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headings list	keywords list	title stringlengths 20 281	id stringlengths 20 20	toc stringlengths 57 522 ⌀	sections list	abstract list	summary list	year stringclasses 13 values
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases", "biology and life sciences", "immunology", "medicine and health sciences" ]	Out-of-Sequence Signal 3 as a Mechanism for Virus-Induced Immune Suppression of CD8 T Cell Responses	journal.ppat.1004357	null	[ [ "The fact that virus infections can induce a transient state of immune suppression was first described over a century ago , as patients acutely infected with the measles virus failed to develop a recall response to tuberculin even though they had previously been immunized [1] .", "Since then , infection w...	[ "Virus infections are known to induce a transient state of immune suppression often associated with an inhibition of T cell proliferation in response to mitogen or cognate-antigen stimulation .", "Recently , virus-induced immune suppression has been linked to responses to type 1 interferon ( IFN ) , a signal 3 cy...	[ "Vaccines are used to protect individuals against infection with a number of different pathogens and depend on the formation of antigen specific memory cells .", "The efficacy of vaccines can be affected by a number of different factors .", "It has been known for some time now that suppression of the immune sys...	2014
[ "Introduction", "Results/Discussion", "Materials And Methods" ]	[ "biochemistry", "computer science/systems and control theory", "biochemistry/bioinformatics", "computational biology/metabolic networks", "computational biology" ]	Automatic Assignment of EC Numbers	journal.pcbi.1000661	null	[ [ "With the several thousand proteins found in each organism a highly developed hierarchical and consistent classification scheme is absolutely essential for a comparison of metabolic capacities of the organisms .", "Unfortunately such a system exists only for the enzymes and not for the other protein class...	[ "A wide range of research areas in molecular biology and medical biochemistry require a reliable enzyme classification system , e . g . , drug design , metabolic network reconstruction and system biology .", "When research scientists in the above mentioned areas wish to unambiguously refer to an enzyme and its fu...	[ "The fundamental understanding of metabolism in organisms which can only be achieved by integrated studies on their biology using a systems biology approach will aid in the design of future metabolic engineering strategies .", "Metabolic network reconstruction provides insight into the molecular mechanisms of a p...	2010
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "protein interactions", "statistics", "metabolic networks", "signaling networks", "computerized simulations", "mathematics", "biostatistics", "regulatory networks", "biology", "proteomics", "microarrays", "biochemistry", "computer science", "proteomic databases", "computational biology" ...	Differential Expression Analysis for Pathways	journal.pcbi.1002967	null	[ [ "Genes and proteins can be grouped into different categories on the basis of many traits: sequence , function , interactions , etc . .", "Grouping genes by biological pathway is often the most relevant approach to biologists .", "For this study , we represent biological pathways as directed graphs , w...	[ "Life science technologies generate a deluge of data that hold the keys to unlocking the secrets of important biological functions and disease mechanisms .", "We present DEAP , Differential Expression Analysis for Pathways , which capitalizes on information about biological pathways to identify important regulato...	[ "The data deluge represents a growing challenge for life sciences .", "Within this sea of data surely lie many secrets to understanding important biological and medical systems .", "To quantify important patterns in this data , we present DEAP ( Differential Expression Analysis for Pathways ) .", "DEAP amalga...	2013
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "invertebrates", "dengue virus", "medicine and health sciences", "body fluids", "immune physiology", "pathology and laboratory medicine", "pathogens", "immunology", "microbiology", "animals", "viruses", "vaccines", "rna viruses", "infectious disease control", "antibodies", "insect vect...	Midgut barriers prevent the replication and dissemination of the yellow fever vaccine in Aedes aegypti	journal.pntd.0007299	null	[ [ "Arboviruses , which are transmitted among vertebrate hosts by blood-feeding arthropod vectors , put billions of people at risk worldwide .", "Viral infection in arthropods is usually persistent .", "Following uptake of an infectious blood meal by a female mosquito , arbovirus must initiate a producti...	[ "To be transmitted to vertebrate hosts via the saliva of their vectors , arthropod-borne viruses have to cross several barriers in the mosquito body , including the midgut infection and escape barriers .", "Yellow fever virus ( YFV ) belongs to the genus Flavivirus , which includes human viruses transmitted by Ae...	[ "Most flaviviruses , including yellow fever virus ( YFV ) , are transmitted between hosts by mosquito bites .", "The yellow fever vaccine ( YFV-17D ) is one of the safest and most effective live virus vaccine ever developed .", "It is also used as a platform for engineering vaccines against other health-threate...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "decision making", "engineering and technology", "statistics", "applied mathematics", "social sciences", "neuroscience", "learning and memory", "simulation and modeling", "algorithms", "decision analysis", "cognitive neuroscience", "cognitive psychology", "mathematics", "animal behavior", ...	Optimizing the depth and the direction of prospective planning using information values	journal.pcbi.1006827	null	[ [ "When confronted with several choices , we need to have an evaluation of how good each option is .", "Each choice has some immediate consequences , but also takes us into a new state where new choices emerge , and so on .", "Think of chess as an example .", "One intuitive way to solve a sequential...	[ "Evaluating the future consequences of actions is achievable by simulating a mental search tree into the future .", "Expanding deep trees , however , is computationally taxing .", "Therefore , machines and humans use a plan-until-habit scheme that simulates the environment up to a limited depth and then exploit...	[ "When faced with several choices in complex environments like chess , thinking about all the potential consequences of each choice , infinitely deep into the future , is simply impossible due to time and cognitive limitations .", "An outstanding question is what is the best direction and depth of thinking about t...	2019
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "polyacrylamide gel electrophoresis", "immune physiology", "pathology and laboratory medicine", "chemical compounds", "blue native polyacrylamide gel electrophoresis", "293t cells", "pathogens", "biological cultures", "immunology", "microbiology", "carbohydrates...	Glycoengineering HIV-1 Env creates ‘supercharged’ and ‘hybrid’ glycans to increase neutralizing antibody potency, breadth and saturation	journal.ppat.1007024	null	[ [ "Neutralizing antibodies ( nAbs ) are likely to be an essential part of the immunity conferred by an effective HIV-1 vaccine [1] .", "NAbs interfere with HIV-1 infection by binding to functional Envelope glycoprotein ( Env ) spikes consisting of gp120/gp41 trimers arrayed on virion surfaces , thereby bloc...	[ "The extensive glycosylation of HIV-1 envelope ( Env ) glycoprotein leaves few glycan-free holes large enough to admit broadly neutralizing antibodies ( bnAb ) .", "Consequently , most bnAbs must inevitably make some glycan contacts and avoid clashes with others .", "To investigate how Env glycan maturation reg...	[ "Here we engineered various changes in the sizes and shapes of sugars that decorate HIV surface spike proteins and tested the effects of these changes on virus susceptibility to neutralizing antibodies .", "In so doing , we were able to define the optimal Env-sugars recognized by prototype bnAbs that recognize va...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "chemical compounds", "enzymes", "enzymology", "parasitic diseases", "organic compounds", "parasitology", "developmental biology", "serine", "peptide libraries", "acidic amino acids", "amino acids", "cysteine", "proteins", "life cycles", "chemistry", "...	Activity profiling of peptidases in Angiostrongylus costaricensis first-stage larvae and adult worms	journal.pntd.0006923	null	[ [ "Angiostrongylus costaricensis is a zoonotic parasitic nematode that causes human abdominal angiostrongyliasis , a severe gastrointestinal disease .", "This helminth was first described in patients from Costa Rica in 1971 [1] .", "Abdominal angiostrongyliasis ( AA ) is currently widespread in Latin Am...	[ "Angiostrongylus costaricensis is a relatively uncharacterized nematode that causes abdominal angiostrongyliasis in Latin America , a human parasitic disease .", "Currently , no effective pharmacological treatment for angiostrongyliasis exists .", "Peptidases are known to be druggable targets for a variety of d...	[ "A . costaricensis is a poorly studied nematode that causes abdominal angiostrongyliasis , a human parasitic disease .", "Peptidases perform several functions in the life cycle of parasites , including nutrition , differentiation and host invasion .", "The present study characterized the repertoire of peptidase...	2018
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "chemical biology/small molecule chemistry", "molecular biology/post-translational regulation of gene expression", "cell biology/cell signaling", "cell biology", "biochemistry/chemical biology of the cell", "biochemistry/cell signaling and trafficking structures", "biochemistry/transcription and transla...	A Quantitative Systems Approach Reveals Dynamic Control of tRNA Modifications during Cellular Stress	journal.pgen.1001247	null	[ [ "The complexity of the transfer RNA ( tRNA ) system confers great potential for its use in cellular regulatory programs .", "There are hundreds of tRNA-encoding genes in S . cerevisiae and human genomes , with extensive post-transcriptional processing that includes enzyme-mediated ribonucleoside modificat...	[ "Decades of study have revealed more than 100 ribonucleoside structures incorporated as post-transcriptional modifications mainly in tRNA and rRNA , yet the larger functional dynamics of this conserved system are unclear .", "To this end , we developed a highly precise mass spectrometric method to quantify tRNA m...	[ "While the genetic code in DNA is read from four nucleobase structures , there are more than 100 ribonucleoside structures incorporated as post-transcriptional modifications mainly in tRNA and rRNA .", "These structures and their biosynthetic machinery are highly conserved , with 20–30 present in any one organism...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "neurogenesis", "genetic mutation", "neuroscience", "gene function", "genetics of disease", "cognitive neuroscience", "animal cognition", "developmental neuroscience", "biology", "mutagenesis", "working memory", "genetic screens", "genetics", "behavioral neuroscience", "genetics and geno...	Mutation of the Diamond-Blackfan Anemia Gene Rps7 in Mouse Results in Morphological and Neuroanatomical Phenotypes	journal.pgen.1003094	null	[ [ "Ribosomes are responsible for constructing the myriad proteins required for the function of each individual cell .", "Ribosomes themselves , which consist of small ( 40S ) and large ( 60S ) subunits , are assembled from about 80 different ribosomal proteins ( RPs ) along with four species of rRNA synthes...	[ "The ribosome is an evolutionarily conserved organelle essential for cellular function .", "Ribosome construction requires assembly of approximately 80 different ribosomal proteins ( RPs ) and four different species of rRNA .", "As RPs co-assemble into one multi-subunit complex , mutation of the genes that enco...	[ "Ribosomes are composed of two subunits that each consist of a large number of proteins , and their function of translating mRNA into protein is essential for cell viability .", "Naturally occurring or genetically engineered mutations within an individual ribosomal protein provide a valuable resource , since the ...	2013
[ "Introduction", "Methods", "Results and Discussion" ]	[]	The Ecological Dynamics of Fecal Contamination and Salmonella Typhi and Salmonella Paratyphi A in Municipal Kathmandu Drinking Water	journal.pntd.0004346	null	[ [ "Enteric ( typhoid ) fever is a severe systemic infection and a common cause of community acquired febrile disease in many low-income countries in Asia and Africa [1] .", "The infection is triggered by the ingestion of the bacteria Salmonella Typhi ( S . Typhi ) and Salmonella Paratyphi A ( S . Paratyphi ...	[ "One of the UN sustainable development goals is to achieve universal access to safe and affordable drinking water by 2030 .", "It is locations like Kathmandu , Nepal , a densely populated city in South Asia with endemic typhoid fever , where this goal is most pertinent .", "Aiming to understand the public healt...	[ "Aiming to understand the ecology of municipal drinking water and measure the potential exposure to pathogens that cause typhoid fever ( Salmonella Typhi and Salmonella Paratyphi A ) in Kathmandu , Nepal , we collected water samples from 10 water sources weekly for one year and subjected them to comprehensive chemi...	2016
[ "Introduction", "Materials and methods", "Discussion" ]	[ "medicine and health sciences", "body fluids", "pathology and laboratory medicine", "pathogens", "geographical locations", "microbiology", "retroviruses", "viruses", "immunodeficiency viruses", "human sexual behavior", "filoviruses", "rna viruses", "africa", "hiv epidemiology", "semen", ...	Development of risk reduction behavioral counseling for Ebola virus disease survivors enrolled in the Sierra Leone Ebola Virus Persistence Study, 2015-2016	journal.pntd.0005827	null	[ [ "Prior to the EVD epidemic , the Demographic Health Survey conducted in 2013 in Sierra Leone showed that condom use was low , with 5% of female and 13% of male respondents reporting having used a condom in the past 12 months .", "Twenty-five percent of men and 6% of women reported having two or more sex p...	[ "During the 2014–2016 West Africa Ebola Virus Disease ( EVD ) epidemic , the public health community had concerns that sexual transmission of the Ebola virus ( EBOV ) from EVD survivors was a risk , due to EBOV persistence in body fluids of EVD survivors , particularly semen .", "The Sierra Leone Ebola Virus Pers...	[ "The 2014–2016 West Africa Ebola Virus Disease ( EVD ) epidemic was large and widespread , affecting thousands of people across Guinea , Liberia , and Sierra Leone .", "Prior to this epidemic , there were limited data on persistence of Ebola virus in body fluids of EVD survivors and the potential risk that viral ...	2017
