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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" ]	[ "staphylococci", "biology", "microbiology", "bacterial pathogens" ]	cAMP and EPAC Are Key Players in the Regulation of the Signal Transduction Pathway Involved in the α-Hemolysin Autophagic Response	journal.ppat.1002664	null	[ [ "Autophagy is a cellular process in response to stress , which is activated when cells are subjected to nutrient limitation , high temperatures , oxidative stress , accumulation of damaged organelles , or infection with certain pathogens [1] .", "When autophagy is activated , various cellular constituents...	[ "Staphylococcus aureus is a microorganism that causes serious diseases in the human being .", "This microorganism is able to escape the phagolysosomal pathway , increasing intracellular bacterial survival and killing the eukaryotic host cell to spread the infection .", "One of the key features of S . aureus inf...	[ "Staphylococcus aureus is a microorganism that causes serious infectious diseases such as pneumonia , endocarditis , osteomyelitis , and wound infections .", "This pathogen can infect various types of non-professional phagocytic cells and after internalization is able to escape the phagolysosomal compartment towa...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "protein interactions", "simulation and modeling", "membrane proteins", "cellular structures and organelles", "thermodynamics", "g protein coupled receptors", "research and analysis methods", "lipids", "proteins", "transmembrane receptors", "cell membranes", "free energy", "cholesterol", "...	Reduced level of docosahexaenoic acid shifts GPCR neuroreceptors to less ordered membrane regions	journal.pcbi.1007033	null	[ [ "Cellular membranes host functional membrane domains ( “lipid rafts’’ ) rich in proteins and cholesterol ( CHOL ) [1] .", "Many G protein-coupled receptors ( GPCRs ) and cognate G proteins are found in these domains [2] , and numerous reports have suggested that CHOL is involved in GPCR function [3–7] .",...	[ "G protein-coupled receptors ( GPCRs ) control cellular signaling and responses .", "Many of these GPCRs are modulated by cholesterol and polyunsaturated fatty acids ( PUFAs ) which have been shown to co-exist with saturated lipids in ordered membrane domains .", "However , the lipid compositions of such domain...	[ "Our current picture of cellular membranes depicts them as laterally heterogeneous sheets of lipids crowded with membrane proteins .", "These proteins often require a specific lipid environment to efficiently perform their functions .", "Certain neuroreceptor proteins are regulated by membrane cholesterol that ...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "developmental biology", "molecular cell biology", "genetics", "biology", "evolutionary biology", "genetics and genomics" ]	RNF12 Activates Xist and Is Essential for X Chromosome Inactivation	journal.pgen.1002001	null	[ [ "X chromosome inactivation ( XCI ) in placental mammals is random with respect to the parental origin of the X chromosome that undergoes inactivation , during early embryonic development [1] .", "In contrast , in marsupials and mouse extra-embryonic tissues XCI is imprinted .", "Imprinted XCI always t...	[ "In somatic cells of female placental mammals , one of the two X chromosomes is transcriptionally silenced to accomplish an equal dose of X-encoded gene products in males and females .", "Initiation of random X chromosome inactivation ( XCI ) is thought to be regulated by X-encoded activators and autosomally enco...	[ "In all placental mammals , the males have only one X chromosome per diploid genome , as compared to the females who have two copies of this relatively large chromosome , carrying more than 1 , 000 genes .", "Hence , the evolution of the heterologous XY sex chromosome pair has resulted in an inevitable need for g...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "herpetology", "public health", "medicine", "biochemistry", "public health and epidemiology", "biology", "zoology", "toxic agents", "toxicology" ]	Allopurinol Reduces the Lethality Associated with Acute Renal Failure Induced by Crotalus durissus terrificus Snake Venom: Comparison with Probenecid	journal.pntd.0001312	null	[ [ "Envenoming resulting from snake bite is recognized nowadays as one of the major neglected public health issue within poor communities living in the rural areas of several countries throughout the world .", "Because of serious misreporting , the true worldwide burden of snake bite is not known , but accor...	[ "Acute renal failure is one of the most serious complications of envenoming resulting from Crotalus durissus terrificus bites .", "This study evaluated the relevance of hyperuricemia and oxidative stress and the effects of allopurinol and probenecid in renal dysfunction caused by direct nephrotoxicity of C . d ."...	[ "In Brazil , among registered snake bites , those by the genus Crotalus originate the highest mortality rate .", "The rattlesnake Crotalus durissus terrificus is the most frequently implicated in these accidents .", "The kidney is a particularly vulnerable organ to the venom of this rattlesnake .", "In fact ,...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "sociology", "tropical diseases", "geographical locations", "social sciences", "surgical and invasive medical procedures", "health care", "bacterial diseases", "human families", "tanzania", "eye diseases", "neglected tropical diseases", "eyes", "patients", ...	Why do patients refuse trichiasis surgery? Lessons and an education initiative from Mtwara Region, Tanzania	journal.pntd.0006464	null	[ [ "Trachoma is an eye disease caused by the bacterium Chlamydia trachomatis .", "It is common in areas of the world that lack access to health care and clean water .", "Repeated infections cause recurrent conjunctivitis , which then leads to significant scarring of the eyelid .", "This scarring caus...	[ "Trachomatous trichiasis is one of the leading causes of preventable blindness worldwide .", "A relatively simple surgery can spare vision .", "Although this surgery is usually performed free of charge in endemic regions , multiple studies indicate that surgical refusal is common .", "Prior studies have attem...	[ "Many international health interventions in resource-limited settings involve treatments that are fully funded by donor organizations and , therefore , available for free to those in need .", "Trachoma , a bacterial eye disease that can cause blindness if left untreated , has frequently been the target of surgica...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "genetics", "biology", "genetics and genomics" ]	The SCFDia2 Ubiquitin E3 Ligase Ubiquitylates Sir4 and Functions in Transcriptional Silencing	journal.pgen.1002846	null	[ [ "Chromatin structure governs a host of cellular processes , including gene expression , DNA replication , and DNA repair [1] .", "In higher eukaryotic cells , chromatin is classified into two major forms , euchromatin and heterochromatin , based on cytological staining .", "Euchromatin , the less dens...	[ "In budding yeast , transcriptional silencing , which is important to regulate gene expression and maintain genome integrity , requires silent information regulator ( Sir ) proteins .", "In addition , Rtt106 , a histone chaperone involved in nucleosome assembly , functions in transcriptional silencing .", "Howe...	[ "Heterochromatin is important for the maintenance of genome stability and regulation of gene expression .", "Heterochromatin protein 1 ( HP1 ) , a protein that binds to histone H3 methylated at lysine 9 ( H3K9me3 ) at heterochromatin loci in mammalian cells , is dynamically regulated during the cell cycle by phos...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "flow cytometry", "gene transfer", "plasmid construction", "mutation", "membrane fusion", "dna construction", "molecular biology techniques", "gene delivery", "glycoproteins", "cellular structures and organelles", "research and analysis methods", "molecular biology", "cell membranes", "spe...	Receptor-Targeted Nipah Virus Glycoproteins Improve Cell-Type Selective Gene Delivery and Reveal a Preference for Membrane-Proximal Cell Attachment	journal.ppat.1005641	null	[ [ "Cell entry as first step in the viral replication cycle is initiated by the attachment of virus particles to distinct cell surface proteins .", "While many viral receptors have been identified , there is only limited knowledge available about the molecular requirements that cell surface proteins have to ...	[ "Receptor-targeted lentiviral vectors ( LVs ) can be an effective tool for selective transfer of genes into distinct cell types of choice .", "Moreover , they can be used to determine the molecular properties that cell surface proteins must fulfill to act as receptors for viral glycoproteins .", "Here we show t...	[ "Pseudotyping of lentiviral vectors ( LVs ) with glycoproteins from other enveloped viruses has not only often been revealing in mechanistic studies of particle assembly and entry , but is also of practical importance for gene delivery .", "LVs pseudotyped with engineered glycoproteins allowing free choice of rec...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "proteins", "virology", "protein structure", "host-pathogen interaction", "biology", "microbiology" ]	Structure of the Parainfluenza Virus 5 (PIV5) Hemagglutinin-Neuraminidase (HN) Ectodomain	journal.ppat.1003534	null	[ [ "The Paramyxoviridae are membrane-enveloped negative-sense single-stranded RNA viruses that infect animals and humans often resulting in significant disease and mortality .", "Most paramyxoviruses enter cells at neutral pH by fusing their envelope with the plasma membrane of a target cell thereby releasin...	[ "Paramyxoviruses cause a wide variety of human and animal diseases .", "They infect host cells using the coordinated action of two surface glycoproteins , the receptor binding protein ( HN , H , or G ) and the fusion protein ( F ) .", "HN binds sialic acid on host cells ( hemagglutinin activity ) and hydrolyzes...	[ "Paramyxoviruses comprise a large family of significant pathogens including Newcastle disease virus ( NDV ) , parainfluenza viruses 1-5 ( PIV1-5 ) , respiratory syncytial virus , the highly transmissible measles virus , and the emerging and deadly Nipah and Hendra viruses .", "Five paramyxoviruses are U . S . Dep...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "reproductive system", "3' utr", "messenger rna", "germ cells", "alternative splicing", "developmental biology", "oocytes", "untranslated regions", "molecular biology techniques", "embryos", "research and analysis methods", "embryology", "artificial gene amp...	Nuclear m6A reader YTHDC1 regulates alternative polyadenylation and splicing during mouse oocyte development	journal.pgen.1007412	null	[ [ "More than one hundred different RNA modifications are known in eukaryotes [1] .", "N6-methyladenosine ( m6A ) is the most prevalent internal modification in eukaryote mRNAs , occurring in transcripts of approximately one third of genes in human and mouse [2–4] .", "Globally , m6A is enriched in the 3...	[ "The N6-methyladenosine ( m6A ) modification is the most prevalent internal RNA modification in eukaryotes .", "The majority of m6A sites are found in the last exon and 3’ UTRs .", "Here we show that the nuclear m6A reader YTHDC1 is essential for embryo viability and germline development in mouse .", "Specifi...	[ "The N6-methyladenosine ( m6A ) modification , one type of RNA methylation , is the most abundant internal RNA modification in eukaryote messenger RNAs .", "m6A is specifically recognized by RNA-binding reader proteins .", "Here we report an essential role of the nuclear m6A reader , YTHDC1 , in embryo developm...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	General Relationship of Global Topology, Local Dynamics, and Directionality in Large-Scale Brain Networks	journal.pcbi.1004225	null	[ [ "Current large-scale initiatives are attempting to construct a map of the structural and functional network connections in the brain [1 , 2] .", "One critical goal of these initiatives is to understand the mechanism by which local and functionally specialized neural activity becomes globally integrated to...	[ "The balance of global integration and functional specialization is a critical feature of efficient brain networks , but the relationship of global topology , local node dynamics and information flow across networks has yet to be identified .", "One critical step in elucidating this relationship is the identifica...	[ "Current brain connectome projects are attempting to construct a map of the structural and functional network connections in the brain .", "One goal of these projects is to understand how network organization determines local functions and information transfer patterns , which is essential to achieve higher cogni...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Structural Similarities and Differences between Amyloidogenic and Non-Amyloidogenic Islet Amyloid Polypeptide (IAPP) Sequences and Implications for the Dual Physiological and Pathological Activities of These Peptides	journal.pcbi.1003211	null	[ [ "The Islet Amyloid Polypeptide/IAPP ( also known as amylin ) is coexpressed and cosecreted with insulin by pancreatic islet β-cells [1]–[3] and acts as a synergistic partner of insulin to limit after-meal glucose excursions [4] .", "IAPP belongs to the calcitonin ( CT ) family of peptides ( See Table S1 i...	[ "IAPP , a 37 amino-acid peptide hormone belonging to the calcitonin family , is an intrinsically disordered protein that is coexpressed and cosecreted along with insulin by pancreatic islet β-cells in response to meals .", "IAPP plays a physiological role in glucose regulation; however , in certain species , IAPP...	[ "IAPP , a 37 amino-acid peptide hormone belonging to the calcitonin family , is an intrinsically disordered peptide produced along with insulin by pancreatic islet β-cells in response to meals .", "In its functional form , IAPP acts as a synergic partner of insulin to reduce blood glucose .", "IAPP can , howeve...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular biology/rna-protein interactions", "virology/viral replication and gene regulation", "infectious diseases/respiratory infections" ]	The Structure of a Biologically Active Influenza Virus Ribonucleoprotein Complex	journal.ppat.1000491	null	[ [ "The influenza A viruses belong to the family Orthomyxoviridae and are genetically and antigenically heterogeneous .", "They are responsible for annual epidemics of respiratory disease and represent an important public-health problem [1] .", "All viral subtypes can be found in their natural reservoir ...	[ "The influenza viruses contain a segmented , single-stranded RNA genome of negative polarity .", "Each RNA segment is encapsidated by the nucleoprotein and the polymerase complex into ribonucleoprotein particles ( RNPs ) , which are responsible for virus transcription and replication .", "Despite their importan...	[ "The influenza viruses cause annual epidemics of respiratory disease and occasional pandemics that constitute a major public-health issue .", "The recent spillover of avian H5N1 and H1N1 swine influenza viruses to humans poses a serious threat of a new pandemic .", "These viruses contain a segmented RNA genome ...	2009
