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headings list	keywords list	title stringlengths 20 281	id stringlengths 20 20	toc stringlengths 57 522 ⌀	sections list	abstract list	summary list	year stringclasses 13 values
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/nosocomial and healthcare-associated infections", "infectious diseases/bacterial infections", "microbiology/cellular microbiology and pathogenesis", "microbiology/medical microbiology", "cell biology/cytoskeleton" ]	Staphylococcus aureus Host Cell Invasion and Virulence in Sepsis Is Facilitated by the Multiple Repeats within FnBPA	journal.ppat.1000964	null	[ [ "Staphylococcus aureus is a major human pathogen and the continuous emergence and spread of antibiotic resistant strains ( e . g . MRSA , VRSA ) mean treatment options are often severely limited [1] , [2] .", "Despite its normal role as a commensal organism living asymptomatically in the nasal cavities of...	[ "Entry of Staphylococcus aureus into the bloodstream can lead to metastatic abscess formation and infective endocarditis .", "Crucial to the development of both these conditions is the interaction of S . aureus with endothelial cells .", "In vivo and in vitro studies have shown that the staphylococcal invasin F...	[ "Staphylococcus aureus is a frequent cause of bacteremia and sepsis .", "Adhesion to and invasion of endothelial cells lining blood vessels by S . aureus can lead to colonization of the heart valves and/or dissemination into surrounding tissues and the establishment of secondary ( metastatic ) infections .", "U...	2010
[ "Introduction", "Model", "Results", "Discussion" ]	[ "action potentials", "medicine and health sciences", "engineering and technology", "signal processing", "applied mathematics", "membrane potential", "random variables", "electrophysiology", "neuroscience", "covariance", "motor neurons", "simulation and modeling", "algorithms", "mathematics...	Inferring oscillatory modulation in neural spike trains	journal.pcbi.1005596	null	[ [ "Neural oscillations have generated considerable interest for their roles in cognition and as indicators for disease [1–14] .", "Electroencephalograms ( EEGs ) and local field potential ( LFPs ) recordings have revealed transient oscillations in many cortical and subcortical structures , to which neurons ...	[ "Oscillations are observed at various frequency bands in continuous-valued neural recordings like the electroencephalogram ( EEG ) and local field potential ( LFP ) in bulk brain matter , and analysis of spike-field coherence reveals that spiking of single neurons often occurs at certain phases of the global oscill...	[ "Oscillatory modulation of neural activity in the brain is widely observed under conditions associated with a variety of cognitive tasks and mental states .", "Within individual neurons , oscillations may be uncovered in the moment-to-moment variation in neural firing rate .", "This , however , is often challen...	2017
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "virology/virus evolution and symbiosis", "genetics and genomics/gene expression", "infectious diseases/neglected tropical diseases", "biotechnology/applied microbiology", "virology/animal models of infection", "public health and epidemiology/infectious diseases", "microbiology/applied microbiology", ...	Viral Paratransgenesis in the Malaria Vector Anopheles gambiae	journal.ppat.1000135	null	[ [ "Transmitted by Anopheles mosquitoes , malaria is a disease responsible for inordinate mortality , morbidity and economic loss worldwide [1] .", "Failure of traditional control methodologies has stimulated efforts to develop novel genetic strategies to control the mosquito vectors , particularly An .", ...	[ "Paratransgenesis , the genetic manipulation of insect symbiotic microorganisms , is being considered as a potential method to control vector-borne diseases such as malaria .", "The feasibility of paratransgenic malaria control has been hampered by the lack of candidate symbiotic microorganisms for the major vect...	[ "Paratransgenesis , the genetic manipulation of mosquito symbiotic microorganisms , is being considered as a potential strategy to control malaria .", "Microorganisms associated with Anopheles mosquitoes could be manipulated to alter the mosquito's ability to become infected with and transmit the malaria parasite...	2008
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "infectious diseases/protozoal infections", "infectious diseases/neglected tropical diseases", "immunology/immunity to infections", "immunology/innate immunity" ]	Cognitive Dysfunction Is Sustained after Rescue Therapy in Experimental Cerebral Malaria, and Is Reduced by Additive Antioxidant Therapy	journal.ppat.1000963	null	[ [ "Malaria , together with tuberculosis and human immunodeficiency virus/acquired immunodeficiency syndrome ( HIV/AIDS ) , is one of three most important infectious diseases worldwide , with devastating morbidity and mortality and deleterious economic consequences [1] .", "More than 400 million people suffe...	[ "Neurological impairments are frequently detected in children surviving cerebral malaria ( CM ) , the most severe neurological complication of infection with Plasmodium falciparum .", "The pathophysiology and therapy of long lasting cognitive deficits in malaria patients after treatment of the parasitic disease i...	[ "Cerebral malaria ( CM ) is a deadly consequence of Plasmodium falciparum infection .", "Severe neurologic deficits are frequent during CM .", "Although most resolve within 6 months , several retrospective studies have described high frequencies of long-lasting cognitive impairment after an episode of CM .", ...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "mus (mouse)", "genetics and genomics" ]	Mouse Pachytene Checkpoint 2 (Trip13) Is Required for Completing Meiotic Recombination but Not Synapsis	journal.pgen.0030130	null	[ [ "The genesis of gametes containing an intact , haploid genome is critical for the prevention of birth defects , and is highly dependent upon the fidelity of chromosome dynamics before the first meiotic division .", "Homologous chromosomes must pair , synapse , undergo recombination , and segregate properl...	[ "In mammalian meiosis , homologous chromosome synapsis is coupled with recombination .", "As in most eukaryotes , mammalian meiocytes have checkpoints that monitor the fidelity of these processes .", "We report that the mouse ortholog ( Trip13 ) of pachytene checkpoint 2 ( PCH2 ) , an essential component of the...	[ "It is critical that the chromosomes carried by sperm and eggs contain faithful representations of the genome of the individual that produced them .", "During the process of meiosis , the maternal and paternal copies of each chromosome “synapse” with each other ( become tightly associated ) , exchange genetic mat...