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headings list	keywords list	title stringlengths 20 281	id stringlengths 20 20	toc stringlengths 57 522 ⌀	sections list	abstract list	summary list	year stringclasses 13 values
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "immunology", "adipocytes", "connective tissue cells", "cytotoxic t cells", "bacteria", "lipids", "white blood cells", "animal cells", "fats", "gene expression", "t cells", "connective tissue", "biological tissue", "actin...	Mycobacterium tuberculosis infection modulates adipose tissue biology	journal.ppat.1006676	null	[ [ "In 2015 , tuberculosis ( TB ) affected 10 . 4 million individuals leading to 1 . 8 million deaths globally [1 , 2] .", "TB is primarily a disease of the lung , which serves as port of entry and site of disease manifestation .", "In the lung , Mycobacterium tuberculosis ( Mtb ) is preferentially entra...	[ "Mycobacterium tuberculosis ( Mtb ) primarily resides in the lung but can also persist in extrapulmonary sites .", "Macrophages are considered the prime cellular habitat in all tissues .", "Here we demonstrate that Mtb resides inside adipocytes of fat tissue where it expresses stress-related genes .", "Moreov...	[ "In 2015 , tuberculosis ( TB ) affected 10 . 4 million individuals causing 1 . 8 million deaths per year .", "Yet , a much larger group– 2 billion people–harbors latent TB infection ( LTBI ) without clinical symptoms , but at lifelong risk of reactivation .", "The physiological niches of Mycobacterium tuberculo...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases/helminth infections", "biotechnology/protein chemistry and proteomics" ]	Brugia malayi Excreted/Secreted Proteins at the Host/Parasite Interface: Stage- and Gender-Specific Proteomic Profiling	journal.pntd.0000410	null	[ [ "The parasitic nematodes , Brugia malayi and Wuchereria bancrofti are lymphatic dwelling filariae that induce a spectrum of clinical manifestations ( ranging from clinically asymptomatic [or subclinical] microfilaremia to the deforming elephantiasis ) felt to reflect the nature of the filarial specific immune...	[ "Relatively little is known about the filarial proteins that interact with the human host .", "Although the filarial genome has recently been completed , protein profiles have been limited to only a few recombinants or purified proteins of interest .", "Here , we describe a large-scale proteomic analysis using ...	[ "Human lymphatic filariasis caused by the nematode parasites Brugia malayi and Wuchereria bancrofti are a major cause of concern in tropical countries .", "Studies over several decades have identified various proteins of these parasites that have highlighted their role in host–parasite interactions and possible c...	2009
[ "Introduction", "Results and Discussion", "Materials and Methods" ]	[]	Co-evolution of Bacterial Ribosomal Protein S15 with Diverse mRNA Regulatory Structures	journal.pgen.1005720	null	[ [ "RNA-protein interactions and ribonucleoprotein complexes play key roles in many cellular processes including transcriptional regulation , translation , epigenetic regulation , and post-transcriptional silencing [1] .", "Furthermore , aberrant RNA-protein recognition and binding has been linked to multipl...	[ "RNA-protein interactions are critical in many biological processes , yet how such interactions affect the evolution of both partners is still unknown .", "RNA and protein structures are impacted very differently by mechanisms of genomic change .", "While most protein families are identifiable at the nucleotide...	[ "RNA-protein interactions are important for many biological processes , and aberrant interactions have been implicated in many human diseases .", "However , how the specificity of such interactions may change over time and impact the evolution of both partners is still largely unexplored .", "In this work we ex...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "phosphorylation", "cell motility", "swimming", "medicine and health sciences", "pathology and laboratory medicine", "xanthomonas campestris", "pathogens", "biological locomotion", "mutation", "plant science", "plant pathology", "cellular structures and organelles", "bacteria", "cell swimm...	Cyclic-di-GMP binds to histidine kinase RavS to control RavS-RavR phosphotransfer and regulates the bacterial lifestyle transition between virulence and swimming	journal.ppat.1007952	null	[ [ "The two-component signalling system ( TCS ) is one of the predominant molecular machineries used by almost all bacteria to monitor and adaptively respond to environmental cues [1 , 2] .", "The prototypical TCS is composed of a membrane-bound histidine kinase ( HK ) and a cytosolic response regulator ( RR...	[ "The two-component signalling system ( TCS ) comprising a histidine kinase ( HK ) and a response regulator ( RR ) is the predominant bacterial sense-and-response machinery .", "Because bacterial cells usually encode a number of TCSs to adapt to various ecological niches , the specificity of a TCS is in the centre...	[ "c-di-GMP is a multifunctional bacterial second messenger that controls various physiological processes .", "The nucleotide derivative binds to riboswitches or proteins as effectors during regulation .", "Here , we found that c-di-GMP physically binds to a histidine kinase , RavS , of a plant pathogenic bacteri...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell death", "cellular stress responses", "cancer genetics", "microbiology", "host-pathogen interaction", "signaling in selected disciplines", "epithelial cells", "animal models", "c-jun n-terminal kinase signaling cascade", "drosophila melanogaster", "model organisms", "apoptotic signaling",...	Transgenic Expression of the Helicobacter pylori Virulence Factor CagA Promotes Apoptosis or Tumorigenesis through JNK Activation in Drosophila	journal.ppat.1002939	null	[ [ "Infection with Helicobacter pylori is the strongest risk factor for the development of gastric carcinoma , which is the second most common cause of cancer-related death worldwide [1] .", "Although approximately half the world's population is infected with H . pylori , most of those individuals will devel...	[ "Gastric cancer development is strongly correlated with infection by Helicobacter pylori possessing the effector protein CagA .", "Using a transgenic Drosophila melanogaster model , we show that CagA expression in the simple model epithelium of the larval wing imaginal disc causes dramatic tissue perturbations an...	[ "The gastric pathogen Helicobacter pylori infects an estimated 50% of the world's population and is a major risk factor for the development of gastric cancer .", "Strains of H . pylori that can inject the CagA effector protein into host cells are known to be more virulent , but the potential contributions of host...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "tropical diseases", "microbiology", "health care", "multivariate analysis", "bacterial diseases", "mathematics", "statistics (mathematics)", "global health", "neglected tropical diseases", "population biology", "statistical inference", "research and analysis ...	Household Transmission of Vibrio cholerae in Bangladesh	journal.pntd.0003314	null	[ [ "Cholera disproportionately affects less-developed areas of Asia , Africa , and Latin America , leading to an estimated 3–5 million cases and 100–130 thousand deaths per year [1] .", "Vibrio cholerae O1/O139 transmission is associated with two general modes of exposure to infection .", "Community-to-p...	[ "Vibrio cholerae infections cluster in households .", "This study's objective was to quantify the relative contribution of direct , within-household exposure ( for example , via contamination of household food , water , or surfaces ) to endemic cholera transmission .", "Quantifying the relative contribution of ...	[ "Since John Snow's ground-breaking investigations of the devastating outbreaks in 19th-century London , cholera has been considered the quintessential waterborne human infection , transmitting via fecal contamination of environmental water sources .", "Recently , renewed interest has been paid to the potential im...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "developmental biology", "plant science", "plant growth and development", "molecular development", "plant genomics", "plant biology", "biology" ]	Chromosome Fragile Sites in Arabidopsis Harbor Matrix Attachment Regions That May Be Associated with Ancestral Chromosome Rearrangement Events	journal.pgen.1003136	null	[ [ "Genome integrity depends upon the coordination of replicon and centriole duplication , chromatin condensation , and the assembly and action of the spindle apparatus .", "Several checkpoints regulate the progression of the chromosomal and cytoskeletal events [1] , and repair systems are recruited as neede...	[ "Mutations in the BREVIPEDICELLUS ( BP ) gene of Arabidopsis thaliana condition a pleiotropic phenotype featuring defects in internode elongation , the homeotic conversion of internode to node tissue , and downward pointing flowers and pedicels .", "We have characterized five mutant alleles of BP , generated by E...	[ "Chromosome evolution involves both small-scale ( e . g . single nucleotide ) changes , as well as large-scale rearrangements such as inversions , translocations , and fusion events .", "We investigated mutations of the BREVIPEDICELLUS gene of Arabidopsis , which is a master regulator of inflorescence architectur...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology" ]	C-Terminal Region of EBNA-2 Determines the Superior Transforming Ability of Type 1 Epstein-Barr Virus by Enhanced Gene Regulation of LMP-1 and CXCR7	journal.ppat.1002164	null	[ [ "Epstein-Barr Virus ( EBV ) is a B-lymphotropic gamma herpesvirus which persistently infects over 90% of the adult population world-wide .", "EBV infection is usually asymptomatic , although in some cases the virus can be the causative agent of infectious mononucleosis [1] .", "EBV is also involved in...	[ "Type 1 Epstein-Barr virus ( EBV ) strains immortalize B lymphocytes in vitro much more efficiently than type 2 EBV , a difference previously mapped to the EBNA-2 locus .", "Here we demonstrate that the greater transforming activity of type 1 EBV correlates with a stronger and more rapid induction of the viral on...	[ "Epstein-Barr virus ( EBV ) is a common human virus that is involved in several types of cancer and directly causes human B lymphocytes to proliferate when they become infected .", "EBV occurs naturally as two different viral types ( type 1 and type 2 ) .", "The genomes of these viruses are mostly very similar ...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "public health and epidemiology/epidemiology", "genetics and genomics/genetics of disease", "genetics and genomics/complex traits", "genetics and genomics/cancer genetics" ]	Evaluation of Candidate Stromal Epithelial Cross-Talk Genes Identifies Association between Risk of Serous Ovarian Cancer and TERT, a Cancer Susceptibility “Hot-Spot”	journal.pgen.1001016	null	[ [ "Ovarian cancer is the seventh leading cause of cancer mortality among women globally , accounting for 4 . 2% of cancer deaths [1] , due in part to the lack of practical screening methods and detectable symptoms in the early stages of tumor progression [2] .", "Although the aetiology of ovarian cancer has...	[ "We hypothesized that variants in genes expressed as a consequence of interactions between ovarian cancer cells and the host micro-environment could contribute to cancer susceptibility .", "We therefore used a two-stage approach to evaluate common single nucleotide polymorphisms ( SNPs ) in 173 genes involved in ...	[ "In this article , we report the findings from a large-scale analysis of common variation in genes that are expressed as a consequence of interactions between ovarian cancer cells and their host micro-environment that could influence serous ovarian cancer risk .", "We evaluated 1 , 302 common variants within or n...	2010
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "animals", "molecular biology techniques", "molecular genetics", "insect vectors", "research and analysis methods", "agrochemicals", "infectious diseases", "artificial gene amplification and extension", "aedes aegypti", "hyperexpression techniqu...	CYP-mediated permethrin resistance in Aedes aegypti and evidence for trans-regulation	journal.pntd.0006933	null	[ [ "Aedes aegypti is an important pest capable of transmitting four important human disease viruses: dengue , yellow fever , chikungunya , and Zika .", "Dengue , for example , causes morbidity and mortality in 141 countries across the tropical and subtropical regions of the world and is estimated to be a ris...	[ "Aedes aegypti poses a serious risk to human health due to its wide global distribution , high vector competence for several arboviruses , frequent human biting , and ability to thrive in urban environments .", "Pyrethroid insecticides remain the primary means of controlling adult A . aegypti populations during d...	[ "Cytochrome P450 monooxygenases ( CYPs ) are one of the most important mechanism of insecticide resistance in mosquitoes .", "These CYP enzymes break down insecticides into non-toxic forms that can be readily excreted .", "An increase of CYP-mediated detoxification is commonly found in pyrethroid resistant Aede...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases", "immunology", "homo (human)" ]	A Novel TLR4-Mediated Signaling Pathway Leading to IL-6 Responses in Human Bladder Epithelial Cells	journal.ppat.0030060	null	[ [ "The innate immune system is the first line of defense against infection and is thought to primarily be mediated by phagocytic immune cells such as macrophages and dendritic cells .", "These cells recognize microorganisms via a limited number of germline-encoded pattern recognition receptors ( PRRs ) that...	[ "The vigorous cytokine response of immune cells to Gram-negative bacteria is primarily mediated by a recognition molecule , Toll-like receptor 4 ( TLR4 ) , which recognizes lipopolysaccharide ( LPS ) and initiates a series of intracellular NF-κB–associated signaling events .", "Recently , bladder epithelial cells...	[ "In spite of frequent cross contamination by bacteria from the gut , urinary tract infections are relatively infrequent .", "Although much of the credit goes to cells lining the urinary tract , such as bladder cells , how this is achieved remains unclear .", "Human bladder cells display , on their surfaces , sp...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "systems biology", "biology", "computational biology", "genetics and genomics" ]	Biomolecular Events in Cancer Revealed by Attractor Metagenes	journal.pcbi.1002920	null	[ [ "Despite their type-specific features , cancers share some common traits , or “hallmarks , ” related to , e . g . , the abilities of some cancer cells to divide uncontrollably or to invade surrounding tissues [1] .", "Furthermore , it has been recognized that gene expression signatures resulting from anal...	[ "Mining gene expression profiles has proven valuable for identifying signatures serving as surrogates of cancer phenotypes .", "However , the similarities of such signatures across different cancer types have not been strong enough to conclude that they represent a universal biological mechanism shared among mult...	[ "Cancer is known to be characterized by several unifying biological capabilities or “hallmarks . ”", "However , attempts to computationally identify patterns , such as gene expression signatures , shared across many different cancer types have been largely unsuccessful .", "A typical approach has been to classi...	2013
