebrates", "animals", "mammals", "hemorrhagic fever with renal syndrome", "phylogenetic analysis", "genome analysis", "molecular biology techniques", "pop...	Genetic Diversity and Reassortment of Hantaan Virus Tripartite RNA Genomes in Nature, the Republic of Korea	journal.pntd.0004650	null	[ [ "Viruses in the Hantavirus genus of the family Bunyaviridae are negative-sense single-stranded RNA virus containing Large ( L ) , Medium ( M ) , and Small ( S ) segments [1] .", "Hantaviruses pose an emerging public health threat , with about 200 , 000 cases of human disease annually worldwide and fatalit...	[ "Hantaan virus ( HTNV ) , a negative sense tripartite RNA virus of the Family Bunyaviridae , is the most prevalent hantavirus in the Republic of Korea ( ROK ) .", "It is the causative agent of Hemorrhagic Fever with Renal Syndrome ( HFRS ) in humans and maintained in the striped field mouse , Apodemus agrarius , ...	[ "Hemorrhagic Fever with Renal Syndrome ( HFRS ) and Hantavirus Pulmonary Syndrome ( HPS ) are endemic zoonotic infectious diseases caused by hantaviruses that belong to the Family Bunyaviridae containing negative-sense tripartite RNA genomes .", "Hantaviruses pose a critical emerging public health threat , with u...	2016
[ "Introduction", "Method", "Results", "Discussion" ]	[ "livestock", "medicine and health sciences", "pathology and laboratory medicine", "education", "pathogens", "immunology", "tropical diseases", "geographical locations", "vertebrates", "microbiology", "social sciences", "sociology", "animals", "mammals", "dogs", "north america", "prev...	Knowledge, attitudes, and practices regarding rabies in Grenada	journal.pntd.0007079	null	[ [ "Rabies is a zoonotic disease that is endemic in many countries , including in the Caribbean region [1] .", "The World Health Organization ( WHO ) reported that the disease kills tens of thousands of people every year [2] .", "Most deaths occur in developing countries and rural communities [3 , 4] .",...	[ "While Grenada attained a zero-human-rabies case status since 1970 , the authors conducted the first study to assess knowledge , attitudes , and practices that may contribute to this status as well as to receive feedback on the rabies control program in Grenada .", "A cross-sectional survey was conducted in July ...	[ "About 62% of households in Grenada owned animals that are susceptible to rabies .", "Pets , particularly dogs , were more commonly owned than livestock .", "Males were more likely to correctly identify animals that are susceptible to rabies .", "The level of participation in the animal vaccination program wa...	2019
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "public and occupational health", "medicine and health sciences", "global health", "biology and life sciences", "microbiology" ]	A Novel Live-Attenuated Vaccine Candidate for Mayaro Fever	journal.pntd.0002969	null	[ [ "Mayaro virus ( MAYV ) is an important and growing human health concern in the neotropics .", "First isolated in Mayaro county , Trinidad in 1954 , cases of Mayaro fever ( MAY ) have since been reported in 9 different countries in northern South America [1] .", "In addition , serological surveys sugge...	[ "Mayaro virus ( MAYV ) is an emerging , mosquito-borne alphavirus that causes a dengue-like illness in many regions of South America , and which has the potential to urbanize .", "Because no specific treatment or vaccine is available for MAYV infection , we capitalized on an IRES-based approach to develop a live-...	[ "Mayaro virus ( MAYV ) is a mosquito-borne alphavirus that causes severe and sometimes chronic arthralgia in persons in South America , where it circulates in forest habitats .", "It is widely neglected because it is typically mistaken for dengue due to the overlap in the clinical signs and symptoms , and the lac...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "reverse transcriptase-polymerase chain reaction", "medicine and health sciences", "immune physiology", "pathology and laboratory medicine", "biopsy", "spleen", "liver diseases", "surgical and invasive medical procedures", "autopsy", "signs and symptoms", "gastroenterology and hepatology", "mo...	Ultrasound-guided minimally invasive autopsy as a tool for rapid post-mortem diagnosis in the 2018 Sao Paulo yellow fever epidemic: Correlation with conventional autopsy	journal.pntd.0007625	null	[ [ "In the last decades , we have been globally identifying an unprecedented number of emerging infections [1] .", "As a result , considerable effort is currently being made by several actors from governmental and non-governmental institutions for better preparedness for the next expected emerging threats to...	[ "New strategies for collecting post-mortem tissue are necessary , particularly in areas with emerging infections .", "Minimally invasive autopsy ( MIA ) has been proposed as an alternative to conventional autopsy ( CA ) , with promising results .", "Previous studies using MIA addressed the cause of death in adu...	[ "Reliable mortality information is of paramount importance to establish sound public health policies .", "Autopsy is an important tool not only for determining the cause of death , but also for the detection of novel diseases .", "In the last decades , we have been globally identifying an unprecedented number o...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "physics", "tissue mechanics", "developmental biology", "pattern formation", "biology", "computational biology", "biophysics", "biomechanics" ]	Dynamics and Mechanical Stability of the Developing Dorsoventral Organizer of the Wing Imaginal Disc	journal.pcbi.1002153	null	[ [ "Patterning processes in multicellular organisms rely on faithful mechanisms of cell segregation and segmentation [1] , [2] .", "These ideas are beautifully illustrated by the morphogenetic events that the imaginal discs of Drosophila undergo during metamorphosis [3]–[7] .", "There , the combined acti...	[ "Shaping the primordia during development relies on forces and mechanisms able to control cell segregation .", "In the imaginal discs of Drosophila the cellular populations that will give rise to the dorsal and ventral parts on the wing blade are segregated and do not intermingle .", "A cellular population that...	[ "During development , tissues are shaped in order to form organs with specific functionalities .", "This process relies on mechanisms that control cell segregation and migration .", "These concepts are beautifully illustrated by the morphogenetic events that the imaginal discs of Drosophila undergo during metam...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "hiv infections", "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "pathogens", "immunology", "microbiology", "vertebrates", "animals", "mammals", "retroviruses", "throat", "immunodeficiency viruses", "viruses", "primates", "animal m...	Follicular Regulatory CD8 T Cells Impair the Germinal Center Response in SIV and Ex Vivo HIV Infection	journal.ppat.1005924	null	[ [ "In chronic HIV and SIV infection , viral replication is concentrated in B cell follicles in secondary lymphoid tissues [1–5] , although factors that promote this are not fully understood .", "Follicular helper T cells ( TFH ) , which reside in the secondary lymphoid follicles , are highly permissive to H...	[ "During chronic HIV infection , viral replication is concentrated in secondary lymphoid follicles .", "Cytotoxic CD8 T cells control HIV replication in extrafollicular regions , but not in the follicle .", "Here , we show CXCR5hiCD44hiCD8 T cells are a regulatory subset differing from conventional CD8 T cells ,...	[ "HIV is a chronic infection and is never completely cleared from the body , despite successful antiretroviral therapy that reduces plasma viral loads to undetectable levels and restores CD4 T cell counts .", "While undetectable in plasma , HIV is able to hide in various niches throughout the body .", "One such ...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Human CD8+ T-cells Recognizing Peptides from Mycobacterium tuberculosis (Mtb) Presented by HLA-E Have an Unorthodox Th2-like, Multifunctional, Mtb Inhibitory Phenotype and Represent a Novel Human T-cell Subset	journal.ppat.1004671	null	[ [ "Tuberculosis ( TB ) remains a major global threat because current interventions are unable to prevent or treat infection adequately .", "Mycobacterium tuberculosis ( Mtb ) is an intracellular pathogen that has evolved a myriad of effective evasion strategies to thwart host defence mechanisms .", "Due...	[ "Mycobacterial antigens are not exclusively presented to T-cells by classical HLA-class Ia and HLA-class II molecules , but also through alternative antigen presentation molecules such as CD1a/b/c , MR1 and HLA-E .", "We recently described mycobacterial peptides that are presented in HLA-E and recognized by CD8+ ...	[ "Pathogens like Mycobacterium tuberculosis ( Mtb ) are recognized by human T-cells following their presentation in HLA molecules .", "HLA class I molecules can be divided into two types , classical as well as non-classical HLA molecules .", "Here we studied the non-classical HLA family member , HLA-E , which di...	2015
[ "Introduction", "Methods", "Results and discussion" ]	[ "dengue virus", "invertebrates", "medicine and health sciences", "enzyme-linked immunoassays", "pathology and laboratory medicine", "togaviruses", "pathogens", "immunology", "geographical locations", "microbiology", "animals", "alphaviruses", "health care", "viruses", "chikungunya virus"...	Zika virus epidemiology in Bolivia: A seroprevalence study in volunteer blood donors	journal.pntd.0006239	null	[ [ "Zika virus ( ZIKV ) is an arthropod-borne Flavivirus transmitted to humans mainly by Aedes mosquitoes .", "It has been responsible over the last decade for outbreaks in Pacific Islands [1] ( Yap Island , 2007 [2]; French Polynesia , 2013 [3]; New Caledonia , Cook Islands and Easter Island , 2014 [4]; Van...	[ "Zika virus ( ZIKV ) , was widely reported in Latin America and has been associated with neuropathologies , as microcephaly , but only few seroprevalence studies have been published to date .", "Our objective was to determine the seroprevalence amongst Bolivian blood donors and estimate the future potential circu...	[ "Zika virus ( ZIKV ) is a virus of African origin , transmitted by Aedes mosquitoes , and related to dengue and yellow fever virus .", "It was originally believed to be responsible for a mild febrile illness in Africa and South-east Asia .", "However , in recent years , ZIKV has been responsible for outbreaks i...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "infographics", "taxonomy", "genome evolution", "phylogenetics", "data management", "mathematics", "algebra", "genome analysis", "dna", "homologous recombination", "computer and information sciences", "genomics", "molecular evolution", "evolutionary systematics", "evolutionary genetics",...	Inference of Ancestral Recombination Graphs through Topological Data Analysis	journal.pcbi.1005071	null	[ [ "Since the publication of the first draft of the human genome [1 , 2] , there has been an explosion in genomic data .", "The genomes of thousands of different human individuals have been sequenced [3] , several hundreds of eukaryotic genomes have been characterized , and new viral , bacterial and archaeal...	[ "The recent explosion of genomic data has underscored the need for interpretable and comprehensive analyses that can capture complex phylogenetic relationships within and across species .", "Recombination , reassortment and horizontal gene transfer constitute examples of pervasive biological phenomena that cannot...	[ "Evolution occurs through different mechanisms , including point mutations , gene duplication , horizontal gene transfer , and recombinations .", "Some of these mechanisms cannot be captured by tree graphs .", "We present a framework , based on the mathematical tools of computational topology , that can explici...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	High Rates of Asymptomatic, Sub-microscopic Plasmodium vivax Infection and Disappearing Plasmodium falciparum Malaria in an Area of Low Transmission in Solomon Islands	journal.pntd.0003758	null	[ [ "Nations in the Southwest Pacific have endured considerable malaria transmission , with the highest Plasmodium falciparum burden outside the African continent and possibly the highest Plasmodium vivax transmission in the world [1] .", "Historically , transmission has ranged from hyperendemic areas in West...	[ "Solomon Islands is intensifying national efforts to achieve malaria elimination .", "A long history of indoor spraying with residual insecticides , combined recently with distribution of long lasting insecticidal nets and artemether-lumefantrine therapy , has been implemented in Solomon Islands .", "The impact...	[ "Solomon Islands , an island nation in the Southwest Pacific that has seen dramatic reductions in malaria transmission over the past 20 years , is aiming for malaria elimination .", "There is an increasing recognition that a substantial reservoir of asymptomatic and often sub-microscopic Plasmodium spp .", "inf...