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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", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "schistosomiasis", "neglected tropical diseases", "parasitic diseases" ]	Prevalence and Associated Factors of Schistosomiasis among Children in Yemen: Implications for an Effective Control Programme	journal.pntd.0002377	null	[ [ "Schistosomiasis or bilharzia , one of the most prevalent neglected tropical diseases ( NTDs ) , is still a public health problem in many developing countries in the tropics and subtropics with approximately 240 million infected people and about 700 million people worldwide are at risk of this infection [1] ....	[ "Schistosomiasis , one of the most prevalent neglected tropical diseases , is a life-threatening public health problem in Yemen especially in rural communities .", "This cross-sectional study aims to determine the prevalence and associated risk factors of schistosomiasis among children in rural Yemen .", "Urine...	[ "Schistosomiasis remains one of the most serious and prevalent diseases worldwide .", "Despite intensive control efforts by the government and international bodies , schistosomiasis is the second cause of death , after malaria , in Yemen , with an estimated 3 million cases .", "We screened 400 children in rural...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "infectious diseases/hiv infection and aids", "immunology/immune response", "infectious diseases/viral infections" ]	Similar Impact of CD8+ T Cell Responses on Early Virus Dynamics during SIV Infections of Rhesus Macaques and Sooty Mangabeys	journal.pcbi.1000901	null	[ [ "The simian immunodeficiency virus ( SIV ) occurs as a natural infection in several Old-world monkey species , such as sooty mangabeys ( SM ) or African green monkeys [1] , [2] .", "In striking contrast to HIV infection of humans , SIV infection does not cause disease in natural hosts .", "The levels ...	[ "Despite comparable levels of virus replication , simian immunodeficiency viruses ( SIV ) infection is non-pathogenic in natural hosts , such as sooty mangabeys ( SM ) , whereas it is pathogenic in non-natural hosts , such as rhesus macaques ( RM ) .", "Comparative studies of pathogenic and non-pathogenic SIV inf...	[ "Simian immunodeficiency viruses ( SIV ) are typically non-pathogenic in their natural hosts .", "However , if the same virus infects a non-natural host it often leads to AIDS-like symptoms .", "Therefore , comparing SIV infections in these two types of host might help explain the pathogenesis of SIV in non-nat...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The Incubation Period of Primary Epstein-Barr Virus Infection: Viral Dynamics and Immunologic Events	journal.ppat.1005286	null	[ [ "Epstein-Barr virus ( EBV ) is a ubiquitous human herpesvirus .", "As with all herpesviruses , EBV causes lifelong infection in its host .", "Infection is associated with autoimmune diseases [1 , 2] and is known to cause several types of cancer , representing 1% of the worldwide cancer burden [3] .", ...	[ "Epstein-Barr virus ( EBV ) is a human herpesvirus that causes acute infectious mononucleosis and is associated with cancer and autoimmune disease .", "While many studies have been performed examining acute disease in adults following primary infection , little is known about the virological and immunological eve...	[ "Chronic viral infections are ubiquitous in the human population .", "Many of these viruses persist in spite of the host immune response .", "Epstein-Barr virus ( EBV ) is a human herpesvirus and the primary causative agent of acute infectious mononucleosis .", "The virus is primarily transmitted through sali...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "immunology", "biology", "microbiology", "molecular cell biology" ]	Tetherin/BST-2 Antagonism by Nef Depends on a Direct Physical Interaction between Nef and Tetherin, and on Clathrin-mediated Endocytosis	journal.ppat.1003487	null	[ [ "Mammalian cells express a number of proteins that inhibit specific steps of virus replication .", "One such factor , tetherin ( BST-2 or CD317 ) , impairs the release of enveloped viruses from infected cells [1] , [2] , [3] , [4] , [5] .", "Tetherin is a type II integral membrane protein with a topol...	[ "Nef is the viral gene product employed by the majority of primate lentiviruses to overcome restriction by tetherin ( BST-2 or CD317 ) , an interferon-inducible transmembrane protein that inhibits the detachment of enveloped viruses from infected cells .", "Although the mechanisms of tetherin antagonism by HIV-1 ...	[ "Tetherin ( BST-2 , CD317 or HM1 . 24 ) is an interferon-inducible cellular restriction factor that prevents the release of enveloped viruses from infected cells .", "Human and simian immunodeficiency viruses have evolved to use different viral proteins to overcome the anti-viral effects of tetherin .", "Wherea...	2013
[ "Introduction", "Results", "Discussion", "Material and Methods" ]	[]	Transcriptional and Linkage Analyses Identify Loci that Mediate the Differential Macrophage Response to Inflammatory Stimuli and Infection	journal.pgen.1005619	null	[ [ "At the cellular level , innate immune cells , such as macrophages , are central to the development and prevention of infectious diseases .", "On engagement of surface signaling receptors or pattern recognition receptors ( PRRs ) such as toll-like receptors ( TLRs ) , RIG-I-like receptors ( RLRs ) and the...	[ "Macrophages display flexible activation states that range between pro-inflammatory ( classical activation ) and anti-inflammatory ( alternative activation ) .", "These macrophage polarization states contribute to a variety of organismal phenotypes such as tissue remodeling and susceptibility to infectious and in...	[ "Macrophages provide a first line of defense against invading pathogens and play an important role in the initiation and resolution of immune responses .", "When in contact with pathogens or immune factors , such as cytokines , macrophages assume activation states that range between pro-inflammatory ( classical a...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "linear discriminant analysis", "statistics", "human genomics", "data mining", "genomic databases", "mathematics", "genome analysis", "mammalian genomics", "information technology", "research and analysis methods", "sequence analysis", "computer and information sciences", "bioinformatics", ...	A computational framework to assess genome-wide distribution of polymorphic human endogenous retrovirus-K In human populations	journal.pcbi.1006564	null	[ [ "Endogenous retroviruses ( ERVs ) are derived from infectious retroviruses that integrated into a host germ cell at some time in the evolutionary history of a species [1–5] .", "ERVs in humans ( HERVs ) comprise up to 8% of the genome and have contributed important functions to their host [6–8] .", "T...	[ "Human Endogenous Retrovirus type K ( HERV-K ) is the only HERV known to be insertionally polymorphic; not all individuals have a retrovirus at a specific genomic location .", "It is possible that HERV-Ks contribute to human disease because people differ in both number and genomic location of these retroviruses ....	[ "Human Endogenous Retrovirus type K ( HERV-K ) is the youngest of retrovirus families in the human genome and is the only group of endogenous retroviruses that has polymorphic members; a locus containing a HERV-K can be occupied in one individual but empty in others .", "HERV-Ks could contribute to disease risk o...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genomics", "biology", "computational biology", "microbiology", "genetics and genomics" ]	A Semi-Quantitative, Synteny-Based Method to Improve Functional Predictions for Hypothetical and Poorly Annotated Bacterial and Archaeal Genes	journal.pcbi.1002230	null	[ [ "Gene function prediction is currently one of the fundamental problems in microbiology [1] .", "The improvement in DNA sequencing technologies has allowed for the sequencing of hundreds of full Bacterial and Archaeal genomes .", "However , in the dataset of full Bacterial and Archaeal genomes from NCB...	[ "During microbial evolution , genome rearrangement increases with increasing sequence divergence .", "If the relationship between synteny and sequence divergence can be modeled , gene clusters in genomes of distantly related organisms exhibiting anomalous synteny can be identified and used to infer functional con...	[ "Based on trends between gene sequence divergence and gene order divergence over time , we developed a new synteny-based method to refine functional annotation .", "This method uses these trends to determine the probability that any two syntenous genes ( genes that are sequential in two organisms ) are functional...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "genetic diseases", "mutation", "hereditary nonpolyposis colorectal cancer", "forecasting", "mathematics", "statistics (mathematics)", "genome analysis", "nonsense mutation", "molecular biology techniques", "autosomal dominant diseases", "research and analysis m...	Hereditary cancer genes are highly susceptible to splicing mutations	journal.pgen.1007231	null	[ [ "As the cost of sequencing technologies is declining , the number of genomes and exomes sequenced is increasing , resulting in an expanding archive of genetic variation in both diseased and healthy individuals [1 , 2] .", "To keep pace with the ever growing variant archive , in silico tools are being crea...	[ "Substitutions that disrupt pre-mRNA splicing are a common cause of genetic disease .", "On average , 13 . 4% of all hereditary disease alleles are classified as splicing mutations mapping to the canonical 5′ and 3′ splice sites .", "However , splicing mutations present in exons and deeper intronic positions ar...	[ "To understand the extent to which disrupted pre-mRNA splicing causes human disease , we re-analyzed coding mutations in MLH1 , one of the causal genes of Lynch Syndrome .", "We found that a high fraction of the MLH1 coding mutations resulted in disrupted splicing .", "To further investigate a more general role...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Evidence of Reversible Bradycardia and Arrhythmias Caused by Immunogenic Proteins Secreted by T. cruzi in Isolated Rat Hearts	journal.pntd.0003512	null	[ [ "Chagas disease is an important public health problem in Latin America currently affecting an estimated 8 million people in 21 countries and spreading by human migration to a number of non-endemic regions [1] .", "The protozoan Trypanosoma cruzi is the etiologic agent of the disease in mammals; the parasi...	[ "Chagas cardiomyopathy , caused by the protozoan Trypanosoma cruzi , is characterized by alterations in intracellular ion , heart failure and arrhythmias .", "Arrhythmias have been related to sudden death , even in asymptomatic patients , and their molecular mechanisms have not been fully elucidated .", "The ai...	[ "Chagas disease , caused by the parasite Trypanosoma cruzi , is an endemic disease of Latin-American countries , affecting an estimated 8 million people in 21 countries .", "It is spread by the bite of triatomine reduvid bug .", "Due to immigration towards non-endemic regions , the disease can spread and affect...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The Multi-allelic Genetic Architecture of a Variance-Heterogeneity Locus for Molybdenum Concentration in Leaves Acts as a Source of Unexplained Additive Genetic Variance	journal.pgen.1005648	null	[ [ "Genome Wide Association ( GWA ) analysis is a powerful approach to study the genetic basis of complex traits in natural populations .", "It is widely used to study the genetics of human disease , but is equally useful in studies of other populations .", "For example , it has been used to dissect the ...	[ "Genome-wide association ( GWA ) analyses have generally been used to detect individual loci contributing to the phenotypic diversity in a population by the effects of these loci on the trait mean .", "More rarely , loci have also been detected based on variance differences between genotypes .", "Several hypoth...	[ "Most biological traits vary in natural populations , and understanding the genetic basis of this variation remains an important challenge .", "Genome-wide association ( GWA ) studies have emerged as a powerful tool to address this challenge by dissecting the genetic architecture of trait variation into the contr...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "phosphorylation", "chemical compounds", "applied mathematics", "reactants", "organic compounds", "dna transcription", "simulation and modeling", "algorithms", "systems science", "mathematics", "chemical equilibrium", "algebra", "basic amino acids", "amino acids", "polynomials", "physi...	Identifying parameter regions for multistationarity	journal.pcbi.1005751	null	[ [ "Mathematical models in the form of parameterized systems of ordinary differential equations ( ODEs ) are valuable tools in biology .", "Often , qualitative properties of the ODEs are associated with macroscopic biological properties and biological functions [1–4] .", "It is therefore important that w...	[ "Mathematical modelling has become an established tool for studying the dynamics of biological systems .", "Current applications range from building models that reproduce quantitative data to identifying systems with predefined qualitative features , such as switching behaviour , bistability or oscillations .", ...	[ "Mathematical modelling has become an important tool in biology .", "As modelling requires separating the essential from the ordinary , there is never just one model but a collection thereof .", "To understand biology through modelling it is therefore crucial to be able to tell which of these models are capable...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models	journal.pcbi.1004542	null	[ [ "Protein dynamics plays a key role in describing the function of most proteins and protein complexes .", "The importance of protein dynamics studies has been increasingly recognized alongside the importance of the structures themselves .", "Experimentally , protein dynamics can be studied using nuclea...	[ "Dynamics can provide deep insights into the functional mechanisms of proteins and protein complexes .", "For large protein complexes such as GroEL/GroES with more than 8 , 000 residues , obtaining a fine-grained all-atom description of its normal mode motions can be computationally prohibitive and is often unnec...	[ "Proteins and other biomolecules are not static but are constantly in motion .", "Moreover , they possess intrinsic collective motion patterns that are tightly linked to their functions .", "Thus , an accurate and detailed description of their motions can provide deep insights into their functional mechanisms ....	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell physiology", "invertebrates", "medicine and health sciences", "reproductive system", "animals", "cell differentiation", "cell formation", "germ cells", "animal models", "developmental biology", "drosophila melanogaster", "model organisms", "stem cells", "experimental organism systems...	Specification and spatial arrangement of cells in the germline stem cell niche of the Drosophila ovary depend on the Maf transcription factor Traffic jam	journal.pgen.1006790	null	[ [ "Stem cells retain the capacity for development in differentiated organisms , which is important for tissue growth , homeostasis and regeneration , and for long-term reproductive capability .", "Stem cells are often associated with a specialized microenvironment , a niche that is essential for the formati...	[ "Germline stem cells in the Drosophila ovary are maintained by a somatic niche .", "The niche is structurally and functionally complex and contains four cell types , the escort , cap , and terminal filament cells and the newly identified transition cell .", "We find that the large Maf transcription factor Traff...	[ "Establishment and maintenance of stem cells often depends on associated niche cells .", "The germline stem cell niche of the Drosophila ovary has been a long-standing model for the analysis of the interactions between stem cells and niche cells .", "Surprisingly little is known , however , about the mechanisms...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "computational biology/protein homology detection" ]	Detecting Remote Evolutionary Relationships among Proteins by Large-Scale Semantic Embedding	journal.pcbi.1001047	null	[ [ "Using sequence similarity between proteins to detect evolutionary relationships—protein homology detection—is one of the most fundamental and longest studied problems in computational biology .", "A protein's function is strongly correlated with its 3D structure , and due to evolutionary pressure , prote...	[ "Virtually every molecular biologist has searched a protein or DNA sequence database to find sequences that are evolutionarily related to a given query .", "Pairwise sequence comparison methods—i . e . , measures of similarity between query and target sequences—provide the engine for sequence database search and ...	[ "Searching a protein or DNA sequence database to find sequences that are evolutionarily related to a query is one of the foundational problems in computational biology .", "These database searches rely on pairwise comparisons of sequence similarity between the query and targets , but despite years of method refin...	2011