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics", "biology", "microbiology", "molecular cell biology", "genetics and genomics", "toxicology" ]	Alkylation Base Damage Is Converted into Repairable Double-Strand Breaks and Complex Intermediates in G2 Cells Lacking AP Endonuclease	journal.pgen.1002059	null	[ [ "DNA double-strand breaks ( DSBs ) are important sources of genome instability , giving rise to chromosomal aberrations and severe biological consequences including tumorigenesis and cell death [1] , [2] .", "We and others also showed that regions adjacent to DSBs are prone to mutagenesis through a variet...	[ "DNA double-strand breaks ( DSBs ) are potent sources of genome instability .", "While there is considerable genetic and molecular information about the disposition of direct DSBs and breaks that arise during replication , relatively little is known about DSBs derived during processing of single-strand lesions , ...	[ "DNA double-strand breaks ( DSBs ) are an important source of genome instability that can lead to severe biological consequences including tumorigenesis and cell death .", "Although much is known about DSBs induced directly by ionizing radiation and radiomimetic cancer drugs , there is a relative dearth of inform...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "pathology/pathophysiology", "neurological disorders", "genetics and genomics/disease models" ]	Pathogenic VCP/TER94 Alleles Are Dominant Actives and Contribute to Neurodegeneration by Altering Cellular ATP Level in a Drosophila IBMPFD Model	journal.pgen.1001288	null	[ [ "IBMPFD is a progressive autosomal dominant disorder , characterized by the adult onset of muscle degeneration , abnormal bone metabolism , and drastic behavior changes .", "This disease has been linked to mutations in VCP ( known as p97 in mouse or CDC48 in yeast ) , a hexameric AAA ( ATPase associated w...	[ "Inclusion body myopathy with Paget's disease of bone and frontotemporal dementia ( IBMPFD ) is caused by mutations in Valosin-containing protein ( VCP ) , a hexameric AAA ATPase that participates in a variety of cellular processes such as protein degradation , organelle biogenesis , and cell-cycle regulation .", ...	[ "Inclusion body myopathy with Paget's disease of bone and frontotemporal dementia ( IBMPFD ) is a progressive autosomal dominant disease , characterized by the adult onset of muscle degeneration , abnormal bone metabolism , and drastic behavior changes .", "IBMPFD is caused by specific mutations in the highly con...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular biology/recombination", "molecular biology/chromosome structure", "genetics and genomics/chromosome biology", "genetics and genomics/disease models", "molecular biology/transcription elongation", "genetics and genomics/cancer genetics", "molecular biology/chromatin structure", "molecular bi...	Spt2p Defines a New Transcription-Dependent Gross Chromosomal Rearrangement Pathway	journal.pgen.1000290	null	[ [ "Maintaining genomic stability is crucial for cell survival and normal cell growth .", "Different genetic disorders , including cancers , display different forms of genomic instabilities .", "There is growing evidence supporting the hypothesis that gross chromosomal rearrangements ( GCRs ) found in di...	[ "Large numbers of gross chromosomal rearrangements ( GCRs ) are frequently observed in many cancers .", "High mobility group 1 ( HMG1 ) protein is a non-histone DNA-binding protein and is highly expressed in different types of tumors .", "The high expression of HMG1 could alter DNA structure resulting in GCRs ....	[ "Transmitting genetic information without creating deleterious genetic alternations is one of the cell's most important tasks .", "When cells cannot repair DNA damage properly , it leads to genomic instability and results in genetic disorders , including cancer .", "Many studies , including ours , have started ...	2008
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing techniques", "organoids", "medicine and health sciences", "breast tumors", "reproductive system", "biological cultures", "dna-binding proteins", "cancers and neoplasms", "animal models", "oncology", "model organisms", "experimental organism systems", "epigenetics", "molecular b...	Canonical PRC2 function is essential for mammary gland development and affects chromatin compaction in mammary organoids	journal.pbio.2004986	null	[ [ "A central question in biology is how different cell types maintain distinct cell fates despite containing the same genetic material .", "Organization of DNA into open or closed chromatin states by posttranslational modifications ( PTMs ) of histones has emerged as a critical mechanism underpinning cell d...	[ "Distinct transcriptional states are maintained through organization of chromatin , resulting from the sum of numerous repressive and active histone modifications , into tightly packaged heterochromatin versus more accessible euchromatin .", "Polycomb repressive complex 2 ( PRC2 ) is the main mammalian complex re...	[ "The formation of mammary glands requires the tight regulation of many genes that govern cell fate decisions in the cells that form them .", "However , most of these genes remain undefined .", "The Polycomb repressive complex 2 ( PRC2 ) has a role in gene silencing , and it is comprised of several subunits , wh...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "quantitative trait loci", "model organisms", "dna recombination", "dna", "mammalian genomics", "homologous recombination", "inbred strains", "research and analysis methods", "chromosome biology", "genetic loci", "animal genomics", "biochemistry", "cell biology", "nucleic acids", "geneti...	Hybrid Sterility Locus on Chromosome X Controls Meiotic Recombination Rate in Mouse	journal.pgen.1005906	null	[ [ "Meiotic recombination of homologous chromosomes enhances genetic diversity of species and safeguards proper segregation of chromosomes into gametes .", "In the mouse the process begins at the leptotene stage of the first meiotic prophase with chromatin modification by PRDM9-directed trimethylation at lys...	[ "Meiotic recombination safeguards proper segregation of homologous chromosomes into gametes , affects genetic variation within species , and contributes to meiotic chromosome recognition , pairing and synapsis .", "The Prdm9 gene has a dual role , it controls meiotic recombination by determining the genomic posit...	