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "biotechnology", "antimicrobials", "medicine and health sciences", "chemical compounds", "small molecules", "drugs", "microbiology", "vertebrates", "organic compounds", "animals", "animal models", "osteichthyes", "bacterial diseases", "developmental biology", "antibiotic resistance", "...	High-throughput identification and rational design of synergistic small-molecule pairs for combating and bypassing antibiotic resistance	journal.pbio.2001644	null	[ [ "Small-molecule antimicrobial therapy facilitated one of the greatest increases in lifespan in history but is endangered by the rise of antimicrobial-resistant “superbugs” [1] .", "The CDC estimates that antibiotic-resistant bacteria cause more than 2 million infections and 23 , 000 deaths annually in the...	[ "Antibiotic-resistant infections kill approximately 23 , 000 people and cost $20 , 000 , 000 , 000 each year in the United States alone despite the widespread use of small-molecule antimicrobial combination therapy .", "Antibiotic combinations typically have an additive effect: the efficacy of the combination mat...	[ "Antibiotic resistance is a growing problem that threatens our ability to treat systemic bacterial infections .", "One strategy to combat antibiotic resistance is the use of synergistic antibiotic pairs that , when combined , have activity that is considerably greater than the sum of each individual drug’s activi...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "connectomics", "neuroanatomy", "anatomy", "nervous system", "biology and life sciences", "neuroscience" ]	Influence of Wiring Cost on the Large-Scale Architecture of Human Cortical Connectivity	journal.pcbi.1003557	null	[ [ "The physical brain is a network of extraordinary complexity on multiple spatial scales .", "On the macroscopic scale , regions are connected by a large number of white-matter projections that form an intricate system: the connectome [1] .", "Understanding the principles of the large-scale architectur...	[ "In the past two decades some fundamental properties of cortical connectivity have been discovered: small-world structure , pronounced hierarchical and modular organisation , and strong core and rich-club structures .", "A common assumption when interpreting results of this kind is that the observed structural pr...	[ "Macroscopic regions in the grey matter of the human brain are intricately connected by white-matter pathways , forming the extremely complex network of the brain .", "Analysing this brain network may provide us insights on how anatomy enables brain function and , ultimately , cognition and consciousness .", "V...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The Contribution of Network Organization and Integration to the Development of Cognitive Control	journal.pbio.1002328	This study reveals that although the organization of functional brain networks remains stable during adolescence, between-network integration continues to increase, underlying maturation in cognitive control.	[ [ "Cognitive control refers to the ability to execute voluntary , goal-directed behavior [1–3] .", "It requires flexible and adaptive coordination of core executive systems that are supported by integration among widely distributed , specialized brain circuitries [4] .", "The core components of cognitiv...	[ "Cognitive control , which continues to mature throughout adolescence , is supported by the ability for well-defined organized brain networks to flexibly integrate information .", "However , the development of intrinsic brain network organization and its relationship to observed improvements in cognitive control ...	[ "Adolescence is a unique period of brain development , with major changes occurring across the brain at many different levels of brain functioning .", "At the macroscopic level , the brain is composed of individual regions that collaborate in networks to perform diverse cognitive functions .", "Some networks of...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The Polymerase Activity of Mammalian DNA Pol ζ Is Specifically Required for Cell and Embryonic Viability	journal.pgen.1005759	null	[ [ "In eukaryotes , DNA polymerase ζ ( pol ζ ) is critical for the tolerance of many types of DNA replication blocks , by playing a central role in translesion DNA synthesis ( TLS ) .", "Primary replicative DNA polymerases ( pol δ or pol ε ) are stalled when they encounter many types of template DNA adducts ...	[ "DNA polymerase ζ ( pol ζ ) is exceptionally important for maintaining genome stability .", "Inactivation of the Rev3l gene encoding the polymerase catalytic subunit causes a high frequency of chromosomal breaks , followed by lethality in mouse embryos and in primary cells .", "Yet it is not known whether the D...	[ "Translesion synthesis allows DNA replication to occur in the presence of damaged DNA .", "This process is mediated by low-fidelity DNA polymerases ( such as pol ζ or pol η ) that maintain genomic stability .", "The action of these polymerases is crucial to limit cancer .", "In mice , complete deletion of DNA...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases/neglected tropical diseases", "infectious diseases/helminth infections", "public health and epidemiology/infectious diseases", "public health and epidemiology/screening", "infectious diseases/epidemiology and control of infectious diseases" ]	Helminth and Intestinal Protozoa Infections, Multiparasitism and Risk Factors in Champasack Province, Lao People's Democratic Republic	journal.pntd.0001037	null	[ [ "Lao People's Democratic Republic ( Lao PDR ) is a landlocked country situated in the Great Mekong sub-region of Southeast Asia , where socioeconomic and eco-epidemiological characteristics vary greatly according to location .", "In the northern part similar ecosystems are found as in southern People's Re...	[ "Detailed investigations of multiparasitism are scarce in the Mekong River basin .", "We assessed helminth ( trematode , nematode , and cestode ) , and intestinal protozoa infections , and multiparasitism in random population samples from three different eco-epidemiological settings in Champasack province , south...	[ "Multiparsitism is a general public health concern in tropical countries , and is of particular importance in the Mekong River basin of Southeast Asia .", "Here , we report results obtained from an in-depth study of hepato-biliary and intestinal multiparasitism and associated risk factors in three settings of the...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "body fluids", "pathology and laboratory medicine", "immune physiology", "pathogens", "immunology", "microbiology", "vertebrates", "animals", "mammals", "retroviruses", "primates", "immunodeficiency viruses", "viruses", "...	Paradoxical myeloid-derived suppressor cell reduction in the bone marrow of SIV chronically infected macaques	journal.ppat.1006395	null	[ [ "Myeloid-derived Suppressor Cells ( MDSCs ) are immature cells of myeloid origin , frequently found in tumor microenvironments and in the blood of cancer patients [1–3] .", "Bone marrow ( BM ) is the reservoir for MDSCs .", "Under homeostatic conditions , there is a delicate balance between the immatu...	[ "Myeloid derived suppressor cells ( MDSCs ) , which suppress anti-tumor or anti-viral immune responses , are expanded in the peripheral blood and tissues of patients/animals with cancer or viral infectious diseases .", "We here show that in chronic SIV infection of Indian rhesus macaques , the frequency of MDSCs ...	[ "Both cancer and infectious diseases including HIV/AIDS lead to the accumulation of myeloid-derived suppressor cells ( MDSCs ) , which can effectively suppress anti-tumor and anti-viral T cell responses to dampen protective immunity .", "Using a macaque model , we found unexpectedly that the MDSCs in bone marrow ...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "immune physiology", "engineering and technology", "synthetic biology", "immunology", "mutation", "synthetic biotherapeutics", "mathematics", "forecasting", "statistics (mathematics)", "protein structure prediction", "protein structure", "research and analysis...	Population-specific design of de-immunized protein biotherapeutics	journal.pcbi.1005983	null	[ [ "Protein-based drugs ( biotherapeutics ) are increasingly used to treat a wide variety of diseases[1 , 2] .", "Although biotherapeutics show high activity and specificity at the initiation of treatment , the gradual build-up of a patient immune response is a bottleneck for even wider usage[3] .", "The...	[ "Immunogenicity is a major problem during the development of biotherapeutics since it can lead to rapid clearance of the drug and adverse reactions .", "The challenge for biotherapeutic design is therefore to identify mutants of the protein sequence that minimize immunogenicity in a target population whilst retai...	[ "Therapeutic proteins have become an important area of pharmaceutical research and have been successfully applied to treat many diseases in the last decades .", "However , biotherapeutics suffer from the formation of anti-drug antibodies , which can reduce the efficacy of the drug or even result in severe adverse...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "cell physiology", "medicine", "arrhythmias", "electrophysiology", "physiology", "biology", "anatomy and physiology", "cardiovascular system", "biophysics", "computational biology", "cardiovascular" ]	NHE Inhibition Does Not Improve Na+ or Ca2+ Overload During Reperfusion: Using Modeling to Illuminate the Mechanisms Underlying a Therapeutic Failure	journal.pcbi.1002241	null	[ [ "Ischemia-reperfusion ( IR ) injury represents a constellation of pathological events that occur when previously ischemic myocardium experiences a restoration of normal tissue perfusion .", "IR injury , which can manifest as dangerous arrhythmias such as ventricular tachycardias and fibrillation , reduced...	[ "Reperfusion injury results from pathologies of cardiac myocyte physiology that develop when previously ischemic myocardium experiences a restoration of normal perfusion .", "Events in the development of reperfusion injury begin with the restoration of a proton gradient upon reperfusion , which then allows the so...	[ "Myocardial ischemia , commonly observed when arteries supplying the heart become occluded , results when cardiac tissue receives inadequate blood perfusion .", "In order to minimize the amount of cardiac damage , ischemic tissue must be reperfused .", "However , reperfusion can result in deleterious effects th...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "children", "ecology and environmental sciences", "medicine and health sciences", "rivers", "education", "sociology", "tropical diseases", "geographical locations", "teachers", "social sciences", "parasitic diseases", "age groups", "physiological processes", "tanzania", "aquatic environm...	Community Knowledge, Perceptions, and Practices Associated with Urogenital Schistosomiasis among School-Aged Children in Zanzibar, United Republic of Tanzania	journal.pntd.0004814	null	[ [ "Schistosomiasis is a debilitating disease that affects poor and deprived population groups , especially in rural Africa [1] .", "The global impact is enormous with more than 200 million people infected with blood flukes of the genus Schistosoma [2] .", "Urogenital schistosomiasis , caused by S . haem...	[ "On the Zanzibar islands , United Republic of Tanzania , elimination of urogenital schistosomiasis is strived for in the coming years .", "This qualitative study aimed to better understand community knowledge , perceptions , and practices associated with schistosomiasis among school-aged children on Unguja and Pe...	[ "On the Zanzibar islands , United Republic of Tanzania , elimination of urogenital schistosomiasis , a disease caused by infection with a blood fluke ( Schistosoma haematobium ) , locally known as kichocho , is strived for in the coming years .", "This study used qualitative research methods of focus groups and i...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The Catalytic and Non-catalytic Functions of the Brahma Chromatin-Remodeling Protein Collaborate to Fine-Tune Circadian Transcription in Drosophila	journal.pgen.1005307	null	[ [ "Circadian clocks are endogenous timekeeping mechanisms that drive rhythms in physiology and behavior with an approximately 24-hour period , allowing organisms from all kingdoms of life to anticipate and operate through predictable daily environmental changes .", "Much progress has been made in understand...	[ "Daily rhythms in gene expression play a critical role in the progression of circadian clocks , and are under regulation by transcription factor binding , histone modifications , RNA polymerase II ( RNAPII ) recruitment and elongation , and post-transcriptional mechanisms .", "Although previous studies have shown...	[ "The circadian clock is an endogenous timing system that enables organisms to anticipate daily changes in their external environment and temporally coordinate key biological functions that are important to their survival .", "Central to Drosophila clockwork is a key transcription factor CLOCK ( CLK ) .", "CLK a...	2015
[ "Introduction", "Results and Discussion", "Materials and Methods" ]	[ "oncology", "medicine", "cancer genetics", "ovarian cancer", "gynecological tumors", "genetics", "biology", "cancers and neoplasms" ]	Low Frequency of ESRRA–C11orf20 Fusion Gene in Ovarian Carcinomas	journal.pbio.1001784	A study by Francesca Micci and colleagues shows that the ESRRA-C11orf20 fusion transcript is rare in ovarian carcinoma, contrary to a previously reported frequency of 15%.	[ [ "Cancer of the ovary makes up 30% of all malignant diseases of the female genital tract .", "Prognosis is poor , with a mean 5-year survival rate in Europe of 32% .", "This unfavorable outcome is largely attributable to a lack of early warning symptoms and signs and also a lack of diagnostic tests tha...	[ "The identification of recurrent gene fusions in common epithelial cancers—for example , TMPRSS2/ERG in prostate cancer and EML4/ALK in nonsmall cell lung carcinomas—has raised the question of whether fusion genes are pathogenetically important also in ovarian carcinomas .", "The first recurrent fusion transcript...	[ "The identification of characteristic fusion genes in cancer helps us to understand how a particular cancer arises and also to improve classification and diagnosis , with a view to develop specific medical treatments that target exactly those aberrant molecules that trigger the disease .", "A fusion transcript pr...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "dermatology", "developmental biology", "cell biology/gene expression" ]	Cyclic Expression of Lhx2 Regulates Hair Formation	journal.pgen.1000904	null	[ [ "Hair develops in hair follicles ( HFs ) and embryonic development of HFs ( morphogenesis ) is initiated between embryonic days 12 ( E12 ) to E15 , and is regulated by continuous epithelial-mesenchymal interactions between epidermal and dermal cells [1]–[3] .", "The first morphological sign of HF morphoge...	[ "Hair is important for thermoregulation , physical protection , sensory activity , seasonal camouflage , and social interactions .", "Hair is generated in hair follicles ( HFs ) and , following morphogenesis , HFs undergo cyclic phases of active growth ( anagen ) , regression ( catagen ) , and inactivity ( teloge...	[ "Hair is generated in hair follicles , complex mini-organs in the skin that are devoted to this task .", "All hair follicles are generated during embryonic development .", "The hair follicles generate a new hair shaft by cycling through stages of regression , rest , and growth continuously throughout life .", ...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "borrelia infection", "innate immune system", "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "gene regulation", "immune activation", "immunology", "microbiology", "animal models", "bacterial diseases", "model organisms", "emerging infect...	MicroRNA-146a Provides Feedback Regulation of Lyme Arthritis but Not Carditis during Infection with Borrelia burgdorferi	journal.ppat.1004212	null	[ [ "Lyme Disease is caused by infection with Borrelia burgdorferi , a tick-borne spirochete [1] , and is the most common vector-borne disease in the United States with an estimated 300 , 000 cases per year [2] .", "Often , infection leads to acute arthritis in humans .", "Clinical manifestations of Lyme ...	[ "MicroRNAs have been shown to be important regulators of inflammatory and immune responses and are implicated in several immune disorders including systemic lupus erythematosus and rheumatoid arthritis , but their role in Lyme borreliosis remains unknown .", "We performed a microarray screen for expression of miR...	