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "biophysics/macromolecular assemblies and machines", "biochemistry/rna structure", "molecular biology/rna-protein interactions", "molecular biology/translation mechanisms", "molecular biology/translational regulation", "biophysics/rna structure", "biochemistry/transcription and translation", "biophysi...	SecM-Stalled Ribosomes Adopt an Altered Geometry at the Peptidyl Transferase Center	journal.pbio.1000581	A structure of a ribosome stalled during translation of the SecM peptide provides insight into the mechanism by which the large subunit active site is inactivated.	[ [ "The ribosome is a large macromolecular particle that synthesizes polypeptide chains from the substituent amino acid building blocks .", "The active site for peptide bond formation , the so-called peptidyl transferase center ( PTC ) , is located in a cleft on the intersubunit side of the large ribosomal s...	[ "As nascent polypeptide chains are synthesized , they pass through a tunnel in the large ribosomal subunit .", "Interaction between specific nascent chains and the ribosomal tunnel is used to induce translational stalling for the regulation of gene expression .", "One well-characterized example is the Escherich...	[ "In all cells , ribosomes perform the job of making proteins .", "As the proteins are synthesized they pass through a tunnel in the ribosome , and some growing proteins interact with the tunnel , leading to stalling of protein synthesis .", "Here , we used cryo-electron microscopy to determine the structure of ...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The Analysis of Pendolino (peo) Mutants Reveals Differences in the Fusigenic Potential among Drosophila Telomeres	journal.pgen.1005260	null	[ [ "Telomeres are nucleoprotein complexes that counterbalance incomplete replication of terminal DNA and protect chromosome ends preventing both activation of cell cycle checkpoints and fusion events .", "In most organisms , the end replication problem is solved by telomerase , which mediates the addition of...	[ "Drosophila telomeres are sequence-independent structures that are maintained by transposition to chromosome ends of three specialized retroelements ( HeT-A , TART and TAHRE; collectively designated as HTT ) rather than telomerase activity .", "Fly telomeres are protected by the terminin complex ( HOAP-HipHop-Moi...	[ "Telomeres are specialized structures that protect chromosome ends from incomplete replication , degradation and end-to-end fusion .", "Abnormalities in telomere structure or maintenance can promote a variety of human diseases including premature aging and cancer .", "Although all human telomeres contain the sa...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "amebiasis", "infectious disease epidemiology", "epidemiology", "neglected tropical diseases" ]	Seroprevalence of Entamoeba histolytica Infection among Chinese Men Who Have Sex with Men	journal.pntd.0002232	null	[ [ "Entamoeba histolytica ( E . histolytica ) has a worldwide distribution and is endemic in most developing countries .", "Invasive amebiasis ( IA ) caused by E . histolytica is a very common human gastrointestinal parasitic disease which affected 50 million people worldwide and caused greater than 100 , 00...	[ "Men who have sex with men ( MSM ) were found to be one of the high-risk populations for Entamoeba histolytica ( E . histolytica ) infection .", "Accompanied by the prevalence of human immunodeficiency virus ( HIV ) among MSM , invasive amebiasis caused by E . histolytica has been paid attention to as an opportun...	[ "Entamoeba histolytica ( E . histolytica ) is a very common human gastrointestinal parasitic disease which affects 50 million people worldwide .", "Men who have sex with men ( MSM ) have already been found to be one of the high-risk populations with E . histolytica infection .", "Previous studies have reported ...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	An Outbreak of Chikungunya in Rural Bangladesh, 2011	journal.pntd.0003907	null	[ [ "Chikungunya is an arthropod-borne disease caused by Chikungunya virus ( Alphavirus family , Togaviridae family ) which was initially identified in Tanzania in 1952 [1] .", "Chikungunya outbreaks likely happened before the virus was identified because there were many verifiable depictions of epidemic feve...	[ "The first identified Chikungunya outbreak occurred in Bangladesh in 2008 .", "In late October 2011 , a local health official from Dohar Sub-district , Dhaka District , reported an outbreak of undiagnosed fever and joint pain .", "We investigated the outbreak to confirm the etiology , describe the clinical pres...	[ "Chikungunya virus is transmitted through bites from Aedes mosquitoes and causes outbreaks of fever and polyarthralgia; the geographic range of infection is expanding .", "An outbreak of fever with prolonged joint pain was investigated in Bangladesh in 2011 , where house-to-house surveys were carried out to ident...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "biology" ]	A Systematic Review of High Quality Diagnostic Tests for Chagas Disease	journal.pntd.0001881	null	[ [ "Chagas disease , or American Trypanosomiasis , is caused by the parasite Trypanosoma cruzi .", "The World Health Organization estimates that approximately 10 million individuals are currently infected with T . cruzi and are at risk for developing cardiac or gut pathology normally associated with chronic ...	[ "There is significant heterogeneity in reported sensitivities and specificities of diagnostic serological assays for Chagas disease , as might be expected from studies that vary widely according to setting , research design , antigens employed , and reference standard .", "The purpose of this study is to summariz...	[ "Chagas disease , an infectious disease endemic to Latin America , is caused by the protozoan parasite Trypanosoma cruzi .", "T . cruzi can be transmitted through blood transfusions , organ transplants , or from mother to fetus , although it is most commonly transmitted through insect vectors .", "Infections ca...	2012
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "medicine and health sciences", "genetic networks", "body fluids", "immune physiology", "pathology and laboratory medicine", "immune cells", "immunology", "signs and symptoms", "network analysis", "immune system proteins", "computer and information sciences", "white blood cell...	Interactions between the tumor and the blood systemic response of breast cancer patients	journal.pcbi.1005680	null	[ [ "Breast cancer ( BC ) research has largely focused on understanding the intrinsic properties of the primary tumor in order to therapeutically target key molecular components that drive progression within the tumor epithelial cells [1] .", "For example , tamoxifen and trastuzumab target the estrogen and hu...	[ "Although systemic immunity is critical to the process of tumor rejection , cancer research has largely focused on immune cells in the tumor microenvironment .", "To understand molecular changes in the patient systemic response ( SR ) to the presence of BC , we profiled RNA in blood and matched tumor from 173 pat...	[ "We present a novel system ( MIxT ) to identify genes and pathways in the primary tumor that are tightly linked to genes and pathways in the patient systemic response ( SR ) .", "These results suggest new ways to tackle and monitor the disease by looking outside the tumor and exploiting the patient SR ." ]	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "control theory", "medicine and health sciences", "neural networks", "engineering and technology", "electronics", "neurodegenerative diseases", "signal processing", "neuroscience", "epileptic seizures", "control engineering", "systems science", "mathematics", "epilepsy", "computer and info...	A minimally invasive neurostimulation method for controlling abnormal synchronisation in the neuronal activity	journal.pcbi.1006296	null	[ [ "Synchronisation is one of the key mechanisms responsible for self-organisation and emergence in living organisms [1–3] .", "Regular and periodic activity emerging from the collective behaviour of a set of interacting agents , has been noted to be crucial for the operation of many processes in living orga...	[ "Many collective phenomena in Nature emerge from the -partial- synchronisation of the units comprising a system .", "In the case of the brain , this self-organised process allows groups of neurons to fire in highly intricate partially synchronised patterns and eventually lead to high level cognitive outputs and c...	[ "Synchronisation plays an important role in most of the neuronal activities and in particular in the control of the motor system .", "However , due to biochemical dysfunction in the brain activity , an abnormal and excessive synchronisation may occur being responsible for severe symptoms of several neurological d...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Specific Management of Post-Chikungunya Rheumatic Disorders: A Retrospective Study of 159 Cases in Reunion Island from 2006-2012	journal.pntd.0003603	null	[ [ "Fifty years after its first tropical description in the Newala district of Tanganyika [1 , 2] , chikungunya ( CHIK ) has re-emerged extensively , resulting in 1 . 4 to 6 . 5 million infected individuals between 2004 and 2014 in Africa , as well as regions within the Indian Ocean , Southeast Asia , the Pacifi...	[ "Since 2003 , the tropical arthritogenic chikungunya ( CHIK ) virus has become an increasingly medical and economic burden in affected areas as it can often result in long-term disabilities .", "The clinical spectrum of post-CHIK ( pCHIK ) rheumatic disorders is wide .", "Evidence-based recommendations are need...	[ "With a 6-year insight , we extensively and retrospectively describe clinical profiles and specific treatments of mechanical and inflammatory post-chikungunya rheumatic disorders .", "In the current context of chikungunya’s global spread , we provide the first diagnostic and therapeutic algorithm to guide physici...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "recreation", "education", "decision making", "engineering and technology", "demography", "sociology", "social sciences", "neuroscience", "cell phones", "experimental psychology", "cognition", "games", "behavior", "educational attainment", "communication equipment", "gambling", "peop...	Approach-Induced Biases in Human Information Sampling	journal.pbio.2000638	null	[ [ "Many spheres of human behavior depend upon gathering and understanding evidence appropriately to inform decision-making .", "Yet the best way to sample information is a nontrivial problem , necessitating deciding where to sample information [1 , 2] , when to cease information gathering [3 , 4] , and weig...	[ "Information sampling is often biased towards seeking evidence that confirms one’s prior beliefs .", "Despite such biases being a pervasive feature of human behavior , their underlying causes remain unclear .", "Many accounts of these biases appeal to limitations of human hypothesis testing and cognition , de f...	[ "Human decision-making often appears irrational .", "A major challenge is to explain why apparently irrational behavior occurs and what potential benefits it might have conferred for our evolutionary ancestors .", "A well-studied behavior in experimental psychology is “confirmation bias , ” where we sample info...	2016
[ "Introduction", "Methods", "Results", "Discussion", "Conclusion" ]	[]	Prevalence and Determinants of the Gender Differentials Risk Factors of Child Deaths in Bangladesh: Evidence from the Bangladesh Demographic and Health Survey, 2011	journal.pntd.0003616	null	[ [ "Child deaths , which are one of the most important health indicators for a country , represent the socio-economic development of a population and have received considerable attention from national and international agencies in the last few decades because of their inclusion in the Millennium Development Goal...	[ "The number of child deaths is a potential indicator to assess the health condition of a country , and represents a major health challenge in Bangladesh .", "Although the country has performed exceptionally well in decreasing the mortality rate among children under five over the last few decades , mortality still...	[ "Children are a significant asset of a country .", "Child deaths are an important way to determine the health sector development .", "The effectiveness of the interventions is required to prevent child deaths .", "The purpose of this study is to identify the prevalence and risk factors of child deaths in Bang...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases", "genetics and genomics/functional genomics", "immunology/innate immunity", "immunology", "infectious diseases/bacterial infections", "genetics and genomics" ]	Global Functional Analyses of Cellular Responses to Pore-Forming Toxins	journal.ppat.1001314	null	[ [ "Pore-forming toxins ( PFTs ) are proteinaceous virulence factors that play a major role in bacterial pathogenesis [1] , [2] , [3] .", "PFTs constitute the single largest class of bacterial virulence factors , comprising ∼25–30% of all bacterial protein toxins [3] , [4] .", "PFTs have been demonstrate...	[ "Here we present the first global functional analysis of cellular responses to pore-forming toxins ( PFTs ) .", "PFTs are uniquely important bacterial virulence factors , comprising the single largest class of bacterial protein toxins and being important for the pathogenesis in humans of many Gram positive and Gr...	[ "The plasma membrane surrounds cells and protects their interior from the environment and from attack by disease-causing agents like bacteria and viruses .", "Bacteria that cause disease have discovered that an effective way to attack cells is to secrete proteins ( pore-forming toxins ) that breach , i . e . , fo...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "genome expression analysis", "functional genomics", "environmental sciences", "marine monitoring", "marine biology", "toxicology", "environmental protection", "marine and aquatic sciences", "regulatory networks", "biology", "microarrays", "systems biology", "predictive toxicology", "bioch...	Towards a System Level Understanding of Non-Model Organisms Sampled from the Environment: A Network Biology Approach	journal.pcbi.1002126	null	[ [ "Modelling the responses and compensatory adaptations of living organisms to a changing environment is extremely important both in terms of scientific understanding and for its potential impact on global health .", "Although computational modelling of ecological systems has been utilised in ecotoxicology ...	[ "The acquisition and analysis of datasets including multi-level omics and physiology from non-model species , sampled from field populations , is a formidable challenge , which so far has prevented the application of systems biology approaches .", "If successful , these could contribute enormously to improving ou...	[ "Understanding how living organisms adapt to changes in their natural habitats is of paramount importance particularly in respect to environmental stressors , such as pollution or climate .", "Computational models integrating the multi-level molecular responses with organism physiology are likely to be indispensa...