[ "During differentiation of germ cells into gametes , a maternal and a paternal copy of each chromosome have to find each other , pair , and synapse in order to ensure proper chromosome segregation into the gametes .", "Because of the unique ability to identify homologous DNA sequences between homologous chromosom...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Branched-Chain Aminotransferases Control TORC1 Signaling in Saccharomyces cerevisiae	journal.pgen.1005714	null	[ [ "The Target of Rapamycin Complex 1 ( TORC1 ) is functionally and structurally conserved throughout eukaryotes and senses and responds to nutrients to promote cell growth and inhibit catabolic processes such as autophagy .", "Amino acids , particularly the branched-chain amino acid leucine , control TORC1 ...	[ "The conserved target of rapamycin complex 1 ( TORC1 ) integrates nutrient signals to orchestrate cell growth and proliferation .", "Leucine availability is conveyed to control TORC1 activity via the leu-tRNA synthetase/EGOC-GTPase module in yeast and mammals , but the mechanisms sensing leucine remain only parti...	[ "In all organisms from yeasts to mammals the target of rapamycin TORC1 pathway controls growth in response to nutrients such as leucine , but the leucine sensing mechanisms are only partially characterized .", "We show that both leucine and its α-ketoacid metabolite , α-ketoisocaproate , are similarly capable of ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "bacteriology", "gram positive bacteria", "bacterial diseases", "infectious diseases", "innate immune system", "medicine and health sciences", "pathology and laboratory medicine", "immunity", "medical microbiology", "host-pathogen interactions", "streptococcus", "microbial pathogens", "biolo...	TLR2 Signaling Decreases Transmission of Streptococcus pneumoniae by Limiting Bacterial Shedding in an Infant Mouse Influenza A Co-infection Model	journal.ppat.1004339	null	[ [ "The bacterial pathogen Streptococcus pneumoniae ( the pneumococcus ) robustly colonizes the upper respiratory tract of humans and is commonly carried asymptomatically .", "Colonization rates are highest in early childhood , where they can exceed 80% [1]; in crowded environments such as daycare centers [2...	[ "While the importance of transmission of pathogens is widely accepted , there is currently little mechanistic understanding of this process .", "Nasal carriage of Streptococcus pneumoniae ( the pneumococcus ) is common in humans , especially in early childhood , and is a prerequisite for the development of diseas...	[ "In this study , we sought to identify factors contributing to the transmission of the bacterial pathogen Streptococcus pneumoniae ( the pneumococcus ) , a major cause of otitis media , pneumonia , and septicemia .", "Often found as a co-infection with other bacterial and viral pathogens , the pneumococcus is com...	2014
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "genome-wide association studies", "medicine", "genome analysis tools", "genetic polymorphism", "epidemiology", "genetics", "population genetics", "biology", "genomics", "evolutionary biology", "genetic epidemiology" ]	High Trans-ethnic Replicability of GWAS Results Implies Common Causal Variants	journal.pgen.1003566	null	[ [ "Genome-wide association studies ( GWAS ) have detected hundreds of risk alleles [1] , generating novel biological knowledge and widening the range of diagnostic and treatment tools [2] .", "However , the reported effect sizes of these variants are small and their impact in individual risk prediction rema...	[ "Genome-wide association studies ( GWAS ) have detected many disease associations .", "However , the reported variants tend to explain small fractions of risk , and there are doubts about issues such as the portability of findings over different ethnic groups or the relative roles of rare versus common variants i...	[ "Describing and identifying the genetic variants that increase risk for complex diseases remains a central focus of human genetics and is fundamental for the emergent field of personalized medicine .", "Over the last six years , GWAS have revolutionized the field , discovering hundreds of disease loci .", "Howe...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "ophthalmology", "medicine", "public health", "trachoma" ]	Intestinal Parasite Prevalence in an Area of Ethiopia after Implementing the SAFE Strategy, Enhanced Outreach Services, and Health Extension Program	journal.pntd.0002223	null	[ [ "An integrated strategy of surgery , antibiotics , facial cleanliness , and environmental improvement – the SAFE strategy in short – is recommended to eliminate blinding trachoma in endemic countries by the year 2020 [1] .", "The F and E components aim to reduce the transmission of Chlamydia trachomatis v...	[ "The SAFE strategy aims to reduce transmission of Chlamydia trachomatis through antibiotics , improved hygiene , and sanitation .", "We integrated assessment of intestinal parasites into large-scale trachoma impact surveys to determine whether documented environmental improvements promoted by a trachoma program h...	[ "Part of the SAFE strategy ( surgery , antibiotics , facial cleanliness , and environmental improvement ) to eliminate blinding trachoma involves improving access to , and use of , water and sanitation .", "We combined the assessment of parasitic worm and intestinal protozoa infections with surveys of trachoma in...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "body weight", "medicine and health sciences", "cell differentiation", "developmental biology", "adipocytes", "physiological parameters", "connective tissue cells", "obesity", "bioenergetics", "adipocyte differentiation", "lipids", "animal cells", "fats", "gene expression", "zinc", "co...	Zinc transporter ZIP13 suppresses beige adipocyte biogenesis and energy expenditure by regulating C/EBP-β expression	journal.pgen.1006950	null	[ [ "Obesity and its associated metabolic diseases are caused by a long-term imbalance between energy intake and energy expenditure .", "Adipose tissue , a major factor in controlling the balance of energy , is composed of white and brown adipocytes , which have two distinct functions: white adipocytes store ...	[ "Given the relevance of beige adipocytes in adult humans , a better understanding of the molecular circuits involved in beige adipocyte biogenesis has provided new insight into human brown adipocyte biology .", "Genetic mutations in SLC39A13/ZIP13 , a member of zinc transporter family , are known to reduce adipos...	[ "Inducible brown fat-like cells , named beige adipocytes have recently been a topic of great interest , mainly because they are induced in response to external cues , and are closely associated with adult human brown adipocyte .", "Therefore , the identification of selective molecular circuits involved in beige a...