[ "Introduction", "Results", "Discussion", "Conclusion", "Methods" ]	[ "adenocarcinoma of the lung", "medicine and health sciences", "squamous cell lung carcinoma", "carcinomas", "cancers and neoplasms", "oncology", "histology", "adenocarcinomas", "epigenetics", "dna", "chromatin", "dna methylation", "digestive system", "chromosome biology", "lung and intra...	Comparative transcriptomes of adenocarcinomas and squamous cell carcinomas reveal molecular similarities that span classical anatomic boundaries	journal.pgen.1006938	null	[ [ "The classification of cancers for specific and tailored clinical management has been a topic of ongoing study .", "Historically , cancers have been classified primarily by the organs in which they originate—a convenient strategy that aligns with traditional anatomical divisions of medicine .", "Accor...	[ "Advances in genomics in recent years have provided key insights into defining cancer subtypes “within-a-tissue”—that is , respecting traditional anatomically driven divisions of medicine .", "However , there remains a dearth of data regarding molecular profiles that are shared across tissues , an understanding o...	[ "In clinical practice , the organ in which a cancer arises typically classifies it .", "However , developments in our understanding of cancer have revealed that this method overlooks key aspects of cancer biology relevant to both disease prevention and treatment .", "In fact , work characterizing the genetic ma...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell motility", "signaling networks", "g-protein signaling", "network analysis", "cellular structures and organelles", "g protein coupled receptors", "cytosol", "computer and information sciences", "proteins", "ras signaling", "transmembrane receptors", "cell membranes", "chemotaxis", "bi...	A Model for Direction Sensing in Dictyostelium discoideum: Ras Activity and Symmetry Breaking Driven by a Gβγ-Mediated, Gα2-Ric8 -- Dependent Signal Transduction Network	journal.pcbi.1004900	null	[ [ "In light of the restriction to LatA-treated cells , the backbone of the chemotactic pathway activated in response to changes in extracellular cAMP is Δ cAMP →Δ GPCR occupation →Δ Gαβγ activation →Δ Ras activity .", "We describe this pathway in terms of three modules: the GPCR surface receptors cAR1-4 , G...	[ "Chemotaxis is a dynamic cellular process , comprised of direction sensing , polarization and locomotion , that leads to the directed movement of eukaryotic cells along extracellular gradients .", "As a primary step in the response of an individual cell to a spatial stimulus , direction sensing has attracted nume...	[ "Many eukaryotic cells , including Dictyostelium discoideum ( Dicty ) , neutrophils and other cells of the immune system , can detect and reliably orient themselves in chemoattractant gradients .", "In Dicty , signal detection and transduction involves a G-protein-coupled receptor ( GPCR ) through which extracell...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "molecular neuroscience", "neurodegenerative diseases", "anatomy and physiology", "neuroscience", "animal models", "motor systems", "model organisms", "neurological system", "motor neuron diseases", "biology", "zebrafish", "cellular neuroscience", "neurological disorders", "n...	FUS and TARDBP but Not SOD1 Interact in Genetic Models of Amyotrophic Lateral Sclerosis	journal.pgen.1002214	null	[ [ "ALS is the most common motor neuron disorder and is characterized by loss of upper and lower motor neurons .", "It is the third most common neurological disorder with an incidence of 1–2 people in 100 , 000 , a prevalence of 4–6 per 100 , 000 and with a lifetime risk of 1 in 1 , 000 [1] , [2] .", "AL...	[ "Mutations in the SOD1 and TARDBP genes have been commonly identified in Amyotrophic Lateral Sclerosis ( ALS ) .", "Recently , mutations in the Fused in sarcoma gene ( FUS ) were identified in familial ( FALS ) ALS cases and sporadic ( SALS ) patients .", "Similarly to TDP-43 ( coded by TARDBP gene ) , FUS is a...	[ "Mutations in the SOD1 , TARDBP , and FUS genes have been commonly identified in Amyotrophic Lateral Sclerosis ( ALS ) .", "However , possible interactions between these ALS–causative genetic mutations have not been examined .", "Here we expressed each of three human FUS mutations ( R521H , R521C , and S57Δ ) i...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology/embryology", "genetics and genomics/animal genetics", "genetics and genomics/gene expression", "developmental biology/developmental evolution", "genetics and genomics/chromosome biology", "developmental biology/molecular development", "genetics and genomics/epigenetics" ]	Gene Dosage Effects of the Imprinted Delta-Like Homologue 1 (Dlk1/Pref1) in Development: Implications for the Evolution of Imprinting	journal.pgen.1000392	null	[ [ "Genomic imprinting , the process causing genes to be differentially expressed according to their parental origin acts on a subset of developmentally regulated genes [reviewed in 1] .", "Since imprinting results in functional haploidy of target genes , the evolution of such a mechanism must have conferred...	[ "Genomic imprinting is a normal process that causes genes to be expressed according to parental origin .", "The selective advantage conferred by imprinting is not understood but is hypothesised to act on dosage-critical genes .", "Here , we report a unique model in which the consequences of a single , double , ...	[ "Genomic imprinting , the process that causes genes to be expressed from one of the two chromosome homologues according to parental origin , is likely to act on genes whose dosage is important for their correct function .", "To test this , we compared the phenotype of transgenic mice expressing a double and tripl...	2009
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	A Trypanosoma brucei Kinesin Heavy Chain Promotes Parasite Growth by Triggering Host Arginase Activity	journal.ppat.1003731	null	[ [ "The protozoan flagellate parasite Trypanosoma brucei is responsible for the diseases human sleeping sickness and nagana in cattle .", "In experimental murine models , the host immune response to this blood-borne pathogen involves antibody production against the Variant Surface Glycoprotein ( VSG ) , as w...	[ "In order to promote infection , the blood-borne parasite Trypanosoma brucei releases factors that upregulate arginase expression and activity in myeloid cells .", "By screening a cDNA library of T . brucei with an antibody neutralizing the arginase-inducing activity of parasite released factors , we identified a...	[ "From the first invasive step onwards , African trypanosomes can efficiently undermine the protective immune response of their mammalian host to favor their survival within the host and successful transmission by its vector , the tsetse fly .", "Identifying the parasite factors affecting the protective immune res...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "nucleotides", "gene function", "histone modification", "chromatin", "rna structure", "gene expression", "biology", "molecular biology", "biochemistry", "rna", "rna processing", "nucleic acids", "protein translation", "genetics", "molecular cell biology", "genetics and genomics" ]	Elongator Complex Influences Telomeric Gene Silencing and DNA Damage Response by Its Role in Wobble Uridine tRNA Modification	journal.pgen.1002258	null	[ [ "Elongator complex , first identified in Saccharomyces cerevisiae , consists of a core complex , Elp1–Elp3 and a sub-complex , Elp4–Elp6 [1]–[3] .", "Orthologs of Elp1 to Elp4 has been identified in higher eukaryotes and a six-subunit Elongator complex has been purified from humans [4]–[5] .", "In yea...	[ "Elongator complex is required for formation of the side chains at position 5 of modified nucleosides 5-carbamoylmethyluridine ( ncm5U34 ) , 5-methoxycarbonylmethyluridine ( mcm5U34 ) , and 5-methoxycarbonylmethyl-2-thiouridine ( mcm5s2U34 ) at wobble position in tRNA .", "These modified nucleosides are important...	[ "Elongator is a conserved protein complex in eukaryotes .", "Studies in yeast , worms , and plants have revealed that Elongator complex is required for formation of mcm5 and ncm5 side chains at wobble uridines in a subset of tRNA species .", "The primary function of Elongator complex in yeast is to modify U34 i...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "biofilms", "bacteriology", "ecology and environmental sciences", "medicine and health sciences", "water resources", "microbiome", "pathology and laboratory medicine", "engineering and technology", "pathogens", "microbiology", "protozoans", "opportunistic pathogens", "bacteria", "microbial...	Opportunistic pathogens and large microbial diversity detected in source-to-distribution drinking water of three remote communities in Northern Australia	journal.pntd.0007672	null	[ [ "Water providers in the wet-dry tropics of Northern Australia face significant challenges to keep drinking water safe and free of opportunistic pathogens .", "One such opportunistic pathogen is Burkholderia pseudomallei , an environmental saprophytic bacterium and causative agent of the severe disease mel...	[ "In the wet-dry tropics of Northern Australia , drinking water in remote communities is mostly sourced from bores accessing groundwater .", "Many aquifers contain naturally high levels of iron and some are shallow with surface water intrusion in the wet season .", "Therefore , environmental bacteria such as iro...	[ "Water providers in the wet-dry tropics of Northern Australia face additional challenges to keep drinking water microbiologically safe .", "The source water is often rich in iron-cycling bacteria leading to excessive biofilm formation in pipes and it can also contain the emerging opportunistic pathogen Burkholder...	2019
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "immunology", "biology", "genomics", "microbiology", "genetics and genomics" ]	Ebola Virion Attachment and Entry into Human Macrophages Profoundly Effects Early Cellular Gene Expression	journal.pntd.0001359	null	[ [ "Zaire ebolavirus ( ZEBOV ) is a member of the family Filoviridae within the order Mononegavirales [1] .", "It was discovered in 1976 in what is now the Democratic Republic of the Congo [2] as the etiological agent of a severe human viral hemorrhagic fever known as Ebola Hemorrhagic Fever ( EHF ) .", ...	[ "Zaire ebolavirus ( ZEBOV ) infections are associated with high lethality in primates .", "ZEBOV primarily targets mononuclear phagocytes , which are activated upon infection and secrete mediators believed to trigger initial stages of pathogenesis .", "The characterization of the responses of target cells to ZE...	[ "Ebola virus causes a severe hemorrhagic fever syndrome in man with high case-fatality rates .", "Following infection , monocytes and macrophages are among the first cells targeted by the virus .", "These cells respond by increasing expression of inflammatory cytokines and chemokines that contribute towards pat...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "experimental design", "vertebrates", "social sciences", "neuroscience", "animals", "mammals", "research design", "cognitive psychology", "research and analysis methods", "language", "meta-research article", "peer review", "research assessment", "research reporting guidelines", "psycholo...	Authorization of Animal Experiments Is Based on Confidence Rather than Evidence of Scientific Rigor	journal.pbio.2000598	null	[ [ "Reproducibility is a fundamental principle of the scientific method and distinguishes scientific evidence from mere anecdote .", "The advancement of basic as well as applied research depends on the reproducibility of the findings , and can be seriously hampered if reproducibility is poor .", "However...	[ "Accumulating evidence indicates high risk of bias in preclinical animal research , questioning the scientific validity and reproducibility of published research findings .", "Systematic reviews found low rates of reporting of measures against risks of bias in the published literature ( e . g . , randomization , ...	[ "Scientific validity of research findings depends on scientific rigor , including measures to avoid bias , such as random allocation of animals to treatment groups ( randomization ) and assessing outcome measures without knowing to which treatment groups the animals belong ( blinding ) .", "However , measures aga...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "neural networks", "information processing", "visual object recognition", "social sciences", "neuroscience", "learning and memory", "perception", "cognitive psychology", "recurrent neural networks", "human performance", "cognition", "brain mapping", "artificial intelligence", "memory", "...	Beyond core object recognition: Recurrent processes account for object recognition under occlusion	journal.pcbi.1007001	null	[ [ "There is abundance of feedforward , and recurrent connections in the primate visual cortex [1 , 2] .", "The feedforward connections form a hierarchy of cortical areas along the visual pathway , playing a significant role in various aspects of visual object processing [3] .", "However , the role of re...	[ "Core object recognition , the ability to rapidly recognize objects despite variations in their appearance , is largely solved through the feedforward processing of visual information .", "Deep neural networks are shown to achieve human-level performance in these tasks , and explain the primate brain representati...	[ "In recent years , deep-learning-based computer vision algorithms have been able to achieve human-level performance in several object recognition tasks .", "This has also contributed in our understanding of how our brain may be solving these recognition tasks .", "However , object recognition under more challen...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology/membranes and sorting", "microbiology/innate immunity", "immunology/innate immunity" ]	Stage-Specific Sampling by Pattern Recognition Receptors during Candida albicans Phagocytosis	journal.ppat.1000218	null	[ [ "C . albicans is an opportunistic pathogen , mostly confined to the gastrointestinal , genitourinary tracts and the skin .", "It can cause infections of mucosal tissues and is also able to invade systemically , especially in immunocompromised hosts [1] .", "Immune cells recognize C . albicans mainly t...	[ "Candida albicans is a medically important pathogen , and recognition by innate immune cells is critical for its clearance .", "Although a number of pattern recognition receptors have been shown to be involved in recognition and phagocytosis of this fungus , the relative role of these receptors has not been forma...	[ "Infection by Candida albicans has increased as a result of immunosuppression associated with AIDS and organ transplantation .", "We assessed the role of three pattern recognition receptors , namely Dectin-1 ( a beta glucan receptor ) , the type 3 complement receptor ( CR3 ) , and the mannose receptor , in mediat...	2008
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "blood cells", "t helper cells", "schistosoma", "invertebrates", "medicine and health sciences", "immune cells", "helminths", "immunology", "cloning", "animals", "clinical medicine", "molecular biology techniques", "research and analysis methods", "schistosoma japonicum", "white blood ce...	Blockade of PD-1 Signaling Enhances Th2 Cell Responses and Aggravates Liver Immunopathology in Mice with Schistosomiasis japonica	journal.pntd.0005094	null	[ [ "Schistosomiasis is an infectious disease that affects at least 220 million people worldwide and causes serious morbidity and economic problems in developing countries [1 , 2] .", "During infection with Schistosoma japonicum ( S . japonicum ) or S . mansoni , granulomas form around eggs that are trapped i...	[ "More than 220 million people worldwide are chronically infected with schistosomes , causing severe disease or even death .", "The major pathological damage occurring in schistosomiasis is attributable to the granulomatous inflammatory response and liver fibrosis induced by schistosome eggs .", "The inflammator...	[ "Schistosomiasis is a parasitic disease that affects approximately 220 million people and causes serious morbidity and economic problems mainly in ( sub ) tropical regions .", "After Schistosoma japonicum or Schistosoma mansoni infection , parasite eggs are trapped in host liver and induce liver inflammation and ...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "microbiology", "salmonella typhi", "salmonellosis", "epithelial cells", "bacterial diseases", "enterobacteriaceae", "bacteria", "mapk signaling cascades", "bacterial pathogens", "salmonella typhimurium", "in...	Salmonella enterica serovar-specific transcriptional reprogramming of infected cells	journal.ppat.1006532	null	[ [ "Salmonella enterica encompasses multiple serovars that are associated with distinct pathogenic features and host specificities [1 , 2] .", "Salmonella enterica serovar Typhi ( S . Typhi ) , for example , is the cause of typhoid fever , a systemic disease of humans that leads to an estimated 200 , 000 dea...	[ "Despite their high degree of genomic similarity , different Salmonella enterica serovars are often associated with very different clinical presentations .", "In humans , for example , the typhoidal S . enterica serovar Typhi causes typhoid fever , a life-threatening systemic disease .", "In contrast , the non-...	[ "Salmonella Typhimurium and Salmonella Typhi are associated with very different clinical presentations .", "While S . Typhimurium causes self-limiting gastroenteritis ( i . e . “food poisoning” ) , S . Typhi causes typhoid fever , a systemic , life-threatening disease .", "The bases for these major differences ...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "neurobiology of disease and regeneration", "immunology", "microbiology", "lymphoid organs", "neuroscience", "infectious diseases", "biology", "pathogenesis", "immune system", "clinical immunology", "neurological disorders", "neurology", "molecular cell biology" ]	Lymphotoxin, but Not TNF, Is Required for Prion Invasion of Lymph Nodes	journal.ppat.1002867	null	[ [ "Prions are unusual infectious agents thought to be comprised solely of an abnormally folded , aggregated isoform ( PrPSc ) of the endogenous cellular prion protein ( PrPC ) [1] .", "Deposition of PrPSc aggregates , vacuolation , and neuronal loss in brain tissue are histopathological hallmarks of a group...	[ "Neuroinvasion and subsequent destruction of the central nervous system by prions are typically preceded by a colonization phase in lymphoid organs .", "An important compartment harboring prions in lymphoid tissue is the follicular dendritic cell ( FDC ) , which requires both tumor necrosis factor receptor 1 ( TN...	[ "Prions are unique infectious agents thought to be composed entirely of an abnormal conformer of the endogenous prion protein .", "Prions cause a severe neurological disorder in humans and other animals known as prion disease .", "Though prion disease can arise spontaneously or from genetic mutations in the gen...	2012