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "learning", "medicine and health sciences", "brain", "social sciences", "neuroscience", "learning and memory", "simulation and modeling", "cognitive psychology", "animal behavior", "animal management", "zoology", "animal performance", "research and analysis methods", "behavior", "neostri...	Interactions of spatial strategies producing generalization gradient and blocking: A computational approach	journal.pcbi.1006092	null	[ [ "Neurobehavioral evidence supports a prominent role for interactions between multiple anatomically distinct memory systems in the mammalian brain underlying the coordination of different behavioral strategies during learning ( e . g . , [1] ) : A cognitive memory system , relying on a network comprising the h...	[ "We present a computational model of spatial navigation comprising different learning mechanisms in mammals , i . e . , associative , cognitive mapping and parallel systems .", "This model is able to reproduce a large number of experimental results in different variants of the Morris water maze task , including s...	[ "We present a computational model of navigation that successfully reproduces a set of different experiments involving cognitive mapping and associative phenomena during spatial learning .", "The key ingredients of the model that are responsible for this achievement are", "( i ) the coordination of different nav...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "rna interference", "developmental biology", "immunoprecipitation", "epigenetics", "co-immunoprecipitation", "morphogenesis", "cellular structures and organelles", "research and analysis methods", "lipids", "genetic interference", "proteins", "fats", "gene expression", "ubiquitination", ...	Early girl is a novel component of the Fat signaling pathway	journal.pgen.1007955	null	[ [ "Precise coordination of growth and morphogenesis during development is critical for formation of organs of correct proportions and optimal function .", "This is achieved through the cumulative effect of biochemical signaling through morphogens and biomechanical signals mediated through the actomyosin net...	[ "The Drosophila protocadherins Dachsous and Fat regulate growth and tissue polarity by modulating the levels , membrane localization and polarity of the atypical myosin Dachs .", "Localization to the apical junctional membrane is critical for Dachs function , and the adapter protein Vamana/Dlish and palmitoyl tra...	[ "During development , organs grow to achieve a consistent final size .", "The evolutionarily conserved Hippo signaling network plays a central role in organ size control , and when dysregulated can be associated with cancer and other diseases .", "Fat signaling is one of several upstream pathways that impinge o...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "oncology", "cell biology", "yeast and fungi", "geriatrics", "genetics and genomics", "saccharomyces" ]	Evidence That a RecQ Helicase Slows Senescence by Resolving Recombining Telomeres	journal.pbio.0050160	Yeast cells lacking the RecQ helicase Sgs1p show an accumulation of telomere recombination intermediates associated with premature senescence.	[ [ "Telomeres are critical for genome stability and normal cell physiology because they cap the ends of chromosomes; if uncapped , telomeres behave as DNA breaks and thus elicit damage responses and are subject to nucleolytic degradation and recombination [1 , 2] .", "Capping depends on telomere architecture...	[ "RecQ helicases , including Saccharomyces cerevisiae Sgs1p and the human Werner syndrome protein , are important for telomere maintenance in cells lacking telomerase activity .", "How maintenance is accomplished is only partly understood , although there is evidence that RecQ helicases function in telomere replic...	[ "Because telomeres are situated at the ends of chromosomes , they are both essential for chromosome integrity and particularly susceptible to processes that lead to loss of their own DNA sequences .", "The enzyme telomerase can counter these losses , but there are also other means of telomere maintenance , some o...	2007
[ "Introduction", "Methods", "Results", "Discussion", "Conclusions" ]	[ "medicine and health sciences", "toxins", "pathology and laboratory medicine", "japan", "bibliometrics", "tropical diseases", "geographical locations", "vertebrates", "animals", "toxic agents", "toxicology", "reptiles", "scientometrics", "neglected tropical diseases", "snakebite", "res...	Snakebite Envenoming – A Combined Density Equalizing Mapping and Scientometric Analysis of the Publication History	journal.pntd.0005046	null	[ [ "Snakebites envenomation is a neglected tropical disease and lead to an enormous burden of disease in many parts of the world [1–3] .", "Precise epidemiological data is missing but estimates suggest that 25 , 000–125 , 000 deaths and about 400 , 000 permanent disabilities are caused by snakebites annually...	[ "Estimates suggest that more than 25 , 000 to 125 , 000 people die annually from snakebite envenomation worldwide .", "In contrast to this major disease burden , thorough bibliometric studies do not exist so far that illustrate the overall research activity over a long time span .", "Therefore , the NewQIS-plat...	[ "Snakebite injury is a neglected tropical disease and lead to an enormous burden of disease in many parts of the world with about 25 , 000–125 , 000 estimated deaths .", "Therefore , research on this area of medicine is crucial since new diagnostic and therapeutic pathways may help to diminish disease burden .", ...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "sequencing techniques", "medicine and health sciences", "pulmonology", "simulation and modeling", "methylation", "epigenetics", "dna", "molecular biology techniques", "rna sequencing", "dna methylation", "chromatin", "asthma", "research and analysis methods", "chromosome biology", "gene...	An integrative association method for omics data based on a modified Fisher’s method with application to childhood asthma	journal.pgen.1008142	null	[ [ "Because of major advances in high-throughput biotechnologies , large amounts of omics data have been collected to study the biological mechanisms underlying complex diseases at different levels , such as genomics , epigenomics , and transcriptomics .", "Such different types of omics data can help us unde...	[ "The development of high-throughput biotechnologies allows the collection of omics data to study the biological mechanisms underlying complex diseases at different levels , such as genomics , epigenomics , and transcriptomics .", "However , each technology is designed to collect a specific type of omics data .", ...	[ "In this research , we developed a statistical approach using a modified Fisher’s method ( denoted as Omnibus-Fisher ) to combine separate p-values of association testing for a trait and SNPs , DNA methylation markers , and RNA sequencing , calculated by kernel machine regression into an overall gene-level p-value ...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "fluorescence imaging", "statistical noise", "applied mathematics", "neuroscience", "simulation and modeling", "algorithms", "mathematics", "statistics (mathematics)", "computational neuroscience", "neuroimaging", "research and analysis methods", "gaussian noise", "imaging techniques", "an...	Multi-scale approaches for high-speed imaging and analysis of large neural populations	journal.pcbi.1005685	null	[ [ "A major goal of neuroscience is to understand interactions within large populations of neurons , including their network dynamics and emergent behavior .", "This ideally requires the observation of neural activity over large volumes .", "Recently , light-sheet microscopy and genetically encoded indic...	[ "Progress in modern neuroscience critically depends on our ability to observe the activity of large neuronal populations with cellular spatial and high temporal resolution .", "However , two bottlenecks constrain efforts towards fast imaging of large populations .", "First , the resulting large video data is ch...	[ "The voxel rate of imaging systems ultimately sets the limit on the speed of data acquisition .", "These limits often mean that only a small fraction of the activity of large neuronal populations can be observed at high spatio-temporal resolution .", "For imaging of very large populations with single cell resol...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "ecology and environmental sciences", "honey bees", "population genetics", "invertebrate genomics", "animals", "genetic mapping", "evolutionary adaptation", "population biology", "bees", "hymenoptera", "ecosystems", "animal genomics", "insects", "genetic loci", "arthro...	Two extended haplotype blocks are associated with adaptation to high altitude habitats in East African honey bees	journal.pgen.1006792	null	[ [ "Genetic adaptation to different environmental conditions is a key process in evolution and speciation .", "However , identifying the genetic variants involved in adaptation and the underlying regulatory networks and biological mechanisms by which they impact fitness is challenging .", "There are rela...	[ "Understanding the genetic basis of adaption is a central task in biology .", "Populations of the honey bee Apis mellifera that inhabit the mountain forests of East Africa differ in behavior and morphology from those inhabiting the surrounding lowland savannahs , which likely reflects adaptation to these habitats...	[ "Identifying the genes and genetic changes responsible for environmental adaptation is an important step towards understanding how species evolve .", "The honey bee Apis mellifera has adapted to a variety of habitats across its worldwide geographical distribution .", "Here we aim to identify the genetic basis o...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "cell physiology", "medicine and health sciences", "neurochemistry", "eicosanoids", "metabolic networks", "cell metabolism", "neuroscience", "metabolites", "network analysis", "genome analysis", "pharmacology", "drug metabolism", "computer and information sciences", "lipids", "genomics",...	Model-driven discovery of long-chain fatty acid metabolic reprogramming in heterogeneous prostate cancer cells	journal.pcbi.1005914	null	[ [ "Prostate cancer ( PC ) is the most commonly diagnosed non-cutaneous malignancy among Western men and accounts for the second leading cause of cancer-related death [1] .", "In the majority of cases , PC eventually becomes independent of androgens , resuming growth after androgen-deprivation therapies in a...	[ "Epithelial-mesenchymal-transition promotes intra-tumoral heterogeneity , by enhancing tumor cell invasiveness and promoting drug resistance .", "We integrated transcriptomic data for two clonal subpopulations from a prostate cancer cell line ( PC-3 ) into a genome-scale metabolic network model to explore their m...	[ "The coexistence within the same tumor of a variety of subpopulations , featuring different phenotypes ( intra-tumoral heterogeneity ) represents a challenge for diagnosis , prognosis and targeted therapies .", "In this work , we have explored the metabolic differences underlying tumor heterogeneity by building c...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "vertebrates", "social sciences", "mice", "neuroscience", "animals", "mammals", "learning and memory", "diet", "biological locomotion", "animal models", "perception", "model organisms", "cognitive psychology", "animal behavior", "nutrition", "cognition...	Reciprocal Effects on Neurocognitive and Metabolic Phenotypes in Mouse Models of 16p11.2 Deletion and Duplication Syndromes	journal.pgen.1005709	null	[ [ "Understanding the interactions between genes that determine brain activity , metabolism and behavior is crucial to decipher changes in underlying neurocognitive disorders .", "For syndromes caused by copy number variation at the 16p11 . 2 locus , causal gene discovery is particularly challenging .", ...	[ "The 16p11 . 2 600 kb BP4-BP5 deletion and duplication syndromes have been associated with developmental delay; autism spectrum disorders; and reciprocal effects on the body mass index , head circumference and brain volumes .", "Here , we explored these relationships using novel engineered mouse models carrying a...	[ "The 16p11 . 2 BP4-BP5 deletion and duplication syndromes are frequent copy number variants in humans , and are associated with developmental delay and autism spectrum disorders , with a reciprocal effect on head circumference and body mass index .", "Here we explored gene dosage effect in mouse models and found ...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infographics", "medicine and health sciences", "public policy", "geographical locations", "tropical diseases", "social sciences", "indirect costs", "sociology", "charts", "health care", "ethnicities", "north america", "political science", "welfare (social security)", "neglected tropical...	Calculation of the Average Cost per Case of Dengue Fever in Mexico Using a Micro-Costing Approach	journal.pntd.0004897	null	[ [ "Dengue fever ( DF ) is caused by infection with the dengue virus , a single-stranded positive-sense RNA virus of the Flaviviridae family [1] .", "The virus is transmitted almost exclusively by the mosquito vector Aedes aegypti , and humans are the only known reservoir for the virus [2 , 3] .", "Clini...	[ "The increasing burden of dengue fever ( DF ) in the Americas , and the current epidemic in previously unaffected countries , generate major costs for national healthcare systems .", "There is a need to quantify the average cost per DF case .", "In Mexico , few data are available on costs , despite DF being end...	[ "Dengue fever ( DF ) is caused by infection with the dengue virus , which is spread by the Aedes aegypti mosquito .", "Although the effects of DF are usually mild , in some cases serious illness and even death may result .", "The average costs per case when extrapolated to society may therefore be high , partic...	2016
[ "Introduction", "Results/Discussion", "Methods" ]	[ "biology", "computational biology", "biophysics" ]	The Role of Conserved Waters in Conformational Transitions of Q61H K-ras	journal.pcbi.1002394	null	[ [ "The role of solvent on the structure and function of proteins has been the subject of numerous previous studies [1]–[6] .", "For instance , it has been shown that waters in the dimer interface of hemoglobin play an important role in its transition between deoxy and oxy forms [7] , [8] .", "Water mole...	[ "To investigate the stability and functional role of long-residence water molecules in the Q61H variant of the signaling protein K-ras , we analyzed all available Ras crystal structures and conformers derived from a series of independent explicit solvent molecular dynamics ( MD ) simulations totaling 1 . 76 µs .", ...	[ "K-ras belongs to the Ras family of G-proteins that regulate cell proliferation and development .", "To execute its function , K-ras adopts different conformational states when it is active and inactive .", "In addition to these two states , it samples many transient intermediate conformations as it makes the t...	2012