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Parallel Evolution of Chordate Cis-Regulatory Code for Development	journal.pgen.1003904	null	[ [ "Gene regulation is facilitated by the binding of transcription factors to specific sites in genomic DNA .", "Consequently , accurate control of gene expression in any cell is largely influenced by two variables; the presence of the transcription factor proteins themselves and accessibility to regulatory ...	[ "Urochordates are the closest relatives of vertebrates and at the larval stage , possess a characteristic bilateral chordate body plan .", "In vertebrates , the genes that orchestrate embryonic patterning are in part regulated by highly conserved non-coding elements ( CNEs ) , yet these elements have not been ide...	[ "Vertebrates share many aspects of early development with our closest chordate ancestors , the tunicates .", "However , whilst the repertoire of genes that orchestrate development is essentially the same in the two lineages , the genomic code that regulates these genes appears to be very different , even though i...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "dermatology/pediatric skin diseases, including genetic diseases", "genetics and genomics/functional genomics", "genetics and genomics/disease models", "genetics and genomics/genetics of disease", "cardiovascular disorders/coronary artery disease" ]	A Mouse Model of Harlequin Ichthyosis Delineates a Key Role for Abca12 in Lipid Homeostasis	journal.pgen.1000192	null	[ [ "Harlequin ichthyosis ( HI , OMIM 242500 ) is a rare and devastating congenital disorder characterised by premature delivery and thick , hyperkeratotic , ‘armour’-like skin plaques .", "This immobile skin or ‘collodion membrane’ constricts the embryo causing odema , limb contractures and eversion of the e...	[ "Harlequin Ichthyosis ( HI ) is a severe and often lethal hyperkeratotic skin disease caused by mutations in the ABCA12 transport protein .", "In keratinocytes , ABCA12 is thought to regulate the transfer of lipids into small intracellular trafficking vesicles known as lamellar bodies .", "However , the nature ...	[ "Harlequin Ichthyosis is a severe inherited disease in which the skin develops as thick armour-like plates .", "While many HI patients die at birth , those who survive are subject to dehydration and infection .", "The disease is caused by defects in a protein called ABCA12 , which is thought to function by tran...	2008
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "recreation", "markov models", "applied mathematics", "sociology", "social sciences", "simulation and modeling", "algorithms", "evolutionary computation", "social systems", "probability distribution", "mathematics", "animal behavior", "zoology", "research and analysis methods", "imitatio...	Social Norms of Cooperation in Small-Scale Societies	journal.pcbi.1004709	null	[ [ "Indirect Reciprocity ( IR ) , which involves reputation and status [1] , constitutes , perhaps , the most elaborated and cognitively demanding mechanism of cooperation discovered so-far [2] .", "Unlike other mechanisms of cooperation , IR has been heralded as providing the biological basis of our moralit...	[ "Indirect reciprocity , besides providing a convenient framework to address the evolution of moral systems , offers a simple and plausible explanation for the prevalence of cooperation among unrelated individuals .", "By helping someone , an individual may increase her/his reputation , which may change the pre-di...	[ "The prevalence of cooperation among human societies is a puzzle that has caught the eye of researchers from multiple fields .", "Why is that people are selfless and often incur costs to aid others ?", "Reputations are intimately linked with the answer to this question , and so are the social norms that dictate...	2016
[ "Introduction", "Results/Discussion", "Methods" ]	[ "biophysics/theory and simulation", "cell biology/cytoskeleton" ]	Computational Analysis of Viscoelastic Properties of Crosslinked Actin Networks	journal.pcbi.1000439	null	[ [ "Actin is the most abundant intracellular protein in eukaryotic cells and plays an important role in a wide range of biological and mechanical phenomena [1] .", "Monomeric actin ( G-actin ) self-assembles to a filamentous form , F-actin , which is crosslinked into the actin cytoskeleton by various actin c...	[ "Mechanical force plays an important role in the physiology of eukaryotic cells whose dominant structural constituent is the actin cytoskeleton composed mainly of actin and actin crosslinking proteins ( ACPs ) .", "Thus , knowledge of rheological properties of actin networks is crucial for understanding the mecha...	[ "The actin cytoskeleton provides structural integrity to a cell , is highly dynamic , and plays a central role in a wide variety of phenomena such as migration and the sensation of external forces .", "For years , researchers have studied the mechanics of the cytoskeleton by creating actin gels in the laboratory ...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cognitive neuroscience", "decision making", "computational neuroscience", "biology", "neuroscience" ]	Evidence for Model-based Computations in the Human Amygdala during Pavlovian Conditioning	journal.pcbi.1002918	null	[ [ "Neural computations mediating instrumental conditioning are suggested to depend on two distinct mechanisms: a model-based reinforcement learning system , in which the value of actions are computed on the basis of a rich knowledge of the states of the world and the nature of the transitions between states , a...	[ "Contemporary computational accounts of instrumental conditioning have emphasized a role for a model-based system in which values are computed with reference to a rich model of the structure of the world , and a model-free system in which values are updated without encoding such structure .", "Much less studied i...	[ "A hot topic in the neurobiology of learning is the idea that there may be two distinct mechanisms for learning in the brain: a model-based learning system in which predictions are made with respect to a rich internal model of the learning environment , versus a “model-free” mechanism in which trial-and-error learn...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "virology", "biology", "microbiology", "viral diseases" ]	The Viral Chemokine MCK-2 of Murine Cytomegalovirus Promotes Infection as Part of a gH/gL/MCK-2 Complex	journal.ppat.1003493	null	[ [ "Herpesviruses enter their host cells either by fusion of the viral envelope with the plasma membrane or with membranes of endocytotic vesicles .", "The fusion process is promoted by a concerted action of the conserved viral glycoproteins gB , gH , and gL [1] of which gH and gL consistently form a tight h...	