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Par1b Induces Asymmetric Inheritance of Plasma Membrane Domains via LGN-Dependent Mitotic Spindle Orientation in Proliferating Hepatocytes	journal.pbio.1001739	Proliferating hepatocytes in the liver show an atypical, asymmetric mode of cell division, which is coordinated by Par1b and LGN and may explain the unique tissue architecture of the liver.	[ [ "The liver is a vital organ .", "Hepatocytes occupy more than 85% of the parenchymal liver mass and are responsible for a wide range of biological processes .", "These include the synthesis of plasma proteins and the processing of nutrients and toxic compounds from the blood that passes through the li...	[ "The development and maintenance of polarized epithelial tissue requires a tightly controlled orientation of mitotic cell division relative to the apical polarity axis .", "Hepatocytes display a unique polarized architecture .", "We demonstrate that mitotic hepatocytes asymmetrically segregate their apical plas...	[ "The development and maintenance of the polarized epithelial architecture and function of organs that form tubular “lumen” structures is important for normal physiology and , when deregulated , gives rise to disease .", "Recent studies have highlighted the importance of a strict coordination of the orientation of...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology/persistence and latency", "cell biology/membranes and sorting", "biochemistry/cell signaling and trafficking structures", "virology/viruses and cancer", "virology/immune evasion" ]	Role of Amphipathic Helix of a Herpesviral Protein in Membrane Deformation and T Cell Receptor Downregulation	journal.ppat.1000209	null	[ [ "Lipid rafts are membrane microdomains that take part in coordinating cell signalling functions and membrane trafficking .", "In T cells , upon antigenic stimulation , T cell receptors ( TCRs ) are recruited to lipid rafts , where they transmit signals via several pathways .", "The TCR signals induce ...	[ "Lipid rafts are membrane microdomains that function as platforms for signal transduction and membrane trafficking .", "Tyrosine kinase interacting protein ( Tip ) of T lymphotropic Herpesvirus saimiri ( HVS ) is targeted to lipid rafts in T cells and downregulates TCR and CD4 surface expression .", "Here , we ...	[ "Herpesvirus persists in its host by entering a latent state , periodically reactivating to produce infectious viral particles .", "Some of the herpesviruses have also been known to be related to cancers .", "Herpesvirus saimiri ( HVS ) , an oncogenic monkey herpesvirus , persists in the T lymphocytes of its na...	2008
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "taxonomy", "medicine and health sciences", "toxins", "pathology and laboratory medicine", "pathogens", "vibrio", "tropical diseases", "microbiology", "toxicology", "toxic agents", "bacterial diseases", "phylogenetics", "vibrio cholerae", "data management", "phylogenetic analysis", "ge...	Comparative genome analysis of VSP-II and SNPs reveals heterogenic variation in contemporary strains of Vibrio cholerae O1 isolated from cholera patients in Kolkata, India	journal.pntd.0005386	null	[ [ "Cholera is an acute life-threatening diarrheal disease and remains a major health threat , particularly in developing countries in Asia , Africa , and Latin America [1 , 2] .", "It is estimated that 1 . 4 to 4 . 3 million cases of cholera and 28 , 000 to 142 , 000 deaths due to cholera , occur every year...	[ "Cholera is an acute diarrheal disease and a major public health problem in many developing countries in Asia , Africa , and Latin America .", "Since the Bay of Bengal is considered the epicenter for the seventh cholera pandemic , it is important to understand the genetic dynamism of Vibrio cholerae from Kolkata ...	[ "Seven cholera pandemics have been recorded throughout history , and the sixth , and presumably earlier pandemics , emerged from the Bay of Bengal .", "The seventh pandemic strain also appeared and spread from this area to different area of the world .", "Thus , the Bay of Bengal has always been considered the ...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Health Seeking Behaviour and Treatment Intentions of Dengue and Fever: A Household Survey of Children and Adults in Venezuela	journal.pntd.0004237	null	[ [ "Dengue fever , a viral vector-borne disease spread by the day-biting mosquitoes Aedes aegypti and A . albopictus , is a global health problem of increasing importance [1] .", "Currently , dengue affects over 2 . 5 billion people living in dengue endemic areas , which comprises 40% of the world’s populati...	[ "Dengue in Venezuela is a major public health problem with an increasing incidence of severe cases .", "Early diagnosis and timely treatment influences the outcome of dengue illness , as delay in care-seeking is significantly associated with complications leading to severe dengue .", "We aimed to understand pat...	[ "The rapid spread of dengue in the last decade has brought this disease higher in the public health agenda worldwide .", "Dengue is transmitted by day-biting mosquitoes and typically presents with sudden fever and flu-like symptoms .", "In a proportion of cases , severe disease can ensue which if not promptly t...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "inflammatory diseases", "children", "medicine and health sciences", "microbiome", "pathology and laboratory medicine", "diagnostic radiology", "pathogens", "genetic diseases", "microbiology", "fibrosis", "neuroscience", "pulmonology", "preventive medicine", "age groups", "developmental ...	Initial acquisition and succession of the cystic fibrosis lung microbiome is associated with disease progression in infants and preschool children	journal.ppat.1006798	null	[ [ "Cystic fibrosis ( CF ) is a multisystem genetic disease in which pulmonary manifestations account for the majority of morbidity and mortality .", "CF lung disease is characterized by thickened airway secretions , bacterial infection , and neutrophil dominated inflammation that leads to progressive airway...	[ "The cystic fibrosis ( CF ) lung microbiome has been studied in children and adults; however , little is known about its relationship to early disease progression .", "To better understand the relationship between the lung microbiome and early respiratory disease , we characterized the lower airways microbiome us...	[ "CF lung disease is characterized by persistent airway infection by complex microbial communities .", "These communities often consist of pathogens and endogenous microbes typically associated with the oral cavity .", "The development of these complex communities and their relationship to CF lung disease progre...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Molecular Characterization of Staphylococcus aureus Isolates Transmitted between Patients with Buruli Ulcer	journal.pntd.0004049	null	[ [ "Buruli ulcer ( BU ) is a neglected necrotizing skin disease caused by Mycobacterium ulcerans , with the highest burden of the disease in West Africa , particularly in Benin , Cote d’Ivoire and Ghana [1] .", "The disease usually starts as a nodule , plaque , oedema or papule and progresses to form large u...	[ "Buruli ulcer ( BU ) is a skin infection caused by Mycobacterium ulcerans .", "The wounds of most BU patients are colonized with different microorganisms , including Staphylococcus aureus .", "This study investigated possible patient-to-patient transmission events of S . aureus during wound care in a health car...	[ "Buruli ulcer ( BU ) is a skin infection caused by Mycobacterium ulcerans .", "The wounds of most BU patients are colonized with different microorganisms , including Staphylococcus aureus .", "This study investigated patient-to-patient transmission events during wound care in a health care center .", "S . aur...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "infectious diseases of the nervous system", "clinical laboratory sciences", "diagnostic medicine", "clinical immunology", "neurological disorders", "cysticercosis", "neurology", "neglected tropical diseases", "immunology", "parasitic diseases" ]	Neurocysticercosis: HP10 Antigen Detection Is Useful for the Follow-up of the Severe Patients	journal.pntd.0002096	null	[ [ "Neurocysticercosis ( NC ) is one of the most frequent parasitic diseases affecting the human central nervous system [1] .", "It is transmitted by the ingestion of Taenia solium eggs mainly through the consumption of contaminated vegetables , and is still prevalent in most countries of Asia , Africa and L...	[ "The most severe clinical form of neurocysticercosis ( NC ) occurs when cysticerci are located in the subarachnoid space at the base of the brain ( SaB ) .", "The diagnosis , monitoring and treatment of NC-SaB , constitutes a severe clinical challenge .", "Herein we evaluate the potential of the HP10 antigen de...	[ "Neurocysticercosis is one of the most frequent parasitic diseases affecting the human central nervous system .", "The most severe clinical forms occur when parasites are located in the subarachnoid space at the base of the brain .", "In these instances , cysticidal drug efficacy is reduced and neuroimaging stu...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "blastocystis hominis infection", "infectious diseases", "medicine and health sciences", "emerging infectious diseases", "pathology and laboratory medicine", "host-pathogen interactions", "medical microbiology", "gastroenterology and hepatology", "microbial pathogens", "biology and life sciences",...	Intra-Subtype Variation in Enteroadhesion Accounts for Differences in Epithelial Barrier Disruption and Is Associated with Metronidazole Resistance in Blastocystis Subtype-7	journal.pntd.0002885	null	[ [ "Blastocystis is a unicellular , genetically diverse protist , phylogenetically placed within the Stramenopiles [1] , and it is the only member of this group associated with human pathological changes [2] , [3] .", "It is a species complex comprising 17 subtypes ( STs ) at least 9 of which are found in hu...	[ "Blastocystis is an extracellular , enteric pathogen that induces intestinal disorders in a range of hosts including humans .", "Recent studies have identified potential parasite virulence factors in and host responses to this parasite; however , little is known about Blastocystis-host attachment , which is cruci...	[ "Since it was first described more than a century ago , the question as to whether the protistan parasite Blastocystis causes disease or is a commensal of the human gut still remains unresolved .", "Strain- or subtype-dependent variability in Blastocystis pathogenicity has been proposed to contribute to this cont...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "learning", "cell physiology", "medicine and health sciences", "brain", "vertebrates", "social sciences", "neuroscience", "learning and memory", "mammals", "animals", "rna stem-loop structure", "cognitive psychology", "sensory physiology", "rna structure", "hippocampal formation", "mol...	Probabilistic Learning by Rodent Grid Cells	journal.pcbi.1005165	null	[ [ "Mammals use probabilistic computations to perceive noisy and ambiguous sensory inputs [1–5] .", "It seems likely that learning an internal model of a noisy sensory environment should follow similar statistical inference principles [4] .", "While solid behavioural evidence [1–5] and mounting in vivo e...	[ "Mounting evidence shows mammalian brains are probabilistic computers , but the specific cells involved remain elusive .", "Parallel research suggests that grid cells of the mammalian hippocampal formation are fundamental to spatial cognition but their diverse response properties still defy explanation .", "No ...	[ "Cells in the mammalian hippocampal formation are thought to be central for spatial learning and stable spatial representations .", "Of the known spatial cells , grid cells form strikingly regular and stable patterns of activity , even in darkness .", "Hence , grid cells may provide the universal metric upon wh...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "mathematics/statistics", "computational biology/molecular dynamics", "biophysics/macromolecular assemblies and machines", "cell biology/nuclear structure and function" ]	Intramolecular Cohesion of Coils Mediated by Phenylalanine–Glycine Motifs in the Natively Unfolded Domain of a Nucleoporin	journal.pcbi.1000145	null	[ [ "The nuclear pore complex is a supramolecular protein structure in the nuclear envelope that controls nucleo-cytoplasmic traffic and communication ( Figure 1A ) [1] .", "A key NPC architectural feature is a poorly understood semi-permeable diffusion barrier at its center , which allows passive diffusion o...	[ "The nuclear pore complex ( NPC ) provides the sole aqueous conduit for macromolecular exchange between the nucleus and the cytoplasm of cells .", "Its diffusion conduit contains a size-selective gate formed by a family of NPC proteins that feature large , natively unfolded domains with phenylalanine–glycine repe...	[ "The nuclear pore complex is a molecular filter that gates macromolecular exchange between the cytoplasm and the nucleoplasm of cells .", "It contains a size-selective diffusion barrier at its center composed of proteins named FG nucleoporins .", "These nucleoporins feature large , structurally disordered domai...