[ "Lyme Disease is caused by infection with the bacteria Borrelia burgdorferi , is transmitted through infected deer ticks ( Ixodes scapularis ) , and often leads to arthritis that can persist , even after antibiotic treatment .", "Here , we have identified a microRNA that is critical in modulating Lyme arthritis ,...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "systems biology", "viral immune evasion", "immunity", "virology", "immunity to infections", "immunology", "biology", "microbiology", "host-pathogen interaction", "genetics and genomics" ]	IRGM Is a Common Target of RNA Viruses that Subvert the Autophagy Network	journal.ppat.1002422	null	[ [ "Macroautophagy ( thereafter referred to as autophagy ) is a highly regulated self-degradative mechanism for intracellular clearance and recycling of cytoplasmic contents [1] .", "During this process large portions of the cytoplasm are engulfed into autophagosomes that subsequently fuse with lysosomes to ...	[ "Autophagy is a conserved degradative pathway used as a host defense mechanism against intracellular pathogens .", "However , several viruses can evade or subvert autophagy to insure their own replication .", "Nevertheless , the molecular details of viral interaction with autophagy remain largely unknown .", ...	[ "Autophagy is a highly regulated cellular degradative pathway for recycling of long-lived proteins and damaged organelles .", "Autophagy is also used by host cells as a defense mechanism against intracellular pathogens .", "Autophagy can degrade pathogens or pathogen-derived molecules trapped within specialized...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "microbiology/environmental microbiology", "computational biology/comparative sequence analysis", "computational biology/genomics" ]	The Effects of Alignment Quality, Distance Calculation Method, Sequence Filtering, and Region on the Analysis of 16S rRNA Gene-Based Studies	journal.pcbi.1000844	null	[ [ "The recent advent of massively-parallelized pyrosequencing platforms has enabled a renaissance in the field of microbial ecology [1] , [2] .", "Pyrosequencing has engendered much enthusiasm since it is now possible to obtain nearly 100-times as many sequences by pyrosequencing for the same cost as using ...	[ "Pyrosequencing of PCR-amplified fragments that target variable regions within the 16S rRNA gene has quickly become a powerful method for analyzing the membership and structure of microbial communities .", "This approach has revealed and introduced questions that were not fully appreciated by those carrying out t...	[ "Microbial communities are notoriously difficult to analyze because of their inaccessibility via culturing and high diversity .", "Next generation sequencing technologies have made it possible to obtain deep sampling coverage of the 16S rRNA gene; however , interpretation of the resulting data is complicated by t...	2010
[ "Introduction", "Models", "Results", "Discussion" ]	[]	Highly Loaded Behavior of Kinesins Increases the Robustness of Transport Under High Resisting Loads	journal.pcbi.1003981	null	[ [ "Kinesins move 8 nm per step [1–4] along MT by using energy obtained from ATP hydrolysis [5–7] .", "Among the kinesin superfamily , this study focuses on kinesin–1 ( referred to simply as kinesin ) which has two identical heads [8 , 9] .", "Several experiments have measured the run length of cargoes t...	[ "Kinesins are nano-sized biological motors which walk by repeating a mechanochemical cycle .", "A single kinesin molecule is able to transport its cargo about 1 μm in the absence of external loads .", "However , kinesins perform much longer range transport in cells by working collectively .", "This long range...	[ "Kinesins are molecular motors which work when they bind to tracks called microtubules ( MTs ) .", "In a cell , cargoes of kinesins are transported to very distant destinations compared to a short transport ability of single kinesins .", "To study this difference , we establish a novel quantitative model capabl...	2015
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "ocular anatomy", "brain", "social sciences", "light", "neuroscience", "electromagnetic radiation", "perception", "cognitive psychology", "luminance", "visible light", "vision", "animal cells", "visual cortex", "physics", "psychology", "cellular neuros...	A neural field model for color perception unifying assimilation and contrast	journal.pcbi.1007050	null	[ [ "Color induction , which refers to a change in color appearance of a test stimulus under the influence of spatially neighboring stimuli in the field of view [1] , has been extensively studied in psychophysics [2] .", "This effect has been observed for uniform inducing surrounds [3–7] and geometrically mor...	[ "We address the question of color-space interactions in the brain , by proposing a neural field model of color perception with spatial context for the visual area V1 of the cortex .", "Our framework reconciles two opposing perceptual phenomena , known as simultaneous contrast and chromatic assimilation .", "The...	[ "The color perception produced by an image heavily depends on the spatial distribution of its colors .", "From this “color in context” phenomenon , extensively studied in psychophysics for decades , has arisen the question in neuroscience of how color and space interact in the brain .", "Visual signals are inde...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/animal genetics", "cell biology/nuclear structure and function", "molecular biology/recombination", "molecular biology/chromosome structure", "genetics and genomics/chromosome biology", "genetics and genomics/gene function", "molecular biology/dna repair" ]	Chromosome Axis Defects Induce a Checkpoint-Mediated Delay and Interchromosomal Effect on Crossing Over during Drosophila Meiosis	journal.pgen.1001059	null	[ [ "Meiotic recombination occurs during prophase I when homologous chromosomes are synapsed along their entire length .", "Synapsis is defined as the close and stable association of homologous chromosomes through a proteinaceous structure called the synaptonemal complex ( SC ) .", "In most organisms , th...	[ "Crossovers mediate the accurate segregation of homologous chromosomes during meiosis .", "The widely conserved pch2 gene of Drosophila melanogaster is required for a pachytene checkpoint that delays prophase progression when genes necessary for DSB repair and crossover formation are defective .", "However , th...	[ "Meiosis is a specialized cell division in which diploid organisms form haploid gametes for sexual reproduction .", "This is accomplished by a single round of replication followed by two consecutive divisions .", "At the first meiotic division , the segregation of homologous chromosomes in most organisms is dep...	2010
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "immunopathology", "animal models of infection", "antivirals", "viral persistence and latency", "virology", "viral nucleic acid", "immunology", "biology", "microbiology", "viral replication" ]	A Highly Intensified ART Regimen Induces Long-Term Viral Suppression and Restriction of the Viral Reservoir in a Simian AIDS Model	journal.ppat.1002774	null	[ [ "The study of persistence of viral sanctuaries during antiretroviral therapy ( ART ) and the possibility for their therapeutic targeting is crucial for eradication of HIV-1 .", "Animal models for lentiviral persistence during therapy are therefore needed .", "The creation of such animal models require...	[ "Stably suppressed viremia during ART is essential for establishing reliable simian models for HIV/AIDS .", "We tested the efficacy of a multidrug ART ( highly intensified ART ) in a wide range of viremic conditions ( 103–107 viral RNA copies/mL ) in SIVmac251-infected rhesus macaques , and its impact on the vira...	[ "Novel research aimed at finding a cure for AIDS requires animal models responding to human antiretroviral drugs .", "However , there have been few antiretrovirals cross-active against the simian viruses .", "In this study , we expanded the arsenal of drugs active against the simian retrovirus SIVmac251 and sho...	2012
[ "Introduction", "Methods", "Results and discussion", "Conclusions" ]	[ "medicine and health sciences", "microbiome", "tropical diseases", "microbiology", "parasitic diseases", "parasitic protozoans", "metabolomics", "protozoans", "metabolites", "gastroenterology and hepatology", "neglected tropical diseases", "microbial genomics", "parasitic intestinal diseases...	Experimental Chagas disease-induced perturbations of the fecal microbiome and metabolome	journal.pntd.0006344	null	[ [ "Trypanosoma cruzi are protozoan parasites endemic to Central and South America .", "They cause a range of cardiac and gastrointestinal manifestations collectively known as Chagas disease .", "With increasing travel and immigration , infected individuals are also now found worldwide .", "Six to se...	[ "Trypanosoma cruzi parasites are the causative agents of Chagas disease .", "These parasites infect cardiac and gastrointestinal tissues , leading to local inflammation and tissue damage .", "Digestive Chagas disease is associated with perturbations in food absorption , intestinal traffic and defecation .", "...	[ "Host-parasite interactions are usually studied as a binary system , without considering the role of the host microbiota .", "This work integrates microbiome research into the study of gastrointestinal Chagas disease .", "We show that T . cruzi infection perturbs the fecal microbiome and metabolome , indicating...	2018
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "biochemistry/molecular evolution", "virology/virion structure, assembly, and egress", "biochemistry/protein folding", "virology", "virology/host invasion and cell entry" ]	The Disulfide Bonds in Glycoprotein E2 of Hepatitis C Virus Reveal the Tertiary Organization of the Molecule	journal.ppat.1000762	null	[ [ "The hepatitis C virus ( HCV ) is a major cause of chronic liver disease worldwide , leading to cirrhosis and hepatocellular carcinoma [1] .", "In spite of being the focus of intense research efforts , no vaccine is available against HCV , and current therapeutic treatments have limited efficacy and signi...	[ "Hepatitis C virus ( HCV ) , a major cause of chronic liver disease in humans , is the focus of intense research efforts worldwide .", "Yet structural data on the viral envelope glycoproteins E1 and E2 are scarce , in spite of their essential role in the viral life cycle .", "To obtain more information , we dev...	[ "Little is known about the structure of the envelope glycoproteins of the hepatitis C virus ( HCV ) , in spite of their essential role in the viral cycle of this major human pathogen .", "Here , we determined the connectivity of the 9 disulfide bonds formed by the strictly conserved 18 cysteines of the ectodomain...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Leptomonas seymouri: Adaptations to the Dixenous Life Cycle Analyzed by Genome Sequencing, Transcriptome Profiling and Co-infection with Leishmania donovani	journal.ppat.1005127	null	[ [ "Flagellates of the family Trypanosomatidae are single-celled obligatory parasites .", "They can be either dixenous ( i . e . those with two hosts in their life cycle—Trypanosoma , Leishmania , and Phytomonas spp . ) or monoxenous ( i . e . those having only one host ) .", "For decades , monoxenous tr...	[ "The co-infection cases involving dixenous Leishmania spp .", "( mostly of the L . donovani complex ) and presumably monoxenous trypanosomatids in immunocompromised mammalian hosts including humans are well documented .", "The main opportunistic parasite has been identified as Leptomonas seymouri of the sub-fam...	[ "In this work we performed a comprehensive evaluation of the infective potential of Leptomonas seymouri , repeatedly isolated from kala-azar patients infected by Leishmania donovani in India and neighboring countries , and have tested the capacity of this monoxenous trypanosomatid to utilize the sand fly vectors pe...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/bacterial infections", "microbiology/medical microbiology" ]	Variations in TcdB Activity and the Hypervirulence of Emerging Strains of Clostridium difficile	journal.ppat.1001061	null	[ [ "Clostridium difficile is a gram-positive , spore-forming anaerobe , first described by Hall and O'Toole over 75 years ago [1]; however , the organism was not associated with human disease until 1978 [2] , [3] .", "Over the past three decades C . difficile has become a major nosocomial pathogen and is the...	[ "Hypervirulent strains of Clostridium difficile have emerged over the past decade , increasing the morbidity and mortality of patients infected by this opportunistic pathogen .", "Recent work suggested the major C . difficile virulence factor , TcdB , from hypervirulent strains ( TcdBHV ) was more cytotoxic in vi...	[ "Clostridium difficile is a spore-forming bacterium that contaminates hospitals and infects patients undergoing antibiotic therapy .", "C . difficile is now the leading cause of hospital-acquired diarrhea in developed countries .", "Most concerning has been the recent increase in mortality of C . difficile pati...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "cell physiology", "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "pathogens", "immunology", "microbiology", "vertebrates", "viral structure", "animals", "mammals", "retroviruses", "primates", "immunodeficiency viruses", "viruses", ...	Adapting SHIVs In Vivo Selects for Envelope-Mediated Interferon-α Resistance	journal.ppat.1005727	null	[ [ "The innate immune system presents the first host defense against viral infection .", "Host cells are able to sense the presence of viral infection and respond by producing type-I interferon ( IFN-I ) , which , in turn , leads to the up-regulation of hundreds of host genes that are potentially antiviral [...	[ "Lentiviruses are able to establish persistent infection in their respective hosts despite a potent type-I interferon ( IFN-I ) response following transmission .", "A number of IFN-I-induced host factors that are able to inhibit lentiviral replication in vitro have been identified , and these studies suggest a ro...	[ "The innate immune system is an important host defense against viral infection .", "Recently , there has been significant interest in characterizing the innate immune response to HIV-1 infection , in particular the role of type-I interferon ( IFN-I ) .", "Understanding the interaction of HIV-1 with the innate i...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases", "infectious diseases of the nervous system", "medicine and health sciences", "viral diseases", "encephalitis", "japanese encephalitis" ]	A Molecularly Cloned, Live-Attenuated Japanese Encephalitis Vaccine SA14-14-2 Virus: A Conserved Single Amino Acid in the ij Hairpin of the Viral E Glycoprotein Determines Neurovirulence in Mice	journal.ppat.1004290	null	[ [ "Japanese encephalitis virus ( JEV ) is the most common cause of viral encephalitis in Asia and parts of the Western Pacific , with ∼60% of the world's population at risk of infection [1] .", "Within the family Flaviviridae ( genus Flavivirus ) , JEV belongs to the JE serological group , which also includ...	[ "Japanese encephalitis virus ( JEV ) , a mosquito-borne flavivirus that causes fatal neurological disease in humans , is one of the most important emerging pathogens of public health significance .", "JEV represents the JE serogroup , which also includes West Nile , Murray Valley encephalitis , and St . Louis enc...	[ "A group of mosquito-borne flaviviruses that cause fatal encephalitis in humans is among the most important of all emerging human pathogens of global significance .", "This group includes Japanese encephalitis ( JE ) , West Nile , St . Louis encephalitis , and Murray Valley encephalitis viruses .", "In this wor...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "specimen preparation and treatment", "mechanical treatment of specimens", "cellular neuroscience", "specimen disruption", "neuronal morphology", "computational neuroscience", "single neuron function", "biology and life sciences", "computational biology", "electroporation", "biophysics", "neur...	Spatially Distributed Dendritic Resonance Selectively Filters Synaptic Input	journal.pcbi.1003775	null	[ [ "Neurons are constantly bombarded by thousands of synaptic inputs , so it is essential that neurons are able to listen selectively to subsets of these inputs .", "Throughout the sensory pathways , topographic maps ensure that neurons are able to sample a limited range of the stimulus space [1] .", "Bu...	[ "An important task performed by a neuron is the selection of relevant inputs from among thousands of synapses impinging on the dendritic tree .", "Synaptic plasticity enables this by strenghtening a subset of synapses that are , presumably , functionally relevant to the neuron .", "A different selection mechani...	[ "Neurons are constantly bombarded by thousands of inputs .", "Synaptic plasticity is generally accepted as a mechanism to select certain inputs by strengthening their synapses while reducing the effects of others by weakening them .", "Another biophysical mechanism to select inputs is through membrane resonance...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "homo (human)", "genetics and genomics", "computational biology" ]	The Genographic Project Public Participation Mitochondrial DNA Database	journal.pgen.0030104	null	[ [ "The plethora of human mitochondrial DNA ( mtDNA ) studies in recent years has made this molecule one of the most extensively investigated genetic systems .", "Its abundance in human cells; uniparental , nonrecombining mode of inheritance; and high mutation rate compared to that of the nuclear genome , ha...	[ "The Genographic Project is studying the genetic signatures of ancient human migrations and creating an open-source research database .", "It allows members of the public to participate in a real-time anthropological genetics study by submitting personal samples for analysis and donating the genetic results to th...	[ "The Genographic Project was launched in 2005 to address anthropological questions on a global scale using genetics as a tool .", "Samples are collected in two ways .", "First , the project comprises a consortium of ten scientific teams from around the world united by a core ethical and scientific framework tha...	2007