[ "Human cytomegalovirus ( HCMV ) forms two gH/gL glycoprotein complexes , gH/gL/gO and gH/gL/pUL ( 128 , 130 , 131A ) , which determine the tropism , the entry pathways and the mode of spread of the virus .", "For murine cytomegalovirus ( MCMV ) , which serves as a model for HCMV , a gH/gL/gO complex functionally ...	[ "Several human herpesviruses form alternative gH/gL complexes which determine the tropism for different cell types .", "For murine cytomegalovirus ( MCMV ) , a gH/gL/gO complex has recently been characterized .", "Here , we present the identification and characterization of an alternative gH/gL/MCK-2 complex wh...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "fluorescence imaging", "medicine and health sciences", "fish", "fluorescence", "neural networks", "brain", "vertebrates", "neuroscience", "animals", "electromagnetic radiation", "epileptic seizures", "animal models", "osteichthyes", "model organisms", "hindbrain", "experimental organi...	Calcium imaging and dynamic causal modelling reveal brain-wide changes in effective connectivity and synaptic dynamics during epileptic seizures	journal.pcbi.1006375	null	[ [ "Epileptic seizures are transient disturbances in the brain’s electrical activity causing changes of patients’ behaviours or perceptions .", "Seizures have different causes , from gene mutations to acquired brain injuries [1] .", "The effects of particular pathologies on neuronal dynamics have been st...	[ "Pathophysiological explanations of epilepsy typically focus on either the micro/mesoscale ( e . g . excitation-inhibition imbalance ) , or on the macroscale ( e . g . network architecture ) .", "Linking abnormalities across spatial scales remains difficult , partly because of technical limitations in measuring n...	[ "We show that Bayesian inversion techniques used in electrophysiological data are applicable to calcium imaging data derived from light sheet microscopy in the zebrafish brain .", "Using this approach we can now make inference on the underlying large-scale connectivity changes underlying pathological states such ...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "theoretical biology", "ecology", "biology", "population biology" ]	Strategies for Introducing Wolbachia to Reduce Transmission of Mosquito-Borne Diseases	journal.pntd.0001024	null	[ [ "Mosquito-borne parasites and viruses cause some of the world's most important diseases , disproportionately affecting poor communities and representing a major public health challenge .", "Biological control techniques aimed at suppressing mosquito populations or reducing their capacity to transmit disea...	[ "Certain strains of the endosymbiont Wolbachia have the potential to lower the vectorial capacity of mosquito populations and assist in controlling a number of mosquito-borne diseases .", "An important consideration when introducing Wolbachia-carrying mosquitoes into natural populations is the minimisation of any...	[ "Wolbachia are symbiotic bacteria that are found in many insect species .", "Recent laboratory studies show that certain strains of Wolbachia can reduce the capacity of mosquito species to transmit diseases such as dengue fever and malaria , either by directly inhibiting the pathogen or by shortening lifespan .",...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "chemical compounds", "applied mathematics", "metabolic networks", "enzymology", "carbohydrates", "organic compounds", "simulation and modeling", "xylose", "algorithms", "physiological parameters", "metabolites", "mathematics", "network analysis", "enzyme ...	Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties	journal.pcbi.1007242	null	[ [ "Kinetic models are one of the cornerstones of rational metabolic engineering as they allow us to capture the dynamic behavior of metabolism and to predict dynamic responses of living organisms to genetic and environmental changes .", "With reliable kinetic models , metabolic engineering and synthetic bio...	[ "A persistent obstacle for constructing kinetic models of metabolism is uncertainty in the kinetic properties of enzymes .", "Currently , available methods for building kinetic models can cope indirectly with uncertainties by integrating data from different biological levels and origins into models .", "In this...	[ "Kinetic models are the most promising tool for understanding the complex dynamic behavior of living cells .", "The primary goal of kinetic models is to capture the properties of the metabolic networks as a whole , and thus we need large-scale models for dependable in silico analyses of metabolism .", "However ...	2019
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "diagnostic radiology", "statistics", "prefrontal cortex", "brain", "social sciences", "neuroscience", "magnetic resonance imaging", "analysis of variance", "cognitive psychology", "mathematics", "computational neuroscience", "neuroimaging", "coding mechanis...	Frontostriatal pathways gate processing of behaviorally relevant reward dimensions	journal.pbio.2005722	null	[ [ "Reward is central for goal-directed behavior .", "However , reward is not a unitary concept but characterized by multiple dimensions .", "Activity in reward-processing regions such as the ventral striatum ( VS ) correlates with various reward dimensions , including gains and losses [1] , pleasantness...	[ "The value of rewards arises from multiple hedonic and motivational dimensions .", "Reward-encoding brain regions such as the ventral striatum ( VS ) are known to process these dimensions .", "However , the mechanism whereby distinct reward dimensions are selected for neural processing and guiding behavior rema...	[ "People and animals typically both want and like rewards .", "Here , we show that these two dimensions of value can be dissociated at both the behavioral and the neural level .", "In keeping with rodent findings , our human neuroimaging data indicate that the ventral striatum—a part of the reward system in the ...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "oncology", "viruses", "biochemistry", "infectious diseases", "cell biology", "homo (human)" ]	Viral Oncogene–Induced DNA Damage Response Is Activated in Kaposi Sarcoma Tumorigenesis	journal.ppat.0030140	null	[ [ "Recent findings suggest that DNA damage checkpoints become activated in early stages of human tumorigenesis , leading to growth arrest or apoptosis and thereby hindering tumor progression .", "Likewise , very recent reports have indicated that oncogene-induced senescence triggered by DNA replication stre...	