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Hsp90-Associated Immunophilin Homolog Cpr7 Is Required for the Mitotic Stability of [URE3] Prion in Saccharomyces cerevisiae	journal.pgen.1005567	null	[ [ "Similar to human prion protein ( PrP ) , many yeast proteins have a tendency to undergo conformational conversion into infectious protein particles known as prions [1 , 2] [3] .", "The yeast prions have served as a great model system to understand the mechanistic details of prion induction , propagation ...	[ "The role of Hsp70 chaperones in yeast prion propagation is well established .", "Highly conserved Hsp90 chaperones participate in a number of cellular processes , such as client protein maturation , protein degradation , cellular signalling and apoptosis , but little is known about their role in propagation of i...	[ "Studies on yeast prions have provided insight into the role of various cellular factors involved in amyloid based disorders .", "Among the various cellular components the chaperone network has emerged as a crucial regulator of formation and propagation of yeast prions .", "The chaperone machinery primarily con...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "mathematics", "computational biology", "genetics and genomics", "nematodes" ]	Synonymous Substitution Rates Predict HIV Disease Progression as a Result of Underlying Replication Dynamics	journal.pcbi.0030029	null	[ [ "Although the clinical course of HIV infection is generally well-defined , there is considerable variability among patients in rates of disease progression .", "The highly variable asymptomatic phase , ranging from several months to more than 20 years , most likely reflects differences in the nature of th...	[ "Upon HIV transmission , some patients develop AIDS in only a few months , while others remain disease free for 20 or more years .", "This variation in the rate of disease progression is poorly understood and has been attributed to host genetics , host immune responses , co-infection , viral genetics , and adapta...	[ "During the clinical course of HIV infection , an asymptomatic phase always precedes the acquired immunodeficiency syndrome ( AIDS ) .", "The duration of this asymptomatic phase is highly variable among patients and reflects the rate at which the immune system gradually deteriorates .", "Although humoral and ce...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "action potentials", "neural networks", "nervous system", "membrane potential", "electrophysiology", "neuroscience", "membrane electrophysiology", "bioassays and physiological analysis", "thermodynamics", "research and analysis methods", "computer and informatio...	Modularity Induced Gating and Delays in Neuronal Networks	journal.pcbi.1004883	null	[ [ "Activity gating and control over propagation are fundamental capacities of neural circuits .", "It is widely accepted that population-level gating is strongly affected by changing the balance between excitation and inhibition in connected sub-populations of neurons [1–6] .", "However , while the role...	[ "Neural networks , despite their highly interconnected nature , exhibit distinctly localized and gated activation .", "Modularity , a distinctive feature of neural networks , has been recently proposed as an important parameter determining the manner by which networks support activity propagation .", "Here we u...	[ "The capacity to transmit information between connected parts of a neuronal network is fundamental to its function .", "The organization of network connections ( the topology of the network ) is therefore expected to play an important role in determining network transmission .", "Since modular topology characte...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "infectious diseases/bacterial infections", "immunology/innate immunity" ]	Activation of Human Monocytes by Live Borrelia burgdorferi Generates TLR2-Dependent and -Independent Responses Which Include Induction of IFN-β	journal.ppat.1000444	null	[ [ "Lyme disease ( LD ) , the most commonly reported vector-borne illness in the United States , is a tick-borne , multi-system , inflammatory , infectious disorder caused by the spirochetal bacterium Borrelia burgdorferi ( Bb ) [1] .", "The disease is often heralded in its early stage by erythema migrans ( ...	[ "It is widely believed that innate immune responses to Borrelia burgdorferi ( Bb ) are primarily triggered by the spirochete's outer membrane lipoproteins signaling through cell surface TLR1/2 .", "We recently challenged this notion by demonstrating that phagocytosis of live Bb by peripheral blood mononuclear cel...	[ "Lyme disease is a tick-borne infectious disorder caused by the spirochetal pathogen Borrelia burgdorferi ( Bb ) .", "Innate immune responses to Bb are thought to be triggered by the spirochete's outer membrane lipoproteins signaling through cell surface toll-like receptors ( TLR1/2 ) .", "Using a whole genome ...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/genetics of disease", "neurological disorders/neurogenetics", "genetics and genomics", "neurological disorders/epilepsy" ]	Genome-Wide Copy Number Variation in Epilepsy: Novel Susceptibility Loci in Idiopathic Generalized and Focal Epilepsies	journal.pgen.1000962	null	[ [ "Epilepsy is one of the most common neurological disorders in humans with a prevalence of ∼1% and a lifetime incidence of up to 3% [1] .", "The epilepsies present with a broad range of clinical features , and over 50 distinct epilepsy syndromes are now recognized .", "Particularly in a pediatric setti...	[ "Epilepsy is one of the most common neurological disorders in humans with a prevalence of 1% and a lifetime incidence of 3% .", "Several genes have been identified in rare autosomal dominant and severe sporadic forms of epilepsy , but the genetic cause is unknown in the vast majority of cases .", "Copy number v...	[ "Epilepsy , a common neurological disorder characterized by recurrent seizures , affects up to 3% of the population .", "In some cases , the epilepsy has a clear cause such as an abnormality in the brain or a head injury .", "However , in many cases there is no obvious cause .", "Numerous studies have shown t...	2010
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biotechnology", "genome engineering", "cell death", "engineering and technology", "cell cycle and cell division", "synthetic biology", "cell processes", "synthetic bioengineering", "crispr", "epigenetics", "tubulins", "immunologic techniques", "synthetic genomics", "research and analysis ...	A RUNX2-Mediated Epigenetic Regulation of the Survival of p53 Defective Cancer Cells	journal.pgen.1005884	null	[ [ "Because activated p53 is a potent inducer of apoptosis [1] , the activation of p53-dependent apoptosis provides an important molecular basis for killing cancer cells .", "Chemotherapy and radiotherapy , which cause DNA damage , can activate p53 and induce apoptosis in cancer cells .", "Many cancer ce...	[ "The inactivation of p53 creates a major challenge for inducing apoptosis in cancer cells .", "An attractive strategy is to identify and subsequently target the survival signals in p53 defective cancer cells .", "Here we uncover a RUNX2-mediated survival signal in p53 defective cancer cells .", "The inhibitio...	[ "Because activated p53 is a potent inducer of apoptosis , several approaches centering on p53 activation are designed for killing cancer cells .", "However , more than half of human tumors have p53 inactivation , which renders these p53-activating approaches less effective in killing cancer cells .", "Targeting...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Dual Function of CD81 in Influenza Virus Uncoating and Budding	journal.ppat.1003701	null	[ [ "Influenza virus , the major causal agent of flu , is an enveloped , negative-sense RNA virus containing three viral membrane proteins: hemagglutinin ( HA ) , neuraminidase ( NA ) , and M2 proton channel .", "Encapsulated within the viral envelope is a layer of matrix protein ( M1 ) and a segmented genome...	[ "As an obligatory pathogen , influenza virus co-opts host cell machinery to harbor infection and to produce progeny viruses .", "In order to characterize the virus-host cell interactions , several genome-wide siRNA screens and proteomic analyses have been performed recently to identify host factors involved in in...	[ "As a “Trojan Horse” that only encodes 13 viral proteins , influenza hijacks host cell machinery for productive infection .", "In this work , we studied the role of the host protein CD81 in influenza infection .", "We found that CD81 was important for influenza infection at two distinct stages: virus uncoating ...	2013
[ "Introduction", "Methodology", "Results", "Discussion", "Conclusion" ]	[ "taxonomy", "medicine and health sciences", "ecology and environmental sciences", "pathology and laboratory medicine", "rivers", "pathogens", "vibrio", "variant genotypes", "tropical diseases", "microbiology", "geographical locations", "genetic mapping", "bacterial diseases", "phylogenetic...	Minimal genetic change in Vibrio cholerae in Mozambique over time: Multilocus variable number tandem repeat analysis and whole genome sequencing	journal.pntd.0005671	null	[ [ "Cholera remains a public health concern in developing countries with an estimated burden of 1 . 2–4 . 3 million cases and 28 , 000–142 , 000 deaths per year , worldwide [1] .", "South Asia and sub-Saharan Africa account with the majority of cases and deaths .", "Between 01 January and 03 June 2013 , ...	[ "Although cholera is a major public health concern in Mozambique , its transmission patterns remain unknown .", "We surveyed the genetic relatedness of 75 Vibrio cholerae isolates from patients at Manhiça District Hospital between 2002–2012 and 3 isolates from river using multilocus variable-number tandem-repeat ...	[ "Cholera is a deadly disease caused by the bacterium Vibrio cholerae .", "The ancestral home of cholera is around the Bay of Bengal , but recently cholera has moved to Africa .", "In Africa , cholera occurs in sporadic outbreaks .", "In order prevent cases of cholera , we want to understand the transmission o...	2017
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "molecular cell biology", "global health", "genetics", "biology", "genomics", "microbiology", "genetics and genomics" ]	Transposon-mediated Chromosomal Integration of Transgenes in the Parasitic Nematode Strongyloides ratti and Establishment of Stable Transgenic Lines	journal.ppat.1002871	null	[ [ "Parasitic nematodes have an enormous impact on human welfare , infecting over a billion people and causing debilitating , disfiguring or blinding disease in hundreds of millions [1] , [2] , [3] .", "More insidious effects of these parasites include complications in pregnancy and physical and cognitive de...	[ "Genetic transformation is a potential tool for analyzing gene function and thereby identifying new drug and vaccine targets in parasitic nematodes , which adversely affect more than one billion people .", "We have previously developed a robust system for transgenesis in Strongyloides spp .", "using gonadal mic...	[ "Parasitic roundworms sicken and debilitate over one billion people , most of whom subsist on less than two US dollars per day .", "There are no vaccines and few drugs available to treat and prevent these infections .", "Basic research leading to new therapies has been hampered because we lack methods to study ...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	DNA Damage Regulates Translation through β-TRCP Targeting of CReP	journal.pgen.1005292	null	[ [ "E3 ubiquitin ligases , which facilitate the attachment of anywhere from one to a long chain of the small protein ubiquitin to substrate proteins , are important regulators of the cell cycle and the response to stress .", "The best-studied outcome of ubiquitination is destruction of the substrate by the p...	[ "The Skp1-Cul1-F box complex ( SCF ) associates with any one of a number of F box proteins , which serve as substrate binding adaptors .", "The human F box protein βTRCP directs the conjugation of ubiquitin to a variety of substrate proteins , leading to the destruction of the substrate by the proteasome .", "T...	[ "Approximately 600 human genes encode enzymes that act as ubiquitin ligases , which facilitate the transfer of the small protein ubiquitin to thousands of substrate proteins; “tagging” with ubiquitin often promotes the degradation of the substrate by the proteasome .", "In this paper , we adapt a technique called...	2015