[ "Introduction", "Results", "Discussion", "Models" ]	[]	Anxiety-Like Behavioural Inhibition Is Normative under Environmental Threat-Reward Correlations	journal.pcbi.1004646	null	[ [ "Rodent models of human anxiety commonly involve a conflict between approach and avoidance [1–4] , as exemplified in the Elevated Plus Maze [5–7] , Open Field test [8] , operant conflict tests [9 , 10] , or novelty-suppressed feeding test [11] .", "Behavioural inhibition is a core anxiety-like readout in ...	[ "Behavioural inhibition is a key anxiety-like behaviour in rodents and humans , distinct from avoidance of danger , and reduced by anxiolytic drugs .", "In some situations , it is not clear how behavioural inhibition minimises harm or maximises benefit for the agent , and can even appear counterproductive .", "...	[ "Behavioural inhibition is observed in situations of anxiety , both in animals and humans .", "In some situations , it is not clear how it minimises harm or maximises benefit for the agent , and can even appear counterproductive .", "This prevents an understanding of the underlying neural computations .", "He...	2015
[ "Introduction", "Results", "Materials and Methods" ]	[ "oncology", "medicine", "immune cells", "immunology", "biology" ]	Mesenchymal Transition and Dissemination of Cancer Cells Is Driven by Myeloid-Derived Suppressor Cells Infiltrating the Primary Tumor	journal.pbio.1001162	null	[ [ "Tumor metastasis is the primary cause of death by cancer [1] .", "Metastasis is a multistep process in which cancer cells derived from the primary tumor migrate to regional or distant sites where they re-initiate tumor development [2] .", "Until recently , the first step of metastasis , ( i . e . tum...	[ "In order to metastasize , cancer cells need to acquire a motile phenotype .", "Previously , development of this phenotype was thought to rely on the acquisition of selected , random mutations and thus would occur late in cancer progression .", "However , recent studies show that cancer cells disseminate early ...	[ "Cancer progression has been depicted as a linear process , during which the incipient cancer cell sequentially accumulates mutations that confer the ability to metastasize .", "However , recent studies show that cancer cells disseminate early , before such mutations can accumulate , implying the existence of a d...	2011
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "apolipoproteins", "protein interactions", "parasitic diseases", "protein structure", "neglected tropical diseases", "echinococcosis", "infectious diseases", "lipids", "proteins", "lipoproteins", "biology", "recombinant proteins", "biophysics", "biochemistry", "protein chem...	Direct Interaction between EgFABP1, a Fatty Acid Binding Protein from Echinococcus granulosus, and Phospholipid Membranes	journal.pntd.0001893	null	[ [ "Hydatidosis is a highly pathogenic infection with an almost global incidence caused by the larval stage ( metacestode ) of the cestode Echinococcus granulosus .", "In endemic areas it has serious health effects on humans , livestock and wildlife , representing a major public health and economic burden in...	[ "Growth and maintenance of hydatid cysts produced by Echinococcus granulosus have a high requirement for host lipids for biosynthetic processes , membrane building and possibly cellular and developmental signalling .", "This requires a high degree of lipid trafficking facilitated by lipid transporter proteins .",...	[ "Echinococcus granulosus is the causative agent of hydatidosis , a zoonotic infection that affects humans and livestock , representing a public health and economic burden in many countries .", "Since the parasites are unable to synthesise most of their lipids de novo , they must acquire them from the host and the...	2012
[ "Introduction", "Results", "Discussion", "Conclusion", "Materials and methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "microbiome", "gut bacteria", "pathology and laboratory medicine", "vibrio", "immunology", "microbiology", "vertebrates", "animals", "animal models", "osteichthyes", "model organisms", "signs and symptoms", "enterobacteriac...	The enteric nervous system promotes intestinal health by constraining microbiota composition	journal.pbio.2000689	null	[ [ "The intestinal tract serves to harvest nutrients and energy , protect against harmful toxins and pathogens , and clear out waste .", "These functions can be modulated by both the enteric nervous system ( ENS ) and the trillions of symbiotic bacteria that reside within the gut [1–3] .", "Importantly ,...	[ "Sustaining a balanced intestinal microbial community is critical for maintaining intestinal health and preventing chronic inflammation .", "The gut is a highly dynamic environment , subject to periodic waves of peristaltic activity .", "We hypothesized that this dynamic environment is a prerequisite for a bala...	[ "Intestinal health depends on maintaining a balanced microbial community within the highly dynamic environment of the intestine .", "Every few minutes , this environment is rocked by peristaltic waves of muscular contraction and relaxation through a process regulated by the enteric nervous system ( ENS ) .", "W...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "working memory", "cognitive neuroscience", "computational neuroscience", "psychophysics", "biology", "sensory perception", "neuroscience" ]	No Evidence for an Item Limit in Change Detection	journal.pcbi.1002927	null	[ [ "Visual working memory , the ability to buffer visual information over time intervals of the order of seconds , is a fundamental aspect of cognition .", "It is essential for detecting changes [1]–[3] , integrating information across eye fixations [4]–[5] , and planning goal-directed reaching movements [6]...	[ "Change detection is a classic paradigm that has been used for decades to argue that working memory can hold no more than a fixed number of items ( “item-limit models” ) .", "Recent findings force us to consider the alternative view that working memory is limited by the precision in stimulus encoding , with mean ...	[ "Working memory is a fundamental aspect of human cognition .", "It allows us to remember bits of information over short periods of time and make split-second decisions about what to do next .", "Working memory is often tested using a change detection task: subjects report whether a change occurred between two s...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Natural Rabies Infection in a Domestic Fowl (Gallus domesticus): A Report from India	journal.pntd.0003942	null	[ [ "Rabies is a fatal encephalitis caused by the viruses belonging to the genus Lyssavirus of the family Rhabdoviridae .", "It is a viral disease primarily affecting mammals , though all warm blooded animals are susceptible .", "In India and other Asian countries more than 90% of human infections occur d...	[ "Rabies is a fatal encephalitis caused by viruses belonging to the genus Lyssavirus of the family Rhabdoviridae .", "It is a viral disease primarily affecting mammals , though all warm blooded animals are susceptible .", "Experimental rabies virus infection in birds has been reported , but naturally occurring i...	[ "Rabies is a fatal viral disease affecting humans and other animals .", "Though all warm blooded animals are susceptible to this disease , rabies is commonly observed in mammals .", "Birds can be experimentally infected with this virus; however , naturally occurring rabies infection in birds has been reported v...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology", "neurological disorders", "evolutionary biology" ]	Prion Switching in Response to Environmental Stress	journal.pbio.0060294	A yeast prion protein may promote evolvability by providing a mechanism for the rapid evolution of complex traits that is responsive to environmental stress.	[ [ "[PSI+] is an epigenetic modifier of translation termination in yeast [1 , 2] .", "It is formed by the protein Sup35 , a subunit of the translation termination complex , which carries an intrinsically disordered prion-determining region at its N terminus .", "When this domain switches to an aggregatin...	[ "Evolution depends on the manner in which genetic variation is translated into new phenotypes .", "There has been much debate about whether organisms might have specific mechanisms for “evolvability , ” which would generate heritable phenotypic variation with adaptive value and could act to enhance the rate of ev...	[ "One controversy in evolutionary biology concerns whether there might be plausible explanations for the rapid evolution of complex traits .", "An extreme and fascinating example of protein conformational change , the prion , offers a framework for this concept .", "Prion proteins are responsible for neurodegene...	2008
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience/sensory systems", "computational biology/computational neuroscience" ]	A Neurophysiologically Plausible Population Code Model for Feature Integration Explains Visual Crowding	journal.pcbi.1000646	null	[ [ "Since Korte [1] originally described perceptual phenomena of reading in peripheral vision , a substantial number of studies have shown the important role of spacing for object recognition .", "The phenomenon that an object becomes more difficult to recognize when surrounded by other objects is now popula...	[ "An object in the peripheral visual field is more difficult to recognize when surrounded by other objects .", "This phenomenon is called “crowding” .", "Crowding places a fundamental constraint on human vision that limits performance on numerous tasks .", "It has been suggested that crowding results from spat...	[ "Visual crowding refers to the phenomenon that objects become more difficult to recognize when other objects surround them .", "Recently there has been an explosion of studies on crowding , driven , in part , by the belief that understanding crowding will help to understand a range of visual behaviours , includin...	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "parasite groups", "plasmodium", "tropical diseases", "vertebrates", "parasitic diseases", "parasitic protozoans", "animals", "parasitology", "mammals", "primates", "apicomplexa", "protozoans", "molecular biology techniques", "infectious...	Investigating the Contribution of Peri-domestic Transmission to Risk of Zoonotic Malaria Infection in Humans	journal.pntd.0005064	null	[ [ "The success story of reducing malaria worldwide [1] has been marred by a few notable exceptions where bulk of disease is caused by zoonotic “neglected” malaria species with atypical transmission that makes them less easy to control .", "Zoonotic malaria , such as Plasmodium knowlesi from the long tailed ...	[ "In recent years , the primate malaria Plasmodium knowlesi has emerged in human populations throughout South East Asia , with the largest hotspot being in Sabah , Malaysian Borneo .", "Control efforts are hindered by limited knowledge of where and when people get exposed to mosquito vectors .", "It is assumed t...	[ "The primate knowlesi malaria has now emerged in human populations throughout South East Asia .", "Our limited knowledge of where and when people get exposed to the vector ( Anopheles balabacensis ) has resulted in poor control measures , although it is assumed that exposure occurs primarily when people are worki...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Encoder-Decoder Optimization for Brain-Computer Interfaces	journal.pcbi.1004288	null	[ [ "When the BCI system is closed-loop such that both the user can learn and the decoding algorithm can adapt , we have a setting which permits co-adaptation [3 , 4] .", "Changes in system performance may be driven by distinct types of adaptation: ( 1 ) All of the adaptation may occur due to the decoder and ...	[ "Neuroprosthetic brain-computer interfaces are systems that decode neural activity into useful control signals for effectors , such as a cursor on a computer screen .", "It has long been recognized that both the user and decoding system can adapt to increase the accuracy of the end effector .", "Co-adaptation i...	[ "Brain-computer interfaces are systems which allow a user to control a device in their environment via their neural activity .", "The system consists of hardware used to acquire signals from the brain of the user , algorithms to decode the signals , and some effector in the world that the user will be able to con...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "bacteriology", "gram negative bacteria", "medicine and health sciences", "gut bacteria", "microbiome", "chemical compounds", "phosphates", "nmr spectroscopy", "microbiology", "animal models", "model organisms", "metabolites", "experimental organism systems", "bacteria", "microbial genom...	Para-cresol production by Clostridium difficile affects microbial diversity and membrane integrity of Gram-negative bacteria	journal.ppat.1007191	null	[ [ "Clostridium difficile is a Gram-positive spore-forming enteric pathogen and the leading cause of antibiotic-associated diarrhoea worldwide[1] .", "C . difficile infection ( CDI ) ranges from self-limiting diarrhoea to severe and life threatening pseudomembranous colitis[2] .", "C . difficile spores a...	[ "Clostridium difficile is a Gram-positive spore-forming anaerobe and a major cause of antibiotic-associated diarrhoea .", "Disruption of the commensal microbiota , such as through treatment with broad-spectrum antibiotics , is a critical precursor for colonisation by C . difficile and subsequent disease .", "Fu...	[ "Clostridium difficile is a bacterium responsible for causing the majority of antibiotic associated diarrhoea outbreaks world-wide .", "In the United States of America , C . difficile infects half a million people annually .", "Antibiotics disrupt the natural protective gut microbiota , rendering people suscept...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "epidemiology", "tropical diseases", "malaria", "parasitic diseases" ]	Epidemiology of Disappearing Plasmodium vivax Malaria: A Case Study in Rural Amazonia	journal.pntd.0003109	null	[ [ "Malaria is one of the major tropical infectious diseases for which decades of intensive control efforts have met with only partial success in Brazil [1] .", "With nearly 243 , 000 slide-confirmed infections , this country contributed 52% of all malaria cases reported in the Region of the Americas and the...	[ "New frontier settlements across the Amazon Basin pose a major challenge for malaria elimination in Brazil .", "Here we describe the epidemiology of malaria during the early phases of occupation of farming settlements in Remansinho area , Brazilian Amazonia .", "We examine the relative contribution of low-densi...	[ "Despite decades of control efforts , malaria remains a major public health concern in Brazil .", "A large proportion of the 243 , 000 cases diagnosed per year originate from areas of recent colonization in the densely forested Amazon Basin .", "This population-based longitudinal study addresses the epidemiolog...	2014