[ "Kaposi sarcoma is a tumor consisting of Kaposi sarcoma herpesvirus ( KSHV ) –infected tumor cells that express endothelial cell ( EC ) markers and viral genes like v-cyclin , vFLIP , and LANA .", "Despite a strong link between KSHV infection and certain neoplasms , de novo virus infection of human primary cells ...	[ "Recent findings have indicated that DNA hyper-replication triggered by oncogenes can induce cellular senescence , which together with the oncogene-induced DNA damage checkpoint confers a barrier to tumorigenesis .", "Kaposi sarcoma herpesvirus ( KSHV ) can infect human dermal microvascular endothelial cells ( EC...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "bacterial diseases", "infectious diseases" ]	Vibrio parahaemolyticus Effector Proteins Suppress Inflammasome Activation by Interfering with Host Autophagy Signaling	journal.ppat.1003142	null	[ [ "The innate immune responses play important roles in host defense against the infection by microbial pathogens .", "Several nucleotide-binding , oligomerization domain ( NOD ) leucine-rich repeat proteins ( NLRs ) and PYHIN proteins , such as NLRP1 , NLRP3 , NLRC4 , AIM2 , and IFI16 , form inflammasomes: ...	[ "Bacterial pathogens utilize pore-forming toxins or sophisticated secretion systems to establish infection in hosts .", "Recognition of these toxins or secretion system by nucleotide-binding oligomerization domain leucine-rich repeat proteins ( NLRs ) triggers the assembly of inflammasomes , the multiprotein comp...	[ "V . parahaemolyticus is Gram-negative pathogen that causes a food poisoning in human .", "To date , a number of bacterial factors that play a role in V . parahaemolyticus virulence have been characterized , yet little is known about the host factors contributing to the disease process and susceptibility to these...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Novel Staphylococcal Glycosyltransferases SdgA and SdgB Mediate Immunogenicity and Protection of Virulence-Associated Cell Wall Proteins	journal.ppat.1003653	null	[ [ "Staphylococcus aureus and S . epidermidis are successful human commensals that primarily colonize the nares and skin .", "S . aureus can also invade a variety of tissues , leading to life-threatening infections .", "Recently emerged strains of S . aureus show increased virulence and enhanced ability ...	[ "Infection of host tissues by Staphylococcus aureus and S . epidermidis requires an unusual family of staphylococcal adhesive proteins that contain long stretches of serine-aspartate dipeptide-repeats ( SDR ) .", "The prototype member of this family is clumping factor A ( ClfA ) , a key virulence factor that medi...	[ "Staphylococcus aureus and S . epidermidis are major bacterial pathogens that can cause life-threatening human diseases .", "Following entry into the circulation , S . aureus can infect virtually any organ .", "However , it must first counter antibacterial mechanisms of the innate immune system , including thos...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "urology", "public health and epidemiology", "bladder and ureteric disorders", "infectious disease epidemiology", "microbiology", "host-pathogen interaction", "parasitic diseases", "liver diseases", "gastroenterology and hepatology", "neglected tropical diseases", "portal hypertens...	Bladder Morbidity and Hepatic Fibrosis in Mixed Schistosoma haematobium and S. mansoni Infections: A Population-Wide Study in Northern Senegal	journal.pntd.0001829	null	[ [ "Worldwide more than 207 million people are infected with Schistosoma , 85% of whom live in Africa [1] .", "Due to the large overlap in Schistosoma haematobium- and S . mansoni-endemic areas [2]–[4] many people are at risk of co-infection .", "Yet , little is known about mixed Schistosoma infections a...	[ "The global distribution map of schistosomiasis shows a large overlap of Schistosoma haematobium- and S . mansoni-endemic areas in Africa .", "Yet , little is known about the consequences of mixed Schistosoma infections for the human host .", "A recent study in two neighboring co-endemic communities in Senegal ...	[ "In the developing world , over 207 million people are infected with parasitic Schistosoma worms .", "Schistosoma haematobium and S . mansoni are the most abundant species in Africa and many people carry both .", "Yet , little is known about the consequences of such mixed infections .", "In general , S . haem...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "drosophila", "immunology" ]	Down-Regulation of NF-κB Target Genes by the AP-1 and STAT Complex during the Innate Immune Response in Drosophila	journal.pbio.0050238	After a role in initiating an NF-κB-mediated innate immune response to microbial challenge, AP-1 and STAT act to form part of a repressosome to down-regulate the transcription of antimicrobial peptides and thus to resolve the immune response.	[ [ "The innate immune response triggered by pathogen infection activates signal transduction pathways and elicits diverse humoral and cellular responses [1 , 2] .", "This response requires the activation of several transcription factors to remodel the gene expression pattern of cells [3] .", "NF-κB plays...	[ "The activation of several transcription factors is required for the elimination of infectious pathogens via the innate immune response .", "The transcription factors NF-κB , AP-1 , and STAT play major roles in the synthesis of immune effector molecules during innate immune responses .", "However , the fact tha...	[ "The immune response is designed to target foreign infectious elements , not self , but it can become destructive when it fails to discriminate self from nonself .", "Therefore , it is important to restrain the magnitude and duration of the immune response by several mechanisms including receptor down-regulation ...	2007