[ "Introduction", "Material and methods", "Results", "Discussion" ]	[ "genome-wide association studies", "medicine and health sciences", "body fluids", "random variables", "covariance", "mathematics", "genome analysis", "lipid structure", "trait locus analysis", "molecular genetics", "lipids", "molecular biology", "genetic loci", "probability theory", "bio...	Heritability informed power optimization (HIPO) leads to enhanced detection of genetic associations across multiple traits	journal.pgen.1007549	null	[ [ "Genome-wide association studies of increasingly large sample sizes are continuing to inform genetic basis of complex diseases .", "These studies have now led to identification of scores of susceptibility SNPs underlying a vast variety of individual complex traits and diseases [1–3] .", "Moreover , an...	[ "Genome-wide association studies have shown that pleiotropy is a common phenomenon that can potentially be exploited for enhanced detection of susceptibility loci .", "We propose heritability informed power optimization ( HIPO ) for conducting powerful pleiotropic analysis using summary-level association statisti...	[ "Pleiotropy is a common phenomenon in genetics that one genetic variant has effects on multiple traits .", "The shared genetic information across correlated traits can potentially be exploited for enhanced detection of susceptibility loci .", "Most existing multi-trait methods borrow information across phenotyp...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "viral genomics", "virology", "emerging viral diseases", "genetics", "biology and life sciences", "molecular genetics", "microbiology", "genomics", "microbial genomics" ]	Molecular Epidemiology of Japanese Encephalitis Virus in Mosquitoes in Taiwan during 2005–2012	journal.pntd.0003122	null	[ [ "Japanese encephalitis is a vector-borne zoonotic disease transmitted by the bite of a JEV-infected mosquito .", "Although JE is a vaccine preventable disease , JEV infections are still the leading cause of viral encephalitis in Asia [1] , [2] .", "It is estimated that 67 , 900 JE cases occur annually...	[ "Japanese encephalitis ( JE ) is a mosquito-borne zoonotic disease caused by the Japanese encephalitis virus ( JEV ) .", "Pigs and water birds are the main amplifying and maintenance hosts of the virus .", "In this study , we conducted a JEV survey in mosquitoes captured in pig farms and water bird wetland habi...	[ "Japanese encephalitis ( JE ) is a vector-borne zoonotic disease transmitted by the bite of a Japanese encephalitis virus ( JEV ) infected mosquito .", "Japanese encephalitis is an endemic disease in Taiwan .", "Before 2008 , all known JEV isolates collected in Taiwan belonged to Genotype III of JEV .", "Geno...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "legs", "nucleases", "deoxyribonucleases", "enzymes", "gene regulation", "dna-binding proteins", "enzymology", "limbs (anatomy)", "developmental biology", "artificial intelligence", "epigenetics", "mammalian genomics", "embryos", "chromatin", "embryology...	Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb	journal.pcbi.1005720	null	[ [ "Mammalian body plans are shaped by the precise spatiotemporal execution of transcriptional programs [1] , which have been shown to rely on the coordinated activity of enhancers [2] .", "Despite the increased availability of epigenomic data , the identification of these short , cis-regulatory DNA sequence...	[ "Epigenomic mapping of enhancer-associated chromatin modifications facilitates the genome-wide discovery of tissue-specific enhancers in vivo .", "However , reliance on single chromatin marks leads to high rates of false-positive predictions .", "More sophisticated , integrative methods have been described , bu...	[ "The majority of the human genome does not code for proteins .", "Regulatory roles have been ascribed to a growing fraction of the non-coding genome .", "Enhancers , short stretches of non-coding DNA , confer spatial and temporal specificity to gene expression patterns .", "These regions are essential to the ...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "developmental neuroscience", "cellular neuroscience", "neurogenesis", "ecology", "simulation and modeling", "mathematical and statistical techniques", "biology and life sciences", "evolutionary biology", "neuroscience", "research and analysis methods" ]	An Adaptive Threshold in Mammalian Neocortical Evolution	journal.pbio.1002000	A study of the evolutionary history of cortical folding in mammals, its relationship to physiological and life-history traits and the underlying cortical progenitor behavior during embryogenesis, explains the diversity of folding we see across modern mammals. The diversity of neocortical folding among mammals can be ex...	[ [ "Development of the mammalian , and in particular human , neocortex involves various types of neural stem and progenitor cells that reside in the germinal layers of the cortical wall [1]–[5] .", "An increase in the proliferative capacity of these cells underlies the evolutionary expansion of the neocortex...	[ "Expansion of the neocortex is a hallmark of human evolution .", "However , determining which adaptive mechanisms facilitated its expansion remains an open question .", "Here we show , using the gyrencephaly index ( GI ) and other physiological and life-history data for 102 mammalian species , that gyrencephaly...	[ "What are the key differences in the development and evolution of the cerebral cortex that underlie the differences in its size and degree of folding across mammals ?", "Here , we present phylogenetic evidence that the Jurassic era mammalian ancestor may have been a relatively large-brained species with a folded ...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "protein transport", "phosphorylation", "medicine and health sciences", "cellular stress responses", "immune physiology", "pathology and laboratory medicine", "molecular probe techniques", "pathogens", "cell processes", "immunology", "microbiology", "egfr signaling", "immunoblotting", "vir...	Adenovirus early region 3 RIDα protein limits NFκB signaling through stress-activated EGF receptors	journal.ppat.1008017	null	[ [ "Human adenoviruses provide an excellent example of how viruses adapt host cell machinery to invade cells , gain access to the nucleus to replicate , assemble new viral particles , and spread in the host [1 , 2 , 3] .", "The host limits adenovirus infections by mobilizing innate immune systems that activa...	[ "The host limits adenovirus infections by mobilizing immune systems directed against infected cells that also represent major barriers to clinical use of adenoviral vectors .", "Adenovirus early transcription units encode a number of products capable of thwarting antiviral immune responses by co-opting host cell ...	[ "Although most adenovirus infections produce a mild and self-limiting disease , they can be life threatening for immunocompromised individuals .", "Some serotypes also cause epidemic outbreaks that pose a significant health risk in people with no known predisposing conditions .", "Although the early region 3 ( ...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell death", "viral classification", "immunology", "microbiology", "host-pathogen interaction", "dna viruses", "major histocompatibility complex", "viral immune evasion", "biology", "antigen processing and recognition", "cell biology", "virology", "molecular cell biology" ]	Epstein-Barr Virus Evades CD4+ T Cell Responses in Lytic Cycle through BZLF1-mediated Downregulation of CD74 and the Cooperation of vBcl-2	journal.ppat.1002455	null	[ [ "Successful persistence of viral infection depends on the establishment of a balance between host immune responses and viral immune evasion .", "Epstein-Barr virus ( EBV ) , which is carried by more than 90% of the adult human population worldwide , is a prime example of a persistent virus that is general...	[ "Evasion of immune T cell responses is crucial for viruses to establish persistence in the infected host .", "Immune evasion mechanisms of Epstein-Barr virus ( EBV ) in the context of MHC-I antigen presentation have been well studied .", "In contrast , viral interference with MHC-II antigen presentation is less...	[ "Epstein-Barr virus ( EBV ) is a herpesvirus and an important human pathogen that can cause diseases ranging from non-malignant proliferative disease to fully malignant cancers of lymphocytes and epithelial cells .", "The persistence of EBV in healthy individuals relies on the balance between host immune response...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "methods and resources", "statistics", "light", "neuroscience", "electromagnetic radiation", "multivariate analysis", "mathematics", "artificial light", "computational neuroscience", "neuroimaging", "research and analysis methods", "optic lobes", "imaging te...	Fast near-whole–brain imaging in adult Drosophila during responses to stimuli and behavior	journal.pbio.2006732	null	[ [ "Measuring activity simultaneously in the whole brain is critical to understanding how different brain regions interact to process and control sensory inputs , internal states , and behavior .", "Whole-brain recordings not only reveal which regions are involved in which functions and with what network dyn...	[ "Whole-brain recordings give us a global perspective of the brain in action .", "In this study , we describe a method using light field microscopy to record near-whole brain calcium and voltage activity at high speed in behaving adult flies .", "We first obtained global activity maps for various stimuli and beh...	[ "Whole-brain recordings give us a global perspective of the brain in action .", "This is already possible in humans , for which functional magnetic resonance imaging ( fMRI ) has opened a new chapter in the study of brain activity underlying behavior , but this technique has low spatial and temporal resolution ."...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Auditory Processing in Noise: A Preschool Biomarker for Literacy	journal.pbio.1002196	The neural coding of consonants in noise predicts early literacy skills in pre-reading children, providing a biological marker that may help to target early intervention.	[ [ "Three aspects of auditory-neurophysiological processing have often been associated with literacy: variability of neural firing [1 , 2] , auditory system timing [3 , 4] , and processing detailed acoustic features such as those found in consonants [5 , 6] .", "This neural coding is thought to play a pivota...	[ "Learning to read is a fundamental developmental milestone , and achieving reading competency has lifelong consequences .", "Although literacy development proceeds smoothly for many children , a subset struggle with this learning process , creating a need to identify reliable biomarkers of a child’s future litera...	[ "Learning to read is a chief developmental milestone with lifelong consequences; although there are effective interventions for struggling readers , an ongoing challenge has been to identify candidates for intervention at a young-enough age .", "We measured the precision of the neural coding of consonants in nois...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "antimicrobials", "dermatology", "urology", "medicine and health sciences", "pathology and laboratory medicine", "biopsy", "drugs", "tropical diseases", "microbiology", "rabbits", "vertebrates", "animals", "mammals", "surgical and invasive medical procedures", "animal models", "trepone...	Topical treatment with gallium maltolate reduces Treponema pallidum subsp. pertenue burden in primary experimental lesions in a rabbit model of yaws	journal.pntd.0007076	null	[ [ "Yaws is a neglected tropical disease ( NTD ) [1 , 2] caused by the spirochete bacterium Treponema pallidum subsp .", "pertenue ( Tp pertenue ) , a pathogen closely related to the syphilis agent , Treponema pallidum subsp .", "pallidum ( Tp pallidum ) [3] .", "Yaws mainly affects children less tha...	[ "Gallium is a semi-metallic element known since the 1930s to have antimicrobial activity .", "This activity stems primarily from gallium's ability to mimic trivalent iron and disrupt specific Fe ( III ) -dependent pathways , particularly DNA synthesis ( due to inhibition of ribonucleotide reductase ) .", "Becau...	[ "Yaws is a neglected tropical disease affecting children in underprivileged countries , transmitted through direct skin contact with an active lesion .", "This infection , although rarely fatal , can lead to disfigurement and serious disability .", "The World Health Organization is currently conducting a yaws e...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases", "biology and life sciences", "microbiology", "medicine and health sciences" ]	A Neutralizing Anti-gH/gL Monoclonal Antibody Is Protective in the Guinea Pig Model of Congenital CMV Infection	journal.ppat.1004060	null	[ [ "Human cytomegalovirus ( HCMV ) , a member of the herpesvirus family , is widely distributed in the human population and can cause severe disease in immunocompromised patients and upon infection of the fetus .", "A therapeutic for HCMV infection is a major public health priority for women with primary HCM...	[ "Human cytomegalovirus ( HCMV ) is the most common cause of congenital virus infection .", "Congenital HCMV infection occurs in 0 . 2–1% of all births , and causes birth defects and developmental abnormalities , including sensorineural hearing loss and developmental delay .", "Several key studies have establish...	[ "Human cytomegalovirus ( HCMV ) is the most common cause of congenital virus infection and causes developmental abnormalities , including hearing loss and developmental delay .", "Although there is no therapy for congenital HCMV disease , there is evidence from both human and animal studies that antibodies can ha...