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "chemical characterization", "gene regulation", "dna transcription", "fungi", "sumoylation", "sequence motif analysis", "epigenetics", "dna", "chromatin", "promoter regions", "research and analysis methods", "sequence analysis", "bioinformatics", "proteins", "chromosome biology", "gene...	Sumoylation of DNA-bound transcription factor Sko1 prevents its association with nontarget promoters	journal.pgen.1007991	null	[ [ "Sumoylation is an essential eukaryotic post-translational modification that functions in many , predominantly nuclear , cellular processes , such as DNA repair and transcription , by regulating target protein localization , stability , or interactions with other proteins or with chromatin [1–5] .", "The ...	[ "Sequence-specific transcription factors ( TFs ) represent one of the largest groups of proteins that is targeted for SUMO post-translational modification , in both yeast and humans .", "SUMO modification can have diverse effects , but recent studies showed that sumoylation reduces the interaction of multiple TFs...	[ "Transcription factors bind the genome at specific sites to control the expression of target genes .", "Although the DNA sequence of these sites is critical for determining where they bind , additional factors must act to ensure that only appropriate sites remain bound and regulated by transcription factors .", ...	2019
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Spatio-Temporal Distribution of Aedes aegypti (Diptera: Culicidae) Mitochondrial Lineages in Cities with Distinct Dengue Incidence Rates Suggests Complex Population Dynamics of the Dengue Vector in Colombia	journal.pntd.0003553	null	[ [ "Dengue is one of the major public health problems in the tropics and is the second-most deadly vector-borne disease in the world after malaria [1] .", "The mosquito Aedes aegypti is the main vector of the four serotypes of dengue flaviviruses ( DENV1-4 ) and yellow fever virus ( YFV ) , and is a known ve...	[ "Aedes aegypti is the primary vector of the four serotypes of dengue virus ( DENV1-4 ) , Chikungunya and yellow fever virus to humans .", "Previous population genetic studies have revealed a particular genetic structure among the vector populations in the Americas that suggests differences in the ability to trans...	[ "Knowledge on the population structure of Aedes aegypti , the main vector of the dengue virus ( DENV ) , is essential to improving dengue fever prevention strategies in endemic countries .", "In Colombia , despite the epidemiological relevance of dengue fever , the genetic population structure and phylogeography ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology and life sciences" ]	Tethering Sister Centromeres to Each Other Suggests the Spindle Checkpoint Detects Stretch within the Kinetochore	journal.pgen.1004492	null	[ [ "Faithful chromosome segregation is essential .", "Mistakes lead to aneuploidy [1] , cancer progression [2] , and birth defects [3] .", "To ensure proper division of chromosomes , eukaryotes have evolved the spindle checkpoint , which monitors the kinetochore , a large multi-protein complex that assem...	[ "The spindle checkpoint ensures that newly born cells receive one copy of each chromosome by preventing chromosomes from segregating until they are all correctly attached to the spindle .", "The checkpoint monitors tension to distinguish between correctly aligned chromosomes and those with both sisters attached t...	[ "The spindle checkpoint monitors tension on chromosomes to distinguish between chromosomes that are correctly and incorrectly attached to the spindle .", "Tension is generated across a correctly attached chromosome as microtubules from opposite poles attach to and pull kinetochores apart , but are resisted by the...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Infection with Usutu Virus Induces an Autophagic Response in Mammalian Cells	journal.pntd.0002509	null	[ [ "The variety of factors that have contributed to the emergence of the flavivirus West Nile virus ( WNV ) in the Americas and its re-emergence in other parts of the world could also provide a suitable scenario for the emergence of other arboviruses [1] , [2] , [3] .", "These potential threats for human and...	[ "Usutu virus ( USUV ) is an African mosquito-borne flavivirus closely related to West Nile virus and Japanese encephalitis virus , which host range includes mainly mosquitoes and birds , although infections in humans have been also documented , thus warning about USUV as a potential health threat .", "Circulation...	[ "The identification of cellular components and metabolic pathways involved in virus replication provides valuable information for the development of new antiviral strategies .", "Autophagy is one of these metabolic pathways with multiple implications during viral replication .", "Autophagy literally means self-...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/genomics", "genetics and genomics/microbial evolution and genomics", "evolutionary biology/microbial evolution and genomics", "genetics and genomics/comparative genomics", "evolutionary biology/evolutionary and comparative genetics", "computational biology/comparative sequence analy...	Evidence That Mutation Is Universally Biased towards AT in Bacteria	journal.pgen.1001115	null	[ [ "Mutation generates the variability on which natural selection acts .", "Mutation is not an entirely stochastic process , as it acts according to certain deterministic biases .", "Because of this , biases in the outcome of the evolutionary process result not only from selection but also from the biase...	[ "Mutation is the engine that drives evolution and adaptation forward in that it generates the variation on which natural selection acts .", "Mutation is a random process that nevertheless occurs according to certain biases .", "Elucidating mutational biases and the way they vary across species and within genome...	[ "Natural selection sorts through the variability generated by mutation and biases evolution toward fitter outcomes .", "However , because mutation is itself not entirely random it can also bias the direction of evolution independently of selection .", "For instance , it is often assumed that the extreme variati...	2010
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases/helminth infections", "genetics and genomics/gene discovery", "molecular biology/rna splicing", "pharmacology/drug development" ]	Haemonchus contortus Acetylcholine Receptors of the DEG-3 Subfamily and Their Role in Sensitivity to Monepantel	journal.ppat.1000380	null	[ [ "Throughout the world , successful livestock production of ruminants is hampered by gastro-intestinal nematodes .", "Haemonchus contortus in particular is responsible for substantial losses to the global sheep industry [1] .", "Haemonchus contortus is a blood-feeding nematode that inhabits the abomasu...	[ "Gastro-intestinal nematodes in ruminants , especially Haemonchus contortus , are a global threat to sheep and cattle farming .", "The emergence of drug resistance , and even multi-drug resistance to the currently available classes of broad spectrum anthelmintics , further stresses the need for new drugs active a...	[ "Worldwide , sheep and cattle farming are threatened by anthelmintic-resistant gastro-intestinal nematodes .", "A novel chemical class of synthetic anthelmintics was recently discovered , the Amino-Acetonitrile Derivatives ( AADs ) , which exhibit excellent efficacy against various species of livestock-pathogenic...	2009
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "diagnostic radiology", "pathology and laboratory medicine", "mycetoma", "tropical diseases", "limbs (anatomy)", "surgical and invasive medical procedures", "health care", "magnetic resonance imaging", "x-ray radiography", "signs and symptoms", "neglected tropic...	Hand Mycetoma: The Mycetoma Research Centre Experience and Literature Review	journal.pntd.0004886	null	[ [ "Mycetoma is a highly devastating and distressing neglected tropical disease characterized by painless subcutaneous masses with multiple sinuses draining pus and grains [1 , 2] .", "The disease leads to massive deformities , disabilities with severe adverse bearings on the affected patients [3 , 4 , 5] ."...	[ "Mycetoma is a devastating , neglected tropical disease characterised by extensive tissue involvement resulting in destruction , deformities and disabilities in the affected patients .", "The hand is commonly affected by mycetoma thus compromises its functionality and hinder the patient’s daily activities of livi...	[ "Hand mycetoma is a serious condition due to the complexity of the hand anatomy and functionality .", "The disease and the surgical intervention can both produce distortions , deformities and disabilities which interfere with patient daily activities of living .", "Thus producing huge burden on the patients , t...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Hi-C Chromatin Interaction Networks Predict Co-expression in the Mouse Cortex	journal.pcbi.1004221	null	[ [ "The three dimensional ( 3D ) conformation of chromosomes in the cell nucleus plays an important role in determining which genes are expressed in a cell [1–6] .", "In particular , it has been shown that genes are often regulated by elements that are located far away in terms of the linear genome sequence ...	[ "The three dimensional conformation of the genome in the cell nucleus influences important biological processes such as gene expression regulation .", "Recent studies have shown a strong correlation between chromatin interactions and gene co-expression .", "However , predicting gene co-expression from frequent ...	[ "Regulatory elements can target genes over large genomic distances through long-range chromatin interactions .", "These interactions arise as a result of the three-dimensional ( 3D ) conformation of chromosomes in the cell nucleus .", "This 3D conformation can also result in the co-localization of co-regulated ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	EGFR/Ras Signaling Controls Drosophila Intestinal Stem Cell Proliferation via Capicua-Regulated Genes	journal.pgen.1005634	null	[ [ "EGFR/Ras/MAPK signaling has diverse functions in regulating cell proliferation , growth , differentiation and survival in most animal cells [1] .", "Abundant studies also indicate that epidermal growth factor receptor ( EGFR ) activation is a causal driver of many cancers , including breast , lung , brai...	[ "Epithelial renewal in the Drosophila intestine is orchestrated by Intestinal Stem Cells ( ISCs ) .", "Following damage or stress the intestinal epithelium produces ligands that activate the epidermal growth factor receptor ( EGFR ) in ISCs .", "This promotes their growth and division and , thereby , epithelial...	[ "Studies suggest that epidermal growth factor receptor ( EGFR ) signaling activation is a causal driver of many stem cell-derived epithelial cancers , including colorectal cancer .", "As in the human intestine , epithelial renewal in Drosophila intestine is orchestrated by intestinal stem cells ( ISCs ) .", "EG...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "bacteriophages", "pathogens", "endothelial cells", "microbiology", "pili and fimbriae", "epithelial cells", "viruses", "bacterial diseases", "cellular structures and organelles", "bacteria", "bacterial pathogens", "infec...	A virulence-associated filamentous bacteriophage of Neisseria meningitidis increases host-cell colonisation	journal.ppat.1006495	null	[ [ "Neisseria meningitidis ( Nm ) is a commensal bacterium commonly carried asymptomatically in the human nasopharynx .", "In a small proportion of colonized people , the bacteria invade the bloodstream from where they cause septicaemia and/or meningitis after crossing the blood brain barrier .", "Most m...	[ "Neisseria meningitidis is a commensal of human nasopharynx .", "In some circumstances , this bacteria can invade the bloodstream and , after crossing the blood brain barrier , the meninges .", "A filamentous phage , designated MDAΦ for Meningococcal Disease Associated , has been associated with invasive diseas...	[ "Bacteriophages are bacterial viruses , which in some cases encode for virulence factors and increase bacterial virulence .", "Comparative genomic of several strains of Neisseria meningitidis , a major human pathogen , identified the presence of an 8kb prophage in strains belonging to invasive clonal complexes ."...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Intrinsic MyD88-Akt1-mTOR Signaling Coordinates Disparate Tc17 and Tc1 Responses during Vaccine Immunity against Fungal Pneumonia	journal.ppat.1005161	null	[ [ "The rising incidence rate of life threatening fungal infections in immune-deficient hosts requires preventive measure in at risk individuals .", "CD4+ T cells are the primary effector cells that control fungal infections in healthy hosts , and their loss in lymphopenic patients necessitates targeting res...	[ "Fungal infections have skyrocketed in immune-compromised patients lacking CD4+ T cells , underscoring the need for vaccine prevention .", "An understanding of the elements that promote vaccine immunity in this setting is essential .", "We previously demonstrated that vaccine-induced IL-17A+ CD8+ T cells ( Tc17...	[ "Patients with AIDS , cancer or immune suppressive treatments are vulnerable to infection with invasive fungi .", "We have found that even when helper CD4 T cells are profoundly reduced in a mouse model that mimics this defect in AIDS , other remaining T cells are capable of mounting vaccine immunity against a de...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "fish", "pathology and laboratory medicine", "cardiovascular anatomy", "endothelial cells", "vertebrates", "animals", "epithelial cells", "animal models", "organisms", "osteichthyes", "developmental biology", "model organisms", "signs and symptoms", "exper...	MicroRNA26 attenuates vascular smooth muscle maturation via endothelial BMP signalling	journal.pgen.1008163	null	[ [ "Vascular smooth muscle cells ( vSMCs ) provide structural integrity to the vessel wall .", "Guided control of signalling cascades , including Platelet derived growth factor ( Pdgf ) , Notch , and Transforming Growth Factor-β/Bone morphogenic Protein ( TGF-β/BMP ) recruits and induces differentiation of p...	[ "As small regulatory transcripts , microRNAs ( miRs ) act as genetic ‘fine tuners’ of posttranscriptional events , and as genetic switches to promote phenotypic switching .", "The miR miR26a targets the BMP signalling effector , smad1 .", "We show that loss of miR26a leads to hemorrhage ( a loss of vascular sta...	[ "The structural integrity of a blood vessel is critical to ensure proper vessel support and vascular tone .", "Vascular smooth cells ( vSMCs ) are a key component of the vessel wall and , in their mature state , express contractile proteins that help to constrict and relax the vessel in response to blood flow cha...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/gynecologic infections", "microbiology/immunity to infections", "infectious diseases/viral infections", "public health and epidemiology/infectious diseases", "infectious diseases/skin infections", "infectious diseases/sexually transmitted diseases", "microbiology/medical microbiolog...	Seroprevalence of 34 Human Papillomavirus Types in the German General Population	journal.ppat.1000091	null	[ [ "Papillomaviruses ( PV ) are non-enveloped DNA viruses infecting cutaneous or mucosal epithelia of warm-blooded vertebrates .", "So far at least 118 distinct PV types , more than 100 of them isolated from humans , have been completely described [1] .", "In addition , about 130 L1 sequence fragments ha...	[ "The natural history of infections with many human papillomavirus ( HPV ) types is poorly understood .", "Here , we describe for the first time the age- and sex-dependent antibody prevalence for 29 cutaneous and five mucosal HPV types from 15 species within five phylogenetic genera ( alpha , beta , gamma , mu , n...	[ "Papillomaviruses ( PV ) are a large and highly diverse group of DNA viruses that infect cutaneous and mucosal epithelia of warm-blooded vertebrates .", "Of the more than 100 identified human PV ( HPV ) types , many cause benign lesions like warts and papillomas , and some also cervical , other anogenital , and o...	2008