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "reproductive system", "body fluids", "enzymes", "enzymology", "parasitic diseases", "animals", "nematode infections", "endocrine physiology", "serine proteases", "infectious disease control", "insect vectors", "infectious diseases", "prot...	Insulin receptor knockdown blocks filarial parasite development and alters egg production in the southern house mosquito, Culex quinquefasciatus	journal.pntd.0006413	null	[ [ "Lymphatic filariasis ( LF ) is one of the neglected tropical diseases and a major cause of permanent and long-term disability worldwide .", "The disease is caused by three species of nematode worms ( filariae ) –Wuchereria bancrofti ( Wb ) , Brugia malayi , and Brugia timori , which are transmitted by se...	[ "Lymphatic filariasis , commonly known as elephantiasis , is a painful and profoundly disfiguring disease .", "Wuchreria bancrofti ( Wb ) is responsible for >90% of infections and the remainder are caused by Brugia spp .", "Mosquitoes of the genera Culex ( in urban and semi-urban areas ) , Anopheles ( in rural ...	[ "Lymphatic filariasis ( LF ) is caused by infection with nematodes of the family Filarioidea .", "90% of infections are caused by Wuchereria bancrofti and the remainder by Brugia spp .", "In endemic countries , LF has a major social and economic impact with an estimated annual loss of $1 billion .", "Filarial...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "enzyme structure", "signal transduction", "phosphoinositide signal transduction", "inflammation", "immunity", "enzymes", "allergy and hypersensitivity", "immunology", "signaling pathways", "biology", "molecular cell biology" ]	PKCβ Phosphorylates PI3Kγ to Activate It and Release It from GPCR Control	journal.pbio.1001587	The GPCR-activated PI3Kγ is also a key enzyme downstream of the IgE high affinity receptor FcεRI. PKCβ-dependent phosphorylation of PI3Kγ on Ser582 is the ‘missing link’ that functions as a molecular switch to divert PI3Kγ from GPCR inputs.	[ [ "Class I phosphoinositide 3-kinases ( PI3Ks ) produce the lipid second messenger phosphatidylinositol ( 3 , 4 , 5 ) -trisphosphate [PtdIns ( 3 , 4 , 5 ) P3] and consist of a p110 catalytic and a regulatory subunit .", "The class IA catalytic subunits , p110α , β , and δ , are constitutively bound to p85-r...	[ "All class I phosphoinositide 3-kinases ( PI3Ks ) associate tightly with regulatory subunits through interactions that have been thought to be constitutive .", "PI3Kγ is key to the regulation of immune cell responses activated by G protein-coupled receptors ( GPCRs ) .", "Remarkably we find that PKCβ phosphoryl...	[ "Phosphoinositide 3-kinases ( PI3Ks ) are involved in most essential cellular processes .", "Class I PI3Ks are heterodimers: class IA PI3Ks are made up of one of a group of regulatory p85-like subunits and one p110α , p110β , or p110δ catalytic p110 subunit , and are activated via binding of their p85 subunit to ...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "computational biology/macromolecular structure analysis", "molecular biology/molecular evolution", "biochemistry/protein folding", "biophysics/theory and simulation", "molecular biology/bioinformatics", "computational biology/macromolecular sequence analysis" ]	Tradeoff Between Stability and Multispecificity in the Design of Promiscuous Proteins	journal.pcbi.1000627	null	[ [ "Proteins engage in numerous protein-protein interactions , which together regulate the outcome of all biological processes in the cell .", "By some estimates , over a third of all mammalian proteins participate in two or more highly specific protein-protein interactions [1] .", "Proteins that can int...	[ "Natural proteins often partake in several highly specific protein-protein interactions .", "They are thus subject to multiple opposing forces during evolutionary selection .", "To be functional , such multispecific proteins need to be stable in complex with each interaction partner , and , at the same time , t...	[ "In nature , some proteins are more social than others , interacting with a large number of partners .", "These “promiscuous” proteins play key roles in cellular signaling pathways whose disruption may lead to diseases such as cancer .", "The amino acid sequences of such proteins must have evolved to be optimal...	2009
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "systems biology", "biophysic al simulations", "biology", "computational biology" ]	Optimal Dynamics for Quality Control in Spatially Distributed Mitochondrial Networks	journal.pcbi.1003108	null	[ [ "All eukaryotic cells contain mitochondria , whose number and structure can vary substantially during the cell cycle [1] and between cell types [2] .", "One of the primary functions of mitochondria is the production of ATP through utilization of the electrochemical potential across the inner membrane ( ) ...	[ "Recent imaging studies of mitochondrial dynamics have implicated a cycle of fusion , fission , and autophagy in the quality control of mitochondrial function by selectively increasing the membrane potential of some mitochondria at the expense of the turnover of others .", "This complex , dynamical system creates...	[ "Mitochondria are the powerhouses of eukaryotic cells , oxidizing glucose to produce ATP .", "Most cells harbor tens to hundreds of mitochondria in a constant state of flux , in which they fuse with one another , undergo fission , import proteins to grow larger , and eventually are recycled by autophagy .", "Th...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "biotechnology", "engineering and technology", "brassica", "dna-binding proteins", "fungi", "plant science", "model organisms", "genetically modified plants", "experimental organism systems", "epigenetics", "molecular biology techniques", "plants", "chromatin", "genetic engineering", "ar...	Methyl-CpG-binding domain 9 (MBD9) is required for H2A.Z incorporation into chromatin at a subset of H2A.Z-enriched regions in the Arabidopsis genome	journal.pgen.1008326	null	[ [ "Nucleosomes , the fundamental units of chromatin that consist of ~147 bp of DNA wrapped around a histone octamer , efficiently condense large eukaryotic DNA molecules inside the nucleus .", "At the same time , nucleosomes present a physical barrier that restricts the access of DNA-binding proteins to reg...	[ "The SWR1 chromatin remodeling complex , which deposits the histone variant H2A . Z into nucleosomes , has been well characterized in yeast and animals , but its composition in plants has remained uncertain .", "We used the conserved SWR1 subunit ACTIN RELATED PROTEIN 6 ( ARP6 ) as bait in tandem affinity purific...	[ "The histone H2A variant , H2A . Z , is found in all known eukaryotes and plays important roles in transcriptional regulation .", "H2A . Z is selectively incorporated into nucleosomes within many genes by the activity of a conserved ATP-dependent chromatin remodeling complex in yeast , insects , and mammals .", ...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Exploring Bacterial Organelle Interactomes: A Model of the Protein-Protein Interaction Network in the Pdu Microcompartment	journal.pcbi.1004067	null	[ [ "Cellular organization has long been considered to be much simpler in bacteria than in eukaryotic cells .", "However , accumulating evidence indicates a higher-order organization in terms of cellular compartmentalization [1–3] and cell structure [4 , 5] .", "In particular , electron microscopy and hig...	[ "Bacterial microcompartments ( MCPs ) are protein-bound organelles that carry out diverse metabolic pathways in a wide range of bacteria .", "These supramolecular assemblies consist of a thin outer protein shell , reminiscent of a viral capsid , which encapsulates sequentially acting enzymes .", "The most compl...	[ "Many bacteria produce giant proteinaceous structures within their cells , which they use to carry out special metabolic reactions in their interior .", "Much has been learned recently about the individual components—shell proteins and encapsulated enzymes—that assemble together , thousands of subunits in all , t...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "immunology", "experimental design", "database searching", "research design", "probability distribution", "mathematics", "research and analysis methods", "information retrieval", "sequence analysis", "white blood cells", "seque...	DART-ID increases single-cell proteome coverage	journal.pcbi.1007082	null	[ [ "Advancements in the sensitivity and discriminatory power of protein mass-spectrometry ( MS ) have enabled the quantitative analysis of increasingly limited amounts of samples .", "Recently , we have developed Single Cell Proteomics by Mass Spectrometry ( SCoPE-MS ) .", "SCoPE-MS uses a barcoded carri...	[ "Analysis by liquid chromatography and tandem mass spectrometry ( LC-MS/MS ) can identify and quantify thousands of proteins in microgram-level samples , such as those comprised of thousands of cells .", "This process , however , remains challenging for smaller samples , such as the proteomes of single mammalian ...	[ "Identifying and quantifying proteins in single cells gives researchers the ability to tackle complex biological problems that involve single cell heterogeneity , such as the treatment of solid tumors .", "Mass spectrometry analysis of peptides can identify their sequence from their masses and the masses of their...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genomics", "functional genomics", "genome evolution", "genetics", "biology and life sciences", "comparative genomics", "computational biology" ]	8.2% of the Human Genome Is Constrained: Variation in Rates of Turnover across Functional Element Classes in the Human Lineage	journal.pgen.1004525	null	[ [ "“What proportion of the human genome is functional ? ” remains a contentious question [1]–[3] .", "In great part this reflects the use of definitions of ‘function’ that differ from the traditional definition that is based on fitness and selection ( see e . g . [4] for a discussion ) .", "For instance...	[ "Ten years on from the finishing of the human reference genome sequence , it remains unclear what fraction of the human genome confers function , where this sequence resides , and how much is shared with other mammalian species .", "When addressing these questions , functional sequence has often been equated with...	[ "Nearly 99% of the human genome does not encode proteins , and while there recently has been extensive biochemical annotation of the remaining noncoding fraction , it remains unclear whether or not the bulk of these DNA sequences have important functional roles .", "By comparing the genome sequences of different ...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "molecular biology/bioinformatics", "microbiology/microbial physiology and metabolism", "microbiology" ]	Characterization of the Oral Fungal Microbiome (Mycobiome) in Healthy Individuals	journal.ppat.1000713	null	[ [ "Organisms residing in the oral cavity and their collective genome–the oral microbiome–are critical components of health and disease .", "Disruption of the oral microbiome has been proposed to indicate , trigger , or influence the course of oral diseases , especially among immunocompromised patients ( e ....	[ "The oral microbiome–organisms residing in the oral cavity and their collective genome–are critical components of health and disease .", "The fungal component of the oral microbiota has not been characterized .", "In this study , we used a novel multitag pyrosequencing approach to characterize fungi present in ...	[ "We characterized the fungal microbiome ( mycobiome ) of the oral cavity in healthy individuals .", "Our results demonstrate that the fungal component of the oral microbiome is diverse as revealed by the presence of 74 culturable and 11 non-culturable fungal genera in the oral cavity .", "A total of 101 species...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "eubacteria", "computational biology" ]	UV-Induced Mutagenesis in Escherichia coli SOS Response: A Quantitative Model	journal.pcbi.0030041	null	[ [ "The SOS response in the bacterium E . coli encompasses many proteins involved in detecting and repairing DNA damaged by a variety of agents , such as UV radiation , or chemicals such as mitomycin and bleomycin [1] .", "A complex regulatory network , comprising both transcriptional and post-translational ...	[ "Escherichia coli bacteria respond to DNA damage by a highly orchestrated series of events known as the SOS response , regulated by transcription factors , protein–protein binding , and active protein degradation .", "We present a dynamical model of the UV-induced SOS response , incorporating mutagenesis by the e...	[ "Ultraviolet light damages the DNA of cells , which prevents duplication and thereby cell division .", "Bacteria respond to such damage by producing a number of proteins that help to detect , bypass , and repair the damage .", "This SOS response system displays intricate dynamical behavior—in particular the tig...	2007
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "sequencing techniques", "invertebrates", "rna interference", "gene regulation", "invertebrate genomics", "animals", "animal models", "drosophila melanogaster", "model organisms", "experimental organism systems", "sequence motif analysis", "epigenetics", "molecular biology techniques", "rn...	Rewired RNAi-mediated genome surveillance in house dust mites	journal.pgen.1007183	null	[ [ "House dust mites are ubiquitous inhabitants of human dwellings , and are the primary cause of indoor allergy [1] .", "Dust mites have an unusual evolutionary history , descending from a parasitic ancestor [2] .", "Parasite genomes are typically highly modified; possibly to accommodate genetic novelty...	[ "House dust mites are common pests with an unusual evolutionary history , being descendants of a parasitic ancestor .", "Transition to parasitism is frequently accompanied by genome rearrangements , possibly to accommodate the genetic change needed to access new ecology .", "Transposable element ( TE ) activity...	[ "Investigation of small RNA populations in dust mites revealed absence of the piwi-associated RNA ( piRNA ) pathway .", "Apart from several nematode and platyhelminths lineages , piRNAs are an essential component of animal genome surveillance , actively targeting and silencing transposable elements .", "In dust...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell physiology", "carbohydrate metabolism", "medicine and health sciences", "pathology and laboratory medicine", "chemical compounds", "pathogens", "metabolic networks", "experimental design", "bacillus", "microbiology", "carbohydrates", "glucose metabolism", "cell metabolism", "organic ...	SUMOFLUX: A Generalized Method for Targeted 13C Metabolic Flux Ratio Analysis	journal.pcbi.1005109	null	[ [ "Metabolic fluxes describe the in vivo flow of organic matter through the biochemical reaction network , as defined by enzymes and transporters .", "An improved knowledge of metabolic fluxes is crucial if we are to understand how cells utilize nutrients , and how they regulate metabolism in the face of dy...	[ "Metabolic fluxes are a cornerstone of cellular physiology that emerge from a complex interplay of enzymes , carriers , and nutrients .", "The experimental assessment of in vivo intracellular fluxes using stable isotopic tracers is essential if we are to understand metabolic function and regulation .", "Flux es...	[ "Living cells adapt to ever-changing environments by regulating metabolic fluxes , the rates of nutrient flow through the metabolic network , to produce metabolites that are currently in demand .", "13C-labeling techniques coupled with metabolic flux analyses are widely used to estimate metabolic fluxes and provi...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "evolutionary biology/microbial evolution and genomics", "evolutionary biology/genomics", "cell biology/membranes and sorting", "evolutionary biology/developmental molecular mechanisms", "evolutionary biology/morphogenesis and cell biology" ]	Comprehensive Analysis Reveals Dynamic and Evolutionary Plasticity of Rab GTPases and Membrane Traffic in Tetrahymena thermophila	journal.pgen.1001155	null	[ [ "Cells can respond to and shape their environments by taking up and releasing macromolecules .", "Both in- and outbound transport is facilitated by a network of membrane-bound compartments that represent one of the hallmarks of eukaryotic cells [1] .", "Traffic through the network is highly regulated ...	[ "Cellular sophistication is not exclusive to multicellular organisms , and unicellular eukaryotes can resemble differentiated animal cells in their complex network of membrane-bound structures .", "These comparisons can be illuminated by genome-wide surveys of key gene families .", "We report a systematic analy...	[ "Single-celled organisms appear simple compared to multicellular organisms , but this may not be true at the level of the individual cell .", "In fact , microscopic observations suggest that protists can possess networks of organelles just as elaborate as those in animal cells .", "Consistent with this idea , r...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biotechnology", "genome engineering", "engineering and technology", "synthetic biology", "genomic library screening", "invertebrate genomics", "synthetic bioengineering", "crispr", "genomic databases", "genome analysis", "mammalian genomics", "molecular biology techniques", "synthetic genom...	Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion	journal.pcbi.1005341	null	[ [ "CRISPR/Cas9 is a simple and versatile method for genome editing that can be applied to deleting virtually any genomic region for loss-of-function studies .", "Deletion requires the design of optimal pairs of single guide RNA ( sgRNA ) molecules that hybridise to sequences flanking the target region .", ...	[ "CRISPR-Cas9 technology can be used to engineer precise genomic deletions with pairs of single guide RNAs ( sgRNAs ) .", "This approach has been widely adopted for diverse applications , from disease modelling of individual loci , to parallelized loss-of-function screens of thousands of regulatory elements .", ...	[ "CRISPR-Cas9 is a revolutionary biological technique for precisely editing cells’ genomes .", "Amongst its many capabilities is the deletion of defined regions of DNA , creating a wide range of applications from modelling rare human diseases , to performing very large knock-out screens of candidate regulatory DNA...	2017