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "cognitive neuroscience", "psychology", "social and behavioral sciences", "biology", "neuroscience" ]	Human Visual Search Does Not Maximize the Post-Saccadic Probability of Identifying Targets	journal.pcbi.1002342	null	[ [ "For many detection and discrimination tasks , performance decreases rapidly with increasing distance from the center of vision .", "Observers overcome this limitation by making discrete eye movements ( saccades ) as often as three times per second , in effect scanning the environment .", "Such serial...	[ "Researchers have conjectured that eye movements during visual search are selected to minimize the number of saccades .", "The optimal Bayesian eye movement strategy minimizing saccades does not simply direct the eye to whichever location is judged most likely to contain the target but makes use of the entire ret...	[ "Vision is most sensitive to fine detail at the center of gaze ( the fovea ) .", "We typically move our eyes several times a second to build up an accurate picture of the world around us and find objects of interest .", "Very recently , researchers have developed models of how a visual system like ours could se...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "viruses", "infectious diseases", "ecology", "virology", "evolutionary biology" ]	Phylogenetic Analysis Reveals the Global Migration of Seasonal Influenza A Viruses	journal.ppat.0030131	null	[ [ "Influenza A virus is able to persistently re-infect human populations by continually evading host immunity through the rapid evolution of surface antigens ( “antigenic drift” ) [1] .", "Influenza virus epidemics strike temperate latitudes of the world each winter , from November to March in the northern ...	[ "The winter seasonality of influenza A virus in temperate climates is one of the most widely recognized , yet least understood , epidemiological patterns in infectious disease .", "Central to understanding what drives the seasonal emergence of this important human pathogen is determining what becomes of the virus...	[ "The winter seasonality of influenza A virus in temperate climates is one of the most puzzling epidemiological patterns in infectious disease .", "To help resolve the issue of influenza seasonality , we studied , using viral genome sequence data , the patterns of global migration of influenza A virus , particular...	2007
[ "Introduction", "Results and discussion", "Materials and methods" ]	[ "biofilms", "medicine and health sciences", "chemical compounds", "pathology and laboratory medicine", "gene regulation", "pathogens", "microbiology", "galactose", "carbohydrates", "organic compounds", "regulator genes", "fungi", "model organisms", "animal behavior", "experimental organi...	Cyc8p and Tup1p transcription regulators antagonistically regulate Flo11p expression and complexity of yeast colony biofilms	journal.pgen.1007495	null	[ [ "In nature , microorganisms preferentially live within multicellular communities such as different types of biofilms and colonies [1–5] .", "Yeast biofilms are complex uniquely organized structures , in which cells are protected from hostile environments , including antifungals , host immune systems , and...	[ "Yeast biofilms are complex multicellular structures , in which the cells are well protected against drugs and other treatments and thus highly resistant to antifungal therapies .", "Colony biofilms represent an ideal system for studying molecular mechanisms and regulations involved in development and internal or...	[ "Yeast biofilms have become an increasingly important clinical problem over the years .", "Biofilms are often associated with infections resistant to antifungals , which are particularly prevalent in immunosuppressed patients .", "High resistance is mediated by cell reprogramming leading to the specific organiz...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	NECAP 1 Regulates AP-2 Interactions to Control Vesicle Size, Number, and Cargo During Clathrin-Mediated Endocytosis	journal.pbio.1001670	The endocytic protein NECAP 1 cooperates with the endocytic adapter protein AP-2 to modulate interactions with accessory proteins and clathrin and to control the size, number, and cargo content of clathrin-coated vesicles.	[ [ "Clathrin-mediated endocytosis is the major vesicular entry route in mammalian cells .", "The formation of endocytic clathrin-coated vesicles ( CCVs ) depends on a complex protein machinery that deforms the planar plasma membrane into small , cargo-laden vesicles that are released into the cytosol [1] , [...	[ "AP-2 is the core-organizing element in clathrin-mediated endocytosis .", "During the formation of clathrin-coated vesicles , clathrin and endocytic accessory proteins interact with AP-2 in a temporally and spatially controlled manner , yet it remains elusive as to how these interactions are regulated .", "Here...	[ "Clathrin-mediated endocytosis is the major entry portal for cargo molecules such as nutrient and signaling receptors in eukaryotic cells .", "Generation of clathrin-coated vesicles involves a complex protein machinery that both deforms the membrane to generate a vesicle and selects appropriate cargo .", "The e...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "computational biology/protein structure prediction", "computational biology/molecular dynamics" ]	A Computational Analysis of ATP Binding of SV40 Large Tumor Antigen Helicase Motor	journal.pcbi.1000514	null	[ [ "Helicases are a family of ATPase motors that couple the energy of ATP binding and hydrolysis to conformation changes , which in turn is coupled to the unwinding and translocation of DNA [1] .", "Simian Virus 40 ( SV40 ) large tumor antigen ( LTag ) is an efficient hexameric helicase that belongs to the h...	[ "Simian Virus 40 Large Tumor Antigen ( LTag ) is an efficient helicase motor that unwinds and translocates DNA .", "The DNA unwinding and translocation of LTag is powered by ATP binding and hydrolysis at the nucleotide pocket between two adjacent subunits of an LTag hexamer .", "Based on the set of high-resolut...	[ "The Large Tumor antigen ( LTag ) encoded by Simian Virus 40 ( SV40 ) is a marvelous molecule that is not only a viral oncogene , but also an efficient molecular machine as a helicase that unwinds double helix DNA for genome replication , an essential process in all living organisms .", "LTag hexameric helicase u...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "evolutionary biology", "viruses", "primates", "virology" ]	A Challenge to the Ancient Origin of SIVagm Based on African Green Monkey Mitochondrial Genomes	journal.ppat.0030095	null	[ [ "More than 30 nonhuman primate species in sub-Saharan Africa are naturally infected with simian immunodeficiency virus ( SIV ) [1]; however , the evolutionary forces shaping SIV diversity remain unclear .", "One of the most important unanswered questions regarding SIV evolution is whether it is an ancient...	[ "While the circumstances surrounding the origin and spread of HIV are becoming clearer , the particulars of the origin of simian immunodeficiency virus ( SIV ) are still unknown .", "Specifically , the age of SIV , whether it is an ancient or recent infection , has not been resolved .", "Although many instances...	[ "Elucidating the factors that influence the emergence of viral pathogens is of great importance to the study of infectious disease .", "HIV is understood to have originated from simian immunodeficiency viruses ( SIVs ) infecting nonhuman African primates , but the length of time the virus has been present in thes...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology/mechanisms of resistance and susceptibility, including host genetics", "virology/immunodeficiency viruses", "virology/host antiviral responses" ]	Species-Specific Activity of HIV-1 Vpu and Positive Selection of Tetherin Transmembrane Domain Variants	journal.ppat.1000300	null	[ [ "Eukaryotic cells can constitutively or inducibly express a variety of molecules that inhibit the replication of viruses .", "Among these antiviral defenses are components of the type-I interferon ( IFN ) -induced innate immune system [1] , [2] .", "In turn , viruses have evolved to express proteins t...	[ "Tetherin/BST-2/CD317 is a recently identified antiviral protein that blocks the release of nascent retrovirus , and other virus , particles from infected cells .", "An HIV-1 accessory protein , Vpu , acts as an antagonist of tetherin .", "Here , we show that positive selection is evident in primate tetherin se...	[ "Tetherin is a cell surface protein that acts as an antiviral defense .", "It functions by tethering newly assembled HIV-1 particles to the surface of the infected cell , such that the viral particle is unable to depart and disseminate to other , uninfected cells .", "HIV-1 possesses an antagonist of tetherin ,...	2009
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	The Schistosome Esophagus Is a ‘Hotspot’ for Microexon and Lysosomal Hydrolase Gene Expression: Implications for Blood Processing	journal.pntd.0004272	null	[ [ "Adult schistosome worms reside in the host vascular system actively feeding on blood that contains antibodies , complement factors and effector leucocytes , yet they are apparently unaffected by this ‘toxic’ diet .", "Indeed , their attested longevity in the hepatic portal system ( Schistosoma mansoni an...	[ "The schistosome esophagus is divided into anterior and posterior compartments , each surrounded by a dense cluster of gland cell bodies , the source of distinct secretory vesicles discharged into the lumen to initiate the processing of ingested blood .", "Erythrocytes are lysed in the lumen , leucocytes are teth...	[ "Schistosomes feed on blood and we have previously shown that its processing begins in the esophagus , which does not act simply as a conduit .", "It comprises anterior and posterior compartments , each surrounded by glands that secrete proteins into the lumen .", "Erythrocytes are ruptured as they pass through...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "urology", "cell death", "keratinocytes", "medicine and health sciences", "pathology and laboratory medicine", "cell processes", "microbiology", "cell differentiation", "epithelial cells", "oncology", "developmental biology", "sexually transmitted diseases", "infectious diseases", "human p...	The CXCL12/CXCR4 Signaling Pathway: A New Susceptibility Factor in Human Papillomavirus Pathogenesis	journal.ppat.1006039	null	[ [ "Human papillomaviruses ( HPVs ) are a family of highly related non-enveloped epitheliotropic viruses that have co-evolved with their human host and developed powerful strategies to establish persistent infection [1] .", "Many reports have described HPVs as commensal viruses that can persist on healthy sk...	[ "The productive human papillomavirus ( HPV ) life cycle is tightly linked to the differentiation and cycling of keratinocytes .", "Deregulation of these processes and stimulation of cell proliferation by the action of viral oncoproteins and host cell factors underlies HPV-mediated carcinogenesis .", "Severe HPV...	[ "Human papillomaviruses ( HPV ) are epitheliotropic tumor viruses causing mostly benign warts but that have developed strategies to establish persistent infections .", "Although host immune responses clear most infections , persistence of some HPV types causes ~5% of human cancers and severe pathogenesis in immun...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "retrovirology and hiv immunopathogenesis", "immunology", "microbiology", "host-pathogen interaction", "infectious diseases", "viral immune evasion", "hiv", "biology", "viral evolution", "immune response", "virology", "viral diseases", "immunoglobulins" ]	Viral Escape from Neutralizing Antibodies in Early Subtype A HIV-1 Infection Drives an Increase in Autologous Neutralization Breadth	journal.ppat.1003173	null	[ [ "Protective vaccines against viral infections generally elicit nAb responses that are comparable to those in natural infections [1] .", "It is , therefore , widely accepted that an optimal vaccine against HIV-1 will need to produce nAbs , but features such as the high genetic diversity and mutability of H...	[ "Antibodies that neutralize ( nAbs ) genetically diverse HIV-1 strains have been recovered from a subset of HIV-1 infected subjects during chronic infection .", "Exact mechanisms that expand the otherwise narrow neutralization capacity observed during early infection are , however , currently undefined .", "Her...	[ "Since cases were first recognized in the United States in 1981 , human immunodeficiency virus ( HIV-1 ) has infected over one million Americans .", "Globally , this scale reaches into the tens of millions , but no effective vaccine exists .", "Of those infected , approximately 20–30% of patients will develop b...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "syllables", "medicine and health sciences", "vocalization", "linguistics", "nervous system", "vertebrates", "marmosets", "social sciences", "animals", "mammals", "animal signaling and communication", "lungs", "animal models", "primates", "respiratory system", "animal behavior", "exp...	Vocal development through morphological computation	journal.pbio.2003933	null	[ [ "It is well established ( though often ignored ) that central pattern generators ( CPGs ) are constrained and modulated by the body in which they are embedded [1 , 2] .", "Moreover , in the field of robotics , much work has demonstrated how the shape and material properties of the body can be exploited to...	[ "The vocal behavior of infants changes dramatically during early life .", "Whether or not such a change results from the growth of the body during development—as opposed to solely neural changes—has rarely been investigated .", "In this study of vocal development in marmoset monkeys , we tested the putative cau...	[ "In robotics , the shape and material properties of the robot body can be exploited to make central control processes simpler; this is known as “morphological computation . ”", "In this view , the body is not a device to simply be controlled by the brain , but rather is directly involved in making some behaviors ...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "public health and epidemiology/epidemiology", "immunology/genetics of the immune system", "neurological disorders/multiple sclerosis and related disorders", "immunology/autoimmunity" ]	Expression of the Multiple Sclerosis-Associated MHC Class II Allele HLA-DRB1*1501 Is Regulated by Vitamin D	journal.pgen.1000369	null	[ [ "Multiple sclerosis ( MS ) is a common inflammatory disease of the central nervous system characterized by myelin loss , axonal pathology , and progressive neurological dysfunction [1] .", "The aetiology of MS is unknown , however it is clear that genetic and environmental components are important [1] , [...	[ "Multiple sclerosis ( MS ) is a complex trait in which allelic variation in the MHC class II region exerts the single strongest effect on genetic risk .", "Epidemiological data in MS provide strong evidence that environmental factors act at a population level to influence the unusual geographical distribution of ...	[ "Multiple Sclerosis ( MS ) is a complex neurological disease with a strong genetic component .", "The Major Histocompatibility Complex ( MHC ) on chromosome 6 exerts the strongest genetic effect on disease risk .", "A region at or near the HLA-DRB1 locus in the MHC influences the risk of MS . HLA-DRB1 has over ...	2009