[ "Introduction", "Results and discussion" ]	[ "mutagenesis", "biochemistry", "mutation", "dna damage", "point mutation", "dna polymerase", "mutant strains", "polymerases", "dna replication", "nucleic acids", "proteins", "genetics", "biology and life sciences", "dna", "dna-binding proteins", "frameshift mutation" ]	Processing closely spaced lesions during Nucleotide Excision Repair triggers mutagenesis in E. coli	journal.pgen.1006881	null	[ [ "Many endogenous and exogenous chemicals as well as radiations covalently damage DNA leading to major perturbations of DNA metabolism such as in replication and transcription .", "Cells have evolved sophisticated mechanisms to deal with DNA damage , collectively referred to as DNA Repair mechanisms .", ...	[ "It is generally assumed that most point mutations are fixed when damage containing template DNA undergoes replication , either right at the fork or behind the fork during gap filling .", "Here we provide genetic evidence for a pathway , dependent on Nucleotide Excision Repair , that induces mutations when proces...	[ "In this paper , we report the surprising finding that in addition to the well-known properties of Nucleotide Excision Repair ( NER ) in efficiently repairing a large number of DNA lesions , NER entails a mutagenic sub-pathway .", "Our data suggest that closely spaced lesions are processed by NER into a toxic DNA...	2017
[ "Introduction", "Methods", "Results/Discussion" ]	[]	Understanding the Connection between Epigenetic DNA Methylation and Nucleosome Positioning from Computer Simulations	journal.pcbi.1003354	null	[ [ "In eukaryotic cells gene function is modulated by a myriad of epigenetic marks and interactions with signal molecules that control synergistically the production of RNA and proteins .", "Epigenetic marks are a set of heritable but reversible chemical changes of the DNA and histones that can trigger gene ...	[ "Cytosine methylation is one of the most important epigenetic marks that regulate the process of gene expression .", "Here , we have examined the effect of epigenetic DNA methylation on nucleosomal stability using molecular dynamics simulations and elastic deformation models .", "We found that methylation of Cp...	[ "In Eukaryotic cells , control of the patterns of DNA cytosine methylation – a mechanism that acts on top of the genetic code – plays a key role in the regulation of gene expression .", "The large prevalence of DNA methylation in vivo , suggests a connection between the physical properties of methylated and un-me...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "cost-effectiveness analysis", "decision making", "engineering and technology", "economic analysis", "tropical diseases", "social sciences", "neuroscience", "parasitic diseases", "cognitive psychology", "cognition", "neglected tropical diseases", "molecular bi...	Calculating the prevalence of soil-transmitted helminth infection through pooling of stool samples: Choosing and optimizing the pooling strategy	journal.pntd.0007196	null	[ [ "Prevalence is a key epidemiological measure for assessing the burden of soil-transmitted helminths ( STH ) in human communities .", "The majority of data collected within national surveillance and treatment programs are in the form of prevalence , although infection intensity data based on egg counts fro...	[ "Prevalence is a common epidemiological measure for assessing soil-transmitted helminth burden and forms the basis for much public-health decision-making .", "Standard diagnostic techniques are based on egg detection in stool samples through microscopy and these techniques are known to have poor sensitivity for i...	[ "Current diagnostic methods for assessing prevalence of soil-transmitted helminths ( STHs ) largely rely on microscopic visualization of helminth eggs , an inexpensive but insensitive method of detection .", "However , growing interest in going beyond control to break transmission of STH through mass drug adminis...	2019
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "public health and epidemiology/infectious diseases", "developmental biology", "immunology/immune response" ]	Development and Evaluation of Two Simple, Rapid Immunochromatographic Tests for the Detection of Yersinia pestis Antibodies in Humans and Reservoirs	journal.pntd.0000421	null	[ [ "Plague , a bacterial infection caused by Yersinia pestis , is essentially a zoonosis of small mammals such as rodents .", "It is occasionally transmitted to man by the bite of an infective flea [1] .", "The bubonic form in humans can evolve rapidly to pneumonic form if not treated early .", "Plag...	[ "Tools for plague diagnosis and surveillance are not always available and affordable in most of the countries affected by the disease .", "Yersinia pestis isolation for confirmation is time-consuming and difficult to perform under field conditions .", "Serologic tests like ELISA require specific equipments not ...	[ "Plague is due to the bacterium Yersinia pestis .", "It is accidentally transmitted to humans by the bite of infected fleas .", "Currently , approximately 20 developing countries with very limited infrastructure are still affected .", "A plague case was defined according to clinical , epidemiological and biol...	2009
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Functionality of Dengue Virus Specific Memory T Cell Responses in Individuals Who Were Hospitalized or Who Had Mild or Subclinical Dengue Infection	journal.pntd.0003673	null	[ [ "Dengue viral infections are one of the most important emerging virus infections in the world [1] causing 390 million dengue infections annually , of which 96 million are clinically apparent [2][3] .", "70% of infections occur in Asia and as a result of the high disease burden , dengue has been declared a...	[ "Although antibody responses to dengue virus ( DENV ) in naturally infected individuals have been extensively studied , the functionality of DENV specific memory T cell responses in relation to clinical disease severity is incompletely understood .", "Using ex vivo IFNγ ELISpot assays , and by determining cytokin...	[ "Although dengue viral infections cause severe clinical disease , the majority of individuals infected with the dengue virus ( DENV ) develop asymptomatic infection .", "The function of DENV specific memory T cells in relation to past clinical disease severity is incompletely understood .", "In this study , we ...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Energy Landscape Reveals That the Budding Yeast Cell Cycle Is a Robust and Adaptive Multi-stage Process	journal.pcbi.1004156	null	[ [ "Stochasticity is an inherent property of living cells [1–6] .", "However , it is still difficult to quantify the robustness and adaptivity of cellular networks , even for a small cellular network perturbed by intrinsic random fluctuations , due to the massive cross regulations and nonlinear nature of suc...	[ "Quantitatively understanding the robustness , adaptivity and efficiency of cell cycle dynamics under the influence of noise is a fundamental but difficult question to answer for most eukaryotic organisms .", "Using a simplified budding yeast cell cycle model perturbed by intrinsic noise , we systematically explo...	[ "Quantitatively understanding the dynamic behavior of the yeast cell cycle process under noise perturbations is a fundamental problem in theoretical biology .", "By constructing a global energy landscape for a simplified yeast cell-cycle regulatory network , we provide a systematic study of this issue .", "Our ...	2015
[ "Introduction", "Results and discussion", "Materials and methods" ]	[ "comparative sequence analysis", "crystal structure", "applied mathematics", "condensed matter physics", "simulation and modeling", "algorithms", "optimization", "mathematics", "protein structure", "crystallography", "research and analysis methods", "sequence analysis", "solid state physics"...	Rosetta:MSF: a modular framework for multi-state computational protein design	journal.pcbi.1005600	null	[ [ "Since the 1990s , computational protein design ( CPD ) has been a powerful tool of protein engineering .", "For example , CPD has been successfully utilized to increase thermostability of proteins [1–3] and to design new or altered binding specificities for metals [4] , DNA [5] or other ligands [6 , 7] ....	[ "Computational protein design ( CPD ) is a powerful technique to engineer existing proteins or to design novel ones that display desired properties .", "Rosetta is a software suite including algorithms for computational modeling and analysis of protein structures and offers many elaborate protocols created to sol...	[ "Protein engineering , i .", "e .", "the targeted modification or design of proteins has tremendous potential for medical and industrial applications .", "One generally applicable strategy for protein engineering is rational protein design: based on detailed knowledge of structure and function , computer prog...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	TIGIT Marks Exhausted T Cells, Correlates with Disease Progression, and Serves as a Target for Immune Restoration in HIV and SIV Infection	journal.ppat.1005349	null	[ [ "During chronic viral infections , high antigenic loads continually stimulate T cells leading to progressive loss of function termed “T cell exhaustion” [1] .", "Throughout this period , T cells increase expression of several inhibitory immune receptors that raise the threshold for activation , resulting ...	[ "HIV infection induces phenotypic and functional changes to CD8+ T cells defined by the coordinated upregulation of a series of negative checkpoint receptors that eventually result in T cell exhaustion and failure to control viral replication .", "We report that effector CD8+ T cells during HIV infection in blood...	[ "HIV-1 infection contributes substantially to global morbidity and mortality , with no immediate promise of an effective vaccine .", "One major obstacle to vaccine development and therapy is to understand why HIV-1 replication persists in a person despite the presence of viral specific immune responses .", "The...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "microbiology/microbial physiology and metabolism", "microbiology/medical microbiology" ]	Role of Acetyl-Phosphate in Activation of the Rrp2-RpoN-RpoS Pathway in Borrelia burgdorferi	journal.ppat.1001104	null	[ [ "The enzootic life-cycle of Borrrelia burgdorferi is complex and typically involves transmission between an arthropod vector ( Ixodes ticks ) and a mammalian host ( e . g . , Peromyscus rodents ) [1] .", "Accumulated evidence have shown that the alternative sigma factor RpoS plays a central role in this c...	[ "Borrelia burgdorferi , the Lyme disease spirochete , dramatically alters its transcriptome and proteome as it cycles between the arthropod vector and mammalian host .", "During this enzootic cycle , a novel regulatory network , the Rrp2-RpoN-RpoS pathway ( also known as the σ54–σS sigma factor cascade ) , plays ...	[ "Borrelia burgdorferi , the causative agent of Lyme disease , is maintained in nature in a complex enzootic cycle involving Ixodes ticks and mammals .", "A novel regulatory network , the Rrp2-RpoN-RpoS pathway , which governs differential expression of numerous genes of B . burgdorferi , is essential for this com...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "dna metabolism", "genetic mutation", "small molecules", "microbiology", "model organisms", "mutation types", "dna", "dna structure", "biology", "molecular biology", "mutagenesis", "biochemistry", "nucleic acids", "genetics", "yeast and fungal models", "dna repair", "saccharomyces ce...	Stimulation of Gross Chromosomal Rearrangements by the Human CEB1 and CEB25 Minisatellites in Saccharomyces cerevisiae Depends on G-Quadruplexes or Cdc13	journal.pgen.1003033	null	[ [ "Some chromosomal regions are more prone to rearrangement than others and thus are the source of genetic diseases and cancer .", "Among “at risk” sequences , tandem repeats like microsatellites and minisatellites that differ by the length of their repeat unit ( 1–10 nt and 10–100 nt , respectively ) are p...	[ "Genomes contain tandem repeats that are at risk of internal rearrangements and a threat to genome integrity .", "Here , we investigated the behavior of the human subtelomeric minisatellites HRAS1 , CEB1 , and CEB25 in Saccharomyces cerevisiae .", "In mitotically growing wild-type cells , these GC–rich tandem a...	[ "All genomes contain particular DNA sequences that are prone to break and rearrange .", "They can be lost or rescued at the expense of sequence variations and complex rearrangements .", "Using a sensitive yeast model system , we examined the fragility of the HRAS1 , CEB1 , and CEB25 GC-rich human minisatellites...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Gene Amplification and Point Mutations in Pyrimidine Metabolic Genes in 5-Fluorouracil Resistant Leishmania infantum	journal.pntd.0002564	null	[ [ "The protozoan parasites Leishmania are distributed worldwide and cause different symptoms including cutaneous , mucocutaneous or visceral leishmaniasis , the latter potentially fatal if left untreated [1] , [2] .", "Treatments include pentavalent antimonials , amphotericin B , paromomycin or miltefosine ...	[ "The human protozoan parasites Leishmania are prototrophic for pyrimidines with the ability of both de novo biosynthesis and uptake of pyrimidines .", "Five independent L . infantum mutants were selected for resistance to the pyrimidine analogue 5-fluorouracil ( 5-FU ) in the hope to better understand the metabol...	[ "The human protozoan parasites Leishmania present the ability of both de novo biosynthesis and uptake of pyrimidines .", "The pyrimidine pathway is not well understood in these parasites .", "In the hope to better understand the pyrimidine pathway in Leishmania , five independent L . infantum mutants were selec...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biotechnology", "infectious diseases", "none", "microbiology", "computational biology", "molecular biology" ]	Comprehensive DNA Signature Discovery and Validation	journal.pcbi.0030098	null	[ [ "Recent increases in the amount of available genomic sequence have made it possible to largely automate the design and screening of probes via computational search algorithms .", "Large-scale computational prediction of DNA signatures was first undertaken for the Biological Aerosol Sentry and Information ...	[ "DNA signatures are nucleotide sequences that can be used to detect the presence of an organism and to distinguish that organism from all other species .", "Here we describe Insignia , a new , comprehensive system for the rapid identification of signatures in the genomes of bacteria and viruses .", "With the av...	[ "Now that the genome sequences of hundreds of bacteria and viruses are known , we can design tests that will rapidly detect the presence of these species based solely on their DNA .", "Such tests have a wide range of applications , from diagnosing infections to detecting harmful microbes in a water supply .", "...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "host-pathogen interaction", "microbiology", "bacterial diseases", "emerging infectious diseases", "neglected tropical diseases", "microbial growth and development", "bacterial pathogens", "veterinary science", "infectious diseases", "veterinary diseases", "microbial physiology", ...	