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "helminths", "tropical diseases", "geographical locations", "parasitic diseases", "animals", "invertebrate genomics", "trematodes", "organisms", "clonorchis sinensis", "foodborne trematodiases", "neglected tropical diseases", "molecular biol...	Application of a loop-mediated isothermal amplification (LAMP) assay targeting cox1 gene for the detection of Clonorchis sinensis in human fecal samples	journal.pntd.0005995	null	[ [ "Clonorchiasis is an important human parasitic infection and is highly prevalent in eastern Asian countries , including China , Korea , and Vietnam [1 , 2] .", "In Korea , the Clonorchis sinensis egg positive rate in the general population is 1 . 9% , and approximately 1 million people are estimated to be...	[ "Clonorchiasis is prevalent in the Far East , and a major health problem in endemic areas .", "Infected persons may experience , if not treated , serious complications such as bile stone formation , pyogenic cholangitis , and even cholangiocarcinoma .", "Early diagnosis and treatment are important to prevent se...	[ "Clonorchiasis , a parasitic infection by Clonorchis sinensis , is one of the major public health problems in eastern Asian countries , including China , Korea , and Vietnam , causing cholangiocarcinoma if not treated .", "The definitive diagnosis is important for successful treatment and prevention of the infect...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetic mutation", "genome evolution", "mitosis", "telomeres", "molecular genetics", "chromosome biology", "biology", "evolutionary genetics", "mutagenesis", "genetics", "gene duplication", "genomics", "evolutionary biology", "genomic evolution", "genetics and genomics" ]	Mitotic Evolution of Plasmodium falciparum Shows a Stable Core Genome but Recombination in Antigen Families	journal.pgen.1003293	null	[ [ "Although the global burden of malaria has declined over the last few years to 216 million cases and 655 , 000 deaths in 2010 [1] , the overall goal of global eradication is still out of reach .", "Emerging resistance to artemisinin , a frontline chemotherapeutic for which resistance is not widespread , h...	[ "Malaria parasites elude eradication attempts both within the human host and across nations .", "At the individual level , parasites evade the host immune responses through antigenic variation .", "At the global level , parasites escape drug pressure through single nucleotide variants and gene copy amplificatio...	[ "Malaria is one of the six diseases that together are responsible for 90% of all infectious disease deaths throughout the world .", "The five species of Plasmodium that cause human malaria take over 655 , 000 lives each year .", "Parasites evade the immune response through antigenic variation and develop resist...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "flow cytometry", "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "evolutionary biology", "pathogens", "immunology", "population genetics", "microbiology", "dna-binding proteins", "gene pool", "dna transcription", "retroviruses", "virus...	The KAT5-Acetyl-Histone4-Brd4 axis silences HIV-1 transcription and promotes viral latency	journal.ppat.1007012	null	[ [ "The recent development of novel immunotherapeutic agents such as the bispecific dual-affinity retargeting ( DART ) antibodies that can engage a bound cytotoxic T cell to destroy an HIV-infected cell through recognizing the viral envelope proteins on the latter’s surface has fueled new optimism for finding a ...	[ "The bromodomain protein Brd4 promotes HIV-1 latency by competitively inhibiting P-TEFb-mediated transcription induced by the virus-encoded Tat protein .", "Brd4 is recruited to the HIV LTR by interactions with acetyl-histones3 ( AcH3 ) and AcH4 .", "However , the precise modification pattern that it reads and ...	[ "A major impediment to the cure of HIV/AIDS is the viral latency .", "Previous studies have identified the bromodomain protein Brd4 as a promoter of HIV latency by binding to the viral LTR to inhibit Tat-induced transcription .", "Here , we discover that the LTR of latent HIV has low acetylated histone H3 ( AcH...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biotechnology", "transgenic plants", "plant biology", "botany", "anatomy and physiology", "histology", "plant science", "plant morphology", "plant pathology", "genetically modified organisms", "biology", "agriculture", "physiology", "plant pathogens", "molecular cell biology", "plant ...	Feeding Cells Induced by Phytoparasitic Nematodes Require γ-Tubulin Ring Complex for Microtubule Reorganization	journal.ppat.1002343	null	[ [ "Root-knot nematodes ( RKN ) Meloidogyne spp .", "are minuscule worms which are widespread in the soil .", "They are obligate sedentary phyto-endoparasites known to infect above 3000 plant species .", "In the course of a compatible interaction , the nematodes of the genera Meloidogyne are able to ...	[ "Reorganization of the microtubule network is important for the fast isodiametric expansion of giant-feeding cells induced by root-knot nematodes .", "The efficiency of microtubule reorganization depends on the nucleation of new microtubules , their elongation rate and activity of microtubule severing factors .",...	[ "Among plant pathogens , sedentary endoparasitic nematodes are one of the most damaging pests in global agriculture .", "Nematodes are greatly resistant due to a broad physiological variability , consequently difficult to fight against .", "The use of pesticides is highly pollutant to the environment and theref...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Structures of B-Lymphotropic Polyomavirus VP1 in Complex with Oligosaccharide Ligands	journal.ppat.1003714	null	[ [ "The B-Lymphotropic Polyomavirus ( LPyV ) was originally isolated from African Green Monkey lymph node cultures [1] and attracted interest because of its narrow tropism for the human B-lymphoblastoid tumor cell line BJA-B .", "In addition , significant antibody binding to LPyV was observed in human sera ,...	[ "B-Lymphotropic Polyomavirus ( LPyV ) serves as a paradigm of virus receptor binding and tropism , and is the closest relative of the recently discovered Human Polyomavirus 9 ( HPyV9 ) .", "LPyV infection depends on sialic acid on host cells , but the molecular interactions underlying LPyV-receptor binding were u...	[ "Viruses must engage specific receptors on host cells in order to initiate infection .", "The type of receptor and its concentration on cells determine viral spread and tropism , but for many viruses , the receptor and the mode of recognition by the virus are not known .", "We have characterized the structural ...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "united states", "invertebrates", "medicine and health sciences", "body fluids", "chikungunya infection", "geographical locations", "saliva", "animals", "north america", "caribbean", "insect vectors", "guadeloupe", "infectious diseases", "south america", "epidemiology", "brazil", "di...	Differential Susceptibilities of Aedes aegypti and Aedes albopictus from the Americas to Zika Virus	journal.pntd.0004543	null	[ [ "Zika virus ( ZIKV; family Flaviviridae , genus Flavivirus ) was first isolated from a sentinel rhesus monkey in the Zika forest of Uganda in 1947 [[1]] .", "Since then , it has emerged outside of its natural range of distribution , Africa and Asia: Yap Island ( Micronesia ) in 2007 [2] , French Polynesia...	[ "Since the major outbreak in 2007 in the Yap Island , Zika virus ( ZIKV ) causing dengue-like syndromes has affected multiple islands of the South Pacific region .", "In May 2015 , the virus was detected in Brazil and then spread through South and Central America .", "In December 2015 , ZIKV was detected in Fre...	[ "Zika virus ( ZIKV ) is an emerging mosquito-borne arbovirus causing dengue-like symptoms .", "This virus was commonly detected in Africa and Asia .", "Since its emergence in Yap Island in Micronesia in 2007 , ZIKV reemerged in the South Pacific region in 2013 and ultimately reached the American continent in 20...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biophysics", "biology", "computational biology" ]	Assembly of Nsp1 Nucleoporins Provides Insight into Nuclear Pore Complex Gating	journal.pcbi.1003488	null	[ [ "Nuclear pore complexes ( NPCs ) are large protein assemblies embedded in the nuclear membrane that provide the only conduit for exchange of molecules between cytoplasm and nucleoplasm , a process defined as nucleocytoplasmic transport ( NCT ) .", "While the membrane bound nucleus of a eukaryotic cell pro...	[ "Nuclear pore complexes ( NPCs ) form gateways for material transfer across the nuclear envelope of eukaryotic cells .", "Disordered proteins , rich in phenylalanine-glycine repeat motifs ( FG-nups ) , form the central transport channel .", "Understanding how nups are arranged in the interior of the NPC may exp...	[ "Cells of higher life forms separate their genomes from the rest of the cell in a nucleus that surrounds the genome by a nuclear envelope .", "Hundreds of pores , each a complex made of many proteins , assure traffic into and out of the nucleus through highly selective transport: small biomolecules can pass unhin...	2014
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma mansoni", "schoolchildren", "medicine and health sciences", "education", "helminths", "sociology", "tropical diseases", "social sciences", "diet", "parasitic diseases", "physical activity", "animals", "health care", "nutrition", "neglected...	Diet and hygiene practices influence morbidity in schoolchildren living in Schistosomiasis endemic areas along Lake Victoria in Kenya and Tanzania—A cross-sectional study	journal.pntd.0006373	null	[ [ "Schistosomiasis , also known as bilharzia , is an infectious disease caused by parasitic flatworms of the genus Schistosoma .", "Schistosomiasis is considered as one of the Neglected Tropical Diseases ( NTDs ) and is estimated to affect at least 230 million people annually [1] with a majority in sub-Saha...	[ "Since 2011 , cohorts of schoolchildren in regions bordering Lake Victoria in Kenya and Tanzania have been investigated for morbidity caused by Schistosoma mansoni infection .", "Despite being neighbouring countries with similar lifestyles and ecological environments , Tanzanian schoolchildren had lower S . manso...	[ "Millions of school-age children in Kenya and Tanzania are at risk for infection with Schistosoma mansoni , which has an impact on their physical health .", "A total of 490 schoolchildren ( 163 from Kenya and 327 from Tanzania ) aged 9–11 years living along the shores of Lake Victoria in Kenya and Tanzania provid...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "social sciences", "neuroscience", "surgical and invasive medical procedures", "visual acuity", "health care", "regression analysis", "optical properties", "mathematics", "statistics (mathematics)", "materials science", "vision", "eyes", "research and analys...	Impact of Trichiasis Surgery on Quality of Life: A Longitudinal Study in Ethiopia	journal.pntd.0004627	null	[ [ "Trachoma , an eye disease caused by Chlamydia trachomatis , is the leading infectious cause of blindness worldwide [1] .", "The infection can lead to progressive conjunctival scarring and subsequently trachomatous trichiasis , the in-turning of eyelashes .", "Trichiasis in turn can cause constant pai...	[ "Trachomatous trichiasis significantly reduces vision and health related quality of life ( QoL ) .", "Although trichiasis surgery is widely performed to treat trichiasis , there is little data on the effect of surgery on QoL .", "We measured the impact of trichiasis surgery on vision and health related QoL in a...	[ "We previously reported that Trachomatous Trichiasis ( TT ) has a profound impact on vision and heath related quality of life ( QoL ) , even when vision is not impaired .", "The World Health Organization ( WHO ) recommends corrective eyelid surgery for trichiasis to reduce the risk of vision loss .", "However ,...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "invertebrate genomics", "animals", "animal models", "drosophila melanogaster", "model organisms", "mathematics", "materials science", "experimental organism systems", "epigenetics", "dna", "dna structure", "macromolecules", "structural genomics", "chromatin", "drosoph...	A maximum-entropy model for predicting chromatin contacts	journal.pcbi.1005956	null	[ [ "In higher-complexity organisms , the packaged molecule of DNA inside the nucleus of a cell consists not only of the DNA polymer but also a large number of DNA-associated protein and RNA complexes that together form what is known as chromatin .", "These complexes bind to the DNA by either sequence affinit...	[ "The packaging of DNA inside a nucleus shows complex structure stabilized by a host of DNA-bound factors .", "Both the distribution of these factors and the contacts between different genomic locations of the DNA can now be measured on a genome-wide scale .", "This has advanced the development of models aimed a...	[ "The three-dimensional folding of DNA inside the nucleus into specific conformations is necessary for the proper functioning of cells .", "These structures can be measured by chromosome conformation capture methods ( Hi-C ) that report the number of times that each pair of genomic sites are found in proximal loca...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell physiology", "fish", "medicine and health sciences", "vesicles", "ocular anatomy", "vertebrates", "social sciences", "neuroscience", "animals", "animal models", "osteichthyes", "membrane fusion", "model organisms", "experimental organism systems", "cellular structures and organelle...	Loss-of-function of the ciliopathy protein Cc2d2a disorganizes the vesicle fusion machinery at the periciliary membrane and indirectly affects Rab8-trafficking in zebrafish photoreceptors	journal.pgen.1007150	null	[ [ "Ciliopathies are an expanding group of human disorders caused by primary cilium dysfunction and unified by a wide array of overlapping phenotypes: cystic kidneys , central nervous system malformations and retinal degeneration among others [1–3] .", "Primary cilia are ubiquitous organelles that consist of...	[ "Ciliopathies are human disorders caused by dysfunction of primary cilia , ubiquitous organelles involved in transduction of environmental signals such as light sensation in photoreceptors .", "Concentration of signal detection proteins such as opsins in the ciliary membrane is achieved by RabGTPase-regulated pol...	[ "Ciliopathies are human disorders caused by dysfunction of primary cilia , ubiquitous organelles involved in transduction of environmental signals to the cells .", "Concentration and regulation of signal detection proteins in the ciliary membrane is therefore tightly regulated through polarized vesicle traffickin...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "neuroscience/theoretical neuroscience", "neuroscience/sensory systems" ]	Analyzing Short-Term Noise Dependencies of Spike-Counts in Macaque Prefrontal Cortex Using Copulas and the Flashlight Transformation	journal.pcbi.1000577	null	[ [ "So far , it is still unknown which statistics are crucial for analysis in order to understand the neural code .", "One approach is to analyze simultaneous spike-counts of neural populations .", "Responses from populations of sensory neurons vary even when the same stimulus is presented repeatedly , a...	[ "Simultaneous spike-counts of neural populations are typically modeled by a Gaussian distribution .", "On short time scales , however , this distribution is too restrictive to describe and analyze multivariate distributions of discrete spike-counts .", "We present an alternative that is based on copulas and can...	[ "The brain has an enormous number of neurons that do not work alone but in an ensemble .", "Yet , mostly individual neurons were measured in the past and therefore models were restricted to independent neurons .", "With the advent of new multi-electrode techniques , however , it becomes possible to measure a gr...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "sequencing techniques", "medicine and health sciences", "immune cells", "gene regulation", "metabolic processes", "immediate early genes", "immunology", "dna transcription", "gene types", "sequence motif analysis", "molecular biology techniques", "research and analysis method...	Ups and Downs of Poised RNA Polymerase II in B-Cells	journal.pcbi.1004821	null	[ [ "Transcription of protein-coding genes by RNA polymerase II ( Pol II ) is a complex , multistep process [1–5] .", "Potentially each of the transcription steps such as polymerase II recruitment , pre-initiation complex ( PIC ) assembly , open complex formation , promoter escape , pausing , elongation , and...	[ "Recent genome-wide analyses have uncovered a high accumulation of RNA polymerase II ( Pol II ) at the 5′ end of genes .", "This elevated Pol II presence at promoters , referred to here as Poll II poising , is mainly ( but not exclusively ) attributed to temporal pausing of transcription during early elongation w...	[ "Accumulation of RNA polymerase II ( Pol II ) in the promoter proximal region has been proposed to be important for rapid gene activation , but the full regulatory role of Pol II dynamics is yet to be delineated .", "Defining polymerase poising as a significant enrichment of accumulation of Pol II near the promot...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "nucleic acids", "dna", "biology", "dna repair" ]	Increased RPA1 Gene Dosage Affects Genomic Stability Potentially Contributing to 17p13.3 Duplication Syndrome	journal.pgen.1002247	null	[ [ "Variously sized contiguous deletions within 17p13 . 3-pter are associated with complex clinical features in humans including structural brain abnormalities ( lissencephaly , agyria , microcephaly ) , growth retardation and developmental delay [1] .", "Multiple pathogenomic studies have identified haploin...	[ "A novel microduplication syndrome involving various-sized contiguous duplications in 17p13 . 3 has recently been described , suggesting that increased copy number of genes in 17p13 . 3 , particularly PAFAH1B1 , is associated with clinical features including facial dysmorphism , developmental delay , and autism spe...	[ "The widespread use of genomic array technology has lead to the identification of a plethora of novel human genomic disorders .", "These complex conditions occur as a consequence of structural genomic alterations ( deletions , amplifications , complex rearrangements ) .", "Understanding the specific consequence...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "computational biology/population genetics", "genetics and genomics/genetics of the immune system", "evolutionary biology/human evolution", "immunology/genetics of the immune system", "genetics and genomics/population genetics" ]	Absence of Evidence for MHC–Dependent Mate Selection within HapMap Populations	journal.pgen.1000925	null	[ [ "The MHC locus contains genes central to acquired immunity , as well as numerous olfactory receptors [1] .", "It is reported to influence mate selection in a number of vertebrates , and is thought to act through the sense of smell to favor genetic dissimilarity between parents and thus heterozygosity in o...	[ "The major histocompatibility complex ( MHC ) of immunity genes has been reported to influence mate choice in vertebrates , and a recent study presented genetic evidence for this effect in humans .", "Specifically , greater dissimilarity at the MHC locus was reported for European-American mates ( parents in HapMa...	[ "There is evidence in numerous species that genes involved in immunity influence mate choice .", "Factors like body odor may subconsciously favor partners with different immunity alleles , to avoid inbreeding and/or endow offspring with broad resistance to pathogens .", "A previous study , based on HapMap genot...	2010