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "mycetoma", "tropical diseases", "patient advocacy", "geographical locations", "sudan", "surgical and invasive medical procedures", "health care", "signs and symptoms", "neglected tropical diseases", "fungal diseases", "afr...	A holistic approach to the mycetoma management	journal.pntd.0006391	null	[ [ "Mycetoma is a common neglected tropical disease , reported worldwide but endemic in many tropical and subtropical regions in what is known as the mycetoma belt and Sudan seems to have the highest endemicity [1 , 2] .", "It is a chronic granulomatous inflammatory disease caused by several true fungi or ce...	[ "Mycetoma , one of the badly neglected tropical diseases , it is a localised chronic granulomatous inflammatory disease characterised by painless subcutaneous mass and formation of multiple sinuses that produce purulent discharge and grains .", "If untreated early and appropriately , it usually spread to affect t...	[ "Mycetoma enjoys all the neglected tropical diseases ( NTDs ) characteristics .", "It frequently affects the poorest of the poor in poor communities in remote regions .", "The affected population are of low socio-economic status , of low visibility and low political and social voice and hence they are neglected...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "urea", "swimming", "pathology and laboratory medicine", "chemical compounds", "ureases", "enzymes", "pathogens", "microbiology", "enzymology", "organic compounds", "biomechanics", "biological locomotion", "helicobacter", "stomach", "bacteria", "bacter...	Multiple Acid Sensors Control Helicobacter pylori Colonization of the Stomach	journal.ppat.1006118	null	[ [ "Helicobacter pylori is a bacterium that has co-evolved with humans since the origin of the human species [1 , 2] .", "This intimate association with the human host has allowed it to develop a number of survival strategies to persist in one of the most challenging environments in the human body—the stomac...	[ "Helicobacter pylori’s ability to respond to environmental cues in the stomach is integral to its survival .", "By directly visualizing H . pylori swimming behavior when encountering a microscopic gradient consisting of the repellent acid and attractant urea , we found that H . pylori is able to simultaneously de...	[ "Helicobacter pylori is a bacterium that chronically infects the stomachs of 50% of humans , and infection can lead to serious diseases like peptic ulcers and stomach cancer .", "To survive , H . pylori rapidly senses acid and swims away to the protective mucus layer covering the stomach surface .", "The bacter...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "cell physiology", "carbohydrate metabolism", "medicine and health sciences", "chemical compounds", "enzymes", "oxygen", "enzymology", "carbohydrates", "glucose metabolism", "organic compounds", "glucose", "cell metabolism", "physiological processes", "enzyme metabolism", "enzyme kinetic...	Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield	journal.pcbi.1006010	null	[ [ "Metabolic networks are shaped by evolution .", "In well-mixed , nutrient-rich environments , fast-growing bacteria are favored by natural selection .", "Such environments are commonly studied in laboratory settings , but natural environments are more diverse .", "In isolated ecological niches wit...	[ "Microbes may maximize the number of daughter cells per time or per amount of nutrients consumed .", "These two strategies correspond , respectively , to the use of enzyme-efficient or substrate-efficient metabolic pathways .", "In reality , fast growth is often associated with wasteful , yield-inefficient meta...	[ "When cells compete for nutrients , those that grow faster and produce more offspring per time are favored by natural selection .", "In contrast , when cells need to maximize the cell number at a limited nutrient supply , fast growth does not matter and an efficient use of nutrients ( i . e . high biomass yield )...	2018
[ "Introduction", "Materials and Methods", "Discussion" ]	[]	Genomic Heritability: What Is It?	journal.pgen.1005048	null	[ [ "Whole-genome regression ( WGR ) methods [1] are becoming increasingly used for analysis and prediction of complex traits , quantitative or categorical .", "These methods were first developed for prediction in plant and animal breeding ( e . g . , [2 , 3] ) .", "More recently , there has been an incre...	[ "Whole-genome regression methods are being increasingly used for the analysis and prediction of complex traits and diseases .", "In human genetics , these methods are commonly used for inferences about genetic parameters , such as the amount of genetic variance among individuals or the proportion of phenotypic va...	[ "Whole-genome regression ( WGR ) methods are being increasingly used for inferring the proportion of variance that can be explained by a linear regression on a massive number of markers , called ‘genomic heritability . ’ However , the statistical assumptions involved in WGRs are somewhat at odds with important quan...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "geography", "public health and epidemiology", "mathematics", "environmental sciences", "ecology", "earth sciences", "statistics", "biology", "public health", "physical geography", "veterinary science", "veterinary medicine" ]	Combining Climatic Projections and Dispersal Ability: A Method for Estimating the Responses of Sandfly Vector Species to Climate Change	journal.pntd.0001407	null	[ [ "Globally , the number of vector-borne infections in humans and animals increases rapidly , meanwhile causing almost one third of all cases of emerging infectious diseases [1] .", "In the Old World , sandfly species of the genus Phlebotomus serve as vectors for sandfly-borne pathogens such as Leishmania ,...	[ "In the Old World , sandfly species of the genus Phlebotomus are known vectors of Leishmania , Bartonella and several viruses .", "Recent sandfly catches and autochthonous cases of leishmaniasis hint on spreading tendencies of the vectors towards Central Europe .", "However , studies addressing potential future...	[ "Growing evidence exists on the emergence of sandfly-borne diseases in the light of climate change .", "Determining the principle responses of phlebotomine sandflies to climatic changes supports our understanding of future regions that will be threatened by new-establishments of this important group of disease ve...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "gastroenterology and hepatology/gastrointestinal cancers", "genetics and genomics/gene expression", "hematology/acute myeloid leukemia", "molecular biology/dna methylation", "oncology/gastrointestinal cancers", "genetics and genomics/epigenetics", "oncology/hematological malignancies", "molecular bio...	An Sp1/Sp3 Binding Polymorphism Confers Methylation Protection	journal.pgen.1000162	null	[ [ "Causes of promoter DNA hypermethylation in cancer are unknown .", "Possibilities range from random events selected for to a model whereby an initial drop of transcription rate allows elimination of active chromatin boundaries and spreading of DNA methylation from “DNA methylation centers”- perhaps , repe...	[ "Hundreds of genes show aberrant DNA hypermethylation in cancer , yet little is known about the causes of this hypermethylation .", "We identified RIL as a frequent methylation target in cancer .", "In search for factors that influence RIL hypermethylation , we found a 12-bp polymorphic sequence around its tran...	[ "The factors that guide DNA hypermethylation in cancer are poorly understood .", "We identified the candidate tumor-suppressor gene , RIL , as a frequent methylation target in cancer .", "Here , we report on a 12-bp polymorphic sequence around its transcription start site that creates a long allele .", "Methy...	2008
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "systems biology", "virology", "biology", "microbiology", "host-pathogen interaction", "genetics and genomics" ]	Large Scale Genotype Comparison of Human Papillomavirus E2-Host Interaction Networks Provides New Insights for E2 Molecular Functions	journal.ppat.1002761	null	[ [ "Papillomaviruses are non-enveloped small DNA viruses , of which over 140 types infect humans ( HPV ) .", "HPV are strictly epitheliotropic , with specificity for stratified epithelia of the skin ( cutaneous HPV ) or genital and oral mucosa ( mucosal HPV ) .", "They are either associated with asymptom...	[ "Human Papillomaviruses ( HPV ) cause widespread infections in humans , resulting in latent infections or diseases ranging from benign hyperplasia to cancers .", "HPV-induced pathologies result from complex interplays between viral proteins and the host proteome .", "Given the major public health concern due to...	[ "Over 100 types of human papillomaviruses are responsible for widespread infections in humans .", "They cause a wide range of pathologies , ranging from inapparent infections to benign lesions , hyperplasia or cancers .", "Such heterogeneity results from variable interplay among viral and host cell proteins .",...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "blood cells", "medicine and health sciences", "immune cells", "immunology", "microbiology", "immunodeficiency viruses", "infectious diseases", "white blood cells", "animal cells", "medical microbiology", "hiv", "t cells", "microbial pathogens", "immune response", "cell biology", "clin...	T-bet and Eomes Are Differentially Linked to the Exhausted Phenotype of CD8+ T Cells in HIV Infection	journal.ppat.1004251	null	[ [ "An effective CD8+ T cell response is required to eradicate or control intracellular pathogens .", "During the acute phase of an infection , pathogen-specific CD8+ T cells expand and differentiate into effector cells to clear the microbe .", "In the wake of antigen clearance , long-lived memory CD8+ T...	[ "CD8+ T cell exhaustion represents a major hallmark of chronic HIV infection .", "Two key transcription factors governing CD8+ T cell differentiation , T-bet and Eomesodermin ( Eomes ) , have previously been shown in mice to differentially regulate T cell exhaustion in part through direct modulation of PD-1 .", ...	[ "CD8+ T cells display numerous traits of severe dysfunction in both treated and untreated HIV infection .", "Previous studies have demonstrated that HIV-specific CD8+ T cells in most individuals possess poor polyfunctionality , and an immature/skewed maturation phenotype .", "However , it remains unclear which ...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "molecular dynamics", "protein structure prediction", "protein structure", "intrinsically disordered proteins", "research and analysis methods", "protein structure determination", "proteins", "biological databases", "structural proteins", "chemistry", "proteomics", "biophysics", "molecular b...	Modeling disordered protein interactions from biophysical principles	journal.pcbi.1005485	null	[ [ "Intrinsically disordered proteins ( IDP ) , which have evolved to not adopt a stable structure under physiological conditions , are a departure from the traditional paradigm of structured proteins [1] .", "After initial recognition of their critical biological functions in the 1990s [1] , IDPs quickly ga...	[ "Disordered protein-protein interactions ( PPIs ) , those involving a folded protein and an intrinsically disordered protein ( IDP ) , are prevalent in the cell , including important signaling and regulatory pathways .", "IDPs do not adopt a single dominant structure in isolation but often become ordered upon bin...	[ "A substantial fraction of the proteins encoded in genomes are intrinsically disordered proteins ( IDPs ) , which lack a single stable structure in the native state .", "IDPs serve many functions including mediating protein-protein interactions ( PPIs ) .", "Such disordered PPIs are prevalent in important regul...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "olives", "cell physiology", "action potentials", "medicine and health sciences", "neural networks", "nervous system", "membrane potential", "junctional complexes", "electrophysiology", "neuroscience", "gap junctions", "network analysis", "plants", "computer and information sciences", "a...	Quasiperiodic rhythms of the inferior olive	journal.pcbi.1006475	null	[ [ "A multitude of behavioral studies leave little doubt that the olivo-cerebellar system organizes appropriate timing in motor behavior [1–3] , perceptual function [4–6] and motor learning [7–10] .", "Furthermore , the role of the inferior olive in motor function is evinced in ( permanent and transient ) cl...	[ "Inferior olivary activity causes both short-term and long-term changes in cerebellar output underlying motor performance and motor learning .", "Many of its neurons engage in coherent subthreshold oscillations and are extensively coupled via gap junctions .", "Studies in reduced preparations suggest that these...	[ "Activity of the inferior olive , transmitted via climbing fibers to the cerebellum , regulates initiation and amplitude of movements , signals unexpected sensory feedback , and directs cerebellar learning .", "It is characterized by widespread subthreshold oscillations and synchronization promoted by strong elec...	2019