A Model System for Studying the Transcriptomic and Physiological Changes Associated with Mammalian Host-Adaptation by Leptospira interrogans Serovar Copenhageni	journal.ppat.1004004	null	[ [ "Leptospirosis is a neglected disease of global significance [1] , [2] .", "Pathogenic leptospires , shed in animal urine or free-living within contaminated water , enter the host through small abrasions in the skin or contact with mucous membranes of the eyes , nose or throat .", "Organisms dissemina...	[ "Leptospirosis , an emerging zoonotic disease with worldwide distribution , is caused by spirochetes belonging to the genus Leptospira .", "More than 500 , 000 cases of severe leptospirosis are reported annually , with >10% of these being fatal .", "Leptospires can survive for weeks in suitably moist conditions...	[ "Leptospirosis , a global disease caused by the unusual bacterium Leptospira , is transmitted from animals to humans .", "Pathogenic species of Leptospira are excreted in urine from infected animals and can continue to survive in suitable environments before coming into contact with a new reservoir or accidental ...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "plant anatomy", "cell motility", "medicine and health sciences", "enzyme-linked immunoassays", "pathology and laboratory medicine", "aspergillus", "enzymes", "immunology", "enzymology", "parasitic protozoans", "fungal molds", "acanthamoeba", "pollen", "fungi", "plant science", "clinic...	Acanthamoeba profilin elicits allergic airway inflammation in mice	journal.pntd.0006979	null	[ [ "Allergic airway inflammation is characterized by the production of allergen-specific immunoglobulin ( Ig ) E and Th2 cytokines including interleukin ( IL ) -4 , IL-5 , and IL-13 which lead to the immune cell recruitment and sensitization of effector cells such as eosinophils , basophils , and mast cells [1] ...	[ "In previous studies , we suggested that Acanthamoeba is a new aero-allergen and that patients who showed positive results for the skin-prick test response to Acanthamoeba cross-reacted with several pollen allergens .", "Additionally , patients with common antibodies reacted to the 13–15 kDa Acanthamoeba unknown ...	[ "Recently , the number of asthma patients have increased sharply .", "Among patients with asthma have a high serum IgE titer , but despite this , some of these patients do not react to known allergens in skin prick tests , that suggests the presence of unknown environmental allergens .", "The protozoa Acanthamo...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "viral transmission and infection", "293t cells", "pathogens", "biological cultures", "vector-borne diseases", "microbiology", "rna extraction", "retroviruses", "viruses", "immunodeficiency viruses", "viral vectors", "mut...	HIV-1 capsids from B27/B57+ elite controllers escape Mx2 but are targeted by TRIM5α, leading to the induction of an antiviral state	journal.ppat.1007398	null	[ [ "ECs are a rare ( <0 . 5% ) and heterogeneous subset of HIV-1-infected subjects grouped together because they maintain undetectable viremia ( <50 copies⁄ml ) and normal CD4+ T cell counts in the absence of antiretroviral therapy ( ART ) .", "Peripheral virus is usually not detectable by conventional PCR m...	[ "Elite controllers ( ECs ) are a rare subset of HIV-1 slow progressors characterized by prolonged viremia suppression .", "HLA alleles B27 and B57 promote the cytotoxic T lymphocyte ( CTL ) -mediated depletion of infected cells in ECs , leading to the emergence of escape mutations in the viral capsid ( CA ) .", ...	[ "Some HIV-1-infected individuals show a natural capacity to control viral propagation .", "In individuals that have the HLA B27 or B57 allele , HIV-1 control is associated with mutations in viral proteins that arise as a result of immune pressure from cytotoxic T lymphocytes .", "HIV-1 capsid protein mutations ...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "fungal spores", "medicine and health sciences", "yeast infections", "cryptococcus", "immune cells", "fungal spore germination", "immunology", "cell processes", "animal models", "fungi", "model organisms", "lymph nodes", "lymphatic system", "experimental organism systems",...	Infectious particle identity determines dissemination and disease outcome for the inhaled human fungal pathogen Cryptococcus	journal.ppat.1007777	null	[ [ "Through the act of breathing , the mammalian lung is regularly exposed to a wide variety of airborne particles , such as dust , air pollutants , and microbes .", "Both physical and immunological barriers have evolved to keep the lung clear of foreign agents and facilitate efficient respiration .", "I...	[ "The majority of invasive human fungal pathogens gain access to their human hosts via the inhalation of spores from the environment into the lung , but relatively little is known about this infectious process .", "Among human fungal pathogens the most frequent cause of inhaled fatal fungal disease is Cryptococcus...	[ "Little is known about how inhaled spores from human fungal pathogens cause infections and spread to other parts of the body .", "The most frequent cause of inhaled fatal fungal disease is Cryptococcus , which causes meningitis .", "To understand how Cryptococcus causes disease , we evaluated pathogenesis of tw...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "gene regulation", "pathogens", "microbiology", "plasmid construction", "viruses", "dna replication", "dna viruses", "hpv-31", "dna construction", "molecular biology techniques", "dna", "human papillomavirus", "hpv-1", ...	Interaction of NCOR/SMRT Repressor Complexes with Papillomavirus E8^E2C Proteins Inhibits Viral Replication	journal.ppat.1005556	null	[ [ "Human papillomaviruses ( HPV ) constitute one of the largest human pathogenic virus families known to date .", "HPV Infections can cause skin warts , ano-genital warts and papillomas derived from mucosal or cutaneous epithelium .", "Persistent infections with certain HPV types such as HPV16 , 18 , 31...	[ "Infections with high-risk human papillomaviruses ( HR-HPV ) such as HPV16 and 31 can lead to ano-genital and oropharyngeal cancers and HPV types from the beta genus have been implicated in the development of non-melanoma skin cancer .", "HPV replicate as nuclear extrachromosomal plasmids at low copy numbers in u...	[ "Human papillomaviruses ( HPV ) have been shown to cause ano-genital and oropharyngeal cancers and have been also implicated in non-melanoma skin cancer .", "HPV have a two-stage replication cycle: in undifferentiated keratinocytes only a low level of genome replication without virus production can be observed wh...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biotechnology", "bioengineering", "biological systems engineering", "engineering and technology", "synthetic biology", "biology and life sciences" ]	Accurate, Model-Based Tuning of Synthetic Gene Expression Using Introns in S. cerevisiae	journal.pgen.1004407	null	[ [ "Advancements and innovations in synthetic and computational biology have revolutionized our ability to rationally engineer libraries of single synthetic genetic elements ( such as promoters or ribosome binding sites ) and have increased our capacity to finely tune the expression of genes according to specifi...	[ "Introns are key regulators of eukaryotic gene expression and present a potentially powerful tool for the design of synthetic eukaryotic gene expression systems .", "However , intronic control over gene expression is governed by a multitude of complex , incompletely understood , regulatory mechanisms .", "Despi...	[ "Synthetic biology is gradually expanding our capability to engineer biology through rational genetic engineering of synthetic gene expression systems .", "These developments are already paving the way for the accelerated study of biology and applying engineered biological systems to major environmental and healt...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Rescheduling Behavioral Subunits of a Fixed Action Pattern by Genetic Manipulation of Peptidergic Signaling	journal.pgen.1005513	null	[ [ "Innate behaviors are stereotypic patterns of movement inherited from birth that require no prior experience for proper execution .", "Among such behaviors are fixed action patterns that , once initiated , run to completion independent of sensory inputs .", "Examples include courtship rituals , aggres...	[ "The ecdysis behavioral sequence in insects is a classic fixed action pattern ( FAP ) initiated by hormonal signaling .", "Ecdysis triggering hormones ( ETHs ) release the FAP through direct actions on the CNS .", "Here we present evidence implicating two groups of central ETH receptor ( ETHR ) neurons in sched...	[ "In Drosophila , the pupal ecdysis behavioral sequence is composed of three distinct steps: pre-ecdysis , ecdysis , and post-ecdysis .", "We hypothesize that release of ecdysis-triggering-hormone ( ETH ) from endocrine Inka cells drives these stereotypical behaviors through sequential activation of peptidergic ET...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "systems biology", "developmental biology", "organism development", "gene expression", "genetics", "biology", "genetics and genomics", "dna transcription", "gene function" ]	Hormonal Signal Amplification Mediates Environmental Conditions during Development and Controls an Irreversible Commitment to Adulthood	journal.pbio.1001306	A dual mechanism regulates the developmental fate choice in C. elegans in response to population density: variation of the threshold of DA hormone required to commit to a certain fate and a positive feedback loop that amplifies this hormonal signal to ensure an organism-wide developmental fate choice.	[ [ "During development , organisms often face unpredictable and unfavorable environmental conditions that may decrease their fitness .", "In some cases , organisms of the same genotype develop into alternate phenotypes , each better adapted to a particular environment .", "Alternative phenotypes entail c...	[ "Many animals can choose between different developmental fates to maximize fitness .", "Despite the complexity of environmental cues and life history , different developmental fates are executed in a robust fashion .", "The nematode Caenorhabditis elegans serves as a powerful model to examine this phenomenon be...	[ "During development , many animals choose between mutually exclusive fates , such as workers , soldiers , or queens in bees or ants .", "The choice between states is uniform throughout the animal since mixtures of these fates are not observed in the wild .", "The nematode Caenorhabditis elegans larvae integrate...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry", "transmembrane proteins", "proteins", "protein folding", "protein structure", "biology", "microbiology", "host-pathogen interaction", "biophysics" ]	Dual Chaperone Role of the C-Terminal Propeptide in Folding and Oligomerization of the Pore-Forming Toxin Aerolysin	journal.ppat.1002135	null	[ [ "Many organisms , as diverse as bacteria , parasites , sea anemones or plants , produce membrane damaging proteins to protect themselves or to modify the behavior of their host [1] .", "Amongst these pore-forming proteins ( PFPs ) , we find bacterial pore-forming toxins ( PFTs ) .", "These are produce...	[ "Throughout evolution , one of the most ancient forms of aggression between cells or organisms has been the production of proteins or peptides affecting the permeability of the target cell membrane .", "This class of virulence factors includes the largest family of bacterial toxins , the pore-forming toxins ( PFT...	[ "Many pathogenic bacteria produce proteins , called pore-forming toxins , designed to perforate the plasma membrane of target cells thus perturbing host cell integrity and functionality .", "It is , however , important that these toxins do not form pores in the producing bacterium .", "To prevent this , bacteri...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology/virulence factors and mechanisms", "virology/viral replication and gene regulation", "virology/virion structure, assembly, and egress", "gastroenterology and hepatology/hepatology", "cell biology", "virology", "infectious diseases/viral infections", "molecular biology" ]	Essential Role of Domain III of Nonstructural Protein 5A for Hepatitis C Virus Infectious Particle Assembly	journal.ppat.1000035	null	[ [ "The hepatitis C virus ( HCV ) is a major causative agent of acute and chronic liver diseases worldwide [1] .", "A hallmark of HCV infection is the high persistence , which is unusual for a virus of this group and which has been explained by numerous active and passive immune evasion strategies [2] , [3] ...	[ "Persistent infection with the hepatitis C virus ( HCV ) is a major risk factor for the development of liver cirrhosis and hepatocellular carcinoma .", "With an estimated about 3% of the world population infected with this virus , the lack of a prophylactic vaccine and a selective therapy , chronic hepatitis C cu...	[ "The hepatitis C virus ( HCV ) is a major cause of acute and chronic liver diseases worldwide .", "In spite of high medical need there is no selective antiviral therapy available and a prophylactic vaccine is not in sight .", "Their development requires cellular replication systems that have become available ju...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "endocrine tumors", "carcinomas", "cancers and neoplasms", "oncology", "mutation", "histology", "signaling cascades", "gene types", "mapk signaling cascades", "chromosome biology", "lung and intrathoracic tumors", "gene expression", "thyroid", "fusion gene...	Comprehensive Analysis of the Transcriptional and Mutational Landscape of Follicular and Papillary Thyroid Cancers	journal.pgen.1006239	null	[ [ "Most thyroid cancers are classified as either classical papillary thyroid carcinoma ( cPTC ) , follicular variant of PTC ( FVPTC ) , or follicular thyroid carcinoma ( FTC ) based on histological architecture [1] .", "However , the distinction between follicular-patterned thyroid tumors , such as FVPTC , ...	[ "Follicular thyroid carcinoma ( FTC ) and benign follicular adenoma ( FA ) are indistinguishable by preoperative diagnosis due to their similar histological features .", "Here we report the first RNA sequencing study of these tumors , with data for 30 minimally invasive FTCs ( miFTCs ) and 25 FAs .", "We also c...	[ "Recently , The Cancer Genome Atlas proposed an improved classification of the subtypes of papillary thyroid carcinoma ( PTC ) based on gene expression profiles , which better represents cell signaling and differentiation .", "However , a molecular characterization of follicular thyroid carcinoma ( FTC ) , which ...	2016