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biophysics", "biophysics/experimental biophysical methods", "biophysics/structural genomics", "biophysics/membrane proteins and energy transduction" ]	Structure and Inhibition of the SARS Coronavirus Envelope Protein Ion Channel	journal.ppat.1000511	null	[ [ "Coronaviruses ( family Coronaviridae , genus Coronavirus [1] ) are enveloped viruses that cause common colds in humans and a variety of lethal diseases in birds and mammals [2]–[4] .", "The virus species in the genus Coronavirus have been organized into 3 groups , using genetic and antigenic criteria [5]...	[ "The envelope ( E ) protein from coronaviruses is a small polypeptide that contains at least one α-helical transmembrane domain .", "Absence , or inactivation , of E protein results in attenuated viruses , due to alterations in either virion morphology or tropism .", "Apart from its morphogenetic properties , p...	[ "Coronaviruses are viral pathogens that cause a variety of lethal diseases in birds and mammals , and common colds in humans .", "In 2003 , however , an animal coronavirus was able to infect humans and produced severe acute respiratory syndrome ( SARS ) , causing a near pandemic .", "Such events are likely to r...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "bacterial diseases", "infectious diseases" ]	Dual Pili Post-translational Modifications Synergize to Mediate Meningococcal Adherence to Platelet Activating Factor Receptor on Human Airway Cells	journal.ppat.1003377	null	[ [ "Type IV fimbriae , or pili , are long filamentous structures that extend from the bacterial surface and primarily consist of the monomer pilin protein [1] .", "Pili are shown to play a major role in promoting colonization of the mucosal epithelium by several human pathogens and , thus , are generally con...	[ "Pili of pathogenic Neisseria are major virulence factors associated with adhesion , twitching motility , auto-aggregation , and DNA transformation .", "Pili of N . meningitidis are subject to several different post-translational modifications .", "Among these pilin modifications , the presence of phosphorylcho...	[ "Neisseria meningitidis is an important human pathogen that can cause rapidly progressing , life threatening meningitis and sepsis in humans .", "There is no fully protective vaccine against this pathogen in current use and the key processes that dictate the transition from harmless carriage of the bacterium in t...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "aging", "developmental biology", "organism development", "genetic polymorphism", "coevolution", "biology and life sciences", "population genetics", "evolutionary biology", "evolutionary processes" ]	G×G×E for Lifespan in Drosophila: Mitochondrial, Nuclear, and Dietary Interactions that Modify Longevity	journal.pgen.1004354	null	[ [ "The extension of longevity by dietary or caloric restriction ( DR or CR ) has been demonstrated in a wide range of organisms , suggesting evolutionarily conserved pathways that regulate this response [1] , [2] , [3] , [4] , [5] .", "However , dissecting the genetic and cellular mechanisms of DR remains a...	[ "Dietary restriction ( DR ) is the most consistent means of extending longevity in a wide range of organisms .", "A growing body of literature indicates that mitochondria play an important role in longevity extension by DR , but the impact of mitochondrial genotypes on the DR process have received little attentio...	[ "It is widely recognized that mitochondrial function plays an important role in longevity and healthy aging .", "Considerable attention has been focused on the extension of longevity by caloric or dietary restriction and mutations that alter this process , and these interventions commonly are associated with shif...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The Sex Determination Gene transformer Regulates Male-Female Differences in Drosophila Body Size	journal.pgen.1005683	null	[ [ "Drosophila is a well-established model to study the mechanisms that control animal growth [1 , 2] .", "Drosophila body size is determined by various developmental cues that coordinate tissue patterning with growth , and by environmental cues such as nutrients and oxygen , that regulate whole body metabol...	[ "Almost all animals show sex differences in body size .", "For example , in Drosophila , females are larger than males .", "Although Drosophila is widely used as a model to study growth , the mechanisms underlying this male-female difference in size remain unclear .", "Here , we describe a novel role for the ...	[ "Female-biased sexual size dimorphism is common in invertebrates , yet the mechanisms underlying increased female body size remain unclear .", "We uncovered a key role for sex determination gene transformer ( tra ) in promoting increased growth in females .", "Interestingly , we found that sex differences in bo...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "dengue virus", "medicine and health sciences", "clinical laboratory sciences", "pathology and laboratory medicine", "pathogens", "tropical diseases", "geographical locations", "india", "microbiology", "viruses", "rna viruses", "neglected tropical diseases", "infectious disease control", "...	Dengue infection in India: A systematic review and meta-analysis	journal.pntd.0006618	null	[ [ "Dengue is the most extensively spread mosquito-borne disease , transmitted by infected mosquitoes of Aedes species .", "Dengue infection in humans results from four dengue virus serotypes ( DEN-1 , DEN-2 , DEN-3 , and DEN-4 ) of Flavivirus genus .", "As per the WHO 1997 classification , symptomatic d...	[ "Dengue is the most extensively spread mosquito-borne disease; endemic in more than 100 countries .", "Information about dengue disease burden , its prevalence , incidence and geographic distribution is critical in planning appropriate control measures against dengue fever .", "We conducted a systematic review ...	[ "Dengue fever , an extensively spread mosquito-borne disease , is endemic in more than 100 countries .", "Information about dengue disease burden , its prevalence and incidence and geographic distribution is necessary to guide in planning appropriate control measures including the dengue vaccine that has recently...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "innate immune system", "medicine and health sciences", "immune cells", "immune physiology", "cytokines", "spleen", "immunology", "tropical diseases", "parasitic diseases", "parasitology", "cell differentiation", "parasitemia", "developmental biology", "molecular developme...	Protection by and maintenance of CD4 effector memory and effector T cell subsets in persistent malaria infection	journal.ppat.1006960	null	[ [ "Malaria accounts for an estimated 438 , 000 deaths annually , with over 3 billion people at risk of infection [1] .", "Plasmodium infection can be considered chronic both for the repetitious exposure in hyperendemic areas [2] , as well as for the ability of both P . falciparum and P . vivax infections to...	[ "Protection at the peak of Plasmodium chabaudi blood-stage malaria infection is provided by CD4 T cells .", "We have shown that an increase in Th1 cells also correlates with protection during the persistent phase of malaria; however , it is unclear how these T cells are maintained .", "Persistent malaria infect...	[ "Malaria causes significant mortality but current vaccine candidates have poor efficacy and duration , as does natural immunity to malaria .", "T helper cells ( CD4+ ) are essential to protection from malaria , but it is unknown what kinds of T cells would be both protective and long-lasting .", "Here , we expl...