[ "Introduction", "Model", "Discussion", "Methods" ]	[]	Enhancer Runaway and the Evolution of Diploid Gene Expression	journal.pgen.1005665	null	[ [ "The evolution of gene expression has become a subject of intensive research in the last years , sparking debates upon its role in adaptive evolution and speciation [1–6] .", "Clearly , protein folding , expression levels , timing and tissue localization of expression are important regulatory traits under...	[ "Evidence is mounting that the evolution of gene expression plays a major role in adaptation and speciation .", "Understanding the evolution of gene regulatory regions is indeed an essential step in linking genotypes and phenotypes and in understanding the molecular mechanisms underlying evolutionary change .", ...	[ "With the advent of new sequencing technologies , the evolution of gene expression regulation is becoming a subject of intensive research .", "In this paper , we report an entirely new phenomenon acting on the evolution of gene regulatory sequences .", "We show that in a small genomic region around genes there ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "invertebrates", "cell motility", "medicine and health sciences", "neurochemistry", "nose", "face", "pathology and laboratory medicine", "caenorhabditis", "nervous system", "pathogens", "neuroscience", "biological locomotion", "biomechanics", "animals", "animal models", "caenorhabditis...	NPR-9, a Galanin-Like G-Protein Coupled Receptor, and GLR-1 Regulate Interneuronal Circuitry Underlying Multisensory Integration of Environmental Cues in Caenorhabditis elegans	journal.pgen.1006050	null	[ [ "Neuronal circuits integrate various environmental stimuli to alter behavioral phenotypes .", "Characterization of the mechanisms underlying multisensory integration is essential to understanding how organisms perceive their environment .", "Disruptions to neural signaling pathways have been linked to...	[ "C . elegans inhabit environments that require detection of diverse stimuli to modulate locomotion in order to avoid unfavourable conditions .", "In a mammalian context , a failure to appropriately integrate environmental signals can lead to Parkinson’s , Alzheimer’s , and epilepsy .", "Provided that the circui...	[ "Multiple environmental cues are sensed by an organism in order to coordinate behavioral responses .", "Consequently , organisms must be able to simultaneously detect and integrate multiple external stimuli in order to appropriately modify their behavior .", "Identifying the unique circuits mediating the respon...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "control theory", "sleep", "applied mathematics", "anatomy and physiology", "physiological processes", "control engineering", "mathematics", "computational neuroscience", "biology", "nonlinear dynamics", "systems biology", "control systems", "physiology", "computational biology", "engine...	Reconstructing Mammalian Sleep Dynamics with Data Assimilation	journal.pcbi.1002788	null	[ [ "Great strides have been made in understanding the physiological basis for sleep regulation [1] in terms of the interacting neuronal cell groups and their neurotransmitter mediated interactions .", "This physiology is now increasingly being embodied into complex mathematical models of sleep dynamics [2]–[...	[ "Data assimilation is a valuable tool in the study of any complex system , where measurements are incomplete , uncertain , or both .", "It enables the user to take advantage of all available information including experimental measurements and short-term model forecasts of a system .", "Although data assimilatio...	[ "Mathematical models are developed to better understand interactions between components of a system that together govern the overall behavior .", "Mathematical models of sleep have helped to elucidate the neuronal cell groups that are involved in promoting sleep and wake behavior and the transitions between them ...	2012
[ "Introduction", "Results", "Discussion" ]	[ "neuroscience", "neurobiology of disease and regeneration", "medicine and health sciences", "signs and symptoms", "pathology and laboratory medicine", "migraine", "gene regulatory networks", "genetic association studies", "neurology", "genetics", "biology and life sciences", "human genetics", ...	Selectivity in Genetic Association with Sub-classified Migraine in Women	journal.pgen.1004366	null	[ [ "Migraine is one of the most common and debilitating neurological disorders and its clinical presentation can be quite variable [1] .", "Even when the diagnosis of migraine meets consensus criteria and can in most cases be clearly distinguished from other types of headaches ( e . g . tension-type headache...	[ "Migraine can be sub-classified not only according to presence of migraine aura ( MA ) or absence of migraine aura ( MO ) , but also by additional features accompanying migraine attacks , e . g . photophobia , phonophobia , nausea , etc . all of which are formally recognized by the International Classification of H...	[ "Migraine is among the most common and debilitating neurological disorders .", "Diagnostic criteria for migraine recognize a variety of symptoms including a primary dichotomous classification for the presence or absence of aura , typically a visual disturbance phenomenon , as well as others such as sensitivity to...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "viral hemorrhagic fevers", "infectious diseases", "neglected tropical diseases", "viral diseases", "ebola hemorrhagic fever" ]	Serologic Cross-Reactivity of Human IgM and IgG Antibodies to Five Species of Ebola Virus	journal.pntd.0001175	null	[ [ "The genus Ebolavirus , family Filoviridae , has five identified ( including one proposed ) viral species [1] .", "Of these , four viral species , Zaire ebolavirus ( ZEBOV ) , Sudan ebolavirus ( SEBOV ) , Côte d'Ivoire ebolavirus ( CIEBOV ) , and Bundibugyo ebolavirus ( BEBOV ) are known to cause Ebola he...	[ "Five species of Ebola virus ( EBOV ) have been identified , with nucleotide differences of 30–45% between species .", "Four of these species have been shown to cause Ebola hemorrhagic fever ( EHF ) in humans and a fifth species ( Reston ebolavirus ) is capable of causing a similar disease in non-human primates ....	[ "Ebola virus ( EBOV ) is a highly pathogenic virus , capable of causing Ebola hemorrhagic fever in humans and non-human primates .", "Five species of EBOV have been identified .", "To examine whether infection with one EBOV species results in antibodies that cross-react with other EBOV species , we selected gro...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology/immunodeficiency viruses" ]	Real-Time Visualization of HIV-1 GAG Trafficking in Infected Macrophages	journal.ppat.1000015	null	[ [ "The human immunodeficiency virus type 1 ( HIV-1 ) Gag polyprotein precursor , Pr55Gag , plays an essential role in virus assembly and release .", "Its expression alone is able to generate virus-like particles ( VLPs ) [1] , [2] .", "All four domains of Pr55Gag–matrix ( MA ) , capsid ( CA ) , nucleoca...	[ "HIV-1 particle production is driven by the Gag precursor protein Pr55Gag .", "Despite significant progress in defining both the viral and cellular determinants of HIV-1 assembly and release , the trafficking pathway used by Gag to reach its site of assembly in the infected cell remains to be elucidated .", "Th...	[ "The viral Gag protein is both necessary and sufficient for the assembly of a new generation of virus particles .", "There has been a significant amount of debate in recent years regarding the site in the cell at which HIV-1 assembly takes place .", "Of particular interest has been the site of assembly in macro...	2008
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Quantifying Chaperone-Mediated Transitions in the Proteostasis Network of E. coli	journal.pcbi.1003324	null	[ [ "Protein homeostasis ( proteostasis ) is essential for the viability of an organism .", "The disruption of protein homeostasis involving the misfolding and subsequent aggregation of proteins is implicated in many diseases , including Down's syndrome , type-II diabetes , Alzheimer's , Parkinson's and Hunti...	[ "For cells to function , the concentrations of all proteins in the cell must be maintained at the proper levels ( proteostasis ) .", "This task – complicated by cellular stresses , protein misfolding , aggregation , and degradation – is performed by a collection of chaperones that alter the configurational landsc...	[ "To maintain proper amounts of folded , functional proteins , cells use systems of chaperones to correct misfolded proteins , disassemble aggregates , and provide sheltered environments in which proteins fold to their native structure .", "Typically , an individual system is studied in isolation , and its effects...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "biochemistry", "biology", "microbiology", "molecular cell biology" ]	Structure-Activity Relationship Studies on the Macrolide Exotoxin Mycolactone of Mycobacterium ulcerans	journal.pntd.0002143	null	[ [ "The macrolide exotoxin mycolactone is a key virulence factor of M . ulcerans and plays a central role in the pathogenesis of Buruli ulcer [1] .", "Mycolactones have been shown to act both in vivo and in vitro on various mammalian cell types , including fibroblasts [1]–[6] , adipocytes [7] , keratinocytes...	[ "Mycolactones are a family of polyketide-derived macrolide exotoxins produced by Mycobacterium ulcerans , the causative agent of the chronic necrotizing skin disease Buruli ulcer .", "The toxin is synthesized by polyketide synthases encoded by the virulence plasmid pMUM .", "The apoptotic , necrotic and immunos...	[ "Buruli ulcer is a chronic necrotizing skin disease caused by Mycobacterium ulcerans .", "The characteristic histopathological features of Buruli ulcer , severe destruction of subcutaneous tissue with minimal inflammation in the core of the lesion , are primarily attributed to the cytotoxic activity of mycolacton...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "sequence analysis", "genome expression analysis", "genome analysis tools", "genomics", "rna processing", "gene expression", "genetics", "biology", "computational biology", "genetics and genomics", "transcriptomes" ]	Identification of Widespread Ultra-Edited Human RNAs	journal.pgen.1002317	null	[ [ "Post-transcriptional modification of RNA molecules increases the complexity of the transcriptome and constitutes an additional mechanism for controlling gene activity .", "One of the most frequent modifications in primates is Adenosine-to-Inosine ( A-to-I ) RNA editing of pre-mRNA .", "Since inosine ...	[ "Adenosine-to-inosine modification of RNA molecules ( A-to-I RNA editing ) is an important mechanism that increases transciptome diversity .", "It occurs when a genomically encoded adenosine ( A ) is converted to an inosine ( I ) by ADAR proteins .", "Sequencing reactions read inosine as guanosine ( G ) ; there...	[ "The traditional view of mRNA as a pure intermediate between DNA and protein has changed in the last decades since the discovery of numerous RNA processing pathways .", "A frequent RNA modification is A-to-I editing , or the conversion of adenosine ( A ) to inosine ( I ) .", "Since inosine is read as a guanosin...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "biotechnology", "plant anatomy", "stem anatomy", "engineering and technology", "cell cycle and cell division", "cell processes", "brassica", "stomata", "plant science", "model organisms", "experimental organism systems", "plant genomics", "sequence motif analysis", "seedlings", "plants"...	BZU2/ZmMUTE controls symmetrical division of guard mother cell and specifies neighbor cell fate in maize	journal.pgen.1008377	null	[ [ "The development of the stomatal complex in maize ( Zea mays ) , consisting of a pair of dumbbell-shaped guard cells ( GCs ) flanked by two subsidiary cells ( SCs ) , provides an excellent model system to study the signals controlling fate determination of adjacent cells by intercellular communication .", ...	[ "Intercellular communication in adjacent cell layers determines cell fate and polarity , thus orchestrating tissue specification and differentiation .", "Here we use the maize stomatal apparatus as a model to investigate cell fate determination .", "Mutations in ZmBZU2 ( bizui2 , bzu2 ) confer a complete absenc...	[ "In the grasses , individual stomatal complexes comprise a pair of dumbbell-shaped guard cells associated with two subsidiary cells and the pore , which together play essential roles in the exchange of CO2 and O2 , in xylem transport , and in transpiration .", "However , little is known about grass stomatal compl...	2019
[ "Introduction", "Results/Discussion", "Methods" ]	[ "biology" ]	Probing the Mutational Interplay between Primary and Promiscuous Protein Functions: A Computational-Experimental Approach	journal.pcbi.1002558	null	[ [ "Proteins are capable to perform molecular tasks with impressive efficiency and , often , with exquisite specificity .", "Nevertheless , many proteins possess weak promiscuous functions , which are more or less related to the primary activity , but involve different substrates or different chemical altera...	[ "Protein promiscuity is of considerable interest due its role in adaptive metabolic plasticity , its fundamental connection with molecular evolution and also because of its biotechnological applications .", "Current views on the relation between primary and promiscuous protein activities stem largely from laborat...	[ "Interpretations of evolutionary processes at the molecular level have been determined to a significant extent by the concept of “trade-off” , the idea that improving a given feature of a protein molecule by mutation will likely bring about deterioration in other features .", "For instance , if a protein is able ...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biotechnology", "bioengineering", "biomedical engineering", "engineering and technology", "biology and life sciences", "computational biology", "biophysics", "biophysical simulations" ]	Disrupted Calcium Release as a Mechanism for Atrial Alternans Associated with Human Atrial Fibrillation	journal.pcbi.1004011	null	[ [ "Atrial fibrillation ( AF ) is currently the most common cardiac rhythm disorder , posing a significant medical and economic challenge for the US health care system [1] , [2] .", "This burden is likely to increase as the population ages and AF prevalence rises [3] .", "Effective prevention and treatme...	[ "Atrial fibrillation ( AF ) is the most common cardiac arrhythmia , but our knowledge of the arrhythmogenic substrate is incomplete .", "Alternans , the beat-to-beat alternation in the shape of cardiac electrical signals , typically occurs at fast heart rates and leads to arrhythmia .", "However , atrial altern...	[ "Atrial fibrillation is an irregular heart rhythm affecting millions of people worldwide .", "Effective treatment of this cardiac disorder relies upon our detailed knowledge and understanding of the mechanisms that lead to arrhythmia .", "Recent clinical observations have suggested that alternans , a phenomenon...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "viruses", "infectious diseases", "virology", "immunology", "microbiology", "mus (mouse)" ]	A Two-Phase Innate Host Response to Alphavirus Infection Identified by mRNP-Tagging In Vivo	journal.ppat.0030199	null	[ [ "At the interface of pathogen infection and host response lies a complex network of regulated interactions .", "As the host seeks to eradicate the pathogen and maintain survival , the pathogen itself seeks to continue its own proliferation at whatever cost is necessary to the host cell .", "Therefore ...	[ "A concept fundamental to viral pathogenesis is that infection induces specific changes within the host cell , within specific tissues , or within the entire animal .", "These changes are reflected in a cascade of altered transcription patterns evident during infection .", "However , elucidation of this cascade...	[ "A major element of viral pathogenesis is the induction of specific changes within the infected host , often reflected in altered gene expression patterns .", "However , revealing these changes in vivo has been limited by an inability to distinguish changes within the minority of infected cells from that in surro...	2007