[ "Introduction", "Methods and material", "Results", "Discussion" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "chemical compounds", "clinical research design", "tropical diseases", "geographical locations", "parasitic diseases", "parasitic protozoans", "organic compounds", "research design", "clinical medicine", "protozoans", "sign...	Failure of fluconazole in treating cutaneous leishmaniasis caused by Leishmania guyanensis in the Brazilian Amazon: An open, nonrandomized phase 2 trial	journal.pntd.0006225	null	[ [ "Cutaneous leishmaniasis ( CL ) is one of the 17 neglected diseases , with 350 million people at risk in 98 endemic countries [1] .", "Latin America is a highly endemic region with a documented 30% increase in the number of reported cases during a period of ten years ( 2001–2011 ) [2] .", "Brazil toge...	[ "The treatment of Leishmaniasis caused by Leishmania ( Viannia ) guyanensis is based on a weak strength of evidence from very few clinical trials and some case series reports .", "Current treatment guidelines recommend pentamidine isethionate or meglumine antimoniate ( Glucantime ) as the first-line choices .", ...	[ "The main agent causing localized cutaneous leishmaniasis in the Guianan Ecoregion Complex , a region that covers Guiana , Suriname , French Guiana , the southern portion of Venezuela and the northern portion of the Amazon Basin , is Leishmania ( Viannia ) guyanensis .", "The current treatment regimens for treati...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biomacromolecule-ligand interactions", "medicine", "viruses and cancer", "emerging viral diseases", "microbiology", "viral structure", "oncology", "oncology agents", "proteins", "biology", "biochemistry", "virology", "antivirals", "glycobiology" ]	Structures of Merkel Cell Polyomavirus VP1 Complexes Define a Sialic Acid Binding Site Required for Infection	journal.ppat.1002738	null	[ [ "The human Merkel cell polyomavirus ( MCPyV or MCV ) was discovered in 2008 and found to be clonally integrated into Merkel cell carcinomas ( MCCs ) , establishing it as the first human oncovirus from the polyomavirus family [1] .", "MCPyV infection is common , with 50–80% of adults being seropositive [2]...	[ "The recently discovered human Merkel cell polyomavirus ( MCPyV or MCV ) causes the aggressive Merkel cell carcinoma ( MCC ) in the skin of immunocompromised individuals .", "Conflicting reports suggest that cellular glycans containing sialic acid ( Neu5Ac ) may play a role in MCPyV infectious entry .", "To add...	[ "Viruses must interact with specific receptor molecules on their host cells in order to first attach to the cell and second gain entry into it .", "Therefore , a viral entry pathway is a sequence of precisely regulated binding events between viral proteins and their cellular receptors , which can be proteins or o...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "chemical compounds", "phosphates", "fluorophotometry", "elution", "thermodynamics", "research and analysis methods", "separation processes", "spectrum analysis techniques", "rna structure", "fluorescence resonance energy transfer", "magnesium", "chemistry", "molecular biology", "spectroph...	A magnesium-induced triplex pre-organizes the SAM-II riboswitch	journal.pcbi.1005406	null	[ [ "Non-coding RNAs are currently thought to account for over 75% of the human genome [1] .", "In bacteria , non-coding RNAs play important roles in gene regulation .", "One such class of RNAs , riboswitches , regulates metabolite production .", "Here , a single RNA sequence folds into one of two or ...	[ "Our 13C- and 1H-chemical exchange saturation transfer ( CEST ) experiments previously revealed a dynamic exchange between partially closed and open conformations of the SAM-II riboswitch in the absence of ligand .", "Here , all-atom structure-based molecular simulations , with the electrostatic effects of Mannin...	[ "The presence of positively charged metal ions is essential to maintain the structural fold and function of RNA .", "Among different metal ions , magnesium is particularly important for the stability of RNA because it can efficiently support a close assembly of negatively charged phosphate groups in an RNA fold ....	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cholesterol", "biochemistry", "carbohydrate metabolism", "lipids", "medicine and health sciences", "dyslipidemia", "nutrition", "lipid metabolism", "biology and life sciences", "diet", "metabolism", "metabolic disorders", "glucose metabolism" ]	In vivo and in silico dynamics of the development of Metabolic Syndrome	journal.pcbi.1006145	null	[ [ "The simultaneous presentation of obesity , dyslipidemia , insulin resistance and hypertension is generally referred to as the Metabolic Syndrome ( MetS ) [1–5] .", "Together , these factors impose increased risk for the development of co-morbidities including cardiovascular disease , type 2 diabetes and ...	[ "The Metabolic Syndrome ( MetS ) is a complex , multifactorial disorder that develops slowly over time presenting itself with large differences among MetS patients .", "We applied a systems biology approach to describe and predict the onset and progressive development of MetS , in a study that combined in vivo an...	[ "Obesity is becoming a growing health problem , with the risk of running into a disease state called the Metabolic Syndrome ( MetS ) .", "It is difficult to study MetS in humans as it develops over a long period of time while many processes and organs are involved .", "Moreover , each patient may present itself...	2018
[ "Introduction", "Results/Discussion", "Methods" ]	[ "computer science", "chemistry", "biology" ]	Partially Glycosylated Dendrimers Block MD-2 and Prevent TLR4-MD-2-LPS Complex Mediated Cytokine Responses	journal.pcbi.1002095	null	[ [ "Dendrimers are a class of spherical macromolecules that can be distinguished from conventional linear polymers by their highly branched and symmetrical architecture .", "Polyamidoamine ( PAMAM ) dendrimers are , by far , the best studied of the commercialised and divergently synthesised dendrimers .", ...	[ "The crystal structure of the TLR4-MD-2-LPS complex responsible for triggering powerful pro-inflammatory cytokine responses has recently become available .", "Central to cell surface complex formation is binding of lipopolysaccharide ( LPS ) to soluble MD-2 .", "We have previously shown , in biologically based ...	[ "Dendrimers are well-defined branched symmetrical macromolecules .", "In biologically based experiments , we have shown that a generation 3 . 5 PAMAM dendrimer whose surface was modified with 8 surface glucosamine molecules inhibited TLR4 mediated cytokine inflammation in both primary human cells and a clinically...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "vero cells", "hela cells", "biological cultures", "microbiology", "light microscopy", "virus effects on host gene expression", "microscopy", "viral genome", "cell cultures", "microbial genetics", "microbial genomics", "research and analysis methods", "viral genomics", "fluorescence micros...	Gene Expression Correlates with the Number of Herpes Viral Genomes Initiating Infection in Single Cells	journal.ppat.1006082	null	[ [ "Cell-to-cell variability is an important factor in cancer , development , evolution , host-pathogen interactions and other key biological processes [1–3] .", "The variability observed among single cells mainly arises from deterministic factors , i . e . preexisting molecular regulatory mechanisms [3 , 4]...	[ "Viral gene expression varies significantly among genetically identical cells .", "The sources of these variations are not well understood and have been suggested to involve both deterministic host differences and stochastic viral host interactions .", "For herpesviruses , only a limited number of incoming vira...	[ "Single cell variation is of major interest in understanding key biological processes , like cancer , development and host pathogen interaction .", "During viral infection , these cell to cell variations can change the outcome of the whole organism infection .", "We suggested that differences in the number of p...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology/immunodeficiency viruses", "virology/viral replication and gene regulation", "virology/new therapies, including antivirals and immunotherapy", "immunology/innate immunity" ]	PPARγ and LXR Signaling Inhibit Dendritic Cell-Mediated HIV-1 Capture and trans-Infection	journal.ppat.1000981	null	[ [ "Worldwide , heterosexual transmission accounts for most new HIV-1 infections , with a majority of these occurring in developing countries [1] , [2] .", "Clearly , controlling heterosexual transmission of HIV-1 would be a significant step toward reducing this global pandemic .", "To achieve this goal ...	[ "Dendritic cells ( DCs ) contribute to human immunodeficiency virus type 1 ( HIV-1 ) transmission and dissemination by capturing and transporting infectious virus from the mucosa to draining lymph nodes , and transferring these virus particles to CD4+ T cells with high efficiency .", "Toll-like receptor ( TLR ) -...	[ "Heterosexual transmission is the primary mode of HIV transmission worldwide .", "In the absence of an effective vaccine , there is an increasing demand for the development of effective microbicides that block HIV sexual transmission .", "Dendritic cells ( DCs ) play a critical role in HIV transmission by effic...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "computational neuroscience", "neuroscience", "biology and life sciences", "computational biology" ]	Modeling Higher-Order Correlations within Cortical Microcolumns	journal.pcbi.1003684	null	[ [ "Electrophysiology is rapidly moving towards high density recording techniques capable of capturing the simultaneous activity of large populations of neurons .", "This raises the challenge of understanding how networks encode and process information in ways that go beyond tuning properties or feedforward ...	[ "We statistically characterize the population spiking activity obtained from simultaneous recordings of neurons across all layers of a cortical microcolumn .", "Three types of models are compared: an Ising model which captures pairwise correlations between units , a Restricted Boltzmann Machine ( RBM ) which allo...	[ "Communication between neurons underlies all perception and cognition .", "Hence , to understand how the brain's sensory systems such as the visual cortex work , we need to model how neurons encode and communicate information about the world .", "To this end , we simultaneously recorded the activity of many neu...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "chromosome structure and function", "dna", "signaling in cellular processes", "chromosome biology", "biology", "molecular biology", "signal transduction", "autosomal recessive", "cell biology", "nucleic acids", "genetics", "dna repair", "human genetics", "molecular cell biology", "genet...	CtIP Mutations Cause Seckel and Jawad Syndromes	journal.pgen.1002310	null	[ [ "Seckel syndrome ( SS ) belongs to the group of genome instability disorders collectively referred to as DNA-damage response ( DDR ) and repair defective syndromes [1] .", "While cancer predisposition is often associated with such syndromes , only a few cancers have been reported for SS patients .", "...	