[ "Introduction", "Materials and methods", "Discussion" ]	[ "fourier analysis", "engineering and technology", "signal processing", "social sciences", "vertebrates", "neuroscience", "animals", "mammals", "kernel functions", "mathematics", "ganglion cells", "amniotes", "interneurons", "vision", "research and analysis methods", "operator theory", ...	Firing-rate based network modeling of the dLGN circuit: Effects of cortical feedback on spatiotemporal response properties of relay cells	journal.pcbi.1006156	null	[ [ "Visually evoked signals pass the dorsal geniculate nucleus ( dLGN ) on the route from retina to primary visual cortex in the early visual pathway .", "This is however not a simple feedforward flow of information , as there is a significant feedback from primary visual cortex back to dLGN .", "Cortica...	[ "Visually evoked signals in the retina pass through the dorsal geniculate nucleus ( dLGN ) on the way to the visual cortex .", "This is however not a simple feedforward flow of information: there is a significant feedback from cortical cells back to both relay cells and interneurons in the dLGN .", "Despite fou...	[ "On route from the retina to primary visual cortex , visually evoked signals have to pass through the dorsal lateral geniculate nucleus ( dLGN ) .", "However , this is not an exclusive feedforward flow of information as feedback exists from neurons in the cortex back to both relay cells and interneurons in the dL...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell physiology", "medicine and health sciences", "neural networks", "nervous system", "astrocytes", "membrane potential", "junctional complexes", "electrophysiology", "neuroscience", "macroglial cells", "epileptic seizures", "gap junctions", "research and analysis methods", "curve fittin...	Astrocytic Kir4.1 channels and gap junctions account for spontaneous epileptic seizure	journal.pcbi.1005877	null	[ [ "Temporal lobe epilepsy , which has a specific clinical presentation of seizures arising from the hippocampus [1] , is a serious health risk to affected individuals .", "Extensive experimental and theoretical studies have shown that elevated K+ concentration in the extracellular microenvironment ( [K+]o )...	[ "Experimental recordings in hippocampal slices indicate that astrocytic dysfunction may cause neuronal hyper-excitation or seizures .", "Considering that astrocytes play important roles in mediating local uptake and spatial buffering of K+ in the extracellular space of the cortical circuit , we constructed a nove...	[ "Astrocytes are critical regulators of normal physiological activity in the central nervous system , and one of their key functions is removing extracellular K+ .", "In recent years , numerous biological studies have shown that astrocytic Kir4 . 1 channels and gap junctions between astrocytes act as major K+ clea...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "body weight", "medicine and health sciences", "pathology and laboratory medicine", "migraine", "headaches", "physiological parameters", "signs and symptoms", "obesity", "mood disorders", "genetic epidemiology", "epidemiology", "hypertension", "blood pressure", "mental health and psychiatr...	Comorbidities in the diseasome are more apparent than real: What Bayesian filtering reveals about the comorbidities of depression	journal.pcbi.1005487	null	[ [ "It has long been recognised that medical disorders frequently co-occur in the same individual [1] but the significance of comorbidity in revealing shared mechanisms of pathogenesis and outcome is a more recent realisation [2–4] .", "For a given disease or for a focused disease group , the exploration of ...	[ "Comorbidity patterns have become a major source of information to explore shared mechanisms of pathogenesis between disorders .", "In hypothesis-free exploration of comorbid conditions , disease-disease networks are usually identified by pairwise methods .", "However , interpretation of the results is hindered...	[ "Depression is one of the most common of psychiatric disorders and its causation is correspondingly multifactorial , complex and heterogeneous .", "It occurs in combination with a number of physical illnesses far more commonly than expected by chance .", "Such comorbidities may be important clues pointing to sh...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell motility", "actin filaments", "cell processes", "parasitic protozoans", "guanine nucleotide exchange factors", "molecular motors", "actin motors", "protozoans", "motor proteins", "contractile proteins", "actins", "proteins", "entamoeba histolytica", "phagocytosis", "biochemistry", ...	EhFP10: A FYVE family GEF interacts with myosin IB to regulate cytoskeletal dynamics during endocytosis in Entamoeba histolytica	journal.ppat.1007573	null	[ [ "Entamoeba histolytica is the causative agent of amoebiasis disease in humans , a major public health problem in developing countries .", "Amoebiasis is the third-leading cause of deaths resulting from parasitic infections [1 , 2] .", "The ability of E . histolytica to phagocytose cells of the intesti...	[ "Motility and phagocytosis are key processes that are involved in invasive amoebiasis disease caused by intestinal parasite Entamoeba histolytica .", "Previous studies have reported unconventional myosins to play significant role in membrane based motility as well as endocytic processes .", "EhMyosin IB is the ...	[ "Entamoeba histolyica is a highly motile human pathogen which eats the blood cells and immune cells by phagocytosis during progression of Amoebiasis disease .", "E . histolytica infections are a major concern in the developing countries .", "Myosins are motor proteins that move over actin cytoskeleton to drive ...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "markov models", "engineering and technology", "pathogens", "microbiology", "decision analysis", "bacterial diseases", "mathematics", "management engineering", "enterobacteriaceae", "bacteria", "bacterial pathogens", "sal...	Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica	journal.pgen.1007333	null	[ [ "Understanding how bacteria adapt to new niches and hosts and thus emerge or re-emerge as a cause of infectious disease in human and animals is of critical importance to anticipating and preventing epidemic disease [1 , 2] .", "With the decreasing cost of genome sequencing , comparative genomics has becom...	[ "Emerging pathogens are a major threat to public health , however understanding how pathogens adapt to new niches remains a challenge .", "New methods are urgently required to provide functional insights into pathogens from the massive genomic data sets now being generated from routine pathogen surveillance for e...	[ "Researchers are now collecting a wealth of genomic data from bacterial pathogens , and this will continue to grow with the introduction of routine sequencing for disease surveillance .", "However , our ability to use this data to predict how changes in genome sequence lead to differences in disease is limited ."...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "animal types", "animal genetics", "immunology", "lymphoid organs", "veterinary diagnostics", "veterinary science", "veterinary medicine", "biology", "immune system", "veterinary immunology", "genetics of the immune system", "large animals", "bone marrow", "genetics", "genetics of diseas...	Identification of a Mutation Associated with Fatal Foal Immunodeficiency Syndrome in the Fell and Dales Pony	journal.pgen.1002133	null	[ [ "The Fell and Dales are related sturdy pony breeds traditionally used as pack animals to carry goods over the difficult upland terrain of northern England .", "Both breeds experienced near extinction during WWII , and the current populations are descended from very few animals .", "It is likely that t...	[ "The Fell and Dales are rare native UK pony breeds at risk due to falling numbers , in-breeding , and inherited disease .", "Specifically , the lethal Mendelian recessive disease Foal Immunodeficiency Syndrome ( FIS ) , which manifests as B-lymphocyte immunodeficiency and progressive anemia , is a substantial thr...	[ "Foal Immunodeficiency Syndrome ( FIS ) is a genetic disease that affects two related British pony breeds , namely the Fell and the Dales .", "Foals with FIS appear to be normal at birth but within a few weeks develop evidence of infection such as diarrhoea , pneumonia , etc .", "The infections are resistant to...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "transfer rna", "medicine and health sciences", "liver", "oxidative stress", "animal models", "developmental biology", "model organisms", "mitochondria", "bioenergetics", "embryos", "cellular structures and organelles", "research and analysis methods", "embryology", "animal cells", "gene...	Mtu1-Mediated Thiouridine Formation of Mitochondrial tRNAs Is Required for Mitochondrial Translation and Is Involved in Reversible Infantile Liver Injury	journal.pgen.1006355	null	[ [ "Transfer RNA ( tRNA ) is an adaptor molecule that converts genetic information into an amino acid sequence in protein synthesis .", "tRNAs contain a wide variety of modified nucleosides that are introduced post-transcriptionally [1 , 2] .", "In mammalian mitochondria , 22 subtypes of tRNAs encoded in...	[ "Reversible infantile liver failure ( RILF ) is a unique heritable liver disease characterized by acute liver failure followed by spontaneous recovery at an early stage of life .", "Genetic mutations in MTU1 have been identified in RILF patients .", "MTU1 is a mitochondrial enzyme that catalyzes the 2-thiolatio...	[ "Mitochondrial transfer tRNA ( mt-tRNA ) contains a variety of chemical modifications that are introduced post-transcriptionally .", "Three mt-tRNAs for Lys , Gln and Glu contain 5-taurinomethyl-2-thiouridine ( τm5s2U ) in their anticodons .", "It is known that the loss of 2-thiolation of τm5s2U is strongly ass...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "biology and life sciences", "immunology", "developmental biology" ]	Basement Membrane and Cell Integrity of Self-Tissues in Maintaining Drosophila Immunological Tolerance	journal.pgen.1004683	null	[ [ "The discovery of Toll-like receptors and other categories of pattern recognition receptors has greatly enhanced our understanding of how the immune system recognizes different types of pathogens [1] , [2]; however , it is less clear why the immune system often turns its arsenal toward self-tissues .", "I...	[ "The mechanism underlying immune system recognition of different types of pathogens has been extensively studied over the past few decades; however , the mechanism by which healthy self-tissue evades an attack by its own immune system is less well-understood .", "Here , we established an autoimmune model of melan...	[ "Autoimmune diseases may be caused by failures in the immune system or by altered selfness in target tissues; however , which of these is more critical is controversial .", "To better understand such diseases , it is necessary to first define the molecular mechanisms that provide self-tolerance to healthy tissues...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The RNA Template Channel of the RNA-Dependent RNA Polymerase as a Target for Development of Antiviral Therapy of Multiple Genera within a Virus Family	journal.ppat.1004733	null	[ [ "The family Picornaviridae contains 12 genera , and includes many human and animal pathogens ( reviewed in [1] ) .", "Among these is the genus Enterovirus which contains four human enterovirus species ( HEV-A , -B , -C , -D ) , three human rhinovirus species ( HRV-A , -B , -C ) , simian enterovirus , bovi...	[ "The genus Enterovirus of the family Picornaviridae contains many important human pathogens ( e . g . , poliovirus , coxsackievirus , rhinovirus , and enterovirus 71 ) for which no antiviral drugs are available .", "The viral RNA-dependent RNA polymerase is an attractive target for antiviral therapy .", "Nucleo...	[ "Virus replication relies on multiplication of viral genomes by viral polymerases .", "For enteroviruses , a large group of clinically important human pathogens for which no antiviral therapy is available , this function is performed by 3Dpol , the RNA-dependent RNA polymerase .", "3Dpol is therefore an attract...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "cell motility", "engineering and technology", "caenorhabditis", "cell cycle and cell division", "signal processing", "cell processes", "animals", "noise reduction", "animal models", "developmental biology", "regulator genes", "caenorhabditis elegans", "model organisms", ...	Temporal precision of regulated gene expression	journal.pcbi.1006201	null	[ [ "Proper timing is crucial for biological processes , including cell division [1–3] , cell differentiation [4] , cell migration [5] , viral infection [6] , embryonic development [7 , 8] , and cell death [9] .", "These processes are governed by molecular events inside cells , i . e . , production , degradat...	[ "Important cellular processes such as migration , differentiation , and development often rely on precise timing .", "Yet , the molecular machinery that regulates timing is inherently noisy .", "How do cells achieve precise timing with noisy components ?", "We investigate this question using a first-passage-t...	[ "Cells control important processes with precise timing , even though their underlying molecular machinery is inherently imprecise .", "In the case of Caenorhabditis elegans development , migrating neuroblast cells produce a molecule until a certain abundance is reached , at which time the cells stop moving .", ...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/animal genetics", "genetics and genomics/gene discovery", "nutrition", "genetics and genomics/disease models", "genetics and genomics/genetics of disease", "genetics and genomics/gene function", "neurological disorders/developmental and pediatric neurology", "nutrition/deficienc...	Zebrafish Mutants calamity and catastrophe Define Critical Pathways of Gene–Nutrient Interactions in Developmental Copper Metabolism	journal.pgen.1000261	null	[ [ "Proper maternal nutrition is critical for early embryonic development .", "The Dutch Famine Study examined the consequences of nutrient deprivation on developmental outcome during severe food shortages near the end of the Second World War and clearly demonstrated that inadequate nutrient availability dur...	[ "Nutrient availability is an important environmental variable during development that has significant effects on the metabolism , health , and viability of an organism .", "To understand these interactions for the nutrient copper , we used a chemical genetic screen for zebrafish mutants sensitive to developmental...	[ "Copper is an essential nutrient required for multiple biologic functions .", "Proper uptake , transport , and excretion of copper are critical for use of this metal while reducing its inherent toxicity .", "While several key proteins involved in this process have been identified , there are still gaps in our u...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	PERK Limits Drosophila Lifespan by Promoting Intestinal Stem Cell Proliferation in Response to ER Stress	journal.pgen.1005220	null	[ [ "Three highly conserved UPRER sensors coordinate the cell-autonomous response to ER stress: PERK , the transcription factor ATF6 , and the endoribonuclease IRE1 ( Fig 1B ) [4–10 , 13] .", "IRE1 promotes splicing of the mRNA encoding the transcription factor Xbp1 , PERK phosphorylates and inhibits the tran...	[ "Intestinal homeostasis requires precise control of intestinal stem cell ( ISC ) proliferation .", "In Drosophila , this control declines with age largely due to chronic activation of stress signaling and associated chronic inflammatory conditions .", "An important contributor to this condition is the age-assoc...	[ "The long-term maintenance of tissue homeostasis in barrier epithelia requires precise coordination of cellular stress and inflammatory responses with regenerative processes .", "This coordination is lost with age , resulting in degenerative and proliferative diseases .", "The Unfolded Protein Response of the E...	2015
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "invertebrates", "morphogenic segmentation", "gene regulation", "animals", "blastulas", "animal models", "developmental biology", "drosophila melanogaster", "model organisms", "systems science", "mathematics", "experimental organism systems", "embryos", "morphogenesis", "drosophila", "...	A damped oscillator imposes temporal order on posterior gap gene expression in Drosophila	journal.pbio.2003174	null	[ [ "The segmented body plan of insects is established by two seemingly very different modes of development [1–4] .", "Long-germband insects , such as the vinegar fly D . melanogaster , determine their segments more or less simultaneously during the blastoderm stage , before the onset of gastrulation [5 , 6] ...	[ "Insects determine their body segments in two different ways .", "Short-germband insects , such as the flour beetle Tribolium castaneum , use a molecular clock to establish segments sequentially .", "In contrast , long-germband insects , such as the vinegar fly Drosophila melanogaster , determine all segments s...	[ "Different insect species exhibit one of two distinct modes of determining their body segments ( known as segmentation ) during development: they either use a molecular oscillator to position segments sequentially , or they generate segments simultaneously through a hierarchical gene-regulatory cascade .", "The s...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biotechnology", "ecology" ]	Survival of Migrating Salmon Smolts in Large Rivers With and Without Dams	journal.pbio.0060265	Electronic tagging of two species of salmon smolts reveals similar survival rates during migration down the dammed Columbia and undammed Fraser Rivers, challenging popular notions about factors affecting salmon abundance.	[ [ "Many Columbia River salmon stocks are listed as threatened or endangered [1 , 2] , a result often attributed to the construction and operation of the Columbia River dams [3–5] .", "Here , we examine one phase of the lifecycle of Columbia River and Fraser River salmon stocks by comparing the freshwater su...	[ "The mortality of salmon smolts during their migration out of freshwater and into the ocean has been difficult to measure .", "In the Columbia River , which has an extensive network of hydroelectric dams , the decline in abundance of adult salmon returning from the ocean since the late 1970s has been ascribed in ...	[ "Miniature electronic technologies now allow researchers to track a salmon's migration from its birthplace in a river's headwaters in the Rocky Mountains to the North Pacific , opening a window on the mysteries of migration and survival .", "Surprisingly , outward migrating salmon ( smolts ) have similar survival...	2008