[ "Introduction", "Methods", "Results and Discussion", "Scenario 2: Potential Influence on Infection Resurgence" ]	[]	Human Onchocerciasis: Modelling the Potential Long-term Consequences of a Vaccination Programme	journal.pntd.0003938	null	[ [ "Currently , the predominant onchocerciasis control strategy in Africa is annual mass drug administration ( MDA ) with ivermectin , which Merck & Co . have committed to donate for as long as needed to eliminate onchocerciasis as a public health problem .", "Since 2010 there has been a dramatic shift in on...	[ "Currently , the predominant onchocerciasis control strategy in Africa is annual mass drug administration ( MDA ) with ivermectin .", "However , there is a consensus among the global health community , supported by mathematical modelling , that onchocerciasis in Africa will not be eliminated within proposed time ...	[ "Novel and alternative strategies are required to meet the demanding control and elimination ( of infection ) goals for human onchocerciasis ( river blindness ) in Africa .", "Due to the overlapping distribution of onchocerciasis and loiasis ( African eye worm ) in forested areas of central Africa , millions of p...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "larvicides", "invertebrates", "dengue virus", "medicine and health sciences", "body fluids", "pathology and laboratory medicine", "pathogens", "microbiology", "animals", "viruses", "age groups", "developmental biology", "adults", "rna viruses", "pest control", "infectious disease cont...	Transstadial Effects of Bti on Traits of Aedes aegypti and Infection with Dengue Virus	journal.pntd.0004370	null	[ [ "Aedes aegypti ( Linnaeus ) is regarded as one of the most important vectors of arboviruses that affect human health , including yellow fever , chikungunya , and dengue .", "Protecting humans from the diseases transmitted by this mosquito has historically been achieved by controlling mosquito populations ...	[ "Most mosquito control efforts are primarily focused on reducing the adult population size mediated by reductions in the larval population , which should lower risk of disease transmission .", "Although the aim of larviciding is to reduce larval abundance and thus recruitment of adults , nonlethal effects on adul...	[ "Effective control of mosquito-borne diseases like dengue fever has historically been achieved by controlling vector populations .", "The use of larvicides that kill the larval stages of the yellow fever mosquito is a critical component of effective control .", "However , larvicides may act together with other ...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The Borrelia burgdorferi RelA/SpoT Homolog and Stringent Response Regulate Survival in the Tick Vector and Global Gene Expression during Starvation	journal.ppat.1005160	null	[ [ "The Lyme disease spirochete Borrelia burgdorferi is maintained in an enzootic cycle involving ticks and vertebrates [1–3] .", "Since B . burgdorferi is not transovarially transmitted , the bacterium must be acquired by Ixodes larval ticks feeding on an infected mammal , the host reservoir .", "The la...	[ "As the Lyme disease bacterium Borrelia burgdorferi traverses its enzootic cycle , alternating between a tick vector and a vertebrate host , the spirochete must adapt and persist in the tick midgut under prolonged nutrient stress between blood meals .", "In this study , we examined the role of the stringent respo...	[ "Borrelia burgdorferi , the spirochete responsible for causing Lyme disease , is maintained in nature via cycling between an Ixodes tick vector and a vertebrate host .", "The spirochete must adapt to and survive extreme nutrient deprivation , which may last months between blood meals , to persist in the midgut of...	2015
[ "Introduction", "Results", "Discussion", "Material and Methods" ]	[ "evolutionary biology/genomics", "evolutionary biology/plant genomes and evolution", "evolutionary biology/evolutionary and comparative genetics" ]	Repeated Adaptive Introgression at a Gene under Multiallelic Balancing Selection	journal.pgen.1000168	null	[ [ "The genomes of incipient species diverge at heterogeneous rates , and recently diverged model species are key systems to investigate the causes of this heterogeneity [1]–[3] .", "Hybridization followed by introgression between recently diverged plant and animal species with incomplete reproductive barrie...	[ "Recently diverged species typically have incomplete reproductive barriers , allowing introgression of genetic material from one species into the genomic background of the other .", "The role of natural selection in preventing or promoting introgression remains contentious .", "Because of genomic co-adaptation ...	[ "The role of natural selection in promoting or preventing genomic divergence between nascent species remains highly debated .", "As long as reproductive barriers remain incomplete , genetic material from one species is indeed exposed to natural selection into the genomic background of the other species .", "In ...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics", "biology", "microbiology", "genetics and genomics" ]	Mechanisms Employed by Escherichia coli to Prevent Ribonucleotide Incorporation into Genomic DNA by Pol V	journal.pgen.1003030	null	[ [ "Translesion synthesis ( TLS ) allows living organisms to tolerate DNA damage to their genome .", "The vast majority of TLS in Escherichia coli is catalyzed by the LexA-regulated damage-inducible polymerases II , IV and V , which alone , or in various combinations , are recruited to the sites of DNA damag...	[ "Escherichia coli pol V ( UmuD′2C ) , the main translesion DNA polymerase , ensures continued nascent strand extension when the cellular replicase is blocked by unrepaired DNA lesions .", "Pol V is characterized by low sugar selectivity , which can be further reduced by a Y11A “steric-gate” substitution in UmuC t...	[ "E . coli pol V , a complex formed by umuC and umuD gene products , is a “founding” member of the Y-family of DNA polymerases that have been identified in all domains of life .", "The primary cellular function of Y-family polymerases is the replication of damaged DNA .", "We discovered that pol V is characteriz...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biotechnology", "sequencing techniques", "genome expression analysis", "functional genomics", "gene regulation", "microbiology", "genome sequencing", "fungi", "genome analysis", "molecular genetics", "molecular biology techniques", "applied microbiology", "environmental biotechnology", "m...	Analysis of the Phlebiopsis gigantea Genome, Transcriptome and Secretome Provides Insight into Its Pioneer Colonization Strategies of Wood	journal.pgen.1004759	null	[ [ "The most abundant source of terrestrial carbon is plant biomass , composed primarily of cellulose , hemicellulose , and lignin .", "Numerous microbes utilize cellulose and hemicellulose , but a much smaller group of filamentous fungi has the capacity to degrade lignin , the most recalcitrant component of...	[ "Collectively classified as white-rot fungi , certain basidiomycetes efficiently degrade the major structural polymers of wood cell walls .", "A small subset of these Agaricomycetes , exemplified by Phlebiopsis gigantea , is capable of colonizing freshly exposed conifer sapwood despite its high content of extract...	[ "The wood decay fungus Phlebiopsis gigantea degrades all components of plant cell walls and is uniquely able to rapidly colonize freshly exposed conifer sapwood .", "However , mechanisms underlying its conversion of lignocellulose and resinous extractives have not been explored .", "We report here analyses of t...	2014
[ "Introduction", "Methods", "Results/Discussion" ]	[ "biotechnology", "computer applications", "computer science", "medicinal chemistry", "organic chemistry", "chemistry", "biology" ]	DOGS: Reaction-Driven de novo Design of Bioactive Compounds	journal.pcbi.1002380	null	[ [ "De novo design aims at generating new chemical entities with drug-like properties and desired biological activities in a directed fashion [1] , [2] .", "This goal corresponds to the major task of the early drug discovery process and comprises a considerable fraction of the effort spent by pharmaceutical ...	[ "We present a computational method for the reaction-based de novo design of drug-like molecules .", "The software DOGS ( Design of Genuine Structures ) features a ligand-based strategy for automated ‘in silico’ assembly of potentially novel bioactive compounds .", "The quality of the designed compounds is asses...	[ "The computer program DOGS aims at the automated generation of new bioactive compounds .", "Only a single known reference compound is required to have the computer come up with suggestions for potentially isofunctional molecules .", "A specific feature of the algorithm is its capability to propose a synthesis p...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "systems biology", "developmental biology", "biology", "computational biology", "genetics and genomics" ]	Stochastic De-repression of Rhodopsins in Single Photoreceptors of the Fly Retina	journal.pcbi.1002357	null	[ [ "The ability of Drosophila to perceive color and motion depends on the specific patterning of several Rhodopsin proteins throughout its retina [1]–[3] .", "The fly retina is a complex three-dimensional structure that consists of a lattice of approximately 800 simple eyes known as ommatidia [4] .", "As...	[ "The photoreceptors of the Drosophila compound eye are a classical model for studying cell fate specification .", "Photoreceptors ( PRs ) are organized in bundles of eight cells with two major types – inner PRs involved in color vision and outer PRs involved in motion detection .", "In wild type flies , most PR...	[ "Complex networks of genetic interactions govern the development of multicellular organisms .", "One of the best-characterized networks governs the development of the fruit-fly retina , a highly organized , three-dimensional organ composed of a hexagonal grid of eight types of photoreceptor neurons .", "Each ph...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "bacterial diseases", "infectious diseases", "salmonellosis", "salmonella" ]	Salmonella Typhi in the Democratic Republic of the Congo: Fluoroquinolone Decreased Susceptibility on the Rise	journal.pntd.0001921	null	[ [ "Typhoid fever is endemic in the Democratic Republic of the Congo ( DR Congo ) .", "Although antimicrobial resistance data are sparse for Central Africa , drug resistance to first-line antibiotics is clearly emerging [1] .", "Also in DR Congo , multidrug resistance ( MDR ) [defined as co-resistance to...	[ "Drug resistance of Salmonella enterica serovar Typhi ( Salmonella Typhi ) to first-line antibiotics is emerging in Central Africa .", "Although increased use of fluoroquinolones is associated with spread of resistance , Salmonella Typhi with decreased ciprofloxacin susceptibility ( DCS ) has rarely been reported...	[ "Typhoid fever , caused by infection with Salmonella enterica serovar Typhi ( Salmonella Typhi ) , is an important health problem in sub-Saharan Africa .", "Multidrug resistance of Salmonella Typhi to the first line antibiotics is spreading and treatment of typhoid fever increasingly relies on fluoroquinolone ant...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "microbiology/plant-biotic interactions", "microbiology/microbial physiology and metabolism", "genetics and genomics/gene function", "biochemistry/cell signaling and trafficking structures", "infectious diseases/bacterial infections", "microbiology/microbial growth and development", "microbiology/medica...	A Novel Signaling Network Essential for Regulating Pseudomonas aeruginosa Biofilm Development	journal.ppat.1000668	null	[ [ "Biofilms are composed of microorganisms attached to a solid surface and encased in a hydrated polymeric matrix of their own synthesis .", "Biofilms form when bacteria adhere to surfaces in moist environments .", "Biofilm-associated microorganisms have been shown to colonize a wide variety of medical ...	[ "The important human pathogen Pseudomonas aeruginosa has been linked to numerous biofilm-related chronic infections .", "Here , we demonstrate that biofilm formation following the transition to the surface attached lifestyle is regulated by three previously undescribed two-component systems: BfiSR ( PA4196-4197 )...	[ "Biofilms are complex communities of microorganisms encased in a matrix and attached to surfaces .", "It is well recognized that biofilm cells differ from their free swimming counterparts with respect to gene expression , protein production , and resistance to antibiotics and the human immune system .", "Howeve...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "linguistics", "chemical compounds", "enzymes", "enzymology", "social sciences", "carbohydrates", "neuroscience", "organic compounds", "cognitive psychology", "glycosylation", "glycoproteins", "language", "proteins", "chemistry", "grammar", "biochemistry", "enzyme structure", "muci...	A Knowledge-Based System for Display and Prediction of O-Glycosylation Network Behaviour in Response to Enzyme Knockouts	journal.pcbi.1004844	null	[ [ "Glycosylation is a major post-translational modification of proteins , in which a carbohydrate moiety , called a glycan , is covalently attached to an amino acid of the polypeptide , to form a glycoprotein [1] .", "N-linked glycans are attached to an asparagine ( N ) residue appearing in the consensus se...	[ "O-linked glycosylation is an important post-translational modification of mucin-type protein , changes to which are important biomarkers of cancer .", "For this study of the enzymes of O-glycosylation , we developed a shorthand notation for representing GalNAc-linked oligosaccharides , a method for their graphic...	[ "Our objective being to model the enzymes of mucin-type O-linked glycosylation , we first developed a model language to represent O-glycan structures succinctly in linear string form , to which a set of pattern-matching rules was then applied to simulate the activities of a set of 25 glycosyltransferase and sulfotr...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "computational biology/signaling networks", "mathematics", "computational biology/systems biology", "cell biology/cell signaling" ]	A Critical Quantity for Noise Attenuation in Feedback Systems	journal.pcbi.1000764	null	[ [ "It has been identified that feedback loops play important roles in a variety of biological processes , such as calcium signaling [1] , [2] , p53 regulation [3] , galactose regulation [4] , cell cycle [5]–[8] , and budding yeast polarization [9]–[13] .", "Although the detailed regulation of feedback loops...	[ "Feedback modules , which appear ubiquitously in biological regulations , are often subject to disturbances from the input , leading to fluctuations in the output .", "Thus , the question becomes how a feedback system can produce a faithful response with a noisy input .", "We employed multiple time scale analys...	[ "Many biological systems use feedback loops to regulate dynamic interactions among different genes and proteins .", "Here , we ask how interlinked feedback loops control the timing of signal transductions and responses and , consequently , attenuate noise .", "Drawing on simple modeling along with both analytic...	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "biotechnology", "public and occupational health", "medicine and health sciences", "biology and life sciences", "sociology", "social sciences", "anthropology" ]	Designing a Community Engagement Framework for a New Dengue Control Method: A Case Study from Central Vietnam	journal.pntd.0002794	null	[ [ "The Wolbachia strategy aims to ‘manipulate mosquito populations to make them incapable of transmitting dengue viruses between people’ ( www . eliminatedengue . com ) .", "Its potential emerged following the successful transference of the insect bacterium Wolbachia pipientis from the fruit fly Drosophila ...	[ "The Wolbachia strategy aims to manipulate mosquito populations to make them incapable of transmitting dengue viruses between people .", "To test its efficacy , this strategy requires field trials .", "Public consultation and engagement are recognized as critical to the future success of these programs , but qu...	[ "In recent years , a number of new strategies using novel technologies for the control of dengue fever control have emerged .", "These strategies are notably different from their predecessors and not without controversy .", "Many also require open release field trials to test their efficacy .", "Public consul...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "organismal evolution", "public health and epidemiology", "ecology", "epidemiology", "biology", "evolutionary biology", "zoology", "parasitology" ]	Plasmodium knowlesi: Reservoir Hosts and Tracking the Emergence in Humans and Macaques	journal.ppat.1002015	null	[ [ "Until recently , it was believed that malaria in humans was caused by only four species of parasite ( Plasmodium falciparum , P . vivax , P . malariae and P . ovale ) .", "However , this perception changed when we discovered a large focus of human infections with P . knowlesi in the Kapit Division of Sar...	[ "Plasmodium knowlesi , a malaria parasite originally thought to be restricted to macaques in Southeast Asia , has recently been recognized as a significant cause of human malaria .", "Unlike the benign and morphologically similar P . malariae , these parasites can lead to fatal infections .", "Malaria parasites...	[ "We recently described the first focus of human infections with P . knowlesi , a malaria parasite of monkeys , and subsequently reported that these infections can be fatal .", "Whether mosquito transmission of infection depended on the monkey reservoir or was maintained by the human population was unknown .", "...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "urology", "invertebrates", "medicine and health sciences", "microbiology", "vertebrates", "animals", "mammals", "viruses", "rna viruses", "insect vectors", "infectious diseases", "swine", "birds", "gamefowl", "viral replication", "fowl", "disease vectors", "insects", "poultry", ...	