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "t helper cells", "medicine and health sciences", "immune cells", "enzyme-linked immunoassays", "pathology and laboratory medicine", "respiratory infections", "immunology", "cloning", "pulmonology", "animal models", "model organisms", "signs and symptoms", "experimental orga...	Coincident airway exposure to low-potency allergen and cytomegalovirus sensitizes for allergic airway disease by viral activation of migratory dendritic cells	journal.ppat.1007595	null	[ [ "It is common knowledge in the allergy field that viral respiratory infections and allergic airway diseases ( AADs ) , for instance allergic asthma , can interdepend [1 , 2] .", "In principle , mutual interference may aggravate or dampen either of these medical entities .", "While few publications rep...	[ "Despite a broad cell-type tropism , cytomegalovirus ( CMV ) is an evidentially pulmonary pathogen .", "Predilection for the lungs is of medical relevance in immunocompromised recipients of hematopoietic cell transplantation , in whom interstitial CMV pneumonia is a frequent and , if left untreated , fatal clinic...	[ "From an epidemiological perspective , natural host-to-host transmission of human CMV mostly occurs in early childhood through saliva from virus-shedding intimate contact persons , such as family members or peers .", "The oronasal route of transmission involves also the airway mucosa and airway-draining lymph nod...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "gene expression", "genetics", "epigenetics", "biology", "molecular cell biology" ]	FGF Signalling Regulates Chromatin Organisation during Neural Differentiation via Mechanisms that Can Be Uncoupled from Transcription	journal.pgen.1003614	null	[ [ "Differentiation is directed by extrinsic signals that regulate expression of transcription factors , which determine cell fates .", "A further critical level of regulation is provided by so-called higher order chromatin organisation , which includes changes in local chromatin compaction and nuclear posit...	[ "Changes in higher order chromatin organisation have been linked to transcriptional regulation; however , little is known about how such organisation alters during embryonic development or how it is regulated by extrinsic signals .", "Here we analyse changes in chromatin organisation as neural differentiation pro...	[ "Changes in the position of genes within the nucleus and in their local organisation frequently correlate with whether or not genes are turned on .", "However , little is known about how such nuclear organisation is controlled and whether this can be separated from the mechanisms that promote transcription .", ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	A Large-Scale Functional Analysis of Putative Target Genes of Mating-Type Loci Provides Insight into the Regulation of Sexual Development of the Cereal Pathogen Fusarium graminearum	journal.pgen.1005486	null	[ [ "Fusarium graminearum , a homothallic ( self-fertile ) ascomycetous fungus , causes serious diseases ( e . g . , Fusarium head blight ) in major cereal crops , and produces several mycotoxins in diseased cereals [1] .", "Recently , this species was defined as a member of the F . graminearum species comple...	[ "Fusarium graminearum , the causal agent of Fusarium head blight in cereal crops , produces sexual progeny ( ascospore ) as an important overwintering and dissemination strategy for completing the disease cycle .", "This homothallic ascomycetous species does not require a partner for sexual mating; instead , it c...	[ "The production of sexual propagules via a self-fertile mating strategy in Fusarium graminearum , an important cereal pathogen , is essential for overwintering and dissemination during the recurrent disease cycle caused by this fungus .", "Genome-wide microarray analyses allow the identification of gene sets that...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "cell death", "basic cancer research", "signaling in selected disciplines", "gene function", "oncology", "tyrosine kinase signaling cascade", "signaling in cellular processes", "oncogenic signaling", "ras signaling", "biology", "antiapoptotic signaling", "molecular biology", "s...	Drosophila Activated Cdc42 Kinase Has an Anti-Apoptotic Function	journal.pgen.1002725	null	[ [ "Activated Cdc42 kinases ( Acks ) are non-receptor tyrosine kinases that are evolutionarily conserved .", "The founding member of this family is human ACK1 , which was identified as a protein that binds to CDC42 in its active GTP bound form [1] .", "Since this discovery Ack homologs have been found in...	[ "Activated Cdc42 kinases ( Acks ) are evolutionarily conserved non-receptor tyrosine kinases .", "Activating somatic mutations and increased ACK1 protein levels have been found in many types of human cancers and correlate with a poor prognosis .", "ACK1 is activated by epidermal growth factor ( EGF ) receptor s...	[ "A number of recent studies have uncovered an involvement of Ack family members in human cancer .", "The majority of these studies focus on human ACK1 and suggest that ACK1 regulates diverse cancer-relevant biological functions , including stimulation of proliferation , blocking programmed cell death , and enhanc...	2012
[ "Introduction", "Results", "Materials and methods", "Discussion" ]	[ "cell physiology", "enzymes", "metabolic networks", "enzymology", "cell metabolism", "phosphatases", "metabolomics", "metabolites", "network analysis", "thermodynamics", "computer and information sciences", "proteins", "metabolic pathways", "gene expression", "adenosine triphosphatase", ...	Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models	journal.pcbi.1007036	null	[ [ "The turnover rates of metabolites through a pathway are called fluxes , and genome-wide intracellular metabolic fluxes are the ultimate regulator of cellular physiology .", "Perturbations on the normal physiology , such as those that occur in a disease state , directly influence the metabolic fluxes .", ...	[ "The ever-increasing availability of transcriptomic and metabolomic data can be used to deeply analyze and make ever-expanding predictions about biological processes , as changes in the reaction fluxes through genome-wide pathways can now be tracked .", "Currently , constraint-based metabolic modeling approaches ...	[ "The recent advances in omics technologies have provided us with an unprecedented abundance of data spanning genomes , global gene expression , and metabolomes .", "Though these advancements in high-throughput data collection offer an excellent opportunity for a more thorough understanding of metabolic capacities...	2019
[ "Introduction", "Results", "Discussion", "Models and methods" ]	[ "relaxation time", "coenzymes", "enzymes", "metabolic networks", "enzymology", "systems science", "mathematics", "metabolites", "network analysis", "enzyme metabolism", "enzyme chemistry", "relaxation (physics)", "computer and information sciences", "proteins", "metabolic pathways", "d...	Metabolic dynamics restricted by conserved carriers: Jamming and feedback	journal.pcbi.1005847	null	[ [ "In recent decades , mathematical modeling of metabolic systems has been intensively explored in the field of systems biology [1–6] .", "Several studies have demonstrated that metabolic systems can be quantitatively predicted using mathematical models [7–10] .", "A particularly important feature for t...	[ "To uncover the processes and mechanisms of cellular physiology , it first necessary to gain an understanding of the underlying metabolic dynamics .", "Recent studies using a constraint-based approach succeeded in predicting the steady states of cellular metabolic systems by utilizing conserved quantities in the ...	[ "Although a metabolic shift is essential for the adaptation of cells or organisms to environmental changes , the transient behaviors of metabolic systems are poorly understood .", "When describing the time development of metabolic systems , there are several conserved quantities to consider due to balances of met...	2017
[ "Introduction", "Results", "Discussion" ]	[]	A Critical Role for the Hippocampus in the Valuation of Imagined Outcomes	journal.pbio.1001684	Converging evidence from neuroimaging and clinical data demonstrates the important involvement of the hippocampus in finding the motivation to pursue goals that we need to imagine because they are not within sight.	[ [ "Would you prefer a can of beer today or a bottle of champagne in one week ?", "Intertemporal choices , involving trade-offs between short-term and long-term outcomes , are pervasive in everyday life .", "The propensity to favor short-term pleasures defines a form of impulsivity that may have dramatic...	[ "Many choice situations require imagining potential outcomes , a capacity that was shown to involve memory brain regions such as the hippocampus .", "We reasoned that the quality of hippocampus-mediated simulation might therefore condition the subjective value assigned to imagined outcomes .", "We developed a n...	[ "Economic theory assumes that we assign some sort of value to options that are presented to us in order to choose between them .", "In neuroscience , evidence suggests that memory brain regions , such as the hippocampus , are involved in imagining novel situations .", "We therefore hypothesized that the hippoca...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Examining the Evolution of the Regulatory Circuit Controlling Secondary Metabolism and Development in the Fungal Genus Aspergillus	journal.pgen.1005096	null	[ [ "Filamentous fungi produce diverse repertoires of small molecules known as secondary metabolites ( SMs ) [1] .", "SMs include widely used pharmaceuticals such the antibiotic penicillin [2] , the cholesterol-reducing drug lovastatin [3] , and the immunosuppressant cyclosporin [4] , as well as potent mycoto...	[ "Filamentous fungi produce diverse secondary metabolites ( SMs ) essential to their ecology and adaptation .", "Although each SM is typically produced by only a handful of species , global SM production is governed by widely conserved transcriptional regulators in conjunction with other cellular processes , such ...	[ "Filamentous fungi produce a highly diverse cadre of secondary metabolites , small molecules whose potent toxic activities are integral to the fungal lifestyle .", "Most secondary metabolites are narrowly taxonomically distributed , whereas the transcriptional regulators that control their production , alongside ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "biology" ]	Blockade of Pachytene piRNA Biogenesis Reveals a Novel Requirement for Maintaining Post-Meiotic Germline Genome Integrity	journal.pgen.1003038	null	[ [ "Piwi-interacting RNAs ( piRNAs ) are a diverse class of gonad-specific small interfering RNAs that bind to members of the Piwi subfamily of Argonaute proteins .", "One common function of piRNAs in all species studied so far is the silencing of transposable elements , which is essential for the protection...	[ "Piwi-interacting RNAs are a diverse class of small non-coding RNAs implicated in the silencing of transposable elements and the safeguarding of genome integrity .", "In mammals , male germ cells express two genetically and developmentally distinct populations of piRNAs at the pre-pachytene and pachytene stages o...	[ "Small non-coding RNAs play critical roles during development and in disease .", "The integrity of the germline genome is of paramount importance to the wellbeing of offspring and the survival of species .", "Piwi-interacting RNAs ( piRNAs ) are a class of small non-coding RNAs abundantly expressed in the gonad...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "protein transport", "sequencing techniques", "cell processes", "dna-binding proteins", "materials science", "molecular biology techniques", "materials by structure", "research and analysis methods", "amino acid analysis", "proteins", "biological databases", "proteomics", "recombinant protei...	Single-molecule protein identification by sub-nanopore sensors	journal.pcbi.1005356	null	[ [ "When Church et al . [1] proposed to use nanopores for sequencing biopolymers , they had envisioned both DNA and proteins sequencing .", "However , the progress in protein sequencing turned out to be much slower since it is more difficult to force proteins through a pore systematically and measure the res...	[ "Recent advances in top-down mass spectrometry enabled identification of intact proteins , but this technology still faces challenges .", "For example , top-down mass spectrometry suffers from a lack of sensitivity since the ion counts for a single fragmentation event are often low .", "In contrast , nanopore t...	[ "Protein identification is the key step in many proteomics studies .", "Currently , the most popular technique for intact protein analysis is top-down mass spectrometry which recently enabled high-throughput identification of many proteins and their proteoforms .", "However , this approach requires large amount...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/genomics", "genetics and genomics/animal genetics", "genetics and genomics/gene expression", "genetics and genomics/genome projects", "genetics and genomics" ]	High-Resolution Mapping of Gene Expression Using Association in an Outbred Mouse Stock	journal.pgen.1000149	null	[ [ "Quantitative trait locus ( QTL ) analysis has been the primary tool for geneticists to study complex genetic traits in experimental organisms .", "However , while such QTL mapping has great power to identify loci controlling the traits , resolution of mapping is usually quite low and as a result few cand...	[ "Quantitative trait locus ( QTL ) analysis is a powerful tool for mapping genes for complex traits in mice , but its utility is limited by poor resolution .", "A promising mapping approach is association analysis in outbred stocks or different inbred strains .", "As a proof of concept for the association approa...	[ "In rodents , as in humans , traits such as obesity or diabetes are under the influence of many genes spread throughout the genome .", "Using linkage analysis , the locations of the major contributing genes can be mapped only to very large regions of chromosomes , usually encompassing hundreds of genes .", "Thi...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/genomics", "genetics and genomics/microbial evolution and genomics", "genetics and genomics/comparative genomics", "genetics and genomics/gene expression", "genetics and genomics/functional genomics" ]	Variations in Stress Sensitivity and Genomic Expression in Diverse S. cerevisiae Isolates	journal.pgen.1000223	null	[ [ "A major focus of genetic study is to elucidate the effects of genetic variation on", "phenotypic diversity .", "The evolution of phenotypes is often driven by environmental", "factors and the interactions between each organism and its environment .", "Recently ,", "there has been a renewe...	[ "Interactions between an organism and its environment can significantly influence", "phenotypic evolution .", "A first step toward understanding this process is to", "characterize phenotypic diversity within and between populations .", "We explored", "the phenotypic variation in stress sensitivity and gen...	[ "Much attention has been given to the ways in which organisms evolve new", "phenotypes and the influence of the environment on this process .", "A major focus", "of study is defining the genetic basis for phenotypes important for organismal", "fitness .", "As a first step toward this goal , we surveyed ph...	2008