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "ecology and environmental sciences", "cell cycle and cell division", "applied mathematics", "cell processes", "condensed matter physics", "social sciences", "light", "neuroscience", "electromagnetic radiation", "simulation and modeling", "algorithms", "crystals", "mathematics", "materials...	A local measure of symmetry and orientation for individual spikes of grid cells	journal.pcbi.1006804	null	[ [ "Neurons in the entorhinal cortex are often classified based on their spatial firing patterns .", "Grid cells , in particular , have attracted a lot of attention , because of their highly symmetric hexagonal activity [1 , 2] .", "To decide whether a given cell should be classified as a grid cell or a ...	[ "Grid cells have attracted broad attention because of their highly symmetric hexagonal firing patterns .", "Recently , research has shifted its focus from the global symmetry of grid cell activity to local distortions both in space and time , such as drifts in orientation , local defects of the hexagonal symmetry...	[ "Grid cells are neurons in mammals whose activity depends on the location of the animal in a striking way: grid cells fire spikes at multiple locations that form a symmetric lattice of repeating hexagons .", "Recent experiments have shown that the symmetry of these patterns is not as stable as initially thought ....	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biomacromolecule-ligand interactions", "medicine and health sciences", "pathology and laboratory medicine", "immunology", "microbiology", "bacterial diseases", "immunomodulation", "infectious diseases", "proteins", "medical microbiology", "tuberculosis", "microbial pathogens", "pathogenesis...	Mycobacterium tuberculosis Lipoprotein LprG Binds Lipoarabinomannan and Determines Its Cell Envelope Localization to Control Phagolysosomal Fusion	journal.ppat.1004471	null	[ [ "Tuberculosis is the second leading cause of death from an infectious disease worldwide ( http://www . who . int/mediacentre/factsheets/fs104/en/index . html ) .", "The causative agent , Mycobacterium tuberculosis ( Mtb ) , is an intracellular bacterial pathogen that persists in phagosomes of infected mac...	[ "Mycobacterium tuberculosis ( Mtb ) virulence is decreased by genetic deletion of the lipoprotein LprG , but the function of LprG remains unclear .", "We report that LprG expressed in Mtb binds to lipoglycans , such as lipoarabinomannan ( LAM ) , that mediate Mtb immune evasion .", "Lipoglycan binding to LprG w...	[ "The causative agent of tuberculosis , Mycobacterium tuberculosis ( Mtb ) , persists in phagosomes inside infected macrophages .", "Mtb expresses lipoarabinomannan ( LAM ) , which inhibits fusion of phagosomes with lysosomes as a means for Mtb to evade host defense .", "LAM is present in the cell envelope , whi...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Operational Principles for the Dynamics of the In Vitro ParA-ParB System	journal.pcbi.1004651	null	[ [ "A variety of mechanisms exist within bacteria to spatially localize proteins within the small confines of a bacterial cell , from reaction diffusion processes that set up waves [1] to spatial occlusion due to the highly crowded environment [2–5] .", "One such protein system that has been observed to disp...	[ "In many bacteria the ParA-ParB protein system is responsible for actively segregating DNA during replication .", "ParB proteins move by interacting with DNA bound ParA-ATP , stimulating their unbinding by catalyzing hydrolysis , that leads to rectified motion due to the creation of a wake of depleted ParA .", ...	[ "Segregating genetic material is essential for cell survival over multiple generations .", "The process underlying the required spatio-temporal organization of DNA is mediated by the ParA-ParB-parS system .", "Recently , experiments have shown that directed motion can be reconstituted in vitro .", "In these e...	2015
[ "Introduction", "Methods and models", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "medicine and health sciences", "helminths", "tropical diseases", "parasitic diseases", "animals", "systems science", "gastropods", "mathematics", "neglected tropical diseases", "population biology", "infectious disease control", "snails", "fecundity", "...	The human-snail transmission environment shapes long term schistosomiasis control outcomes: Implications for improving the accuracy of predictive modeling	journal.pntd.0006514	null	[ [ "Schistosomiasis is a neglected tropical disease ( NTD ) having an estimated global prevalence of 240 million infected persons , many of whom experience significant morbidity within the infected communities of Africa , the Mideast , South America , Asia , and the Philippines [1] .", "For global control of...	[ "Schistosomiasis is a chronic parasitic trematode disease that affects over 240 million people worldwide .", "The Schistosoma lifecycle is complex , involving transmission via specific intermediate-host freshwater snails .", "Predictive mathematical models of Schistosoma transmission have often chosen to simpli...	[ "Infection with blood fluke Schistosoma parasites is a major cause of disease burden around the world .", "Control of schistosomiasis , which is transmitted through intermediate host freshwater snails , is a priority for national and global health programs working in at-risk regions of Africa , the Mideast , Asia...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "toxins", "pathology and laboratory medicine", "toxicology", "toxic agents", "simulation and modeling", "luminescent proteins", "phase diagrams", "yellow fluorescent protein", "bioassays and physiological analysis", "color codes", "crystallographic techniques", ...	Effects of stochasticity and division of labor in toxin production on two-strain bacterial competition in Escherichia coli	journal.pbio.2001457	null	[ [ "Interactions like cooperation and competition between different organisms govern ecosystem dynamics , influencing ecosystem composition [1] , maintenance of biodiversity [1–4] , and the microbiota–host relationship [5–9] .", "Despite the detailed knowledge of individual interaction mechanisms on the one ...	[ "In phenotypically heterogeneous microbial populations , the decision to adopt one or another phenotype is often stochastically regulated .", "However , how this stochasticity affects interactions between competing microbes in mixed communities is difficult to assess .", "One example of such an interaction syst...	[ "Competition is the dominant interaction type between species of bacteria .", "Bacterial toxin-mediated competition is often accompanied by a division of labor between toxin-producing cells and reproducers within a species .", "In populations with large cell numbers , the stochastic dynamics that determine if a...	2017
[ "Introduction", "Results and Discussion", "Materials and Methods" ]	[ "diabetes and endocrinology/obesity", "neuroscience/neuronal signaling mechanisms", "neurological disorders/neuroendocrinology and pituitary" ]	Lipoprotein Receptor LRP1 Regulates Leptin Signaling and Energy Homeostasis in the Adult Central Nervous System	journal.pbio.1000575	Lipoprotein receptor LRP1 play critical roles in lipid metabolism, and this study reveals a novel role for LRP1 in controlling food intake and obesity in the central nervous system of the adult mouse.	[ [ "The low-density lipoprotein receptor-related protein 1 ( LRP1 ) is a large cell surface receptor ubiquitously expressed in a variety of organs including adipose tissue , liver , and brain [1] .", "Previous tissue-specific knockout studies showed that hepatic LRP1 mediates the metabolism of apolipoprotein...	[ "Obesity is a growing epidemic characterized by excess fat storage in adipocytes .", "Although lipoprotein receptors play important roles in lipid uptake , their role in controlling food intake and obesity is not known .", "Here we show that the lipoprotein receptor LRP1 regulates leptin signaling and energy ho...	[ "The World Health Organization estimates that at least 1 in 10 adults worldwide are obese , and in some western countries , a far greater percentage ( 25% or more ) is affected .", "Obesity is a serious concern because it increases the risk of cardiovascular disease , type 2 diabetes , and some cancers , among ot...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "biology", "microbiology", "parasitology" ]	In Vitro and In Vivo Activity of a Palladacycle Complex on Leishmania (Leishmania) amazonensis	journal.pntd.0001626	null	[ [ "Protozoan parasites of the Leishmania genus induce cutaneous , mucocutaneous and visceral diseases in man and animals .", "According to the World Health Organization , about 1 . 5 million of new human cases of cutaneous leishmaniasis and 500 , 000 of visceral leishmaniasis are registered annually [1] .",...	[ "Antitumor cyclopalladated complexes with low toxicity to laboratory animals have shown leishmanicidal effect .", "These findings stimulated us to test the leishmanicidal property of one palladacycle compound called DPPE 1 . 2 on Leishmania ( Leishmania ) amazonensis , an agent of simple and diffuse forms of cuta...	[ "Leishmaniasis is an important public health problem with an estimated annual incidence of 1 . 5 million of new human cases of cutaneous leishmaniasis and 500 , 000 of visceral leishmaniasis .", "Treatment of the diseases is limited by toxicity and parasite resistance to the drugs currently in use , validating th...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases", "medicine and health sciences", "genetics", "biology and life sciences", "microbiology", "molecular biology" ]	Whole Genome Sequence of the Treponema pallidum subsp. endemicum Strain Bosnia A: The Genome Is Related to Yaws Treponemes but Contains Few Loci Similar to Syphilis Treponemes	journal.pntd.0003261	null	[ [ "Uncultivable human pathogenic treponemes include T . pallidum subsp .", "pallidum ( TPA ) , causing syphilis , T . pallidum subsp .", "pertenue ( TPE ) , causing yaws , and T . pallidum subsp .", "endemicum ( TEN ) , causing bejel , which is also known as endemic or nonvenereal syphilis .", "...	[ "T . pallidum subsp .", "endemicum ( TEN ) is the causative agent of bejel ( also known as endemic syphilis ) .", "Clinical symptoms of syphilis and bejel are overlapping and the epidemiological context is important for correct diagnosis of both diseases .", "In contrast to syphilis , caused by T . pallidum s...	[ "Uncultivable treponemes represent bacterial species and subspecies that are obligate pathogens of humans and animals causing diseases with distinct clinical manifestations .", "Treponema pallidum subsp .", "pallidum causes sexually transmitted syphilis , a multistage disease characterized in humans by localize...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Cullin4 Is Pro-Viral during West Nile Virus Infection of Culex Mosquitoes	journal.ppat.1005143	null	[ [ "Flaviviruses , such as West Nile virus ( WNV ) and dengue virus ( DENV ) , pose a huge burden on public healthcare system worldwide .", "With more than half of world’s population at risk of infection , the geographic distribution of these mosquito-borne flaviviruses is expanding due to increased travel ,...	[ "Although mosquitoes serve as vectors of many pathogens of public health importance , their response to viral infection is poorly understood .", "It also remains to be investigated whether viruses deploy some mechanism to be able to overcome this immune response .", "Here , we have used an RNA-Seq approach to i...	[ "Mosquitoes are responsible for transmitting a large number of human and livestock viruses , like West Nile , dengue and Japanese encephalitis viruses .", "Infection of female mosquitoes with these viruses during blood feeding elicits an immune response .", "It is not known how the viruses manage to replicate i...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "herpes simplex virus", "medicine and health sciences", "pathology and laboratory medicine", "chemical compounds", "pathogens", "messenger rna", "microbiology", "organic compounds", "geoinformatics", "biochemical analysis", "viruses", "protein synthesis", "dna viruses", "amino acids", "b...	A bimodal switch in global protein translation coupled to eIF4H relocalisation during advancing cell-cell transmission of herpes simplex virus	journal.ppat.1007196	null	[ [ "Much of our understanding of the molecular mechanisms operating during virus infection comes from population studies .", "The classic single-step virus growth cycle , the identification and characterisation of virus encoded transcripts and proteins , and the associated mechanisms governing temporal regul...	[ "We used the bioorthogonal protein precursor , homopropargylglycine ( HPG ) and chemical ligation to fluorescent capture agents , to define spatiotemporal regulation of global translation during herpes simplex virus ( HSV ) cell-to-cell spread at single cell resolution .", "Translational activity was spatially st...	[ "All viruses reprogram protein synthesis within infected cells for the production of their own proteins and for suppression of host antiviral responses .", "On the other hand , cells also modulate translation to suppress virus replication .", "Thus , global protein synthesis in infected cells represents the tem...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "biochemistry", "infectious diseases", "hiv", "drug resistance", "multivariate modelling", "proteases", "computational biology", "retroviruses" ]	A Look Inside HIV Resistance through Retroviral Protease Interaction Maps	journal.pcbi.0030048	null	[ [ "Retroviruses are associated with a broad range of diseases that include tumors , immunodeficiency syndromes , and neurological disorders [1] .", "They affect a large number of species , from fish and birds to mammals and humans , with global socioeconomic negative impacts [1] .", "Each year the HIV p...	[ "Retroviruses affect a large number of species , from fish and birds to mammals and humans , with global socioeconomic negative impacts .", "Here the authors report and experimentally validate a novel approach for the analysis of the molecular networks that are involved in the recognition of substrates by retrovi...	[ "Retroviruses are associated with a broad range of diseases that include tumor formation , neurological disorders , and immunodeficiency syndromes , including those of HIV .", "The extraordinary mutational plasticity of HIV-1 causes the rapid appearance of highly diverse quasi-species in a very short time , leadi...	2007