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "breast tumors", "cancer treatment", "protein interaction networks", "enzymology", "cancers and neoplasms", "hormones", "oncology", "mutation", "network analysis", "aromatase inhibitors", "pharmacology", "estrogens", "enzyme inhibitors", "computer and info...	Network-guided prediction of aromatase inhibitor response in breast cancer	journal.pcbi.1006730	null	[ [ "A number of recent large efforts have focused on collecting genomic data from tumors .", "While these datasets led to several successful studies and insights , in many cases the clinical data available for patients enrolled in these studies is incomplete .", "This makes it hard to use such datasets f...	[ "Prediction of response to specific cancer treatments is complicated by significant heterogeneity between tumors in terms of mutational profiles , gene expression , and clinical measures .", "Here we focus on the response of Estrogen Receptor ( ER ) + post-menopausal breast cancer tumors to aromatase inhibitors (...	[ "Breast cancer is the second most common type of cancer in women , with an incidence rate of over 250 , 000 cases per year , and breast cancer cases show significant heterogeneity in clinical and omic measures .", "Estrogen receptor positive ( ER+ ) tumors typically grow in response to estrogen , and in post meno...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "biology", "veterinary science" ]	Chitohexaose Activates Macrophages by Alternate Pathway through TLR4 and Blocks Endotoxemia	journal.ppat.1002717	null	[ [ "Sepsis and septic shock , one of the most common causes of admission in intensive care units results in death of nearly 3 , 50 , 000 people every year only in US and Europe [1] , [2] .", "The disease is a consequence of systemic bacterial infections that stimulates mediators of inflammation due to hyper ...	[ "Sepsis is a consequence of systemic bacterial infections leading to hyper activation of immune cells by bacterial products resulting in enhanced release of mediators of inflammation .", "Endotoxin ( LPS ) is a major component of the outer membrane of Gram negative bacteria and a critical factor in pathogenesis o...	[ "Sepsis is one of the leading causes of death contributing to mortality as high as 54 percent in intensive care units across the world .", "Hyper inflammation induced by bacteria or bacterial products through Toll like receptors leads to sepsis and hence current approaches are directed towards blockade such recep...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "immune cells", "cytokines", "respiratory infections", "antigen-presenting cells", "immunity to infections", "immunology", "pulmonology", "adaptive immunity", "infectious diseases", "inflammation", "t cells", "biology", "infectious disease modeling", "immune system", "immun...	The Critical Role of Notch Ligand Delta-like 1 in the Pathogenesis of Influenza A Virus (H1N1) Infection	journal.ppat.1002341	null	[ [ "Influenza virus type A causes acute respiratory infections that are highly contagious and cause significant morbidity and mortality in humans and animals [1] , [2] .", "In 2009 , the influenza pandemic caused by the current H1N1 virus affected all the continents of the world [3] .", "In the United St...	[ "Influenza A viral infections have been identified as the etiologic agents for historic pandemics , and contribute to the annual mortality associated with acute viral pneumonia .", "While both innate and acquired immunity are important in combating influenza virus infection , the mechanism connecting these arms o...	[ "Influenza viruses cause annual epidemics and occasional pandemics that have claimed the lives of millions .", "Both innate and acquired immunity are essential for protection against influenza virus , and Notch and Notch ligands provide a key bridge between innate and acquired immunity .", "However , the role o...	2011
[ "Introduction", "Materials and methods", "Results and discussion" ]	[ "invertebrates", "medicine and health sciences", "pruritus", "tropical diseases", "geographical locations", "social sciences", "parasitic diseases", "animals", "neuroscience", "nematode infections", "neglected tropical diseases", "eyes", "africa", "geography", "loiasis", "loa loa", "...	Removal of adult subconjunctival Loa loa amongst urban dwellers in Nigeria	journal.pntd.0006920	null	[ [ "Ethical approval for this report was sort from the Eye Foundation Hospital Institution Review Board and was waived as this work involved only a retrospective reporting of information documented in the patients case records .", "The research was performed according to the principles of the Helsinki declar...	[ "Loiasis is a neglected tropical disease caused by infection with the filarial parasite Loa loa .", "It is a disease considered by many to be benign .", "Several reports of trans border importation of the Loa loa worm amongst immigrants and visitors from endemic regions of the world exist .", "In most cases a...	[ "Subconjunctival adult Loa loa is one of the ocular manifestations of paraisitosis by Loa loa , which is categorized as a neglected benign disease .", "Loa loa transmission has predominantly been amongst inhabitants in rural communities in Nigeria , one of the countries in the endemic belt of Africa .", "Howeve...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/microbial evolution and genomics", "evolutionary biology/microbial evolution and genomics", "microbiology/microbial evolution and genomics" ]	Origin of an Alternative Genetic Code in the Extremely Small and GC–Rich Genome of a Bacterial Symbiont	journal.pgen.1000565	null	[ [ "The GC content of bacterial genomes has been known to vary widely since at least the 1950s [1] .", "Currently sequenced genomes range from 17–75% GC and show a strong correlation between genome size and GC content [2]–[4] ( Figure 1 ) .", "The tiny genomes of symbionts of sap-feeding insects are extr...	[ "The genetic code relates nucleotide sequence to amino acid sequence and is shared across all organisms , with the rare exceptions of lineages in which one or a few codons have acquired novel assignments .", "Recoding of UGA from stop to tryptophan has evolved independently in certain reduced bacterial genomes , ...	[ "The genetic code , which relates DNA sequence to protein sequence , is nearly universal across all life .", "Examples of recodings do exist , but new instances are rare .", "Genomes that exhibit recodings typically have other extreme properties , including reduced size , reduced gene sets , and low guanine plu...	2009
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "livestock", "medicine and health sciences", "pig models", "immunology", "geographical locations", "vertebrates", "animals", "mammals", "animal models", "preventive medicine", "model organisms", "infectious disease control", "vaccination and immunization", "insect vector...	Intensive Circulation of Japanese Encephalitis Virus in Peri-urban Sentinel Pigs near Phnom Penh, Cambodia	journal.pntd.0005149	null	[ [ "Despite the increased use of vaccination in several Asian countries , Japanese Encephalitis ( JE ) remains the most important cause of viral encephalitis in Asia in humans [1–3] .", "A recent review based on updated incidence data estimated that 68 , 000 JE cases occurred annually in the 24 JE-endemic co...	[ "Despite the increased use of vaccination in several Asian countries , Japanese Encephalitis ( JE ) remains the most important cause of viral encephalitis in Asia in humans with an estimated 68 , 000 cases annually .", "Considered a rural disease occurring mainly in paddy-field dominated landscapes where pigs are...	[ "Japanese Encephalitis Virus ( JEV ) is the most important cause of viral encephalitis in Asia in humans with an estimated 68 , 000 cases annually .", "The disease is considered a mainly rural one because it occurs mainly in rural areas dominated by paddy fields where the main mosquito species vector of JEV breed...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "invertebrates", "medicine and health sciences", "immune cells", "engineering and technology", "nucleases", "deoxyribonucleases", "enzymes", "immunology", "manufacturing processes", "dna-binding proteins", "enzymology", "parasitic diseases", "animals", "nematode infections...	Human Leukocytes Kill Brugia malayi Microfilariae Independently of DNA-Based Extracellular Trap Release	journal.pntd.0005279	null	[ [ "Throughout history , parasitic nematode infections have had a major impact on human development , especially of the poorest and most disadvantaged populations .", "Human diseases associated with these infections include lymphatic filariasis ( LF ) and onchocerciasis .", "A hallmark of these infection...	[ "Wuchereria bancrofti , Brugia malayi and Brugia timori infect over 100 million people worldwide and are the causative agents of lymphatic filariasis .", "Some parasite carriers are amicrofilaremic whilst others facilitate mosquito-based disease transmission through blood-circulating microfilariae ( Mf ) .", "R...	[ "Lymphatic filariasis is a disfiguring and debilitating neglected tropical disease caused by filarial parasitic nematodes including Brugia malayi .", "The immune mechanisms that drive host tolerance and host resistance to blood circulating microfilariae are not yet fully understood .", "In this study , we inves...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "agriculture", "biology" ]	Airborne Signals from a Wounded Leaf Facilitate Viral Spreading and Induce Antibacterial Resistance in Neighboring Plants	journal.ppat.1002640	null	[ [ "Plants are exposed to a diverse range of abiotic and biotic stresses [1]–[3] .", "Physical damage to a plant is a potential threat because it provides an opportunity for pathogen entry .", "Localized tissue damage elicits the expression of an array of antimicrobial phytochemicals [4] , proteins [5] ,...	[ "Many plants release airborne volatile compounds in response to wounding due to pathogenic assault .", "These compounds serve as plant defenses and are involved in plant signaling .", "Here , we study the effects of pectin methylesterase ( PME ) -generated methanol release from wounded plants ( “emitters” ) on ...	[ "The mechanical wounding of plant leaves , which is one of the first steps in pathogen infection and herbivore attack , activates signal transduction pathways and airborne signals to fend off harmful organisms .", "The mechanisms by which these signals promote plant immunity remain elusive .", "Here , we demons...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immune cells", "immunity to infections", "immunology", "microbiology", "host-pathogen interaction", "immunodeficiency viruses", "adaptive immunity", "animal models of infection", "viral immune evasion", "t cells", "biology", "viral evolution", "immune response", "viral persistence and lat...	Viral CTL Escape Mutants Are Generated in Lymph Nodes and Subsequently Become Fixed in Plasma and Rectal Mucosa during Acute SIV Infection of Macaques	journal.ppat.1002048	null	[ [ "Human immunodeficiency virus ( HIV ) infection of humans and Simian Immunodeficiency Virus ( SIV ) infection of rhesus macaques ( Macaca mulatta , RM ) results in a progressive and irreversible decline of immune function characterized by depletion of CD4 T cells , chronic immune activation , and high suscept...	[ "SIVmac239 infection of rhesus macaques ( RMs ) results in AIDS despite the generation of a strong antiviral cytotoxic T lymphocyte ( CTL ) response , possibly due to the emergence of viral escape mutants that prevent recognition of infected cells by CTLs .", "To determine the anatomic origin of these SIV mutants...	[ "Strong antiviral CD8+ T lymphocytes limit SIV replication by recognizing short pathogen-derived peptide epitopes .", "The cytotoxic CD8+ T cell responses specific for this highly mutable virus can select for viruses bearing mutations that prevent CD8+ T cell recognition of cells infected with these escape mutant...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "immunology", "biology" ]	Altered Circulating Levels of Matrix Metalloproteinases and Inhibitors Associated with Elevated Type 2 Cytokines in Lymphatic Filarial Disease	journal.pntd.0001681	null	[ [ "Lymphatic filariasis ( LF ) is characterized by dysfunction of lymphatics that can lead to severe and often irreversible lymphedema and elephantiasis [1] , [2] .", "The critical factor in the development of host pathology appears to reflect the parasite-mediated initiation of a cascade of events that lea...	[ "Infection with Wuchereria bancrofti can cause severe disease characterized by subcutaneous fibrosis and extracellular matrix remodeling .", "Matrix metalloproteinases ( MMPs ) are a family of enzymes governing extracellular remodeling by regulating cellular homeostasis , inflammation , and tissue reorganization ...	[ "Lymphatic filariasis afflicts over 120 million people worldwide .", "While the infection is mostly clinically asymptomatic , approximately 40 million people suffer from overt , morbid clinical pathology characterized by swelling of the scrotal area and lower limbs ( hydrocele and lymphedema ) .", "Host immunol...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "molecular biology", "developmental biology" ]	Mutation of RNA Pol III Subunit rpc2/polr3b Leads to Deficiency of Subunit Rpc11 and Disrupts Zebrafish Digestive Development	journal.pbio.0050312	Transcription of tRNAs and other noncoding RNAs by RNA polymerase III is essential for cell proliferation, growth, and survival. With the aide of experiments in the fission yeast,S. pombe, the authors report how a small in-frame deletion in the second largest Pol III subunit, Polr3b, affects tissue progenitor cells in ...	[ [ "RNA Polymerase III ( Pol III ) is a 17-subunit complex that is responsible for the transcription of small noncoding RNAs such as transfer RNAs ( tRNAs ) , 5S ribosomal RNA ( rRNA ) , U6 small nuclear RNA ( snRNA ) , 7SL RNA , and others in eukaryotes [1 , 2] .", "The two largest subunits , Rpc1 ( ∼160 kD...	[ "The role of RNA polymerase III ( Pol III ) in developing vertebrates has not been examined .", "Here , we identify a causative mutation of the second largest Pol III subunit , polr3b , that disrupts digestive organ development in zebrafish slim jim ( slj ) mutants .", "The slj mutation is a splice-site substit...	[ "The transmission of genetic information from DNA to messenger RNA to protein depends on the function of a large number of small noncoding RNA molecules .", "The genes encoding these RNAs are transcribed by RNA polymerase III ( Pol III ) , a 17-subunit protein complex whose structure is closely related to that of...	2007