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biomacromolecule-ligand interactions", "biochemistry", "enzyme structure", "proteins", "enzymes", "biology and life sciences", "enzymology", "biophysics" ]	Structural Basis for the Ubiquitin-Linkage Specificity and deISGylating Activity of SARS-CoV Papain-Like Protease	journal.ppat.1004113	null	[ [ "Ubiquitin ( Ub ) , a 76-amino-acid protein , is the building block for a set of versatile , post-translational modifications that regulate a number of cellular pathways , including many processes associated with combating viral infection [1] .", "Through the action of activating and conjugating enzymes ,...	[ "Severe acute respiratory syndrome coronavirus ( SARS-CoV ) encodes a papain-like protease ( PLpro ) with both deubiquitinating ( DUB ) and deISGylating activities that are proposed to counteract the post-translational modification of signaling molecules that activate the innate immune response .", "Here we exami...	[ "All coronaviruses such as the SARS virus and the recently identified Middle East Respiratory Syndrome ( MERS ) virus encode in their genomes at least one papain-like protease ( PLpro ) enzyme that has two distinct functions in viral pathogenesis .", "The first function is to process the viral polyprotein into in...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology/viral replication and gene regulation", "molecular biology/translation mechanisms", "molecular biology/mrna stability", "oncology/myelomas and lymphoproliferative diseases", "virology/mechanisms of resistance and susceptibility, including host genetics", "infectious diseases/viral infections", ...	MicroRNA Antagonism of the Picornaviral Life Cycle: Alternative Mechanisms of Interference	journal.ppat.1000820	null	[ [ "MicroRNAs ( miRNAs ) are a class of small , ∼22 nt regulatory RNAs that modulate a diverse array of cellular activities .", "Through recognition of sequence complementary target elements found most often in the 3′UTR of cellular mRNAs , miRNAs post-transcriptionally regulate numerous cellular processes b...	[ "In addition to modulating the function and stability of cellular mRNAs , microRNAs can profoundly affect the life cycles of viruses bearing sequence complementary targets , a finding recently exploited to ameliorate toxicities of vaccines and oncolytic viruses .", "To elucidate the mechanisms underlying microRNA...	[ "Virus host range is shaped by cellular determinants such as transcription factors and receptor expression .", "In addition , we have previously shown that tissue-specific microRNAs can be utilized to direct the specificity of a replication competent picornavirus , Coxsackievirus A21 .", "In this report , we de...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "evolutionary biology" ]	Increased Transmission of Mutations by Low-Condition Females: Evidence for Condition-Dependent DNA Repair	journal.pbio.0060030	When female flies were inseminated with mutagenized sperm, the resulting offspring were 30% more likely to carry a lethal mutation if the female was in low rather than high condition.	[ [ "Germ-line mutation is the ultimate source of heritable variation , but the vast majority of new mutations affecting fitness are deleterious .", "The unremitting presence of deleterious mutations causes a reduction in mean fitness , a phenomenon known as mutation load .", "Mutation load can be substan...	[ "Evidence is mounting that mutation rates are sufficiently high for deleterious alleles to be a major evolutionary force affecting the evolution of sex , the maintenance of genetic variation , and many other evolutionary phenomena .", "Though point estimates of mutation rates are improving , we remain largely ign...	[ "A variety of evolutionary phenomena are affected by the rate at which mutations enter a population and how those mutations are distributed amongst individuals .", "Although it is typically assumed that mutations occur randomly among individuals , this may not be the case .", "Individuals in poor condition may ...	2008
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "geomorphology", "medicine and health sciences", "clinical laboratory sciences", "pathology and laboratory medicine", "landforms", "pathogens", "topography", "geographical locations", "microbiology", "neurorehabilitation", "census", "health care", "retroviruses", "viruses", "north americ...	Temporal trends in Human T-Lymphotropic virus 1 (HTLV-1) associated myelopathy/tropical spastic paraparesis (HAM/TSP) incidence in Martinique over 25 years (1986-2010)	journal.pntd.0006304	null	[ [ "Human T-lymphotropic virus type 1 ( HTLV-1 ) is associated with many diseases including HTLV-1-associated myelopathy/tropical spastic paraparesis ( HAM/TSP ) .", "It is estimated that about 10–20 million people are infected with HTLV-1 throughout the world [1] .", "Whereas HTLV-1 seroprevalence is un...	[ "Human T-lymphotropic virus type 1 ( HTLV-1 ) has been discovered in 1980 and has been linked to tropical spastic paraparesis ( HAM/TSP ) in 1985 in Martinique .", "There is no data on HAM/TSP incidence trends .", "We report , in the present work , the temporal trends incidence of HAM/TSP in Martinique over 25 ...	[ "Human T-lymphotropic virus type 1 ( HTLV-1 ) was discovered in 1980 and HTLV-1-associated myelopathy/tropical spastic paraparesis ( HAM/TSP ) was described five years later in 1985 .", "HAM/TSP is a progressive disabling disorder characterized by spastic paraparesis with bladder and bowel dysfunction that consti...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "animal models", "cancer genetics", "model organisms", "genetic polymorphism", "gene expression", "genetics", "gene regulation", "biology and life sciences", "population genetics", "molecular genetics", "genomics", "evolutionary biology", "mouse models", "genetics of disease", "dna trans...	Mouse Pulmonary Adenoma Susceptibility 1 Locus Is an Expression QTL Modulating Kras-4A	journal.pgen.1004307	null	[ [ "The Pulmonary adenoma susceptibility 1 ( Pas1 ) locus , mapping in the distal region of chromosome 6 , is the major modulator of lung tumor susceptibility in mice [1] , [2] .", "In inbred mouse strains , the Pas1 locus has a conserved haplotype consisting of six genes clustered in a ∼450-kb region [3] ."...	[ "Pulmonary adenoma susceptibility 1 ( Pas1 ) is the major locus responsible for lung tumor susceptibility in mice; among the six genes mapping in this locus , Kras is considered the best candidate for Pas1 function although how it determines tumor susceptibility remains unknown .", "In an ( A/J×C57BL/6 ) F4 inter...	[ "A person's risk of developing cancer depends on both genetic and environmental factors .", "To study the genetic predisposition to cancer without the influence of environmental variables , scientists study mice treated with urethane , a chemical carcinogen that induces lung tumors .", "By crossing inbred ( gen...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "mathematics", "caenorhabditis", "computational biology", "drosophila", "saccharomyces" ]	Where Have All the Interactions Gone? Estimating the Coverage of Two-Hybrid Protein Interaction Maps	journal.pcbi.0030214	null	[ [ "Maps of pairwise protein–protein interactions are being generated in increasing numbers by the two-hybrid method [1] .", "Genome-scale two-hybrid screens have now been conducted for Saccharomyces cerevisiae ( yeast ) [2 , 3] , Caenorhabditis elegans ( worm ) [4] , and Drosophila melanogaster ( fly ) [5] ...	[ "Yeast two-hybrid screens are an important method for mapping pairwise physical interactions between proteins .", "The fraction of interactions detected in independent screens can be very small , and an outstanding challenge is to determine the reason for the low overlap .", "Low overlap can arise from either a...	[ "The genome sequence of an organism provides a parts list of proteins , but not an instruction manual for assembling the parts into a cell .", "Assembly instructions now come from experiments such as two-hybrid screens that detect physical interactions between pairs of proteins .", "Defining the resources requi...	2007
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "cingulate cortex", "medicine and health sciences", "diagnostic radiology", "functional magnetic resonance imaging", "data acquisition", "engineering and technology", "signal processing", "brain", "neuroscience", "magnetic resonance imaging", "brain mapping", "neuroimaging", "research and an...	Multiregional integration in the brain during resting-state fMRI activity	journal.pcbi.1005410	null	[ [ "Data-driven models constrained with functional magnetic resonance imaging ( fMRI ) data can elucidate some of the dependencies that involve a combination of multiple brain regions underlying the observed activity .", "Previous studies show that the activity in some brain regions during resting-state fMRI...	[ "Data-driven models of functional magnetic resonance imaging ( fMRI ) activity can elucidate dependencies that involve the combination of multiple brain regions .", "Activity in some regions during resting-state fMRI can be predicted with high accuracy from the activities of other regions .", "However , it rema...	[ "Models of fMRI activity can elucidate underlying dependencies that involve the combination of multiple brain regions .", "However , it remains unclear in which regions activity depends on unique integration of multiple predictor regions .", "To address this question , sparse ( parsimonious ) models could serve...	2017
[ "Introduction", "Results/Discussion", "Material and Methods" ]	[ "evolutionary biology", "genetics and genomics/population genetics" ]	The Evolutionary Dynamics of the Lion Panthera leo Revealed by Host and Viral Population Genomics	journal.pgen.1000251	null	[ [ "Lion fossils trace to the Late Pliocene in Eastern Africa and the Early Pleistocene in Eastern and Southern Africa coincident with the flourishing of grasslands ∼2–1 . 5 million years ago [1] , [2] .", "By Mid Pleistocene ( ∼500 , 000 years ago ) , lions occupied Europe and by the Late Pleistocene ( ∼130...	[ "The lion Panthera leo is one of the world's most charismatic carnivores and is one of Africa's key predators .", "Here , we used a large dataset from 357 lions comprehending 1 . 13 megabases of sequence data and genotypes from 22 microsatellite loci to characterize its recent evolutionary history .", "Patterns...	[ "The lion Panthera leo , a formidable carnivore with a complex cooperative social system , has fascinated humanity since pre-historical times , inspiring hundreds of religious and cultural allusions .", "Here , we use a comprehensive sample of 357 individuals from most of the major lion populations in Africa and ...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The QTL within the H2 Complex Involved in the Control of Tuberculosis Infection in Mice Is the Classical Class II H2-Ab1 Gene	journal.pgen.1005672	null	[ [ "Tuberculosis ( TB ) remains a significant public health problem: one-third of the human population is infected with Mycobacterium tuberculosis ( MTB ) and 10% of those are at a risk of developing overt TB during their lifetime [1 , 2] .", "Although there is growing body of evidence that the outcome of in...	[ "The level of susceptibility to tuberculosis ( TB ) infection depends upon allelic variations in numerous interacting genes .", "In our mouse model system , the whole-genome quantitative trait loci ( QTLs ) scan revealed three QTLs involved in TB control on chromosomes 3 , 9 , and in the vicinity of the H2 comple...	[ "Many genes of the host regulate interactions with Mycobacterium tuberculosis and determine the level of susceptibility to , and severity of , tuberculosis ( TB ) .", "Identification of these genes and their alleles is continuing and contributes new knowledge about the host-pathogen interactions .", "So far , f...	2015
[ "Introduction", "Results/Discussion", "Methods" ]	[ "animal genetics", "heredity", "genetics", "animal management", "biology", "quantitative traits", "genetic determinism", "genetics and genomics", "agriculture" ]	A Missense Mutation in PPARD Causes a Major QTL Effect on Ear Size in Pigs	journal.pgen.1002043	null	[ [ "The external ear is part of the auditory system and plays a vital role in collecting sound as the first step in hearing .", "Multiple congenital anomalies have been documented for human external ears .", "For instance , microtia , characterized by a small and abnormally shaped outer ear , occurs in a...	[ "Chinese Erhualian is the most prolific pig breed in the world .", "The breed exhibits exceptionally large and floppy ears .", "To identify genes underlying this typical feature , we previously performed a genome scan in a large scale White Duroc × Erhualian cross and mapped a major QTL for ear size to a 2-cM r...	[ "A central but challenging objective in current biology is to dissect the genetic basis of quantitative traits .", "Numerous quantitative trait loci ( QTL ) have been uncovered in model and farm animals , providing unexpected insights into the biology of complex traits .", "However , only a few causal variants ...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases/helminth infections", "immunology/immunity to infections", "immunology/immune response", "pathology/histopathology" ]	Elimination of Schistosoma mansoni Adult Worms by Rhesus Macaques: Basis for a Therapeutic Vaccine?	journal.pntd.0000290	null	[ [ "Schistosomiasis remains a major public health problem in the Tropics , with tens of millions infected and many more at risk [1] .", "It has been estimated that greater than 250 , 000 deaths per annum are directly attributable to the disease [2] , and the subtle morbidities associated with chronic infecti...	[ "Among animal models of schistosomiasis , the rhesus macaque is unique in that an infection establishes but egg excretion rapidly diminishes , potentially due to loss of adult worms from the portal system via shunts or death by immune attack .", "To investigate this , six rhesus macaques were exposed to Schistoso...	[ "Infection with blood-dwelling schistosome worms is a major cause of human disease in many tropical countries .", "Despite intensive efforts a vaccine has proved elusive , not least because the chronic nature of the infection provides few pointers for vaccine development .", "The rhesus macaque appears unique a...	2008