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "neglected tropical diseases" ]	Association of Mast Cell-Derived VEGF and Proteases in Dengue Shock Syndrome	journal.pntd.0001505	null	[ [ "Dengue virus infection is associated with disease , ranging from Dengue fever ( DF ) to Dengue hemorrhagic fever ( DHF ) and/or Dengue shock syndrome ( DSS ) .", "As severe diseases typically develop in individuals suffering secondary Dengue virus infection , host immunological factors appear to play a r...	[ "Recent in-vitro studies have suggested that mast cells are involved in Dengue virus infection .", "To clarify the role of mast cells in the development of clinical Dengue fever , we compared the plasma levels of several mast cell-derived mediators ( vascular endothelial cell growth factor [VEGF] , soluble VEGF r...	[ "To clarify the involvement of mast cells in the development of severe Dengue diseases , plasma levels of mast cell-derived mediators , namely vascular endothelial cell growth factor ( VEGF ) , tryptase , and chymase , were estimated in Dengue patients and control subjects in Vietnam .", "The levels of the mediat...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Whole Genome Sequencing of Mycobacterium africanum Strains from Mali Provides Insights into the Mechanisms of Geographic Restriction	journal.pntd.0004332	null	[ [ "Mycobacterium africanum is a member of the Mycobacterium tuberculosis complex ( MTC ) that causes up to half of all tuberculosis cases in West Africa [1] .", "First identified by Castets in 1968 , it was originally characterized as having biochemical characteristics intermediate between Mycobacterium tub...	[ "Mycobacterium africanum , made up of lineages 5 and 6 within the Mycobacterium tuberculosis complex ( MTC ) , causes up to half of all tuberculosis cases in West Africa , but is rarely found outside of this region .", "The reasons for this geographical restriction remain unknown .", "Possible reasons include a...	[ "Mycobacterium africanum consists of two lineages , lineages 5 and 6 , within the Mycobacterium tuberculosis complex ( MTC ) that cause human tuberculosis in West Africa , but are found rarely outside of this region .", "Our analysis of the whole genome sequences of 26 lineage 5 and 6 isolates , and 66 isolates f...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "bacterial diseases", "infectious diseases", "veterinary diseases", "zoonoses", "veterinary epidemiology", "medicine and health sciences", "veterinary microbiology", "biology and life sciences", "q fever", "veterinary science" ]	Emergence of Coxiella burnetii in Ruminants on Reunion Island? Prevalence and Risk Factors	journal.pntd.0003055	null	[ [ "Q fever is a widespread zoonosis that is caused by Coxiella burnetii ( C . burnetii ) , an obligate intracellular bacterium [1]–[4] .", "The reservoir includes mammals , birds and arthropods , mainly ticks [5] .", "Ruminants ( sheep , goats and cattle ) are identified as the main sources of human inf...	[ "Q fever is a widespread zoonosis that is caused by Coxiella burnetii ( C . burnetii ) , and ruminants are identified as the main sources of human infections .", "Some human cases have been described , but very limited information was available about Q fever in ruminants on Reunion Island , a tropical island in t...	[ "Q fever is a disease that could be transmitted from animals ( cattle , sheep and goats ) to humans and caused by a bacterium called Coxiella burnetii ( C . burnetii ) .", "Some human cases exhibiting characteristic clinical signs of that disease have been detected on Reunion Island , a tropical island in the Ind...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing techniques", "microbial mutation", "medicine and health sciences", "pathology and laboratory medicine", "insertion mutation", "pathogens", "microbiology", "viruses", "mutation", "substitution mutation", "dna viruses", "sequence motif analysis", "molecular biology techniques", "...	Genome-Wide Estimation of the Spontaneous Mutation Rate of Human Adenovirus 5 by High-Fidelity Deep Sequencing	journal.ppat.1006013	null	[ [ "DNA viruses have been traditionally viewed as slowly-evolving entities , but this notion has been challenged in the last decade after the discovery of several highly diverse and fast-evolving DNA viruses [1–6] .", "The pace of evolution should be dependent on the rate at which new spontaneous mutations a...	[ "Rates of spontaneous mutation determine the ability of viruses to evolve , infect new hosts , evade immunity and undergo drug resistance .", "Contrarily to RNA viruses , few mutation rate estimates have been obtained for DNA viruses , because their high replication fidelity implies that new mutations typically f...	[ "Next-generation sequencing has provided a powerful tool for studying microbial genetic diversity but suffers from relatively low per-base accuracy , limiting our ability to detect low-frequency polymorphisms and spontaneous mutations .", "However , this limitation has been solved recently by the development of h...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing techniques", "auditory cortex", "medicine and health sciences", "computational biology", "brain", "random variables", "neuroscience", "learning and memory", "probability distribution", "mathematics", "forecasting", "statistics (mathematics)", "cognition", "computational neurosc...	The Representation of Prediction Error in Auditory Cortex	journal.pcbi.1005058	null	[ [ "Organisms often operate in unknown and uncertain environments .", "Therefore , extracting aspects of past observations , which are maximally predictive of the relevant future , is essential for survival .", "It has been suggested that the sensory cortex evolved to extract the statistical regularities...	[ "To survive , organisms must extract information from the past that is relevant for their future .", "How this process is expressed at the neural level remains unclear .", "We address this problem by developing a novel approach from first principles .", "We show here how to generate low-complexity representat...	[ "A crucial aspect of all life is the ability to use past events in order to guide future behavior .", "To do that , creatures need the ability to predict future events .", "Indeed , predictability has been shown to affect neuronal responses in many animals and under many conditions .", "Clearly , the quality ...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Identification of Strain-Specific B-cell Epitopes in Trypanosoma cruzi Using Genome-Scale Epitope Prediction and High-Throughput Immunoscreening with Peptide Arrays	journal.pntd.0002524	null	[ [ "Chagas disease , a zoonosis caused by the protozoan parasite Trypanosoma cruzi , affects approximately 10 million people in the Americas .", "Approximately 14 , 000 deaths occur annually , and 50 , 000–200 , 000 new cases are diagnosed each year [1] .", "During the acute phase of infection , diagnosi...	[ "The factors influencing variation in the clinical forms of Chagas disease have not been elucidated; however , it is likely that the genetics of both the host and the parasite are involved .", "Several studies have attempted to correlate the T . cruzi strains involved in infection with the clinical forms of the d...	[ "Serological tests are preferentially used for the diagnosis of Chagas disease during the chronic phase because of the low parasitemia and high anti-T .", "cruzi antibody titers .", "However , contradictory or inconclusive results , mainly related to the characteristics of the antigens used , are often observed...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "antimicrobials", "medicine and health sciences", "microbiome", "pathology and laboratory medicine", "pathogens", "drugs", "microbiology", "animal models", "fungi", "model organisms", "antibiotics", "experimental organism systems", "pharmacology", "fungal diseases", "fungal pathogens", ...	Expansion of commensal fungus Wallemia mellicola in the gastrointestinal mycobiota enhances the severity of allergic airway disease in mice	journal.ppat.1007260	null	[ [ "The gut microbiome is a dynamic ecosystem that profoundly influences immune function throughout the body [1–3] .", "Commensal microorganisms are recognized by the host immune system and can alter systemic immune response or produce bioactive metabolites which are absorbed into the bloodstream and have ph...	[ "The gastrointestinal microbiota influences immune function throughout the body .", "The gut-lung axis refers to the concept that alterations of gut commensal microorganisms can have a distant effect on immune function in the lung .", "Overgrowth of intestinal Candida albicans has been previously observed to ex...	[ "The microbiome is the ecosystem of bacteria , fungi , viruses , and other microorganisms that live in and on us .", "The intestines are where most of these organisms reside , and the composition of the intestinal microbiota has a profound effect on immune system function throughout the body .", "In this manusc...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "blood cells", "antimicrobials", "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "pathogens", "drugs", "immunology", "microbiology", "retroviruses", "viruses", "preventive medicine", "pre-exposure prophylaxis", "immunodeficiency viruses", "rna viruses...	Mechanistic framework predicts drug-class specific utility of antiretrovirals for HIV prophylaxis	journal.pcbi.1006740	null	[ [ "Pre-exposure prophylaxis ( PrEP ) to prevent HIV infection ( using drugs which are licensed for its treatment ) has been assessed in people at high risk of sexual transmission .", "Of the available agents , once-daily tenofovir and emtricitabine ( Truvada ) have been extensively studied , and demonstrate...	[ "Currently , there is no effective vaccine to halt HIV transmission .", "However , pre-exposure prophylaxis ( PrEP ) with the drug combination Truvada can substantially decrease HIV transmission in individuals at risk .", "Despite its benefits , Truvada-based PrEP is expensive and needs to be taken once-daily ,...	[ "Pre-exposure prophylaxis ( PrEP ) is a novel , promising strategy to halt HIV transmission .", "PrEP with Truvada can substantially decrease the risk of infection .", "However , individuals often inadequately adhere to the once-daily regimen and the drug is expensive .", "These shortcomings may be overcome b...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "cell walls", "innate immune system", "medicine and health sciences", "immune cells", "immune physiology", "pathology and laboratory medicine", "cytokines", "pathogens", "immunology", "microbiology", "mutation", "fungi", "developmental biology", "model organisms", "molec...	Mnn10 Maintains Pathogenicity in Candida albicans by Extending α-1,6-Mannose Backbone to Evade Host Dectin-1 Mediated Antifungal Immunity	journal.ppat.1005617	null	[ [ "Candida albicans is a common fungal microorganism that colonizes the oral , genital and gastrointestinal surfaces of most healthy individuals .", "The maintenance of colonization is the result of a complex balance between fungal proliferation and host immune recognition .", "Despite host immune defen...	[ "The cell wall is a dynamic structure that is important for the pathogenicity of Candida albicans .", "Mannan , which is located in the outermost layer of the cell wall , has been shown to contribute to the pathogenesis of C . albicans , however , the molecular mechanism by which this occurs remains unclear .", ...	[ "Mannan plays a crucial role in cell wall structure and virulence of the opportunistic pathogen Candida albicans .", "Both the invasive ability of the pathogen and the host defense against the pathogen contribute to the outcome of invasive infection .", "In the present study , we identified a novel α-1 , 6-mann...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "plant science", "plant biology", "plant pathogens", "microbial pathogens", "plant pathology", "biology", "microbiology", "host-pathogen interaction", "pathogenesis" ]	The Ustilago maydis Effector Pep1 Suppresses Plant Immunity by Inhibition of Host Peroxidase Activity	journal.ppat.1002684	null	[ [ "The basidiomycete smut fungus Ustilago maydis establishes a biotrophic interaction with its host plant maize which leads to the formation of plant tumors on all aerial parts of the host plant [1] , [2] .", "After penetration of the leaf surface , pathogenic U . maydis hyphae proliferate inside host cells...	[ "The corn smut Ustilago maydis establishes a biotrophic interaction with its host plant maize .", "This interaction requires efficient suppression of plant immune responses , which is attributed to secreted effector proteins .", "Previously we identified Pep1 ( Protein essential during penetration-1 ) as a secr...	[ "The maize pathogen U . maydis establishes a biotrophic interaction with its host plant and causes the formation of plant tumors .", "The U . maydis infection is initiated by a direct penetration of the plant epidermis and relies on living plant tissue .", "Therefore , suppression of the host immune system is e...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "phosphorylation", "meiosis", "medicine and health sciences", "homologous chromosomes", "chromosome structure and function", "cell cycle and cell division", "cell processes", "meiotic prophase", "surgical and invasive medical procedures", "synapsis", "chromosome biology", "proteins", "surgic...	Reduced dosage of the chromosome axis factor Red1 selectively disrupts the meiotic recombination checkpoint in Saccharomyces cerevisiae	journal.pgen.1006928	null	[ [ "Meiosis is a specialized developmental process , in which a diploid cell undergoes two chromosomal divisions without an intervening S phase to produce haploid gametes for sexual reproduction .", "The reduction in ploidy occurs during meiosis I , when homologous chromosomes are segregated .", "To enab...	[ "Meiotic chromosomes assemble characteristic “axial element” structures that are essential for fertility and provide the chromosomal context for meiotic recombination , synapsis and checkpoint signaling .", "Whether these meiotic processes are equally dependent on axial element integrity has remained unclear .", ...	[ "Meiosis is a specialized cellular division that reduces chromosome copy by half to produce four gametes .", "To ensure proper chromosome segregation , a meiotic cell must induce DNA double strand breaks , repair them with the homologous chromosome , and fully align the homologs .", "These aspects of meiosis ar...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "biotechnology", "animal types", "animal diseases", "medicine and health sciences", "immune physiology", "ruminants", "immunology", "vertebrates", "pets and companion animals", "dogs", "animals", "mammals", "animal models", "animal prion diseases", "model organisms", "experimental orga...	Unraveling the key to the resistance of canids to prion diseases	journal.ppat.1006716	null	[ [ "Prion diseases or transmissible spongiform encephalopathies ( TSEs ) , a group of fatal neurodegenerative disorders , have been described since the XVIIIth century when clinical signs of scrapie in sheep were reported in England [1] .", "Prion disorders are caused by misfolding of a protein , the cellula...	[ "One of the characteristics of prions is their ability to infect some species but not others and prion resistant species have been of special interest because of their potential in deciphering the determinants for susceptibility .", "Previously , we developed different in vitro and in vivo models to assess the su...	[ "Detection of individuals or whole species resistant to any infectious disease is vital to understand the determinants of susceptibility and to develop appropriate therapeutic and preventative strategies .", "Canids have long been considered resistant to prion infection given the absence of clinical disease despi...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "dimers (chemical physics)", "microbial mutation", "medicine and health sciences", "crystal structure", "pathology and laboratory medicine", "intracellular pathogens", "pathogens", "biological cultures", "condensed matter physics", "microbiology", "viral structure", "viruses", "rna viruses",...	HCV NS5A dimer interface residues regulate HCV replication by controlling its self-interaction, hyperphosphorylation, subcellular localization and interaction with cyclophilin A	journal.ppat.1007177	null	[ [ "Hepatitis C virus ( HCV ) is a main causative agent associated with chronic liver diseases including chronic hepatitis , cirrhosis and hepatocellular carcinoma [1 , 2] .", "It is an enveloped , positive-stranded RNA virus belonging to the genus hepacivirus within the flaviviridae family [3] .", "A si...	[ "The HCV NS5A protein plays multiple roles during viral replication , including viral genome replication and virus particle assembly .", "The crystal structures of the NS5A N-terminal domain indicated the potential existence of the NS5A dimers formed via at least two or more distinct dimeric interfaces .", "How...	[ "HCV NS5A is a multifunctional protein involved in both viral RNA replication and infectious virus production , and is a target of one of the most potent antivirals available to date .", "However , the mode of action of NS5A inhibitors is still unclear due to the lack of mechanistic detail regarding NS5A function...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "rna", "micrornas", "virology", "biology and life sciences", "microbiology", "metabolism", "energy metabolism" ]	Kaposi's Sarcoma Herpesvirus MicroRNAs Induce Metabolic Transformation of Infected Cells	journal.ppat.1004400	null	[ [ "Viruses are the etiological agents in approximately 12% of human cancers .", "Most of these cancers can be attributed to infections by human papillomavirus ( HPV ) , hepatitis B virus ( HBV ) , hepatitis C virus ( HCV ) , Epstein-Barr virus ( EBV ) , and Kaposi's sarcoma-associated herpesvirus ( KSHV ) [...	[ "Altered cell metabolism is inherently connected with pathological conditions including cancer and viral infections .", "Kaposi's sarcoma-associated herpesvirus ( KSHV ) is the etiological agent of Kaposi's sarcoma ( KS ) .", "KS tumour cells display features of lymphatic endothelial differentiation and in thei...	[ "Kaposi's sarcoma ( KS ) is the most common cancer in HIV-infected untreated individuals .", "Kaposi's sarcoma-associated herpesvirus ( KSHV ) is the infectious cause of this neoplasm .", "The discovery of KSHV and its oncogenic enigmas has enlightened many fields of tumor biology and viral oncogenesis .", "T...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Spinal Cystic Echinococcosis – A Systematic Analysis and Review of the Literature: Part 1. Epidemiology and Anatomy	journal.pntd.0002450	null	[ [ "Hydatid disease or cystic echinococcosis ( CE ) , caused by the larval stage of the cestode Echinococcus granulosus , is a cosmopolitan parasitic zoonosis occurring on every continent except Antarctica .", "Hydatid ( Greek for ‘watery cyst’ ) disease was already recognized by Hippocrates over 2000 years ...	[ "Bone involvement in human cystic echinococcosis ( CE ) is rare , but affects the spine in approximately 50% of cases .", "Despite significant advances in diagnostic imaging techniques as well as surgical and medical treatment of spinal CE , our basic understanding of the parasite's predilection for the spine rem...	[ "Spinal cystic echinococcosis ( CE ) is a rare but malignant form of a truly neglected tropical disease .", "Despite significant advances in diagnostic imaging techniques as well as surgical and medical treatment of spinal CE , our basic understanding of the parasite's predilection for the spine remains poor at b...	2013