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "quantitative trait loci", "alleles", "bone", "network analysis", "genetic interactions", "computer and information sciences", "lipids", "network motifs", "bone density", "fats", "connective tissue", "biological tissue", "genetic loci", "biochemistry", "...	Weak Epistasis Generally Stabilizes Phenotypes in a Mouse Intercross	journal.pgen.1005805	null	[ [ "The relevance of epistasis in genetic architecture is yet unresolved .", "In genetic screens of model systems , the evidence for genetic interaction is abundant [1–4] and has been proven biologically relevant [5–7] .", "However , the situation is less clear in human populations as epistasis is diffic...	[ "The extent and strength of epistasis is commonly unresolved in genetic studies , and observed epistasis is often difficult to interpret in terms of biological consequences or overall genetic architecture .", "We investigated the prevalence and consequences of epistasis by analyzing four body composition phenotyp...	[ "The role of statistical epistasis in the genetic architecture of complex traits has been of great interest to the genetics community since Fisher introduced the concept in 1918 .", "However , assessing epistasis in human and model organism populations has been impeded by limited statistical power .", "To mitig...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "plant anatomy", "electrophoretic mobility shift assay", "gene regulation", "regulatory proteins", "dna-binding proteins", "plant physiology", "plant science", "transcription factors", "seedlings", "molecular biology techniques", "plants", "research and analysis methods", "plant reproduction...	Arabidopsis WRKY6 Transcription Factor Acts as a Positive Regulator of Abscisic Acid Signaling during Seed Germination and Early Seedling Development	journal.pgen.1005833	null	[ [ "Abscisic acid ( ABA ) is a key phytohormone that plays important roles in plant responses to stresses and plant development [1–2] .", "ABA is accumulated in the developing embryo , and modulates seed development and storage product accumulation [1] .", "In addition , ABA prevents premature seed germi...	[ "The phytohormone abscisic acid ( ABA ) plays important roles during seed germination and early seedling development .", "Here , we characterized the function of the Arabidopsis WRKY6 transcription factor in ABA signaling .", "The transcript of WRKY6 was repressed during seed germination and early seedling deve...	[ "The WRKY6 protein is a WRKY transcription factor which plays important roles in plant pathogen defense , phosphate translocation , and arsenate resistance .", "This study demonstrated that the expression of WRKY6 was obviously repressed during seed germination and significantly induced by exogenous ABA .", "In...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "neuroscience/behavioral neuroscience", "neuroscience/sensory systems", "neuroscience/motor systems", "computational biology/computational neuroscience", "evolutionary biology/animal behavior" ]	Energy-Information Trade-Offs between Movement and Sensing	journal.pcbi.1000769	null	[ [ "Animals must constantly negotiate trade-offs in sensory and motor performance .", "The most well known of these trade-offs occur within either movement or sensory systems , rather than between them .", "As an example within motor systems , fish body shapes and styles of movement that maximize cruisin...	[ "While there is accumulating evidence for the importance of the metabolic cost of information in sensory systems , how these costs are traded-off with movement when sensing is closely linked to movement is poorly understood .", "For example , if an animal needs to search a given amount of space beyond the range o...	[ "Animals thrive by sensing their environment and using the information they've gathered to guide their movement .", "But collecting better information can result in less efficient movement: Bicycling while standing up on the pedals may help you see over obstacles ahead of you , but it causes more air drag , forci...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "bacteriology", "organismal evolution", "medicine and health sciences", "gut bacteria", "bacteriophages", "microbiology", "vertebrates", "mice", "animals", "mammals", "viruses", "animal models", "dna damage", "model organisms", "microbial evolution", "bacterial genetics", "dna", "m...	Carriage of λ Latent Virus Is Costly for Its Bacterial Host due to Frequent Reactivation in Monoxenic Mouse Intestine	journal.pgen.1005861	null	[ [ "Bacterial viruses , called bacteriophages or phages , are present in all bacterial communities and have profound impact on bacteria either by killing them or by mediating horizontal gene transfer through lysogeny .", "Lysogeny refers to the ability of temperate phages , as opposed to virulent ones , to r...	[ "Temperate phages , the bacterial viruses able to enter in a dormant prophage state in bacterial genomes , are present in the majority of bacterial strains for which the genome sequence is available .", "Although these prophages are generally considered to increase their hosts’ fitness by bringing beneficial gene...	[ "Dormant bacterial viruses , or prophages , are found in the genomes of almost all bacteria , but their impact on bacterial host fitness is largely unknown .", "Through experiments in mice , supported by a mathematical model , we quantified the activity of Escherichia coli prophage λ in monoxenic mouse gut , as w...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "mathematics", "molecular biology", "computational biology/systems biology" ]	Modeling Recursive RNA Interference	journal.pcbi.1000183	null	[ [ "RNA interference ( RNAi ) is an RNA-mediated pathway of gene silencing mediated by small RNA molecules [1] , [2] .", "During RNAi , introduction of double-stranded RNA ( dsRNA ) encoding a sub-sequence of a gene leads to reduction in expression of the corresponding gene .", "The heart of the RNAi pro...	[ "An important application of the RNA interference ( RNAi ) pathway is its use as a small RNA-based regulatory system commonly exploited to suppress expression of target genes to test their function in vivo .", "In several published experiments , RNAi has been used to inactivate components of the RNAi pathway itse...	[ "RNA interference is a gene regulatory system in which small RNA molecules turn off genes that have similar sequences to the small RNAs .", "This has become a powerful tool because a researcher can use RNA interference to turn off any gene of interest in order to test its function .", "There is great interest i...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Specificity and Dynamics of Effector and Memory CD8 T Cell Responses in Human Tick-Borne Encephalitis Virus Infection	journal.ppat.1004622	null	[ [ "Tick-borne encephalitis virus ( TBEV ) is a single-stranded flavivirus and the causative agent of tick-borne encephalitis ( TBE ) .", "TBEV is transferred to humans from infected Ixodes ticks .", "TBE is an increasing public health problem occuring throughout northern and central Europe and Asia , wi...	[ "Tick-borne encephalitis virus ( TBEV ) is transferred to humans by ticks .", "The virus causes tick-borne encephalitis ( TBE ) with symptoms such as meningitis and meningoencephalitis .", "About one third of the patients suffer from long-lasting sequelae after clearance of the infection .", "Studies of the i...	[ "Tick-borne encephalitis virus ( TBEV ) belongs to the flavivirus family and causes tick-borne encephalitis .", "This is a severe meningoencephalitic disease with no available treatment .", "Detailed studies of the immune response during human TBEV infection are essential to understand host responses to TBE and...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "echinococcosis", "infectious diseases", "biology", "microbiology", "zoology", "parasitic diseases", "parasitology" ]	Molecular Identification of Echinococcus multilocularis Infection in Small Mammals from Northeast, Iran	journal.pntd.0002313	null	[ [ "Echinococcosis is a near cosmopolitan parasitic disease caused by the cestode Echinococcus [1] , [2] , [3] .", "The potentially fatal zoonotic disease , alveolar echinococcosis , is caused by the metacestode of E . multilocularis , which has a sylvatic cycle , comprising wild carnivores as definitive hos...	[ "Alveolar echinococcosis is a zoonotic disease caused by the metacestode of Echinococcus multilocularis .", "Many species of small mammals , including arvicolid rodents or Ochotona spp .", ", are natural intermediate hosts of the cestode .", "The main aim of this study was to identify natural intermediate hos...	[ "Small mammals , especially rodents , coexist with humans , particularly in rural areas where they become infected with the larval stages of Echinococcus multilocularis via ingestion of eggs in feces from infected carnivores .", "As prey for carnivores , small mammals have an important role in the life cycle of E...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "developmental biology", "molecular motors", "cell biology", "fertilization", "symbiosis", "biology and life sciences", "species interactions", "cellular structures and organelles", "mutualism", "parasitology" ]	Co-evolution between an Endosymbiont and Its Nematode Host: Wolbachia Asymmetric Posterior Localization and AP Polarity Establishment	journal.pntd.0003096	null	[ [ "The phylum Nematoda comprises up to 1 million species and is one of the most diverse and successful , with members colonizing all possible ecological niches on earth [1] , [2] .", "Nematodes have an extraordinary ability to adapt to the parasitic life style [3]–[6] and as a result exert profound impacts ...	[ "While bacterial symbionts influence a variety of host cellular responses throughout development , there are no documented instances in which symbionts influence early embryogenesis .", "Here we demonstrate that Wolbachia , an obligate endosymbiont of the parasitic filarial nematodes , is required for proper ante...	[ "Filarial nematodes are responsible for a number of neglected tropical diseases .", "The vast majority of these human parasites harbor the bacterial endosymbiont Wolbachia .", "Wolbachia are essential for filarial nematode survival and reproduction , and thus are a promising anti-filarial drug target .", "Und...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "physics/interdisciplinary physics", "computational biology/transcriptional regulation", "cell biology/morphogenesis and cell biology", "mathematics", "biophysics/theory and simulation", "developmental biology/pattern formation", "biochemistry/theory and simulation", "computational biology/systems bio...	Spatial Bistability Generates hunchback Expression Sharpness in the Drosophila Embryo	journal.pcbi.1000184	null	[ [ "How an embryo achieves pattern and form from an initially undifferentiated state has fascinated people at least since the time of Aristotle .", "Scientific advances on this began over a century ago , with , for example , the experiments of Hans Driesch on sea urchin embryos [1] , from which he proposed t...	[ "During embryonic development , the positional information provided by concentration gradients of maternal factors directs pattern formation by providing spatially dependent cues for gene expression .", "In the fruit fly , Drosophila melanogaster , a classic example of this is the sharp on–off activation of the h...	[ "Pattern formation during embryonic development , or morphogenesis , is one of the most intriguing problems in biology , entailing the sequence of processes by which a relatively simple system , the fertilized egg , becomes a mature organism .", "In these processes , the genetic information , stored at the molecu...	2008
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "cell biology/microbial physiology and metabolism", "computational biology/synthetic biology", "infectious diseases/neglected tropical diseases", "microbiology/parasitology", "infectious diseases/protozoal infections", "infectious diseases/antimicrobials and drug resistance" ]	Metabolomics to Unveil and Understand Phenotypic Diversity between Pathogen Populations	journal.pntd.0000904	null	[ [ "Health professionals are constantly challenged with the clinical polymorphism of infectious diseases .", "Pathogen diversity is known to play a major role in this clinically observed variability in disease manifestation , severity and drug response .", "However , to obtain a greater understanding of ...	[ "Leishmaniasis is a debilitating disease caused by the parasite Leishmania .", "There is extensive clinical polymorphism , including variable responsiveness to treatment .", "We study Leishmania donovani parasites isolated from visceral leishmaniasis patients in Nepal that responded differently to antimonial tr...	[ "Visceral leishmaniasis is caused by a parasite called Leishmania donovani , which every year infects about half a million people and claims several thousand lives .", "Existing treatments are now becoming less effective due to the emergence of drug resistance .", "Improving our understanding of the mechanisms ...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Bromodomain Proteins Contribute to Maintenance of Bloodstream Form Stage Identity in the African Trypanosome	journal.pbio.1002316	The use of specific inhibitors reveals a role for bromodomain proteins in epigenetically switching from the tsetse fly form of the sleeping sickness parasite Trypanosoma brucei to the mammalian bloodstream form.	[ [ "Trypanosoma brucei is a unicellular , protozoan parasite and the causative agent of Human African Trypanosomiasis ( sleeping sickness ) .", "It also causes n'agana in cattle , a disease that imposes a severe economic burden in affected areas .", "The life cycle of Trypanosoma brucei requires adaptati...	[ "Trypanosoma brucei , the causative agent of African sleeping sickness , is transmitted to its mammalian host by the tsetse .", "In the fly , the parasite’s surface is covered with invariant procyclin , while in the mammal it resides extracellularly in its bloodstream form ( BF ) and is densely covered with highl...	[ "Many parasites undergo major changes in lifestyle as they cycle between their vectors and their hosts .", "We use Trypanosoma brucei , the causative agent of human and animal African Trypanosomiasis , as a model to study how these changes are regulated and maintained at the level of gene expression .", "T . br...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Staphylococcus aureus Colonization of the Mouse Gastrointestinal Tract Is Modulated by Wall Teichoic Acid, Capsule, and Surface Proteins	journal.ppat.1005061	null	[ [ "Staphylococcus aureus is a bacterial pathogen that commonly colonizes the nose , skin , and mucosal surfaces of healthy individuals .", "However , S . aureus may also cause a variety of superficial and invasive infections in hospitalized patients , as well as in individuals within the community who lack ...	[ "Staphylococcus aureus colonizes the nose , throat , skin , and gastrointestinal ( GI ) tract of humans .", "GI carriage of S . aureus is difficult to eradicate and has been shown to facilitate the transmission of the bacterium among individuals .", "Although staphylococcal colonization of the GI tract is asymp...	[ "Staphylococcus aureus persistently colonizes ~20% of the human population , and 40–60% of humans are intermittently colonized by this bacterium .", "The most common reservoir for S . aureus is the anterior nares , and the incidence of staphylococcal disease in higher in individuals who are colonized .", "Recta...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "evolutionary biology", "biology and life sciences", "parasitology" ]	The Plasmodium vivax Merozoite Surface Protein 3β Sequence Reveals Contrasting Parasite Populations in Southern and Northwestern Thailand	journal.pntd.0003336	null	[ [ "Of the four species of human malaria parasites , Plasmodium vivax is the second most prevalent and the most geographically widespread parasite .", "Each year , P . vivax infects an estimated 130–391 million people , of which a large majority was in Central and Southeast Asia [1]–[3] .", "Recent data ...	[ "Malaria control efforts have a significant impact on the epidemiology and parasite population dynamics .", "In countries aiming for malaria elimination , malaria transmission may be restricted to limited transmission hot spots , where parasite populations may be isolated from each other and experience different ...	