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "arthropods", "eukaryotes", "evolutionary biology", "drosophila", "animals", "insects" ]	High-Resolution Genome-Wide Dissection of the Two Rules of Speciation in Drosophila	journal.pbio.0050243	A genome-wide introgression analysis of Drosophila mauritiana chromosome segments in an otherwise D. sechellia genetic background confirms the large X effect, a cornerstone of speciation theory, and reveals its cause.	[ [ "Speciation occurs when two populations become reproductively isolated from each other through the evolution of one or more barriers to gene flow [1 , 2] .", "One of the most intensively studied forms of reproductive isolation is intrinsic postzygotic isolation , the inviability or sterility of species hy...	[ "Postzygotic reproductive isolation is characterized by two striking empirical patterns .", "The first is Haldane's rule—the preferential inviability or sterility of species hybrids of the heterogametic ( XY ) sex .", "The second is the so-called large X effect—substitution of one species's X chromosome for ano...	[ "The evolution of reproductive isolation is a fundamental step in the origin of species .", "One kind of reproductive isolation , the sterility and inviability of species hybrids , is characterized by two of the strongest rules in evolutionary biology .", "The first is Haldane's rule: for species crosses in whi...	2007
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[]	Convergent Evolution of Hemoglobin Function in High-Altitude Andean Waterfowl Involves Limited Parallelism at the Molecular Sequence Level	journal.pgen.1005681	null	[ [ "When multiple species evolve similar changes in phenotype in response to a shared environmental challenge , it suggests that the convergently evolved character state is adaptive under the changed conditions and that it evolved under the influence of directional selection .", "A key question in evolutiona...	[ "A fundamental question in evolutionary genetics concerns the extent to which adaptive phenotypic convergence is attributable to convergent or parallel changes at the molecular sequence level .", "Here we report a comparative analysis of hemoglobin ( Hb ) function in eight phylogenetically replicated pairs of hig...	[ "The convergent evolution of similar traits in different species could be due to repeated changes at the genetic level or different changes that produce the same phenotypic effect .", "To investigate the extent to which convergence in phenotype is caused by repeated mutations , we investigated the molecular basis...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biotechnology", "molecular biology/bioinformatics", "computer science", "computational biology/genomics" ]	Integrating Sequencing Technologies in Personal Genomics: Optimal Low Cost Reconstruction of Structural Variants	journal.pcbi.1000432	null	[ [ "The human genome is comprised of approximately 6 billion nucleotides on two pairs of 23 chromosomes .", "Variations between individuals are comprised of ∼6 million single nucleotide polymorphisms ( SNPs ) and ∼1000 relatively large structural variants ( SVs ) of ∼3 kb or larger and many more smaller SVs ...	[ "The goal of human genome re-sequencing is obtaining an accurate assembly of an individual's genome .", "Recently , there has been great excitement in the development of many technologies for this ( e . g . medium and short read sequencing from companies such as 454 and SOLiD , and high-density oligo-arrays from ...	[ "In recent years , the development of high throughput sequencing and array technologies has enabled the accurate re-sequencing of individual genomes , especially in identifying and reconstructing the variants in an individual's genome compared to a “reference” .", "The costs and sensitivities of these technologie...	2009
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "messenger rna", "parasitic protozoans", "parasitology", "trypanosoma brucei", "protozoans", "methylation", "pharmacology", "drug metabolism", "veterinary science", "veterinary parasitology", "gene expression", "chemistry", "pharmacokinetics", "biochemistr...	The trypanocidal benzoxaborole AN7973 inhibits trypanosome mRNA processing	journal.ppat.1007315	null	[ [ "Kinetoplastid protists cause severe human diseases affecting millions of people .", "Trypanosoma cruzi causes Chagas disease in South America , and various Leishmania species cause a spectrum of diseases throughout the tropics .", "Salivarian trypanosomes , the subject of this study , cause sleeping ...	[ "Kinetoplastid parasites—trypanosomes and leishmanias—infect millions of humans and cause economically devastating diseases of livestock , and the few existing drugs have serious deficiencies .", "Benzoxaborole-based compounds are very promising potential novel anti-trypanosomal therapies , with candidates alread...	[ "Trypanosomes and leishmanias infect millions of humans and cause economically devastating diseases of livestock; the few existing drugs have serious deficiencies .", "Trypanosomosis of cattle caused by Trypanosoma congolense and Trypanosoma vivax , is a serious problem in Africa because cattle are used not only ...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience/neuronal signaling mechanisms", "neuroscience/neurobiology of disease and regeneration", "cell biology/gene expression", "cell biology/neuronal signaling mechanisms" ]	Nuclear Calcium Signaling Controls Expression of a Large Gene Pool: Identification of a Gene Program for Acquired Neuroprotection Induced by Synaptic Activity	journal.pgen.1000604	null	[ [ "Physiological levels of synaptic activity are required for neurons to survive [1] .", "Activity-dependent neuroprotection is induced by calcium entry through synaptic NMDA receptors and requires that calcium transients invade the cell nucleus [2]–[6] .", "Procedures that interfere with electrical act...	[ "Synaptic activity can boost neuroprotection through a mechanism that requires synapse-to-nucleus communication and calcium signals in the cell nucleus .", "Here we show that in hippocampal neurons nuclear calcium is one of the most potent signals in neuronal gene expression .", "The induction or repression of ...	[ "The dialogue between the synapse and the nucleus plays an important role in the physiology of neurons because it links brief changes in the membrane potential to the transcriptional regulation of genes critical for neuronal survival and long-term memory .", "The propagation of activity-induced calcium signals to...	2009
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "macromolecular complex analysis", "biochemistry", "protein chemistry", "protein interactions", "proteins", "biology", "computational biology", "biophysics", "macromolecular structure analysis" ]	On the Importance of Polar Interactions for Complexes Containing Intrinsically Disordered Proteins	journal.pcbi.1003192	null	[ [ "In cells , communication is established principally by protein-protein interactions [1] .", "It is clear that proteins have to interact in a specific manner in order for messages/signals to be transmitted correctly .", "Therefore , significant efforts have been made to understand the driving mechanis...	[ "There is a growing recognition for the importance of proteins with large intrinsically disordered ( ID ) segments in cell signaling and regulation .", "ID segments in these proteins often harbor regions that mediate molecular recognition .", "Coupled folding and binding of the recognition regions has been prop...	[ "Protein-protein interactions are essential to communication and signal integration in cells .", "For these processes to be precise , interactions between proteins have to be specific and well coordinated .", "In order to understand the specificity in protein interactions , researches have focused on interfaces...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "diabetes mellitus", "medicine and health sciences", "diabetic endocrinology", "epidemiology", "endocrinology", "genetics", "biology and life sciences", "genetics of disease", "type 2 diabetes", "metabolic disorders", "genetic epidemiology" ]	Meta-Analysis of Genome-Wide Association Studies in African Americans Provides Insights into the Genetic Architecture of Type 2 Diabetes	journal.pgen.1004517	null	[ [ "The prevalence of type 2 diabetes ( T2D ) among adults in the USA is currently 11 . 3% , with substantially higher prevalence in African Americans ( 18 . 7% ) than in European Americans ( 10 . 2% ) [1] .", "To date , genome-wide association studies ( GWAS ) have identified >70 susceptibility loci for T2D...	[ "Type 2 diabetes ( T2D ) is more prevalent in African Americans than in Europeans .", "However , little is known about the genetic risk in African Americans despite the recent identification of more than 70 T2D loci primarily by genome-wide association studies ( GWAS ) in individuals of European ancestry .", "I...	[ "Despite the higher prevalence of type 2 diabetes ( T2D ) in African Americans than in Europeans , recent genome-wide association studies ( GWAS ) were examined primarily in individuals of European ancestry .", "In this study , we performed meta-analysis of 17 GWAS in 8 , 284 cases and 15 , 543 controls to explor...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "bacteriology", "biofilms", "cell physiology", "cell binding", "medicine and health sciences", "chemical characterization", "pathology and laboratory medicine", "fibrinogen", "pathogens", "microbiology", "staphylococcus aureus", "glycoproteins", "bacteria", "bacterial pathogens", "resear...	Host-specialized fibrinogen-binding by a bacterial surface protein promotes biofilm formation and innate immune evasion	journal.ppat.1007816	null	[ [ "Many bacteria evolve strict mutualistic relationships with their host species with limited capacity to colonize and cause disease in other hosts .", "In contrast , other bacteria have the ability to expand into new host-species leading to the emergence of new pathogenic clones .", "Our understanding ...	[ "Fibrinogen is an essential part of the blood coagulation cascade and a major component of the extracellular matrix in mammals .", "The interface between fibrinogen and bacterial pathogens is an important determinant of the outcome of infection .", "Here , we demonstrate that a canine host-restricted skin patho...	[ "Many bacterial pathogens are specialized for a single host-species and rarely cause infections of other hosts .", "Our understanding of the bacterial factors underpinning host-specificity are limited .", "Here we demonstrate that a canine host-restricted bacterial pathogen , Staphylococcus pseudintermedius , p...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biotechnology", "bioengineering", "biomedical engineering", "systems biology", "computer and information sciences", "network analysis", "engineering and technology", "biology and life sciences", "signaling networks", "computational biology" ]	Multiple Model-Informed Open-Loop Control of Uncertain Intracellular Signaling Dynamics	journal.pcbi.1003546	null	[ [ "The ability to predictably manipulate intracellular signaling pathways would provide an unprecedented level of control of cellular processes and could potentially generate new approaches for therapeutic design and research tools in medicine and systems biology .", "Intracellular signaling networks are co...	[ "Computational approaches to tune the activation of intracellular signal transduction pathways both predictably and selectively will enable researchers to explore and interrogate cell biology with unprecedented precision .", "Techniques to control complex nonlinear systems typically involve the application of con...	[ "Most cell behavior arises as a response to external forces .", "Signals from the extracellular environment are passed to the cell's nucleus through a complex network of interacting proteins .", "Perturbing these pathways can change the strength or outcome of the signals , which could be used to treat or preven...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	An Exclusion Zone for Ca2+ Channels around Docked Vesicles Explains Release Control by Multiple Channels at a CNS Synapse	journal.pcbi.1004253	null	[ [ "Transmitter release at CNS synapses happens at active zones of sub-micrometer dimensions , which harbor docked vesicles and vesicle fusion proteins , as well as presynaptic scaffold proteins and voltage-gated Ca2+ channels [1] .", "The number , and distance of Ca2+ channels to readily-releasable vesicles...	[ "The spatial arrangement of Ca2+ channels and vesicles remains unknown for most CNS synapses , despite of the crucial importance of this geometrical parameter for the Ca2+ control of transmitter release .", "At a large model synapse , the calyx of Held , transmitter release is controlled by several Ca2+ channels ...	[ "Ca2+ channels provide the rise in intracellular Ca2+ concentration necessary to initiate the membrane fusion of transmitter—filled vesicles at synapses .", "Because Ca2+ diffuses away from Ca2+ channels , the distance between Ca2+ channels and vesicles on the range of tens of nanometers is a crucial determinant ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/bacterial infections", "microbiology/cellular microbiology and pathogenesis", "microbiology/medical microbiology" ]	Molecular Mechanisms Involved in Vascular Interactions of the Lyme Disease Pathogen in a Living Host	journal.ppat.1000169	null	[ [ "Hematogenous dissemination of pathogenic organisms is an important feature of disease progression .", "However , dissemination is poorly understood , in large part because of the difficulty in studying this process directly in living organisms under the shear stress conditions that characterize the host ...	[ "Hematogenous dissemination is important for infection by many bacterial pathogens , but is poorly understood because of the inability to directly observe this process in living hosts at the single cell level .", "All disseminating pathogens must tether to the host endothelium despite significant shear forces cau...	[ "Many bacterial pathogens can cause systemic illness by disseminating through the blood to distant target sites .", "However , hematogenous dissemination is still poorly understood , in part because of an inability to directly observe this process in living hosts in real time and at the level of individual pathog...	2008
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "cell binding", "cell physiology", "genome-wide association studies", "luciferase assay", "luciferase", "chemical characterization", "enzymes", "enzymology", "biochemical analysis", "enzyme assays", "genome analysis", "bioassays and physiological analysis", "sequence motif analysis", "rese...	GRAM: A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell-type specific manner	journal.pgen.1007860	null	[ [ "Advances in next-generation sequencing ( NGS ) technologies have enabled high-throughput whole genome and exome sequencing [1] , which have led to the identification and characterization of many disease-associated mutations [2] and the vast majority of common single nucleotide variants ( SNVs ) in the human ...	[ "There has been much effort to prioritize genomic variants with respect to their impact on “function” .", "However , function is often not precisely defined: sometimes it is the disease association of a variant; on other occasions , it reflects a molecular effect on transcription or epigenetics .", "Here , we c...	[ "With advances in sequencing technologies , a deluge of genomic data is available; however , only a fraction of non-coding genomic variants are functionally relevant .", "Sifting through this data to prioritize genomic variants with respect to function is an important but challenging task .", "In this study , w...	2019