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "applied mathematics", "social sciences", "neuroscience", "simulation and modeling", "algorithms", "cognitive neuroscience", "mathematics", "statistics (mathematics)", "neuroimaging", "research and analysis methods", "statistical distributions", "meta-research article", "imaging techniques",...	Empirical assessment of published effect sizes and power in the recent cognitive neuroscience and psychology literature	journal.pbio.2000797	null	[ [ "Low power and selection biases , questionable research practices , and errors favoring the publication of statistically significant results have been proposed as major contributing factors in the reproducibility crisis that is heavily debated in many scientific fields [1–5] .", "Here , we aimed to get an...	[ "We have empirically assessed the distribution of published effect sizes and estimated power by analyzing 26 , 841 statistical records from 3 , 801 cognitive neuroscience and psychology papers published recently .", "The reported median effect size was D = 0 . 93 ( interquartile range: 0 . 64–1 . 46 ) for nominal...	[ "Biomedical science , psychology , and many other fields may be suffering from a serious replication crisis .", "In order to gain insight into some factors behind this crisis , we have analyzed statistical information extracted from thousands of cognitive neuroscience and psychology research papers .", "We esta...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "public health and epidemiology/global health", "public health and epidemiology/infectious diseases" ]	Where Do We Go from Here? Prevalence of Trachoma Three Years after Stopping Mass Distribution of Antibiotics in the Regions of Kayes and Koulikoro, Mali	journal.pntd.0000734	null	[ [ "Trachoma , a blinding bacterial disease of the conjunctiva , is targeted for elimination as a public health problem by the year 2020 , yet an estimated 8 . 2 million people remain at immediate risk of blindness or visual impairment due to the disease [1] .", "To achieve the elimination target , the World...	[ "A national survey in 1997 demonstrated that trachoma was endemic in Mali .", "Interventions to control trachoma including mass drug administration ( MDA ) with azithromycin were launched in the regions of Kayes and Koulikoro in 2003 .", "MDA was discontinued after three annual rounds in 2006 , and an impact su...	[ "Trachoma , a blinding bacterial disease , is targeted for elimination by 2020 .", "To achieve the elimination target , the World Health Organization ( WHO ) recommends member states implement the SAFE strategy; surgery , mass administration of antibiotics , promotion of hygiene and facial cleanliness and water a...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biotechnology", "computer applications", "medicine and health sciences", "engineering and technology", "computer-aided design", "social sciences", "optimization", "systems science", "mathematics", "alzheimer disease", "bioengineering", "computer and information sciences", "biomaterials", ...	De Novo Design and Experimental Characterization of Ultrashort Self-Associating Peptides	journal.pcbi.1003718	null	[ [ "In nature , proteins and peptides self-assemble and associate to produce a variety of diverse structures such as cellular nanomachines and multimeric structures , including cellular pumps , cytoskeletal filaments , and fibrils [1] .", "These complex biological structures can serve as templates for the de...	[ "Self-association is a common phenomenon in biology and one that can have positive and negative impacts , from the construction of the architectural cytoskeleton of cells to the formation of fibrils in amyloid diseases .", "Understanding the nature and mechanisms of self-association is important for modulating th...	[ "The self-association of peptides and proteins plays an important role in many serious diseases , such as Alzheimer's disease .", "A complete understanding of how peptides and proteins self-associate is important in creating therapeutics for such diseases .", "Additionally , self-associating peptides can be use...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "livestock", "medicine and health sciences", "diagnostic radiology", "pathology and laboratory medicine", "pig models", "immunology", "brain", "vertebrates", "cerebral hemispheres", "animals", "mammals", "left hemisphere", "magnetic resonance imaging", "animal models", "histology", "mo...	Perilesional Inflammation in Neurocysticercosis - Relationship Between Contrast-Enhanced Magnetic Resonance Imaging, Evans Blue Staining and Histopathology in the Pig Model	journal.pntd.0004869	null	[ [ "Neurocysticercosis ( NCC ) , infection of the brain by the larval stage of the parasite Taenia solium , is a common cause of epilepsy in endemic countries [1] .", "Imaging studies are essential to diagnose NCC .", "Magnetic resonance imaging ( MRI ) is more sensitive than computed axial tomography ( ...	[ "Disease manifestations in neurocysticercosis ( NCC ) are frequently due to inflammation of degenerating Taenia solium brain cysts .", "Exacerbated inflammation post anthelmintic treatment is associated with leakage of the blood brain barrier ( BBB ) using Evans blue ( EB ) staining .", "How well EB extravasati...	[ "Neurocysticercosis ( NCC ) is a frequent parasitic infection of the human brain in developing countries .", "The symptomatology of human NCC after antiparasitic treatment is generally related to inflammation .", "The presence and degree of enhancement after intravascular injection of the contrast agent gadolin...	2016
[ "Introduction", "Results", "Discussion", "Material and Methods" ]	[ "biochemistry/molecular evolution", "molecular biology/dna replication", "molecular biology/dna repair" ]	Subtle Alterations in PCNA-Partner Interactions Severely Impair DNA Replication and Repair	journal.pbio.1000507	Dynamic switching of PCNA-partner interactions is essential for normal DNA replication and repair in yeast.	[ [ "Robustness , the ability to maintain performance in the face of environmental and genetic perturbations , is a fundamental trait of biological processes [1]–[5] .", "Accordingly , many design principles ensuring the robustness of biological processes , such as redundancy , modularity , and feedback mecha...	[ "The robustness of complex biological processes in the face of environmental and genetic perturbations is a key biological trait .", "However , while robustness has been extensively studied , little is known regarding the fragility of biological processes .", "Here , we have examined the susceptibility of DNA r...	[ "Many biological processes are mediated by complex protein-protein interaction networks .", "The most highly connected proteins in such networks , termed hub proteins , precisely regulate biological processes by the regulated and sequential binding and releasing of partner proteins .", "In the case of DNA repli...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "invertebrates", "medicine and health sciences", "reproductive system", "rna interference", "animals", "germ cells", "oocytes", "stem cells", "epigenetics", "planarians", "sperm", "genetic interference", "animal cells", "flatworms", "gene expression", "biochemistry", "rna", "ovarie...	Germline Defects Caused by Smed-boule RNA-Interference Reveal That Egg Capsule Deposition Occurs Independently of Fertilization, Ovulation, Mating, or the Presence of Gametes in Planarian Flatworms	journal.pgen.1006030	null	[ [ "The characterization of developmental processes involved in sexual reproduction has important implications towards reproductive medicine , stockbreeding , farming , and for controlling the dissemination of infectious disease .", "Evolutionarily conserved molecular processes involved in metazoan germline ...	[ "Few animals are known to lay eggs in the absence of ovulation or copulation , as it is presumably energetically wasteful and subjected to negative selection .", "Characterization of Smed-boule , a member of the DAZ family of germline RNA-binding proteins , revealed that egg capsule ( or capsule ) production and ...	[ "Our work shows that production and deposition of egg capsules by planarian flatworms does not require fertilization , mating , ovulation , or even the existence of gametes .", "We also uncovered evidence for the existence of gender-specific germline stem cells in Schmidtea mediterranea , a hermaphroditic species...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "viral immune evasion", "immunity", "virology", "innate immunity", "immunology", "biology", "microbiology", "immune response" ]	The Human Adenovirus Type 5 E1B 55 kDa Protein Obstructs Inhibition of Viral Replication by Type I Interferon in Normal Human Cells	journal.ppat.1002853	null	[ [ "A major obstacle to the therapeutic application and efficacy of adenoviral vectors is the induction of powerful innate and pro-inflammatory immune responses following systemic delivery [1]–[4] , independently of viral gene expression [5]–[9] .", "The constellations of chemokines produced in response to a...	[ "Vectors derived from human adenovirus type 5 , which typically lack the E1A and E1B genes , induce robust innate immune responses that limit their therapeutic efficacy .", "We reported previously that the E1B 55 kDa protein inhibits expression of a set of cellular genes that is highly enriched for those associat...	[ "The most frequently used therapeutic vectors for gene transfer or cancer treatment are derived from human adenovirus type 5 ( Ad5 ) .", "We have observed previously that the E1B 55 kDa protein encoded by a gene routinely deleted from these vectors represses expression of numerous cellular genes regulated by inte...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Human Metapneumovirus Is Capable of Entering Cells by Fusion with Endosomal Membranes	journal.ppat.1005303	null	[ [ "Human metapneumovirus ( HMPV ) , first isolated in 2001 [1] , is a leading cause of lower respiratory infection in infants and children worldwide [2–13] .", "Similar to the closely related respiratory syncytial virus ( RSV ) , HMPV causes inflammation , sloughing , and necrosis of the airway epithelium [...	[ "Human metapneumovirus ( HMPV ) , a member of the Paramyxoviridae family , is a leading cause of lower respiratory illness .", "Although receptor binding is thought to initiate fusion at the plasma membrane for paramyxoviruses , the entry mechanism for HMPV is largely uncharacterized .", "Here we sought to dete...	[ "Human metapneumovirus ( HMPV ) is a paramyxovirus that causes severe lower respiratory tract infections .", "HMPV infection is initiated by the viral surface fusion ( F ) glycoprotein .", "HMPV F attaches to cellular receptors , including RGD-binding integrins , and catalyzes virus membrane fusion with cellula...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "heme", "invertebrates", "medicine and health sciences", "body fluids", "condensed matter physics", "parasitic protozoans", "animals", "protozoans", "crystallography", "insect vectors", "zoology", "crystallization", "oxidation-reduction reactions", "infectious diseases", "solid state phy...	Heme crystallization in a Chagas disease vector acts as a redox-protective mechanism to allow insect reproduction and parasite infection	journal.pntd.0006661	null	[ [ "Chagas disease ( CD ) is a chronic and debilitating illness caused by the protozoa Trypanosoma cruzi [1] , afflicting about 6 million people predominantly in Latin America [2] .", "Despite low relative mortality of CD patients , development of chronic manifestations , such as digestive , cardiovascular a...	[ "Heme crystallization as hemozoin represents the dominant mechanism of heme disposal in blood feeding triatomine insect vectors of the Chagas disease .", "The absence of drugs or vaccine for the Chagas disease causative agent , the parasite Trypanosoma cruzi , makes the control of vector population the best avail...	[ "Chagas disease is a fatal illness caused by Trypanosoma cruzi parasites , which are transmitted by blood sucking triatomine insect vectors .", "Although blood is a natural food source for these insects , its digestion releases toxic products , which poses a dietary challenge for both triatomine insects and trypa...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases" ]	Imipramine Is an Orally Active Drug against Both Antimony Sensitive and Resistant Leishmania donovani Clinical Isolates in Experimental Infection	journal.pntd.0001987	null	[ [ "The disease visceral leishmaniasis or Kala-azar is caused by the protozoan parasite Leishmania donovani ( LD ) and is widening its base in different parts of the world [1] , [2] .", "Pentavalent antimonial or SSG , which has long been the first line drug , is no longer recommended for use as high levels ...	[ "In an endeavor to find an orally active and affordable antileishmanial drug , we tested the efficacy of a cationic amphiphilic drug , imipramine , commonly used for the treatment of depression in humans .", "The only available orally active antileishmanial drug is miltefosine with long half life and teratogenic ...	[ "The disease Kala-azar or visceral leishmaniasis is still a big problem in the Indian subcontinent .", "The antimonials were used for the chemotherapy of Kala-azar but with time its efficacy has reduced dramatically .", "The newer version of orally active drug miltefosine has been introduced , but its efficacy ...	2012