[ "With intensified malaria control in endemic countries , there have been dramatic changes of malaria epidemiology .", "One of such changes is the increased proportion of Plasmodium vivax malaria , a demonstration of resilience of this parasite to control efforts .", "In Thailand , malaria has been largely elimi...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "membrane potential", "ions", "anions", "permeability", "electrophysiology", "materials science", "cations", "cellular structures and organelles", "physical chemistry", "chemistry", "cell membranes", "hyperpolarization", "intracellular membranes", "cell bi...	The logic of ionic homeostasis: Cations are for voltage, but not for volume	journal.pcbi.1006894	null	[ [ "The transmembrane movements of ions during neuronal activity are inevitably associated with changes in ionic concentrations , both intracellularly and extracellularly .", "This activity-dependent redistribution of ions can be osmotically imbalanced and consequently can lead to changes in volume of the ce...	[ "Neuronal activity is associated with transmembrane ionic redistribution , which can lead to an osmotic imbalance .", "Accordingly , activity-dependent changes of the membrane potential are sometimes accompanied by changes in intracellular and/or extracellular volume .", "Experimental data that include distribu...	[ "We have developed software that calculates membrane potential and cell volume that result from redistribution of principal ions ( K+ , Na+ , and Cl- ) during normal cellular activity and experimental manipulations .", "Calculations in the model are done by an iterative charge-difference method that makes few ass...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "blood cells", "cell death", "medicine and health sciences", "immune cells", "body fluids", "viral transmission and infection", "population dynamics", "immunology", "cell processes", "microbiology", "simulation and modeling", "population biology", "viral load", "research and analysis metho...	Large Variations in HIV-1 Viral Load Explained by Shifting-Mosaic Metapopulation Dynamics	journal.pbio.1002567	A novel metapopulation model of HIV suggests that within-host infections are characterized by a highly dynamic process of localized infection followed by clearance within T cell centers.	[ [ "In 1979 , Bormann and Likens introduced the concept of the shifting-mosaic steady state ( SMSS ) to describe biomass in forested ecosystems .", "This concept was based on the intuition that although the patches comprising the forested ecosystem might each be in different phases of ecological succession d...	[ "The viral population of HIV-1 , like many pathogens that cause systemic infection , is structured and differentiated within the body .", "The dynamics of cellular immune trafficking through the blood and within compartments of the body has also received wide attention .", "Despite these advances , mathematical...	[ "When a person is infected with HIV , the initial peak level of virus in the blood is usually very high before a lower , relatively stable level is reached and maintained for the duration of the chronic infection .", "This stable level is known as the set-point viral load ( SPVL ) and is associated with severity ...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "x chromosome inactivation", "gene regulation", "histone acetylation", "euchromatin", "histone modification", "epigenetics", "molecular genetics", "chromatin", "heterochromatin", "chromosome biology", "proteins", "gene expression", "biochemistry", "cell biology", "post-translational modi...	Non-coding roX RNAs Prevent the Binding of the MSL-complex to Heterochromatic Regions	journal.pgen.1004865	null	[ [ "In many animal species with distinct sexes , sex-chromosomes contribute to genetic sex determination .", "In species with male heterogamety such as humans and fruit flies , the male sex-chromosome pair consists of two morphologically and genetically different chromosomes ( one X and one Y ) whereas femal...	[ "Long non-coding RNAs contribute to dosage compensation in both mammals and Drosophila by inducing changes in the chromatin structure of the X-chromosome .", "In Drosophila melanogaster , roX1 and roX2 are long non-coding RNAs that together with proteins form the male-specific lethal ( MSL ) complex , which coats...	[ "In both fruit flies and humans , males and females have different sets of sex chromosomes .", "This generates differences in gene dosage that must be compensated for by adjusting the transcriptional output of most genes located on the X-chromosome .", "The specific recognition and targeting of the X-chromosome...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Impact of Helminth Infection during Pregnancy on Cognitive and Motor Functions of One-Year-Old Children	journal.pntd.0003463	null	[ [ "Intestinal helminths infect more than two billion of the world’s population , with the highest prevalence in Asia and sub-Saharan Africa . [1]", "The burden of intestinal helminth infection is estimated to be five million disability-adjusted life years ( DALYs ) . [2]", "Helminth infections are rarel...	[ "To determine the effect of helminth infection during pregnancy on the cognitive and motor functions of one-year-old children .", "Six hundred and thirty five singletons born to pregnant women enrolled before 29 weeks of gestation in a trial comparing two intermittent preventive treatments for malaria were assess...	[ "The WHO recommends anthelmintics for pregnant women after their first trimester but the benefits remain unequivocal .", "Although the consequences of helminth infection during pregnancy on the health of pregnant women have been well studied , the impact on the early development of offspring has been understudied...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "classical mechanics", "fluid mechanics", "social sciences", "neuroscience", "simulation and modeling", "systems science", "mathematics", "vision", "neuronal tuning", "research and analysis methods", "computer and information sciences", "animal cells", "flow field", "fluid dynamics", "dy...	Competitive Dynamics in MSTd: A Mechanism for Robust Heading Perception Based on Optic Flow	journal.pcbi.1004942	null	[ [ "Heading perception is not only accurate , it is also remarkably robust and stable .", "These qualities warrant further investigation and are the focus of the present study .", "The robustness and stability of heading perception are especially evident in dynamic environments containing independently m...	[ "Human heading perception based on optic flow is not only accurate , it is also remarkably robust and stable .", "These qualities are especially apparent when observers move through environments containing other moving objects , which introduce optic flow that is inconsistent with observer self-motion and therefo...	[ "Humans have little difficulty moving around in dynamic environments containing other moving objects .", "Previous research has demonstrated that moving objects may induce biases in perceived heading in some circumstances .", "Nevertheless , heading perception is surprisingly robust and stable .", "Even when ...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Clustering of Tissue-Specific Sub-TADs Accompanies the Regulation of HoxA Genes in Developing Limbs	journal.pgen.1004018	null	[ [ "The Hox gene family encodes transcription factors with central roles in patterning of the body plan and organogenesis .", "Hox genes are grouped into clusters in most animal species , and mammals possess 39 genes divided into four clusters named HoxA to HoxD .", "In mice , deletion of the HoxA cluste...	[ "HoxA genes exhibit central roles during development and causal mutations have been found in several human syndromes including limb malformation .", "Despite their importance , information on how these genes are regulated is lacking .", "Here , we report on the first identification of bona fide transcriptional ...	[ "Hox genes encode transcription factors with crucial roles during development .", "These genes are grouped in four different clusters names HoxA , B , C , and D . Mutations in genes of the HoxA and D clusters have been found in several human syndromes , affecting in some cases limb development .", "Despite thei...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology", "in vitro", "microbiology", "computational biology", "eubacteria" ]	A Quantitative Study of the Division Cycle of Caulobacter crescentus Stalked Cells	journal.pcbi.0040009	null	[ [ "C . crescentus is a dimorphic bacterium that inhabits freshwater , seawater , and soils , where it plays an important role in global carbon cycling by mineralizing dissolved organic materials [26] .", "C . crescentus normally undergoes an asymmetric cell division resulting in two different progeny cells ...	[ "Progression of a cell through the division cycle is tightly controlled at different steps to ensure the integrity of genome replication and partitioning to daughter cells .", "From published experimental evidence , we propose a molecular mechanism for control of the cell division cycle in Caulobacter crescentus ...	[ "The cell cycle is the sequence of events by which a growing cell replicates all its components and divides them more or less evenly between two daughter cells .", "The timing and spatial organization of these events are controlled by gene–protein interaction networks of great complexity .", "A challenge for co...	2008
[ "Introduction", "Results", "Discussion", "Material and methods" ]	[ "cancer detection and diagnosis", "deletion mutation", "medicine and health sciences", "cancer risk factors", "genetic diseases", "oncology", "mutation", "hereditary nonpolyposis colorectal cancer", "nonsense mutation", "mutation databases", "frameshift mutation", "autosomal dominant diseases"...	Targeted next generation sequencing identifies functionally deleterious germline mutations in novel genes in early-onset/familial prostate cancer	journal.pgen.1007355	null	[ [ "Prostate cancer ( PrCa ) is the most frequent non-cutaneous cancer diagnosed in men worldwide and the third leading cause of male cancer deaths in Europe [1] .", "Despite efforts in early detection and screening strategies [2] , PrCa is estimated to be responsible for the death of 27 , 540 men in the Uni...	[ "Considering that mutations in known prostate cancer ( PrCa ) predisposition genes , including those responsible for hereditary breast/ovarian cancer and Lynch syndromes , explain less than 5% of early-onset/familial PrCa , we have sequenced 94 genes associated with cancer predisposition using next generation seque...	[ "Prostate cancer ( PrCa ) is the most frequent cancer diagnosed in men worldwide , estimated to be responsible for the death of 27 , 540 men in the United States in 2015 .", "Contrarily to other cancer types , the genetic contribution to the 10–20% of PrCa cases occurring in families with aggregation of the disea...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "heredity", "genetics", "biology", "human genetics", "genetics and genomics" ]	Heritability and Genetic Correlations Explained by Common SNPs for Metabolic Syndrome Traits	journal.pgen.1002637	null	[ [ "Obesity associated traits such as central adiposity , dyslipidemia , hypertension , and insulin resistance are major risk factors for type 2 diabetes and cardiovascular complications [1] .", "The constellation of these traits has been termed metabolic syndrome ( MetS ) .", "Understanding the genetic ...	[ "We used a bivariate ( multivariate ) linear mixed-effects model to estimate the narrow-sense heritability ( h2 ) and heritability explained by the common SNPs ( hg2 ) for several metabolic syndrome ( MetS ) traits and the genetic correlation between pairs of traits for the Atherosclerosis Risk in Communities ( ARI...	[ "The narrow-sense heritability of a trait such as body-mass index is a measure of the variability of the trait between people that is accounted for by their additive genetic differences .", "Knowledge of these genetic differences provides insight into biological mechanisms and hence treatments for diseases .", ...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "organismal evolution", "medicine and health sciences", "pathology and laboratory medicine", "influenza", "population genetics", "microbiology", "population modeling", "microbial evolution", "infectious diseases", "viral immune evasion", "infectious disease modeling", "pathogenesis", "host-p...	Identifying Selection in the Within-Host Evolution of Influenza Using Viral Sequence Data	journal.pcbi.1003755	null	[ [ "The overall risk to human health posed by the novel H7N9 influenza virus [1] , while potentially severe , is as yet unknown [2] , [3] .", "Pandemic influenza is a zoonosis [4] , and as such any new pandemic may be expected to arise through a two-step process [5] , [6] , the virus first gaining the abilit...	[ "The within-host evolution of influenza is a vital component of its epidemiology .", "A question of particular interest is the role that selection plays in shaping the viral population over the course of a single infection .", "We here describe a method to measure selection acting upon the influenza virus withi...	[ "The evolution of the influenza virus is of great importance for human health .", "Through evolution , current influenza viruses develop the ability to infect people who have been vaccinated against earlier strains .", "New strains of influenza that infect birds and pigs could evolve to infect and spread betwee...	2014
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "viruses", "infectious diseases", "virology" ]	ART Suppresses Plasma HIV-1 RNA to a Stable Set Point Predicted by Pretherapy Viremia	journal.ppat.0030046	null	[ [ "Infection with HIV-1 results in progressive immunodeficiency and death from opportunistic infection or cancer .", "Current antiretroviral therapy is effective in suppressing plasma viremia to levels below the detection limit of FDA-approved assays ( 50–75 copies HIV-1 RNA/ml ) , restoring immune function...	[ "Current antiretroviral therapy is effective in suppressing but not eliminating HIV-1 infection .", "Understanding the source of viral persistence is essential for developing strategies to eradicate HIV-1 infection .", "We therefore investigated the level of plasma HIV-1 RNA in patients with viremia suppressed ...	[ "Combination antiretroviral therapy is effective in reducing , but not eliminating , HIV-1 replication .", "Residual viremia during suppressive antiretroviral therapy may arise from a number of sources , including reservoirs of long-lived virus-producing cells , or ongoing complete cycles of viral replication .",...	2007
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "medicine and health sciences", "neurochemistry", "chemical compounds", "dopaminergics", "depolarization", "membrane potential", "electrophysiology", "neuroscience", "insect flight", "biological locomotion", "animals", "flight (biology)", "organic compounds", "animal mod...	FMRFa receptor stimulated Ca2+ signals alter the activity of flight modulating central dopaminergic neurons in Drosophila melanogaster	journal.pgen.1007459	null	[ [ "Neuromodulation of animal behavior by neuropeptides is ubiquitous among vertebrates and invertebrates [1 , 2] .", "Unlike fast acting neurotransmitters , neuropeptides and their receptors influence neuronal activity and circuit dynamics by modulating presynaptic neurotransmitter release .", "The mech...	[ "Neuropeptide signaling influences animal behavior by modulating neuronal activity and thus altering circuit dynamics .", "Insect flight is a key innate behavior that very likely requires robust neuromodulation .", "Cellular and molecular components that help modulate flight behavior are therefore of interest a...	[ "Neuropeptides play an important role in modulating neuronal properties such as excitability and synaptic strength and thereby influence innate behavioral outputs .", "In flying insects , neuromodulation of flight has been primarily attributed to monoamines .", "In this study , we have used the genetically amen...	2018

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