[ "Seckel syndrome is a recessively inherited dwarfism disorder characterized by microcephaly and a unique head profile .", "Genetically , it constitutes a heterogeneous condition , with several loci mapped ( SCKL1-5 ) but only three disease genes identified: the ATR , CENPJ , and CEP152 genes that control cellular...	[ "Cellular DNA is frequently damaged through the actions of exogenous and endogenously arising DNA damaging agents .", "To maintain genome integrity , cells have evolved complex mechanisms to detect DNA damage , signal its presence , and mediate its repair .", "The importance of such mechanisms is evident becaus...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "ecology and environmental sciences", "plant cell biology", "cell processes", "chloroplasts", "plant science", "aquatic environments", "microscopy", "plants", "cellular structures and organelles", "marine environments", "sea water", "research and analysis methods", "scanning electron microsc...	“Pomacytosis”—Semi-extracellular phagocytosis of cyanobacteria by the smallest marine algae	journal.pbio.2003502	null	[ [ "In conventional phagocytosis , the caught prey is internalized , i . e . , enclosed by a phagocytic membrane inside the predator cell to form a food vacuole , within which prey is digested and its contents are absorbed through the vacuole membrane [1] .", "Apart from secure isolation of the prey from the...	[ "The smallest algae , less than 3 μm in diameter , are the most abundant eukaryotes of the World Ocean .", "Their feeding on planktonic bacteria of similar size is globally important but physically enigmatic .", "Tiny algal cells tightly packed with the voluminous chloroplasts , nucleus , and mitochondria appea...	[ "The global significance of microorganisms is a consequence of their astronomical numbers .", "This is certainly true for the smallest planktonic algae on earth , which are less than 3 μm in diameter and the most numerous eukaryotic organisms of the oceans .", "Contrary to the general belief that algae use only...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "anatomy and physiology", "pulmonology", "animal models", "developmental biology", "histology", "model organisms", "molecular genetics", "morphogenesis", "respiratory medicine", "biology", "regeneration", "physiology", "genetics", "genetics and genomics" ]	Hepatocyte Growth Factor, a Determinant of Airspace Homeostasis in the Murine Lung	journal.pgen.1003228	null	[ [ "One approach to identifying mediators of alveolar formation and regeneration in the mammalian lung is to delineate the elemental events that attend airspace formation and then systematically investigate candidate proteins that harbor a compatible signaling repertoire in animal or cellular model systems .", ...	[ "The alveolar compartment , the fundamental gas exchange unit in the lung , is critical for tissue oxygenation and viability .", "We explored hepatocyte growth factor ( HGF ) , a pleiotrophic cytokine that promotes epithelial proliferation , morphogenesis , migration , and resistance to apoptosis , as a candidate...	[ "The airspace compartment of the mammalian lung , comprised of spherical sacs termed alveoli , harbors the architecture , cellular composition , and molecular armamentarium to perform the critical function of gas exchange or oxygen uptake .", "Despite the necessity of this alveolar compartment for organismal viab...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "action potentials", "medicine and health sciences", "nervous system", "membrane potential", "brain", "electrophysiology", "random variables", "neuroscience", "covariance", "mathematics", "computational neuroscience", "cerebellum", "coding mechanisms", "cerebral cortex", "animal cells", ...	Robust transmission of rate coding in the inhibitory Purkinje cell to cerebellar nuclei pathway in awake mice	journal.pcbi.1005578	null	[ [ "Transmission of information through firing rate changes in populations of connected neurons is one of the most widely accepted principles of neural coding .", "In motor control , for example , cortical neurons showing firing rate changes as a function of movement direction can be said to dynamically comp...	[ "Neural coding through inhibitory projection pathways remains poorly understood .", "We analyze the transmission properties of the Purkinje cell ( PC ) to cerebellar nucleus ( CN ) pathway in a modeling study using a data set recorded in awake mice containing respiratory rate modulation .", "We find that inhibi...	[ "Detailed computer simulations of biological neurons can make an important contribution to our understanding of how the brain works .", "In this paper we use such a model of a neuron that represents the output from the cerebellum .", "We can show that the inhibition this neuron type receives from Purkinje cells...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "bacterial diseases", "infectious diseases", "immunity", "tuberculosis", "innate immunity", "hiv", "retrovirology and hiv immunopathogenesis", "immunology", "biology", "viral diseases" ]	Vitamin D Inhibits Human Immunodeficiency Virus Type 1 and Mycobacterium tuberculosis Infection in Macrophages through the Induction of Autophagy	journal.ppat.1002689	null	[ [ "Human immunodeficiency virus type-1 ( HIV ) is a global health problem that has infected 60 million people and caused 25 million deaths worldwide .", "Currently , there are an estimated 33 million people living with HIV including 2 million children .", "Despite the immune defense mechanisms that the ...	[ "Low vitamin D levels in human immunodeficiency virus type-1 ( HIV ) infected persons are associated with more rapid disease progression and increased risk for Mycobacterium tuberculosis infection .", "We have previously shown that 1α , 25-dihydroxycholecalciferol ( 1 , 25D3 ) , the active form of vitamin D , inh...	[ "Macroautophagy ( autophagy - ‘self-eating’ , lysosome-dependent degradation and recycling of the intracellular components in response to stress ) is an important host defense mechanism against viral and mycobacterial infections .", "Recent studies have described that activation of autophagy in macrophages reduce...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "immunology/cellular microbiology and pathogenesis", "infectious diseases/neglected tropical diseases", "immunology/immune response", "gastroenterology and hepatology", "infectious diseases/helminth infections", "microbiology/parasitology", "pathology/immunology", "immunology/leukocyte signaling and g...	Temporal Expression of Chemokines Dictates the Hepatic Inflammatory Infiltrate in a Murine Model of Schistosomiasis	journal.pntd.0000598	null	[ [ "Schistosomiasis , a parasitic disease caused by trematodes of the genus Schistosoma , is a significant cause of human morbidity and mortality .", "Furthermore , recent reports suggest that the global burden of disease due to schistosomiasis has been significantly underestimated [1] .", "Chronic infec...	[ "Schistosomiasis continues to be an important cause of parasitic morbidity and mortality world-wide .", "Determining the molecular mechanisms regulating the development of granulomas and fibrosis will be essential for understanding how schistosome antigens interact with the host environment .", "We report here ...	[ "Schistosomiasis , a disease caused by parasitic worms , is a significant cause of illness and death in the developing world .", "Furthermore , recent reports suggest that the global burden of disease due to schistosomiasis has been significantly underestimated .", "Schistosomiasis of the liver arises due to in...	2010
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Circulating miRNAs: Potential Novel Biomarkers for Hepatopathology Progression and Diagnosis of Schistosomiasis Japonica in Two Murine Models	journal.pntd.0003965	null	[ [ "Schistosomiasis is a chronic debilitating parasitic disease of humans .", "Caused by members of the genus Schistosoma , it afflicts more than 200 million individuals worldwide , representing a major health and economic burden in tropical and developing nations [1] .", "The pathology of chronic Schist...	[ "Schistosomiasis remains a major public health issue , with an estimated 230 million people infected worldwide .", "Novel tools for early diagnosis and surveillance of schistosomiasis are currently needed .", "Elevated levels of circulating microRNAs ( miRNAs ) are commonly associated with the initiation and pr...	[ "Schistosomiasis japonica remains a public health problem in Southeast Asia .", "In China , the number of infected individuals has been reduced considerably due to long-term control efforts over the past 50 years , but still 60 million people are at the risk of the disease .", "Development of novel tools for ea...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "bacteremia", "bacterial diseases", "infectious diseases", "bloodstream infections", "q-fever", "salmonellosis", "neglected tropical diseases", "rickettsia", "brucellosis", "leptospirosis" ]	Etiology of Severe Non-malaria Febrile Illness in Northern Tanzania: A Prospective Cohort Study	journal.pntd.0002324	null	[ [ "Fever without a localized cause is one of the most common presenting complaints among persons seeking healthcare in many low- and middle-income countries [1] , [2] .", "However , unlike the syndromes of pneumonia and diarrhea that feature in global disease burden estimates and have well coordinated progr...	[ "The syndrome of fever is a commonly presenting complaint among persons seeking healthcare in low-resource areas , yet the public health community has not approached fever in a comprehensive manner .", "In many areas , malaria is over-diagnosed , and patients without malaria have poor outcomes .", "We prospecti...	[ "The syndrome of fever is caused by a large number of infectious diseases .", "Malaria is thought to have been declining in the tropics since 2004 .", "Increasing use of malaria diagnostic tests reveal a growing proportion of patients with fever who do not have malaria .", "While malaria diagnostic tests may ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "animal models", "biochemistry", "rna", "model organisms", "nucleic acids", "heredity", "genetics", "epigenetics", "biology", "mouse" ]	RNA–Mediated Epigenetic Heredity Requires the Cytosine Methyltransferase Dnmt2	journal.pgen.1003498	null	[ [ "Experimental results on model animals ranging from Caenorhabditis and Drosophila to the mouse have recently provided support for a mode of epigenetic heredity distinct from the canonical Mendelian rules [1]–[10] .", "These findings may help in understanding unexpected epidemiological results showing pate...	[ "RNA–mediated transmission of phenotypes is an important way to explain non-Mendelian heredity .", "We have previously shown that small non-coding RNAs can induce hereditary epigenetic variations in mice and act as the transgenerational signalling molecules .", "Two prominent examples for these paramutations in...	[ "The possibility of a mode of inheritance distinct from the Mendelian model has been considered since the early days of genetics .", "Only recently , however , suitable experimental models were created .", "We now see the development of new experimental systems detecting non-Mendelian inheritance in a variety o...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "blood cells", "medicine and health sciences", "enzyme-linked immunoassays", "immune physiology", "pathology and laboratory medicine", "immune cells", "pathogens", "vibrio", "immunology", "microbiology", "vaccines", "vibrio cholerae", "infectious disease control", "antibodies", "immunolo...	Bivalent oral cholera vaccination induces a memory B cell response to the V. cholerae O1-polysaccharide antigen in Haitian adults	journal.pntd.0007057	null	[ [ "Vibrio cholerae is the causative agent of cholera and responsible for approximately 1 . 3 to 4 million cases of diarrhea and 21 , 000 to 143 , 000 deaths , annually[1] .", "Large cholera epidemics occur frequently and are even more devastating when V . cholerae is introduced into an immunologically naïve...	[ "The bivalent killed whole-cell oral cholera vaccine ( BivWC ) is being increasingly used to prevent cholera .", "The presence of O-antigen-specific memory B cells ( MBC ) has been associated with protective immunity against cholera , yet MBC responses have not been evaluated after BivWC vaccination .", "To add...	[ "Oral cholera vaccines are being increasingly used throughout the world as a key component of cholera prevention programs .", "While several recent studies suggest oral cholera vaccines may provide durable protection , the potential mechanism that generates this long lasting immune memory and protection are unkno...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "fluorescence imaging", "invertebrates", "classical mechanics", "caenorhabditis", "neuroscience", "animals", "animal models", "vector construction", "caenorhabditis elegans", "model organisms", "microscopy", "experimental organism systems", "damage mechanics", "dna construction", "molecu...	