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "caenorhabditis", "nervous system", "enzymes", "enzymology", "neuroscience", "animals", "motor neurons", "animal models", "caenorhabditis elegans", "model organisms", "experimental organism systems", "nerve fibers", "research and analysis ...	Flavin monooxygenases regulate Caenorhabditis elegans axon guidance and growth cone protrusion with UNC-6/Netrin signaling and Rac GTPases	journal.pgen.1006998	null	[ [ "The formation of neural circuits during development depends on the guidance of growing axons to their proper synaptic targets .", "This process relies on the growth cone , a dynamic actin based structure present at the tip of a growing axon .", "Growth cones contain a dynamic lamellipodial body ringe...	[ "The guidance cue UNC-6/Netrin regulates both attractive and repulsive axon guidance .", "Our previous work showed that in C . elegans , the attractive UNC-6/Netrin receptor UNC-40/DCC stimulates growth cone protrusion , and that the repulsive receptor , an UNC-5:UNC-40 heterodimer , inhibits growth cone protrusi...	[ "Mechanisms that guide axons to their targets in the developing nervous system have been elucidated , but how these pathways affect behavior of the growth cone of the axon during outgrowth remains poorly understood .", "We previously showed that the guidance cue UNC-6/Netrin and its receptors UNC-40/DCC and UNC-5...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "motor systems", "biology", "neuroscience" ]	Analysis of Accuracy in Pointing with Redundant Hand-held Tools: A Geometric Approach to the Uncontrolled Manifold Method	journal.pcbi.1002978	null	[ [ "Although highly stereotyped , human movements performed with the same intention are never exactly the same , displaying large variability in consecutive trials .", "Rather than just ‘biological noise’ , many studies have pointed out how variability may in fact provide important clues on the underlying ne...	[ "This work introduces a coordinate-independent method to analyse movement variability of tasks performed with hand-held tools , such as a pen or a surgical scalpel .", "We extend the classical uncontrolled manifold ( UCM ) approach by exploiting the geometry of rigid body motions , used to describe tool configura...	[ "Daily motor tasks typically involve more degrees-of-freedom than strictly required .", "For instance , pressing a button in the elevator only requires positioning the fingertip at a three-dimensional location in space .", "However , to move the arm we need to control many more degrees-of-freedom ( at least sev...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genomics", "functional genomics", "biology", "computational biology", "genetics and genomics" ]	Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes	journal.pcbi.1002957	null	[ [ "Defining the role of proteins in pathways is among the key challenges of human genomics .", "Many successful approaches have been developed for prediction of protein function and pathway membership [1]–[6] , however they rely on prior knowledge in the organism of interest to make new predictions ( i . e ...	[ "A key challenge in genetics is identifying the functional roles of genes in pathways .", "Numerous functional genomics techniques ( e . g . machine learning ) that predict protein function have been developed to address this question .", "These methods generally build from existing annotations of genes to path...	[ "Due to technical and ethical challenges many human diseases or biological processes are studied in model organisms .", "Discoveries in these organisms are then transferred back to human or other model organisms .", "Traditional methods for transferring novel gene function annotations have relied on finding gen...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "social sciences", "neuroscience", "simulation and modeling", "human performance", "vision", "eyes", "neuronal tuning", "research and analysis methods", "animal cells", "behavior", "head", "cellular neuroscience", "psychology", "cell biology", "anatomy",...	A Single Mechanism Can Account for Human Perception of Depth in Mixed Correlation Random Dot Stereograms	journal.pcbi.1004906	null	[ [ "Stereoscopic vision is possible because the left and right eyes receive slightly different images of the world .", "This geometric arrangement gives rise to retinal disparity which can be used to extract depth information from a visual scene .", "A key challenge in stereo vision is determining which ...	[ "In order to extract retinal disparity from a visual scene , the brain must match corresponding points in the left and right retinae .", "This computationally demanding task is known as the stereo correspondence problem .", "The initial stage of the solution to the correspondence problem is generally thought to...	[ "Relating neural activity to perception is one of the most challenging tasks in neuroscience .", "Stereopsis—the ability of many animals to see in stereoscopic 3D—is a particularly tractable problem because the computational and geometric challenges faced by the brain are very well understood .", "In essence , ...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "bacteriology", "bacterial physiology", "medical microbiology", "streptococcus", "microbial pathogens", "biology and life sciences", "microbiology", "bacterial pathogens" ]	Interplay of the Serine/Threonine-Kinase StkP and the Paralogs DivIVA and GpsB in Pneumococcal Cell Elongation and Division	journal.pgen.1004275	null	[ [ "Bacterial cell growth and division are intimately linked .", "Complex webs of proteins interacting with each other temporally and spatially control the cellular events leading to the production of two identical daughter cells [1]–[3] .", "Most of the proteins required for cell division and elongation...	[ "Despite years of intensive research , much remains to be discovered to understand the regulatory networks coordinating bacterial cell growth and division .", "The mechanisms by which Streptococcus pneumoniae achieves its characteristic ellipsoid-cell shape remain largely unknown .", "In this study , we analyze...	[ "Over the last decade , bacterial genomics have revealed the presence of eukaryotic-type serine/threonine protein kinases ( STKPs ) in many bacteria .", "However , their role and mode of action is still elusive .", "Recent studies have suggested that STKPs could play an important role in regulating cell divisio...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "test evaluation", "public health and epidemiology", "diagnostic medicine", "epidemiology", "infectious disease epidemiology", "global health", "neglected tropical diseases", "dengue fever", "viral diseases", "dengue" ]	Utility of the Tourniquet Test and the White Blood Cell Count to Differentiate Dengue among Acute Febrile Illnesses in the Emergency Room	journal.pntd.0001400	null	[ [ "Dengue , the disease caused by four related but distinct dengue viruses ( DENV ) , is now considered the most important arthropod-borne disease worldwide .", "It is transmitted through the bite of an infected mosquito , usually Aedes aegypti or Aedes albopictus [1] , and is endemic to tropical and subtro...	[ "Dengue often presents with non-specific clinical signs , and given the current paucity of accurate , rapid diagnostic laboratory tests , identifying easily obtainable bedside markers of dengue remains a priority .", "Previous studies in febrile Asian children have suggested that the combination of a positive tou...	[ "In the Americas , the incidence and severity of dengue cases has increased dramatically in the past 30 years .", "Early diagnosis and initiation of appropriate therapy can substantially reduce dengue morbidity and mortality .", "However the absence of a point-of-care diagnostic test and the non-specific clinic...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/bacterial infections", "microbiology/microbial growth and development" ]	Attachment and Entry of Chlamydia Have Distinct Requirements for Host Protein Disulfide Isomerase	journal.ppat.1000357	null	[ [ "Fundamental to understanding of intracellular bacterial pathogenesis is knowledge of the mechanism of bacterial attachment and subsequent entry into cells .", "There are two main processes by which bacteria stimulate their entry into nonphagocytic cells: by bacterial contact mediated activation of a cell...	[ "Chlamydia is an obligate intracellular pathogen that causes a wide range of diseases in humans .", "Attachment and entry are key processes in infectivity and subsequent pathogenesis of Chlamydia , yet the mechanisms governing these interactions are unknown .", "It was recently shown that a cell line , CHO6 , t...	[ "Chlamydia is a large burden on global health .", "It is the most common cause of infectious blindness , and the CDC ( Centers for Disease Control and Prevention ) estimates that in the United States alone there are more than 2 million people with sexually transmitted Chlamydia infections .", "Chlamydia is an o...	2009
[ "Introduction", "Methods", "Results", "Discussion", "Disclaimer" ]	[ "children", "medicine and health sciences", "pathology and laboratory medicine", "viral transmission and infection", "pathogens", "microbiology", "parasitic diseases", "health care", "diarrhea", "age groups", "signs and symptoms", "gastroenterology and hepatology", "sanitation", "medical r...	Risk factors for childhood enteric infection in urban Maputo, Mozambique: A cross-sectional study	journal.pntd.0006956	null	[ [ "Diarrheal illness is estimated to cause approximately 1 . 7 million deaths annually and result in over 74 million disability-adjusted life years lost [1] , primarily among children in low-and middle-income countries where fecal contamination of the living environment is common .", "Diarrheal diseases are...	[ "Enteric infections are common where public health infrastructure is lacking .", "This study assesses risk factors for a range of enteric infections among children living in low-income , unplanned communities of urban Maputo , Mozambique .", "We conducted a cross-sectional survey in 17 neighborhoods of Maputo t...	[ "Enteric pathogens such as bacteria , protozoa , and viruses can cause diarrhea and other longer-term health problems .", "Poor sanitary conditions , including inadequate sanitation facilities , can lead to contamination of the living environment and higher risk of exposure to and transmission of enteric pathogen...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "nuclear import", "medicine and health sciences", "nervous system", "cell processes", "brain", "vertebrates", "electrophysiology", "mice", "neuroscience", "animals", "mammals", "animal behavior", "zoology", "neuronal dendrites", "animal cells", "behavior", "rodents", "hippocampus",...	A Jacob/Nsmf Gene Knockout Results in Hippocampal Dysplasia and Impaired BDNF Signaling in Dendritogenesis	journal.pgen.1005907	null	[ [ "Jacob is a protein that shuttles to the nucleus in response to activation of synaptic and extrasynaptic GluN2B-containing N-methyl-D-aspartate receptors ( NMDARs ) [1] and that following long-distance transport and nuclear import , encodes and transduces the synaptic and extrasynaptic origin of NMDAR signals...	[ "Jacob , the protein encoded by the Nsmf gene , is involved in synapto-nuclear signaling and docks an N-Methyl-D-Aspartate receptor ( NMDAR ) -derived signalosome to nuclear target sites like the transcription factor cAMP-response-element-binding protein ( CREB ) .", "Several reports indicate that mutations in NS...	[ "Kallmann syndrome ( KS ) is a neurodevelopmental disorder that is characterized by a migration deficit of GnRH neurons that fail to migrate into the hypothalamus during embryonic development .", "The affected patients suffer from idiopathic hypogonadotropic hypogonadism associated with anosmia or hyposmia .", ...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	The Gyc76C Receptor Guanylyl Cyclase and the Foraging cGMP-Dependent Kinase Regulate Extracellular Matrix Organization and BMP Signaling in the Developing Wing of Drosophila melanogaster	journal.pgen.1005576	null	[ [ "The vein cells that develop from the ectodermal epithelia of the Drosophila melanogaster wing are positioned , elaborated and maintained by a series of well-characterized intercellular signaling pathways .", "The wing is easily visualized , and specific mutant vein phenotypes have been linked to changes ...	[ "The developing crossveins of the wing of Drosophila melanogaster are specified by long-range BMP signaling and are especially sensitive to loss of extracellular modulators of BMP signaling such as the Chordin homolog Short gastrulation ( Sog ) .", "However , the role of the extracellular matrix in BMP signaling ...	[ "Signaling between cells regulates many processes , including the choices cells make between different fates during development and regeneration , and misregulation of such signaling underlies many human pathologies .", "To understand how such signals control developmental decisions , it is necessary to elucidate...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "chemical compounds", "cell division analysis", "cell cycle and cell division", "cell processes", "carbohydrates", "organic compounds", "glucose", "dna replication", "bioassays and physiological analysis", "dna", "sequence motif analysis", "research and analysis methods", "sequence analysis"...	Division-induced DNA double strand breaks in the chromosome terminus region of Escherichia coli lacking RecBCD DNA repair enzyme	journal.pgen.1006895	null	[ [ "Most bacteria have a circular chromosome on which replication is initiated at single origin oriC and proceeds bi-directionally on the two replichores until forks meet in the terminus , opposite to oriC .", "The chromosome terminus is a particularly active region where several important processes take pla...	[ "Marker frequency analysis of the Escherichia coli recB mutant chromosome has revealed a deficit of DNA in a specific zone of the terminus , centred on the dif/TerC region .", "Using fluorescence microscopy of a marked chromosomal site , we show that the dif region is lost after replication completion , at the ti...	[ "RecBCD protein complex is an important player of DSB repair in bacteria and bacteria that cannot repair DNA double-stranded breaks ( DSB ) have a low viability .", "Whole genome sequencing analyses showed a deficit in specific sequences of the chromosome terminus region in recB mutant cells , suggesting terminus...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/fungal infections" ]	Fungal Cell Gigantism during Mammalian Infection	journal.ppat.1000945	null	[ [ "The interaction between a microbe and a host involves a complex response by both the pathogen and the infected individual .", "The host has multiple defence mechanisms to avoid infection , damage and disease .", "Microbial pathogens adapt to survive in a host through multiple changes that include sig...	[ "The interaction between fungal pathogens with the host frequently results in morphological changes , such as hyphae formation .", "The encapsulated pathogenic fungus Cryptococcus neoformans is not considered a dimorphic fungus , and is predominantly found in host tissues as round yeast cells .", "However , the...	[ "In this article we describe the formation of giant cells by the human fungal pathogen Cryptococcus neoformans during infection , involving an approximately 900-fold increase in volume compared to that of yeast cells grown in vitro .", "This switch to gigantism is a dramatic transition that is posited to have imp...	2010
[ "Introduction", "Results and discussion", "Materials and methods" ]	[ "heart rate", "myocardial infarction", "stroke", "medicine and health sciences", "cerebrovascular diseases", "drug-drug interactions", "drug research and development", "vascular medicine", "ischemic stroke", "neurology", "tachycardia", "pharmacology", "hypertension", "blood pressure", "d...	Assessment of the cardiovascular adverse effects of drug-drug interactions through a combined analysis of spontaneous reports and predicted drug-target interactions	journal.pcbi.1006851	null	[ [ "Adverse drug effects ( ADEs ) are one of the top 10 causes of death in developed countries , are one of the main reasons for stopping the development of new drug-candidates and are the main reason for drug recalls from the market [1 , 2] .", "Cardiovascular effects are some of the most serious ADEs that ...	[ "Adverse drug effects ( ADEs ) are one of the leading causes of death in developed countries and are the main reason for drug recalls from the market , whereas the ADEs that are associated with action on the cardiovascular system are the most dangerous and widespread .", "The treatment of human diseases often req...	[ "Assessment of adverse drug effects as well as the influence of drug-drug interactions on their manifestation is a nontrivial task that requires numerous experimental and clinical studies .", "We developed a computational approach for the prediction of adverse effects that are induced by drug-drug interactions , ...	2019
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "bacteriology", "medicine and health sciences", "pathology and laboratory medicine", "chemical compounds", "aliphatic amino acids", "molecular probe techniques", "enzymes", "pathogens", "vibrio", "microbiology", "enzymology", "immunoblotting", "organic compounds", "serine proteases", "me...	C-terminal processing of GlyGly-CTERM containing proteins by rhombosortase in Vibrio cholerae	journal.ppat.1007341	null	[ [ "The type II secretion system ( T2SS ) is a multi-protein complex used by many Gram-negative bacteria to secrete extracellular proteins [1–4] .", "Most notably , Vibrio cholerae , the causative agent of cholera , uses the T2SS to secrete cholera toxin [5 , 6] .", "Cholera toxin and other T2SS substrat...	[ "Vibrio cholerae and a subset of other Gram-negative bacteria , including Acinetobacter baumannii , express proteins with a C-terminal tripartite domain called GlyGly-CTERM , which consists of a motif rich in glycines and serines , followed by a hydrophobic region and positively charged residues .", "Here we show...	[ "The type II secretion system ( T2SS ) critically contributes to pathogenesis of many Gram-negative bacteria by transporting toxins and a variety of enzymes including proteases , lipases , nucleases and carbohydrases to the extracellular environment .", "Cholera toxin , the principal virulence factor of Vibrio ch...	2018

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