[ "Introduction", "Results/Discussion", "Method" ]	[ "computational biology/systems biology", "computational biology/genomics" ]	Inference of Protein Complex Activities from Chemical-Genetic Profile and Its Applications: Predicting Drug-Target Pathways	journal.pcbi.1000162	null	[ [ "The collection of yeast deletion strains has enabled systematic genomewide functional analysis [1] .", "In addition , strain-specific molecular barcodes allow quantitative functional profiling of pooled deletion strains by using TAG oligonucleotide microarrays [1] , [2] .", "One of several types of f...	[ "The chemical-genetic profile can be defined as quantitative values of deletion strains' growth defects under exposure to chemicals .", "In yeast , the compendium of chemical-genetic profiles of genomewide deletion strains under many different chemicals has been used for identifying direct target proteins and a c...	[ "Finding the specific targets of chemicals and deciphering how drugs work in our body is important for the effective development of new drugs .", "Growth profiles of yeast genomewide deletion strains under many different chemicals have been used for identifying target proteins and a common mode-of-action of drugs...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "computational neuroscience", "single neuron function", "biology and life sciences", "computational biology", "neuroscience", "artificial neural networks" ]	Intrinsic Neuronal Properties Switch the Mode of Information Transmission in Networks	journal.pcbi.1003962	null	[ [ "Gain scaling refers to the ability of neurons to scale the gain of their responses when stimulated with currents of different amplitudes .", "A common property of neural systems , gain scaling adjusts the system's response to the size of the input relative to the input's standard deviation [1] .", "T...	[ "Diverse ion channels and their dynamics endow single neurons with complex biophysical properties .", "These properties determine the heterogeneity of cell types that make up the brain , as constituents of neural circuits tuned to perform highly specific computations .", "How do biophysical properties of single...	[ "Differences in ion channel composition endow different neuronal types with distinct computational properties .", "Understanding how these biophysical differences affect network-level computation is an important frontier .", "We focus on a set of biophysical properties , experimentally observed in developing co...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cryptococcus neoformans", "medicine and health sciences", "genetic networks", "cryptococcus", "pathology and laboratory medicine", "pathogens", "cell cycle and cell division", "cell processes", "microbiology", "fungi", "model organisms", "dna replication", "network analysis", "genome anal...	Investigating Conservation of the Cell-Cycle-Regulated Transcriptional Program in the Fungal Pathogen, Cryptococcus neoformans	journal.pgen.1006453	null	[ [ "About 500 million years of evolution separate the fungal phyla Ascomycota and Basidiomycota [1 , 2] .", "The cell cycle is an essential biological process driving cell division of these distantly related yeasts , and therefore may be under strong selective pressure for conservation .", "Both Saccharo...	[ "The pathogenic yeast Cryptococcus neoformans causes fungal meningitis in immune-compromised patients .", "Cell proliferation in the budding yeast form is required for C . neoformans to infect human hosts , and virulence factors such as capsule formation and melanin production are affected by cell-cycle perturbat...	[ "The opportunistic fungal pathogen Cryptococcus neoformans infects immune-compromised humans and causes fungal meningitis by proliferating in the central nervous system .", "The cell cycle has not been studied at the whole transcriptome level in C . neoformans .", "Here , we present the expression dynamics of a...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Protein O-Glucosyltransferase 1 (POGLUT1) Promotes Mouse Gastrulation through Modification of the Apical Polarity Protein CRUMBS2	journal.pgen.1005551	null	[ [ "Glycosylation can regulate protein stability and function by ensuring efficient protein folding and by altering the binding affinity to interacting partners [1–7] .", "The biological importance of this type of protein modification is highlighted by dozens of human diseases caused by congenital disorders ...	[ "Crumbs family proteins are apical transmembrane proteins with ancient roles in cell polarity .", "Mouse Crumbs2 mutants arrest at midgestation with abnormal neural plate morphology and a deficit of mesoderm caused by defects in gastrulation .", "We identified an ENU-induced mutation , wsnp , that phenocopies t...	[ "Post-translational addition of sugar chains is essential for normal activity of many secreted and transmembrane proteins and dozens of human genetic diseases are associated with congenital disorders of glycosylation .", "Protein O-glucosyltransferase 1 ( POGLUT1 ) , which is essential for early mouse development...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The Impact of Different Sources of Fluctuations on Mutual Information in Biochemical Networks	journal.pcbi.1004462	null	[ [ "To survive in challenging conditions , cells need to detect , transduce , and process signals from their environment .", "A cell’s ability to precisely process environmental signals is limited by intrinsic fluctuations and variability of its cellular processes .", "This variability takes root in the ...	[ "Stochastic fluctuations in signaling and gene expression limit the ability of cells to sense the state of their environment , transfer this information along cellular pathways , and respond to it with high precision .", "Mutual information is now often used to quantify the fidelity with which information is tran...	[ "This work demonstrates how different sources of variability within biochemical networks impact the interpretation of information transmission .", "These sources are the intrinsic noise generated within the pathway of a single cell , variability due to initial conditions and/or global parameters across the popula...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology/nuclear structure and function", "molecular biology/recombination", "genetics and genomics/nuclear structure and function", "molecular biology/chromosome structure", "genetics and genomics/chromosome biology", "molecular biology/chromatin structure", "molecular biology/dna repair" ]	The pch2Δ Mutation in Baker's Yeast Alters Meiotic Crossover Levels and Confers a Defect in Crossover Interference	journal.pgen.1000571	null	[ [ "Meiosis generates haploid gametes from diploid progenitor cells .", "The reduction in ploidy results from the segregation of homologous chromosome pairs in the first meiotic division ( MI , [1] ) .", "Prior to MI , each chromosome is joined to its homolog at chiasmata , which serve to tether homologs...	[ "Pch2 is a widely conserved protein that is required in baker's yeast for the organization of meiotic chromosome axes into specific domains .", "We provide four lines of evidence suggesting that it regulates the formation and distribution of crossover events required to promote chromosome segregation at Meiosis I...	[ "During meiosis , cells that ultimately become gametes ( such as eggs or sperm ) undergo a single round of DNA replication followed by two consecutive divisions .", "In most organisms , the segregation of chromosomes at the first meiotic division is dependent upon genetic exchange , or crossing over , at homologo...	2009
[ "Introduction", "Results", "Discussion", "Material and Methods" ]	[ "developmental biology", "developmental biology/stem cells", "developmental biology/cell differentiation", "neuroscience/neurodevelopment", "developmental biology/neurodevelopment", "developmental biology/molecular development", "developmental biology/developmental molecular mechanisms" ]	Segment-Specific Neuronal Subtype Specification by the Integration of Anteroposterior and Temporal Cues	journal.pbio.1000368	To address the question of how neuronal diversity is achieved throughout the CNS, this study provides evidence of modulation of neural progenitor cell “output” along the body axis by integration of local anteroposterior and temporal cues.	[ [ "The generation of distinct neuronal cell types at different axial levels represents a crucial feature of nervous system development .", "This segment-specific neuronal subtype specification relies upon both anteroposterior and temporal cues , and significant progress has been made in understanding each o...	[ "The generation of distinct neuronal subtypes at different axial levels relies upon both anteroposterior and temporal cues .", "However , the integration between these cues is poorly understood .", "In the Drosophila central nervous system , the segmentally repeated neuroblast 5–6 generates a unique group of ne...	[ "An animal's nervous system contains a wide variety of neuronal subtypes generated from neural progenitor ( “stem” ) cells , which generate different types of neurons at different axial positions and time points .", "Hence , the generation and specification of unique neuronal subtypes is dependent upon the integr...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell death", "cellular stress responses", "cell cycle and cell division", "cell processes", "microbiology", "nucleotides", "escherichia coli", "mutation", "prokaryotic models", "model organisms", "nucleic acid components", "dna", "bacterial pathogens", "research and analysis methods", "...	dGTP Starvation in Escherichia coli Provides New Insights into the Thymineless-Death Phenomenon	journal.pgen.1004310	null	[ [ "Starvation of cells for the DNA precursor dTTP can cause rapid cell death in all domains of life [1] .", "This phenomenon , called thymineless death ( TLD ) , was first discovered in 1954 in E . coli upon exposing thymine-requiring ( thyA ) strains to medium lacking thymine [2] .", "As TLD can be pro...	[ "Starvation of cells for the DNA building block dTTP is strikingly lethal ( thymineless death , TLD ) , and this effect is observed in all organisms .", "The phenomenon , discovered some 60 years ago , is widely used to kill cells in anticancer therapies , but many questions regarding the precise underlying mecha...	[ "Starvation of cells for DNA precursor dTTP is strikingly lethal in many organisms , like bacteria , yeast , and human cells .", "This type of death is unusual in that starvation for other nutritional requirements generally results in growth arrest , but not in death .", "The phenomenon is called thymineless de...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "immune cells", "clinical immunology", "immunity", "virology", "viral transmission and infection", "immunology", "biology", "immunologic techniques", "microbiology", "viral diseases" ]	Influenza A Virus Infection of Human Primary Dendritic Cells Impairs Their Ability to Cross-Present Antigen to CD8 T Cells	journal.ppat.1002572	null	[ [ "Influenza A virus ( IAV ) infection is one of the oldest and most common diseases known to mankind , estimated to cause 500 , 000 deaths per year , primarily in infants and elderly [1] .", "In healthy humans , IAV infection typically causes brief but often severe illness .", "Normally , IAV infection...	[ "Influenza A virus ( IAV ) infection is normally controlled by adaptive immune responses initiated by dendritic cells ( DCs ) .", "We investigated the consequences of IAV infection of human primary DCs on their ability to function as antigen-presenting cells .", "IAV was internalized by both myeloid DCs ( mDCs ...	[ "Although the interactions between viruses and dendritic cells ( DCs ) have been studied for many years , surprisingly little is known on the functional relationship between infection and antigen presentation in primary human DCs .", "Here , we asked specifically whether Influenza A virus ( IAV ) infection of hum...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "spectrometric identification of proteins", "cellular structures", "protein interactions", "macromolecular assemblies", "microbiology", "gene function", "immunochemistry", "model organisms", "chaperone proteins", "cell nucleus", "proteins", "biology", "proteomics", "cytoplasm", "biochemi...	The Prefoldin Bud27 Mediates the Assembly of the Eukaryotic RNA Polymerases in an Rpb5-Dependent Manner	journal.pgen.1003297	null	[ [ "Eukaryotic RNA polymerases are a family of multimeric enzymes , RNA pol I , II , and III , responsible for the specific synthesis of different RNAs .", "RNA pol I is specialized in the synthesis of the pre-rRNA precursor of the three largest rRNA and typically account for about 75% of the entire transcri...	[ "The unconventional prefoldin URI/RMP , in humans , and its orthologue in yeast , Bud27 , have been proposed to participate in the biogenesis of the RNA polymerases .", "However , this role of Bud27 has not been confirmed and is poorly elucidated .", "Our data help clarify the mechanisms governing biogenesis of...	[ "The mechanisms governing the assembly and the transport of the three eukaryotic RNA polymerases to the nucleus are in discussion .", "Interesting papers have demonstrated the participation of some proteins in the assembly of the nuclear RNA polymerases and in their transport to the nucleus , but the mechanisms i...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "sequencing techniques", "medicine and health sciences", "face", "disabilities", "enzymes", "enzymology", "alleles", "genome sequencing", "molecular biology techniques", "research and analysis methods", "public and occupational health", "proteins", "guanosine triphosphatase", "recombinant ...	De novo mutations in the GTP/GDP-binding region of RALA, a RAS-like small GTPase, cause intellectual disability and developmental delay	journal.pgen.1007671	null	[ [ "Developmental delay and intellectual disability ( DD/ID ) affect about 1–2% of individuals worldwide [1] .", "Many highly penetrant genetic variants underlying DD/ID have been identified , but a large fraction of disease risk remains unexplained [2 , 3] .", "While some DD/ID-cases may result from env...	[ "Mutations that alter signaling of RAS/MAPK-family proteins give rise to a group of Mendelian diseases known as RASopathies .", "However , among RASopathies , the matrix of genotype-phenotype relationships is still incomplete , in part because there are many RAS-related proteins and in part because the phenotypic...	[ "While many causes of developmental disabilities have been identified , a large number of affected children cannot be diagnosed despite extensive medical testing .", "Previously unknown genetic factors are likely to be the culprits in many of these cases .", "Using DNA sequencing , and by sharing information am...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	A Novel Feedback Loop That Controls Bimodal Expression of Genetic Competence	journal.pgen.1005047	null	[ [ "Cellular differentiation is guided by complex gene regulatory networks that integrate different intra- and extracellular signals .", "This deterministic view has been challenged by the discovery of so-called bistable or bimodal regulation , whereby the decision to differentiate is stochastic .", "A c...	[ "Gene expression can be highly heterogeneous in isogenic cell populations .", "An extreme type of heterogeneity is the so-called bistable or bimodal expression , whereby a cell can differentiate into two alternative expression states .", "Stochastic fluctuations of protein levels , also referred to as noise , p...	[ "Gene expression can be highly heterogeneous in clonal cell populations .", "An extreme type of heterogeneity is the so-called bistable or bimodal expression , whereby a cell can differentiate into two alternative expression states , and consequently a population will be composed of cells that are ‘ON’ and cells ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biotechnology", "cellular structures", "subcellular organelles", "rna interference", "microbiology", "model organisms", "mitochondrial myopathy", "genetics and genomics", "mitochondrial diseases", "gene expression", "biology", "molecular biology", "cell biology", "genetics", "yeast and ...	Polymorphisms in the Mitochondrial Ribosome Recycling Factor EF-G2mt/MEF2 Compromise Cell Respiratory Function and Increase Atorvastatin Toxicity	journal.pgen.1002755	null	[ [ "The primary function of the mitochondria is the aerobic production of ATP , a process that is reliant on a series of protein complexes that comprise the electron transport chain .", "Several components of the electron transport chain are encoded in the mitochondrial genome , the translation of which is g...	[ "Mitochondrial translation , essential for synthesis of the electron transport chain complexes in the mitochondria , is governed by nuclear encoded genes .", "Polymorphisms within these genes are increasingly being implicated in disease and may also trigger adverse drug reactions .", "Statins , a class of HMG-C...	[ "The mitochondria are responsible for producing the cell's energy .", "Energy production is the result of carefully orchestrated interactions between proteins encoded by the mitochondrial DNA and by nuclear DNA .", "Sequence variations in genes encoding these proteins have been shown to cause disease and advers...	2012

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