Automatically tracking neurons in a moving and deforming brain	journal.pcbi.1005517	null	[ [ "Optical neural imaging has ushered in a new frontier in neuroscience that seeks to understand how neural activity generates animal behavior by recording from large populations of neurons at cellular resolution in awake and behaving animals .", "Population recordings have now been used to elucidate mechan...	[ "Advances in optical neuroimaging techniques now allow neural activity to be recorded with cellular resolution in awake and behaving animals .", "Brain motion in these recordings pose a unique challenge .", "The location of individual neurons must be tracked in 3D over time to accurately extract single neuron a...	[ "Computer algorithms for identifying and tracking neurons in images of a brain have struggled to keep pace with rapid advances in neuroimaging .", "In small transparent organism like the nematode C . elegans , it is now possible to record neural activity from all of the neurons in the animal’s head with single-ce...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "plant biology/plant genetics and gene expression", "developmental biology/plant growth and development", "developmental biology/developmental molecular mechanisms" ]	AGAMOUS Controls GIANT KILLER, a Multifunctional Chromatin Modifier in Reproductive Organ Patterning and Differentiation	journal.pbio.1000251	The floral, homeotic protein AGAMOUS coordinates multiple downstream genes through direct transcriptional regulation of the nuclear matrix attachment region binding protein GIANT KILLER.	[ [ "During flower development , many key processes depend on tissue-specific regulation of gene expression achieved by the coordinated interplay of transcription factors .", "The classical ABC model was proposed nearly two decades ago to account for organ identity control in flower development [1] .", "T...	[ "The Arabidopsis homeotic protein AGAMOUS ( AG ) , a MADS domain transcription factor , specifies reproductive organ identity during flower development .", "Using a binding assay and expression analysis , we identified a direct target of AG , GIANT KILLER ( GIK ) , which fine-tunes the expression of multiple gene...	[ "Multicellular development depends on proper expression of thousands of genes .", "Master regulators , such as homeotic proteins , code for transcription factors in both plants and animals and are thought to act by regulating other genes .", "Recent genomic studies in the plant Arabidopsis have shown that over ...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "cell biology", "pharmacology", "chemical biology", "biophysics" ]	Active-Site Inhibitors of mTOR Target Rapamycin-Resistant Outputs of mTORC1 and mTORC2	journal.pbio.1000038	Cells rely on the mammalian target of rapamycin kinase (mTOR) to sense growth factors. Inhibition of all forms of mTOR using newly developed inhibitors of its active site reveals new insights into the function of two mTOR-containing protein complexes and their potential as therapeutic targets.	[ [ "The mammalian target of rapamycin ( mTOR ) is a serine-threonine kinase related to the lipid kinases of the phosphoinositide 3-kinase ( PI3K ) family .", "mTOR exists in two complexes , mTORC1 [1 , 2] and mTORC2 [3 , 4] , which are differentially regulated , have distinct substrate specificities , and ar...	[ "The mammalian target of rapamycin ( mTOR ) regulates cell growth and survival by integrating nutrient and hormonal signals .", "These signaling functions are distributed between at least two distinct mTOR protein complexes: mTORC1 and mTORC2 .", "mTORC1 is sensitive to the selective inhibitor rapamycin and act...	[ "Growth factor pathways are required for normal development but are often inappropriately activated in many cancers .", "One growth-factor–sensitive pathway of increasing interest to cancer researchers relies on the mammalian target of rapamycin ( mTOR ) , a kinase that ( like all kinases ) delivers phosphate gro...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "urinary system procedures", "medicine and health sciences", "organ transplantation", "immunology", "biomarkers", "human genomics", "surgical and invasive medical procedures", "clinical medicine", "renal transplantation", "genome analysis", "kidneys", "transplantation", "immune system protei...	Exome Sequencing and Prediction of Long-Term Kidney Allograft Function	journal.pcbi.1005088	null	[ [ "Survival of patients afflicted with End Stage Renal Disease ( ESRD ) is superior following kidney transplantation compared to dialysis therapy .", "The short-term outcomes of kidney grafts have steadily improved since the early transplants with refinements in immunosuppressive regimens , use of DNA-based...	[ "Current strategies to improve graft outcome following kidney transplantation consider information at the human leukocyte antigen ( HLA ) loci .", "Cell surface antigens , in addition to HLA , may serve as the stimuli as well as the targets for the anti-allograft immune response and influence long-term graft outc...	[ "The article describes a new concept to help match donor organs to recipients for kidney transplantation .", "The concept relies on the ability to measure the individual DNA of potential donors and recipients .", "When the data about genomes ( i . e . , DNA ) of possible donors and recipients are available , th...	2016
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "linguistics", "engineering and technology", "natural antisense transcripts", "gene regulation", "carcinomas", "cancers and neoplasms", "social sciences", "gastrointestinal tumors", "liver diseases", "decision tree learning", "oncology", "decision analysis", ...	Ensemble of decision tree reveals potential miRNA-disease associations	journal.pcbi.1007209	null	[ [ "MicroRNAs ( miRNAs ) are a kind of endogenous non-coding RNA with the length of about 22 nucleotides , regulating the expression of genes by base paring with target messenger RNA ( mRNA ) [1] .", "Since the first two miRNAs , lin-14 and let-7 , both showing positive regulation for gene expression , were ...	[ "In recent years , increasing associations between microRNAs ( miRNAs ) and human diseases have been identified .", "Based on accumulating biological data , many computational models for potential miRNA-disease associations inference have been developed , which saves time and expenditure on experimental studies ,...	[ "MiRNAs are known as gene regulators and play critical roles in various biological processes .", "Many associations between miRNAs and human diseases have been identified , which promotes the understanding towards the molecular mechanisms of diseases and contributes to prevention and treatment of diseases .", "...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "zoonoses", "hantavirus", "immune cells", "clinical immunology", "nk cells", "hantavirus pulmonary syndrome", "immunology", "viral diseases" ]	Hantavirus-infection Confers Resistance to Cytotoxic Lymphocyte-Mediated Apoptosis	journal.ppat.1003272	null	[ [ "Hantaviruses are emerging zoonotic viruses that cause two severe diseases: hemorrhagic fever with renal syndrome ( HFRS ) in Eurasia and hantavirus cardio-pulmonary syndrome ( HCPS; also called hantavirus pulmonary syndrome ( HPS ) ) in the Americas , with case-fatality rates of up to 10% for HFRS and up to ...	[ "Hantaviruses cause hemorrhagic fever with renal syndrome ( HFRS ) and hantavirus cardio-pulmonary syndrome ( HCPS; also called hantavirus pulmonary syndrome ( HPS ) ) , both human diseases with high case-fatality rates .", "Endothelial cells are the main targets for hantaviruses .", "An intriguing observation ...	[ "Rodent-born hantaviruses cause two severe emerging diseases with high case-fatality rates in humans; hemorrhagic fever with renal syndrome ( HFRS ) in Eurasia and hantavirus cardio-pulmonary syndrome ( HCPS; also called hantavirus pulmonary syndrome ( HPS ) ) in the Americas .", "A hallmark of HFRS/HCPS is incre...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "immunology/immune response", "public health and epidemiology/screening" ]	Discovery of Markers of Exposure Specific to Bites of Lutzomyia longipalpis, the Vector of Leishmania infantum chagasi in Latin America	journal.pntd.0000638	null	[ [ "Sand fly salivary proteins play a major role in blood feeding and Leishmania transmission [1]–[3] .", "Exposure to sand fly salivary proteins induces both cellular immunity and specific antibodies [3] , [4] .", "A relationship between the level of specific antibodies to saliva , vector exposure and r...	[ "Sand flies deliver Leishmania parasites to a host alongside salivary molecules that affect infection outcomes .", "Though some proteins are immunogenic and have potential as markers of vector exposure , their identity and vector specificity remain elusive .", "We screened human , dog , and fox sera from endemi...	[ "Leishmania parasites are transmitted by the bite of an infected vector sand fly that injects salivary molecules into the host skin during feeding .", "Certain salivary molecules can produce antibodies and can be used as an indicator of exposure to a vector sand fly and potentially the disease it transmits .", ...	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "resonance frequency", "medicine and health sciences", "classical mechanics", "pathology and laboratory medicine", "chemical compounds", "vibration", "pathogens", "microbiology", "viral structure", "organic compounds", "retroviruses", "viruses", "immunodeficiency viruses", "rna viruses", ...	All-atom normal mode dynamics of HIV-1 capsid	journal.pcbi.1006456	null	[ [ "The recent breakthroughs in experimental technology for structure determination , especially in single-particle cryo-electron microscopy [2] , have helped unveil many large structure assemblies at near atomic resolution for the first time .", "It is well recognized that a thorough knowledge of their dyna...	[ "Dynamics of biomolecular assemblies offer invaluable insights into their functional mechanisms .", "For extremely large biomolecular systems , such as HIV-1 capsid that has nearly 5 millions atoms , obtaining its normal mode dynamics using even coarse-grained models can be a challenging task .", "In this work ...	[ "Supramolecular assemblies are large biomolecular complexes composed of hundreds or even thousands of protein chains .", "They function as molecular machines or as large containers that store or facilitate the chemical reactions of other molecules .", "Whatever they do , their functional mechanisms are tightly ...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "flow cytometry", "cell death", "medicine and health sciences", "dose prediction methods", "cancer treatment", "cell processes", "simulation and modeling", "oncology", "pharmaceutics", "immunoprecipitation", "research and analysis methods", "specimen preparation and treatment", "staining", ...	Quantitative single cell analysis uncovers the life/death decision in CD95 network	journal.pcbi.1006368	null	[ [ "Apoptosis is a program of cell death , which is essential for all multicellular organisms [1] .", "The crosstalk between apoptotic and anti-apoptotic pathways plays a key role in shaping life/death decisions in the cell .", "Furthermore , the success of anti-cancer therapies strongly depends on the e...	[ "CD95/Fas/APO-1 is a member of the death receptor family that triggers apoptotic and anti-apoptotic responses in particular , NF-κB .", "These responses are characterized by a strong heterogeneity within a population of cells .", "To determine how the cell decides between life and death we developed a computati...	[ "Activation of death receptor ( DR ) family has been reported to activate both apoptotic as well as anti-apoptotic responses .", "Molecular mechanisms underlying the intricate details of this crosstalk have not been established yet .", "Here we show that these pathways are triggered simultaneously in one cell ....	2018
[ "Introduction", "Methods", "Results and discussion" ]	[ "antimicrobials", "medicine and health sciences", "chemical compounds", "drugs", "tropical diseases", "microbiology", "parasitic diseases", "acylation", "wolbachia", "antimalarials", "esters", "antibiotics", "neglected tropical diseases", "pharmacology", "onchocerciasis", "bacteria", ...	Discovery of ABBV-4083, a novel analog of Tylosin A that has potent anti-Wolbachia and anti-filarial activity	journal.pntd.0007159	null	[ [ "The filarial worm diseases onchocerciasis ( “river blindness” ) and lymphatic filariasis ( LF , “elephantiasis” ) , though not typically lethal , produce substantial morbidity , social stigma and loss of economic opportunity in tropical and subtropical regions throughout the globe [1 , 2] .", "Nearly 150...	[ "There is a significant need for improved treatments for onchocerciasis and lymphatic filariasis , diseases caused by filarial worm infection .", "In particular , an agent able to selectively kill adult worms ( macrofilaricide ) would be expected to substantially augment the benefits of mass drug administration (...	[ "The Wolbachia bacterium lives symbiotically within the filarial worms that cause onchocerciasis and lymphatic filariasis .", "In the absence of these bacteria juvenile worms cannot mature , females are unable to reproduce , and the worm life-span is significantly shortened .", "Thus , anti-Wolbachia therapy wo...	2019

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