NS2B/NS3 mutations enhance the infectivity of genotype I Japanese encephalitis virus in amplifying hosts	journal.ppat.1007992	null	[ [ "Japanese encephalitis virus ( JEV ) , a mosquito-borne flavivirus , has a single-stranded , positive-sense RNA genome encoding three structural proteins ( capsid , precursor membrane protein , and envelope protein ) and seven non-structural proteins ( NS1 , NS2A , NS2B , NS3 , NS4A , NS4B , and NS5 ) [1] .",...	[ "Genotype I ( GI ) virus has replaced genotype III ( GIII ) virus as the dominant Japanese encephalitis virus ( JEV ) in the epidemic area of Asia .", "The mechanism underlying the genotype replacement remains unclear .", "Therefore , we focused our current study on investigating the roles of mosquito vector an...	[ "Flaviviral vertebrate amplifying host ( s ) , invertebrate vector ( s ) , genetics , and environmental factors shape the viral geographical distribution and epidemic disease pattern .", "Newly emerging dengue virus genotypes , West Nile virus clades , or Zika virus strains exhibited an enhancement in mosquito ve...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "meiosis", "cell biology", "synapsis", "chromosome biology", "cell cycle and cell division", "biology and life sciences", "cell processes", "meiotic prophase" ]	Protein Phosphatase 4 Promotes Chromosome Pairing and Synapsis, and Contributes to Maintaining Crossover Competence with Increasing Age	journal.pgen.1004638	null	[ [ "For a single diploid genome to be partitioned into two haploid genomes in meiosis , chromosomes must undergo a sequence of strictly regulated dynamic events during meiotic prophase .", "Chromosomes must encounter , assess homology , and form close pairing interactions with their homologous partners , to ...	[ "Prior to the meiotic divisions , dynamic chromosome reorganizations including pairing , synapsis , and recombination of maternal and paternal chromosome pairs must occur in a highly regulated fashion during meiotic prophase .", "How chromosomes identify each other's homology and exclusively pair and synapse with...	[ "Meiosis creates gametes by distributing diploid genomes containing homologous chromosome pairs into daughter cells that receive only one of each chromosome .", "To segregate correctly at the first meiotic division , chromosomes must pair and synapse with their homologous partners , and undergo crossover recombin...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "plant science", "plant growth and development", "plant biology", "plant genetics", "biology" ]	MicroRNA–Mediated Repression of the Seed Maturation Program during Vegetative Development in Arabidopsis	journal.pgen.1003091	null	[ [ "Seed maturation is a highly coordinated developmental phase in which storage reserves , including seed storage proteins ( SSPs ) , are synthesized and accumulated to high levels .", "The maturation genes need to be repressed , however , in order to allow seedling development to occur .", "Indeed , th...	[ "The seed maturation program only occurs during late embryogenesis , and repression of the program is pivotal for seedling development .", "However , the mechanism through which this repression is achieved in vegetative tissues is poorly understood .", "Here we report a microRNA ( miRNA ) –mediated repression m...	[ "Seed development can be conceptually divided into two phases: namely the morphogenesis phase , in which cell division is active and all the major organs are formed , and the maturation phase , in which cells enlarge and storage reserves are synthesized and accumulated .", "Expression of the seed maturation progr...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "public and occupational health", "infectious diseases", "medicine and health sciences", "disease eradication", "global health", "vector-borne diseases", "infectious disease control" ]	Neglected Tropical Diseases: A Systematic Evaluation of Research Capacity in Nigeria	journal.pntd.0003078	null	[ [ "The impact of neglected tropical diseases ( NTDs ) on the health and economy of neglected communities is gaining increasing international attention with a call for global efforts to eliminate or eradicate 10 NTDs by 2020 [1][2] .", "NTDs are a group of infections that mainly affect people living in remot...	[ "Nigeria carries the highest burden and diversity of neglected tropical diseases ( NTDs ) in sub-Saharan Africa and is preparing to scale up its efforts to control/eliminate these diseases .", "To achieve this it will require a range of internal technical support and expertise for mapping , monitoring and evaluat...	[ "Nigeria carries the highest burden and diversity of neglected tropical diseases ( NTDs ) in sub-Saharan Africa and is preparing to increase the control and elimination of these diseases .", "The aim of this study was to provide information on the disease focus and type of studies carried out by scientists workin...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing techniques", "schistosoma", "invertebrates", "schistosoma mansoni", "medicine and health sciences", "pathology and laboratory medicine", "helminths", "pathogens", "microbiology", "viral structure", "genomic library construction", "animals", "invertebrate genomics", "retroviruse...	HIV-1 Integrates Widely throughout the Genome of the Human Blood Fluke Schistosoma mansoni	journal.ppat.1005931	null	[ [ "Schistosomiasis is considered the most important helminthic disease of humanity in terms of morbidity and mortality , and is one of the major neglected tropical diseases ( NTDs ) [1–4] .", "Whereas > 90% of cases occur in Africa , where the major burden of disease lies , a recent outbreak in Corsica conf...	[ "Schistosomiasis is the most important helminthic disease of humanity in terms of morbidity and mortality .", "Facile manipulation of schistosomes using lentiviruses would enable advances in functional genomics in these and related neglected tropical diseases pathogens including tapeworms , and including their no...	[ "Schistosomiasis is a major neglected tropical disease ( NTD ) , which afflicts > 200 million people in developing countries .", "The genome sequence of the schistosome parasite has been decoded; it includes > 10 , 000 genes .", "New approaches to control this NTD are sought and genomic information may provide ...	2016
[ "Introduction", "Results and discussion", "Materials and methods" ]	[ "chemical characterization", "medicine and health sciences", "immune physiology", "protein interactions", "statistics", "immunology", "mathematics", "forecasting", "receptor-ligand binding assay", "protein structure prediction", "protein structure", "antibodies", "research and analysis metho...	Protein—protein binding supersites	journal.pcbi.1006704	null	[ [ "Specific protein-protein interactions are essential for maintaining a robust phenotype .", "A deeper understanding of these interactions would allow the identification of cognate ligands[1] and drivers of specificity , opening a pathway to manipulating the corresponding interaction interfaces in drug des...	[ "The lack of a deep understanding of how proteins interact remains an important roadblock in advancing efforts to identify binding partners and uncover the corresponding regulatory mechanisms of the functions they mediate .", "Understanding protein-protein interactions is also essential for designing specific che...	[ "Protein–protein interactions are key to understand the molecular level mechanisms of regulation in the cell .", "However , there is still a limited understanding of what distinguishes a protein-protein binding site from the rest of the surface .", "This lack of knowledge is manifested in the relatively low acc...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "oncology", "viruses", "infectious diseases", "hepatitis", "ubiqutin ligase", "cell biology", "gastroenterology and hepatology", "virology", "rna polymerase", "hepatocellular carcinoma" ]	Hepatitis C Virus Induces E6AP-Dependent Degradation of the Retinoblastoma Protein	journal.ppat.0030139	null	[ [ "Among viruses that infect the human liver , hepatitis C virus ( HCV ) is a leading cause of morbidity and mortality worldwide [1] .", "Chronic infection with HCV is a major risk factor for the development of cirrhosis as well as hepatocellular carcinoma ( HCC ) [2 , 3] .", "The incidence of this canc...	[ "Hepatitis C virus ( HCV ) is a positive-strand RNA virus that frequently causes persistent infections and is uniquely associated with the development of hepatocellular carcinoma .", "While the mechanism ( s ) by which the virus promotes cancer are poorly defined , previous studies indicate that the HCV RNA-depen...	[ "Persons infected with hepatitis C virus ( HCV ) are at increased risk for liver cancer .", "This is remarkable because HCV is an RNA virus with replication confined to the cytoplasm and no potential for integration of its genome into host cell DNA .", "While it is likely that chronic inflammation contributes t...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "meiosis", "plant science", "molecular cell biology", "cell biology", "chromosome biology", "plant biology", "genetics", "biology", "genomics", "genetics and genomics" ]	Meiosis-Specific Loading of the Centromere-Specific Histone CENH3 in Arabidopsis thaliana	journal.pgen.1002121	null	[ [ "Centromeres are loci that direct faithful segregation of chromosomes during eukaryote cell division .", "They provide a platform for the assembly of kinetochores , structures that bind to spindle microtubules and coordinate chromosome movement .", "Centromere behavior must be regulated differently in...	[ "Centromere behavior is specialized in meiosis I , so that sister chromatids of homologous chromosomes are pulled toward the same side of the spindle ( through kinetochore mono-orientation ) and chromosome number is reduced .", "Factors required for mono-orientation have been identified in yeast .", "However , ...	[ "There are two types of cell division in eukaryotes .", "Mitosis produces cells with identical copies of the genome , while meiosis produces gametes with half the number of chromosomes found in the parent cell .", "Faithful genome inheritance is controlled by centromeres , chromosomal structures that allow dupl...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "invertebrates", "neurochemistry", "immune physiology", "caenorhabditis", "gene regulation", "animals", "hormones", "gene function", "endocrine physiology", "animal models", "developmental biology", "caenorhabditis elegans", "model organisms", "organism development", "molecular developme...	An Insulin-to-Insulin Regulatory Network Orchestrates Phenotypic Specificity in Development and Physiology	journal.pgen.1004225	null	[ [ "The organization and integration of multiple signals endow intercellular regulatory networks with information processing capabilities .", "For example , hormones modulate physiology and maintain homeostasis in variable environments [reviewed in 1] , and morphogens give rise to intricate patterns during d...	[ "Insulin-like peptides ( ILPs ) play highly conserved roles in development and physiology .", "Most animal genomes encode multiple ILPs .", "Here we identify mechanisms for how the forty Caenorhabditis elegans ILPs coordinate diverse processes , including development , reproduction , longevity and several speci...	[ "Insulin signaling is widely implicated in regulating diverse physiological processes ranging from metabolism to longevity across many animal species .", "Many animals have multiple insulin-like peptides that can regulate the activity of this signaling pathway .", "For example , while humans have ten , includin...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases/bacterial infections", "infectious diseases/neglected tropical diseases", "ophthalmology/eye infections", "infectious diseases/epidemiology and control of infectious diseases" ]	Targeting Antibiotics to Households for Trachoma Control	journal.pntd.0000862	null	[ [ "Trachoma , a ‘Neglected Tropical Disease’ , is the leading infectious cause of blindness worldwide and there are currently an estimated 46 million people with the active stage of the disease [1] .", "The disease mostly affects impoverished populations where people cannot afford treatment and access to ru...	[ "Mass drug administration ( MDA ) is part of the current trachoma control strategy , but it can be costly and results in many uninfected individuals receiving treatment .", "Here we explore whether alternative , targeted approaches are effective antibiotic-sparing strategies .", "We analysed data on the prevale...	[ "Repeated ocular infection with the bacterium Chlamydia trachomatis leads to the development of trachoma , a major cause of infectious blindness worldwide .", "Mass distribution of antibiotics , a component of the current trachoma control strategy , has had success in reducing infection in some areas , but result...	2010
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry", "mathematics", "cell biology", "computational biology", "neuroscience", "drosophila", "genetics and genomics" ]	Meta-Analysis of Drosophila Circadian Microarray Studies Identifies a Novel Set of Rhythmically Expressed Genes	journal.pcbi.0030208	null	[ [ "Most organisms exhibit rhythms of behavior and physiology that occur with", "“circadian” or daily periods .", "Such rhythms are driven by endogenous", "biological clocks regulated via the rhythmic expression of a core set of pacemaker genes", "[4–7] .", "A salient feature of many", "c...	[ "Five independent groups have reported microarray studies that identify dozens of", "rhythmically expressed genes in the fruit fly Drosophila melanogaster .", "Limited overlap among the lists of discovered genes makes it difficult to determine which ,", "if any , exhibit truly rhythmic patterns of expression ...	[ "Circadian genes regulate many of life's most essential processes , from sleeping and", "eating to cellular metabolism , learning , and much more .", "Many of these genes exhibit", "cyclic transcript expression , a characteristic utilized by an ever-expanding corpus of", "microarray-based studies to discove...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/protozoal infections", "infectious diseases/neglected tropical diseases", "immunology/immunity to infections", "pathology/immunology" ]	Tip-DC Development during Parasitic Infection Is Regulated by IL-10 and Requires CCL2/CCR2, IFN-γ and MyD88 Signaling	journal.ppat.1001045	null	[ [ "Inflammatory immune responses against invading pathogens require the recruitment of immune cells to the site of infection .", "However , the infiltration of infected tissue by activated immune cells may result in tissue injury justifying a profound understanding of the mechanisms underlying the recruitme...	[ "The development of classically activated monocytic cells ( M1 ) is a prerequisite for effective elimination of parasites , including African trypanosomes .", "However , persistent activation of M1 that produce pathogenic molecules such as TNF and NO contributes to the development of trypanosome infection-associa...	[ "Most infections are associated with host inflammatory responses that can result in multiple organ failure and death .", "It is therefore essential to understand the mechanisms balancing host immune response and tissue damage .", "Mouse models of African trypanosome infection represent valuable tools to study t...	2010
[ "Introduction", "Materials and methods", "Results", "Discussion", "Conclusion" ]	[ "eye muscles", "traumatic injury", "medicine and health sciences", "ocular anatomy", "mathematical models", "bone", "network analysis", "bioassays and physiological analysis", "muscle functions", "research and analysis methods", "muscle analysis", "muscle physiology", "musculoskeletal system...	Structure, function, and control of the human musculoskeletal network	journal.pbio.2002811	null	[ [ "The interconnected nature of the human body has long been the subject of both scientific inquiry and superstitious beliefs .", "From the ancient humors linking heart , liver , spleen , and brain with courage , calm , and hope [1] to the modern appreciation of the gut–brain connection [2] , humans tend to...	[ "The human body is a complex organism , the gross mechanical properties of which are enabled by an interconnected musculoskeletal network controlled by the nervous system .", "The nature of musculoskeletal interconnection facilitates stability , voluntary movement , and robustness to injury .", "However , a fun...	[ "While network science is frequently used to characterize networks from genomics , proteomics , and connectomics , its utility in understanding biomechanics , orthopedics , and physical therapy has remained largely unexplored .", "Indeed , current clinical practice and knowledge regarding the musculoskeletal syst...	2018
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "body fluids", "pathology and laboratory medicine", "pathogens", "microbiology", "vertebrates", "saliva", "animals", "viruses", "rna viruses", "sequence motif analysis", "glycosylation", "insect vectors", "research and analysis methods", ...	N-linked glycosylation of the West Nile virus envelope protein is not a requisite for avian virulence or vector competence	journal.pntd.0007473	null	[ [ "Since its identification in North America in 1999 , West Nile virus ( WNV ) has caused large human encephalitis epidemics in the United States resulting in 48 , 183 reported human cases of neuroinvasive and non-neuroinvasive disease and 2 , 114 deaths to date ( http://www . cdc . gov/westnile ) .", "Firs...	[ "The N-linked glycosylation motif at amino acid position 154–156 of the envelope ( E ) protein of West Nile virus ( WNV ) is linked to enhanced murine neuroinvasiveness , avian pathogenicity and vector competence .", "Naturally occurring isolates with altered E protein glycosylation patterns have been observed in...	[ "West Nile virus ( WNV ) has been responsible for the largest human encephalitis epidemics in the continental United States .", "Avians and Culex mosquitoes are the primary hosts for WNV natural transmission cycles .", "The envelope ( E ) protein for WNV contains a variable N-linked glycosylation motif which in...	2019
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "face", "cancer risk factors", "neuroscience", "oncology", "dna damage", "developmental biology", "frontal bones", "organism development", "stem cells", "skeleton", "dna", "embryos", "bone development", "skull", "embryology", "musculoskeletal system", ...	BRCA1 and BRCA2 tumor suppressors in neural crest cells are essential for craniofacial bone development	journal.pgen.1007340	null	[ [ "Abnormal growth of the facial bones causes congenital craniofacial malformations [1] .", "Because most bones in the face derive from multipotent stem cells designated cranial neural crest cells ( CNCCs ) [2 , 3] , craniofacial bone disorders are largely attributed to defects in CNCCs [4 , 5] .", "Imp...	[ "Craniofacial abnormalities , including facial skeletal defects , comprise approximately one-third of all birth defects in humans .", "Since most bones in the face derive from cranial neural crest cells ( CNCCs ) , which are multipotent stem cells , craniofacial bone disorders are largely attributed to defects in...	[ "Craniofacial abnormalities , including facial skeletal defects , comprise approximately one-third of all birth defects in humans .", "Since most bones in the face derive from neural crest cells , which are multipotent stem cells , craniofacial bone disorders are largely attributed to defects in neural crest cell...	2018
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "animal types", "medicine and health sciences", "pathology and laboratory medicine", "ruminants", "domestic animals", "geographical locations", "tropical diseases", "vertebrates", "dogs", "animals", "mammals", "bacterial diseases", "signs and symptoms", "neglected tropical diseases", "zo...	Domestic animals infected with Mycobacterium ulcerans—Implications for transmission to humans	journal.pntd.0006572	null	[ [ "Buruli ulcer ( BU ) , the necrotizing skin disease caused by M . ulcerans ( MU ) remains a major Public Health problem in more than 33 countries worldwide .", "Although the distribution of BU is global , its burden is highest in remote communities of West and Central African regions including Benin , Gha...	[ "The environmental pathogen , Mycobacterium ulcerans ( MU ) can infect both humans and animals and cause Buruli ulcer ( BU ) disease .", "However , its mode ( s ) of transmission from the colonized environment to human/animal hosts remain unclear .", "In Australia , MU can infect both wildlife and domestic mamm...	[ "Buruli ulcer ( BU ) remains a major Public Health problem in rural communities in sub-Saharan Africa .", "There are several reports of the occurrence of BU in Wildlife as well as domestic animals in Australia leading to the suggestion that animals may play a role in the transmission of MU to humans .", "Report...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "livestock", "medicine and health sciences", "chemical characterization", "crystal structure", "pathology and laboratory medicine", "ruminants", "enzymes", "pathogens", "condensed matter physics", "enzymology", "vertebrates", "microbiology", "orthomyxoviruses", "animals", "mammals", "v...	An Open Receptor-Binding Cavity of Hemagglutinin-Esterase-Fusion Glycoprotein from Newly-Identified Influenza D Virus: Basis for Its Broad Cell Tropism	journal.ppat.1005411	null	[ [ "Influenza viruses are enveloped , segmented , single-stranded , negative-sense RNA viruses and belong to the family Orthomyxoviridae [1] .", "The genomes of influenza A virus ( IAV ) and influenza B virus ( IBV ) consist of eight RNA segments , whereas influenza C viruses ( ICV ) only have seven segments...	[ "Influenza viruses cause seasonal flu each year and pandemics or epidemic sporadically , posing a major threat to public health .", "Recently , a new influenza D virus ( IDV ) was isolated from pigs and cattle .", "Here , we reveal that the IDV utilizes 9-O-acetylated sialic acids as its receptor for virus entr...	[ "Of the Orthomyxoviridae family of viruses , influenza A , B and C viruses all can cause disease in humans .", "Recently , a novel influenza D virus ( IDV ) with approximately 50% amino acid identity to human influenza C virus ( ICV ) is found in pigs and cattle .", "This novel virus can establish infection in ...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "animal models", "biochemistry", "developmental biology", "lipids", "embryology", "model organisms", "genetic mutation", "genetics", "biology", "morphogenesis", "sterols", "genetics and genomics" ]	Cholesterol Metabolism Is Required for Intracellular Hedgehog Signal Transduction In Vivo	journal.pgen.1002224	null	[ [ "Hedgehog ( Hh ) ligands have numerous and fundamental roles in both embryonic development [1] , [2] and tumor biology [3] .", "Mammalian hedgehog proteins bind to the transmembrane receptor Patched ( Ptc ) and thereby relieve its repression of Smoothened ( Smo ) .", "Intracellular transduction of Smo...	[ "We describe the rudolph mouse , a mutant with striking defects in both central nervous system and skeletal development .", "Rudolph is an allele of the cholesterol biosynthetic enzyme , hydroxysteroid ( 17-beta ) dehydrogenase 7 , which is an intriguing finding given the recent implication of oxysterols in media...	[ "The molecules and signaling pathways that regulate growth and patterning of the developing embryo are still being elucidated , and one valuable experimental approach is the use of animal models , such as the mouse .", "We have identified a recessive mutation in the mouse , rudolph , that causes abnormal forebrai...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "reproductive system", "gonads", "epithelial cells", "germ cells", "sertoli cells", "developmental biology", "sperm", "animal cells", "gene expression", "biological tissue", "testes", "ovaries", "anatomy", "cell biology", "genetics", "epithelium", "b...	Dual role of DMXL2 in olfactory information transmission and the first wave of spermatogenesis	journal.pgen.1007909	null	[ [ "The DMX-Like 2 ( DMXL2 ) gene encodes a protein with multiple WD40 domains , which mediate protein-protein and protein-DNA interactions [1] , [2] , [3] .", "These WD40 domains correspond to a series of 44- to 60-amino acid sequence repeats with a characteristic sequence terminating in a tryptophan–aspart...	[ "Gonad differentiation is a crucial step conditioning the future fertility of individuals and most of the master genes involved in this process have been investigated in detail .", "However , transcriptomic analyses of developing gonads from different animal models have revealed that hundreds of genes present sex...	[ "DMXL2 gene dysfunction underlies various human diseases , including breast cancer , non-syndromic hearing loss , and polyendocrine-polyneuropathy syndrome , demonstrating the large range of potential actions of DMXL2 .", "We show here that Dmxl2 expression is crucial for survival in mice , as neonates die within...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "children", "medicine and health sciences", "sociology", "tropical diseases", "social sciences", "parasitic diseases", "biological locomotion", "pediatrics", "age groups", "human families", "neglected tropical diseases", "families", "public and occupational health", "elephantiasis", "pod...	Health beliefs of school-age rural children in podoconiosis-affected families: A qualitative study in Southern Ethiopia	journal.pntd.0005564	null	[ [ "Podoconiosis is an example of a lifestyle-related disease that develops later in life and affects millions of people with little experience of preventive behaviour .", "It is non-infectious ( and thus also termed ‘non-filarial elephantiasis’ ) and is characterized by bilateral swelling of the lower legs ...	[ "Several studies have suggested investigation of health beliefs in children to be an important pre-condition for primary prevention of disease .", "However , little effort has been made to understand these in the context of podoconiosis .", "This study therefore aimed to explore the health beliefs of school-age...	[ "Podoconiosis is an example of a lifestyle-related disease that develops after childhood and affects millions of people with little experience of preventive behaviour .", "It is caused by prolonged barefoot exposure to irritant mineral particles , accompanied by inherited susceptibility .", "Children with a fam...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/bacterial infections", "microbiology/cellular microbiology and pathogenesis", "genetics and genomics/bioinformatics", "microbiology/medical microbiology" ]	Functional Analysis of the Quorum-Sensing Streptococcal Invasion Locus (sil)	journal.ppat.1000651	null	[ [ "Group A streptococcus ( GAS ) is a common human pathogen that has major healthcare and economic impacts .", "It causes a variety of human diseases ranging from superficial skin and throat infections to severe life-threatening diseases such as necrotizing fasciitis ( NF ) .", "There are approximately ...	[ "Group A streptococcus ( GAS ) causes a wide variety of human diseases , and at the same time , GAS can also circulate without producing symptoms , similar to its close commensal relative , group G streptococcus ( GGS ) .", "We previously identified , by transposon-tagged mutagenesis , the streptococcal invasion ...	[ "Cell-to-cell communication in bacteria is termed quorum-sensing ( QS ) , which is triggered by signaling molecules called autoinducers .", "In streptococci , autoinducers are synthesized as immature peptides that are processed , secreted , and then sensed by two-component systems ( TCSs ) .", "As a result , th...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular neuroscience", "cellular neuroscience", "model organisms", "biology and life sciences", "yeast and fungal models", "neuroscience", "research and analysis methods" ]	Phosphorylation Modulates Clearance of Alpha-Synuclein Inclusions in a Yeast Model of Parkinson's Disease	journal.pgen.1004302	null	[ [ "Protein misfolding and aggregation is an unavoidable and widespread problem in biology .", "Cells evolved a series of quality control mechanisms to ensure overall proteostasis and , in some cases , to exploit the plasticity of diverse conformational states , including those concealed in protein aggregate...	[ "Alpha-synuclein ( aSyn ) is the main component of proteinaceous inclusions known as Lewy bodies ( LBs ) , the typical pathological hallmark of Parkinson's disease ( PD ) and other synucleinopathies .", "Although aSyn is phosphorylated at low levels under physiological conditions , it is estimated that ∼90% of aS...	[ "Protein aggregation is a common hallmark in neurodegenerative disorders , but is also associated with phenotypic plasticity in a variety of organisms , including yeasts .", "Alpha-synuclein ( aSyn ) forms aggregates that are typical of synucleinopathies , and is phosphorylated at S129 , but the significance of p...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "gene regulation", "rna extraction", "neuroscience", "odorant binding proteins", "extraction techniques", "research and analysis methods", "aggression", "transcriptional control", "animal cells", "proteins", "behavior", "gene expression", "olfactory receptor neurons", "biochemistry", "se...	Odorant binding protein 69a connects social interaction to modulation of social responsiveness in Drosophila	journal.pgen.1007328	null	[ [ "A fundamental question in neuroscience is how do animals integrate sensory information , together with context , internal state and prior social interaction , into an appropriate behavioral response [1] .", "The manner by which prior social interaction affects behavioral responses is a well-described phe...	[ "Living in a social environment requires the ability to respond to specific social stimuli and to incorporate information obtained from prior interactions into future ones .", "One of the mechanisms that facilitates social interaction is pheromone-based communication .", "In Drosophila melanogaster , the male-s...	[ "In this work , we used Drosophila melanogaster as a model organism to explore a basic question in neuroscience: why do different individuals experience the same sensory stimuli , such as smell differently , and moreover , why does one individual experience identical stimuli differently on different occasions ?", ...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "bacteriology", "heterozygosity", "organismal evolution", "population genetics", "radii", "microbiology", "mathematical models", "geometry", "simulation and modeling", "luminescent proteins", "mathematics", "yellow fluorescent protein", "microbial evolution", "population biology", "resea...	Genetic drift and selection in many-allele range expansions	journal.pcbi.1005866	null	[ [ "A competition between stochastic and deterministic effects underlies evolution .", "In a well-mixed system such as a shaken culture of the yeast microorganism Saccharomyces cerevisiae , stochastic competition between individuals , mutations , and selection dictate the dynamics of the population [1] .", ...	[ "We experimentally and numerically investigate the evolutionary dynamics of four competing strains of E . coli with differing expansion velocities in radially expanding colonies .", "We compare experimental measurements of the average fraction , correlation functions between strains , and the relative rates of ge...	[ "Population expansions occur naturally during the spread of invasive species and have played a role in our evolutionary history when humans migrated out of Africa .", "We use a colony of non-motile bacteria expanding into unoccupied , nutrient-rich territory on an agar plate as a model system to explore how an ex...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "genome expression analysis", "gene expression", "genetics", "biology", "genomics", "microbiology", "host-pathogen interaction", "genetics and genomics", "parasitology" ]	Comparative Study of Transcriptome Profiles of Mechanical- and Skin-Transformed Schistosoma mansoni Schistosomula	journal.pntd.0002091	null	[ [ "Schistosomiasis is a parasitic disease caused by platyhelminths of the genus Schistosoma .", "It has been estimated that ∼200 million people are infected and ∼200 , 000 die due to schistosomiasis-related pathologies [1] .", "Without a vaccine , mechanisms of prophylaxis rely primarily on reduction of...	[ "Schistosome infection begins with the penetration of cercariae through healthy unbroken host skin .", "This process leads to the transformation of the free-living larvae into obligate parasites called schistosomula .", "This irreversible transformation , which occurs in as little as two hours , involves castin...	[ "Schistosomiasis is an endemic parasitic disease affecting ∼200 million people in the most socioeconomically deprived regions of the world .", "Human infection occurs during water contact where free-living larvae called cercariae penetrate host skin and become parasitic organisms called schistosomula .", "This ...	2013

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