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "anatomy and physiology", "electrophysiology", "neuroscience", "endocrine physiology", "computational neuroscience", "endocrinology", "diabetes and endocrinology", "biology", "neuroendocrinology", "physiology", "endocrine system", "computational biology" ]	Phasic Firing in Vasopressin Cells: Understanding Its Functional Significance through Computational Models	journal.pcbi.1002740	null	[ [ "Magnocellular vasopressin neurons produce and secrete the antidiuretic hormone vasopressin in response to increases in the osmotic pressure of extracellular fluid [1] .", "They form a key part of the highly robust homeostatic system which maintains osmotic pressure within narrow bounds .", "Each of t...	[ "Vasopressin neurons , responding to input generated by osmotic pressure , use an intrinsic mechanism to shift from slow irregular firing to a distinct phasic pattern , consisting of long bursts and silences lasting tens of seconds .", "With increased input , bursts lengthen , eventually shifting to continuous fi...	[ "Vasopressin is a hormone secreted from specialised brain cells into the bloodstream , acting at the kidneys to control water excretion , and thereby help regulate osmotic pressure .", "This is a cell membrane property determined by the ratio between body salt and water , and its maintenance is essential to the f...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "biology" ]	Accuracy of Urine Circulating Cathodic Antigen Test for the Diagnosis of Schistosoma mansoni in Preschool-Aged Children before and after Treatment	journal.pntd.0002109	null	[ [ "Recognizing the public health impact of schistosomiasis and soil-transmitted helminthiasis , the World Health Organization ( WHO ) has set a minimum target for the control of morbidity due to these parasitic worm infections , urging member states to regularly treat at least 75% and up to 100% , of all school...	[ "The Kato-Katz technique is widely used for the diagnosis of Schistosoma mansoni , but shows low sensitivity in light-intensity infections .", "We assessed the accuracy of a commercially available point-of-care circulating cathodic antigen ( POC-CCA ) cassette test for the diagnosis of S . mansoni in preschool-ag...	[ "The strategy to control morbidity due to infection with the blood fluke Schistosoma mansoni is to regularly treat school-aged children with the drug praziquantel .", "Recent studies suggest that in highly endemic areas preschoolers might need to be included in such deworming campaigns .", "An accurate diagnosi...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology", "plant biology", "virology", "immunology", "molecular biology" ]	A Novel Role for the TIR Domain in Association with Pathogen-Derived Elicitors	journal.pbio.0050068	How do plant resistance gene recognize the cognate pathogen? These authors dissect the interaction of a resistance gene and a viral pathogen.	[ [ "Plants , like animals , are able to launch successful defense responses against invading microorganisms .", "For this purpose , plants have developed a variety of strategies that include molecular , chemical , and physical barriers to infection .", "One of the most important of these defense systems ...	[ "Plant innate immunity is mediated by Resistance ( R ) proteins , which bear a striking resemblance to animal molecules of similar function .", "Tobacco N is a TIR-NB-LRR R gene that confers resistance to Tobacco mosaic virus , specifically the p50 helicase domain .", "An intriguing question is how plant R prot...	[ "Each year , up to 10% of world agricultural production is lost to pests and diseases caused by a variety of pathogens including bacteria , fungi , nematodes , and viruses .", "Scientists have understood for nearly a century that plants carry their own immune system that actively engages pathogens and prevents ma...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "developmental biology", "cell biology", "caenorhabditis", "computational biology", "molecular biology", "genetics and genomics" ]	High-Throughput In Vivo Analysis of Gene Expression in Caenorhabditis elegans	journal.pbio.0050237	Using DNA sequences 5' to open reading frames, the authors construct green fluorescent protein fusions and generate spatial and temporal tissue expression profiles for 10% of all genes in the nematode Caenorhabditis elegans.	[ [ "Determining when and where genes are expressed is often key to determining their function .", "Although expression profiling of genes using Serial Analysis of Gene Expression ( SAGE ) and microarrays is now routine , we still have complete developmental expression profiles for only a small fraction of al...	[ "Using DNA sequences 5′ to open reading frames , we have constructed green fluorescent protein ( GFP ) fusions and generated spatial and temporal tissue expression profiles for 1 , 886 specific genes in the nematode Caenorhabditis elegans .", "This effort encompasses about 10% of all genes identified in this orga...	[ "Knowing where a protein is expressed provides an important clue about its potential function .", "As critical as this information is , we have complete developmental expression profiles for only a small fraction of all genes expressed in any metazoan .", "Here , we have generated spatial and temporal tissue ex...	2007
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "public and occupational health", "ecology and environmental sciences", "medicine and health sciences", "ecology", "global health", "global change ecology", "biology and life sciences" ]	Projected Future Distributions of Vectors of Trypanosoma cruzi in North America under Climate Change Scenarios	journal.pntd.0002818	null	[ [ "Climate change has been implicated in shifts of the geographic distribution of many species[1] , enabling some taxa to increase their distributions into northern latitudes [1] , [2] .", "Thus , changes in climate can potentially alter the spatial range of vector-borne diseases through shifts in geographi...	[ "Chagas disease kills approximately 45 thousand people annually and affects 10 million people in Latin America and the southern United States .", "The parasite that causes the disease , Trypanosoma cruzi , can be transmitted by insects of the family Reduviidae , subfamily Triatominae .", "Any study that attempt...	[ "Chagas disease kills thousands of people annually .", "Triatomine insects ( family Reduviidae , sub-family Triatominae ) , can be potential vectors of the parasite ( Trypanosoma cruzi ) that causes the disease .", "There are often no symptoms until cardiac and digestive system dysfunction ( possibly including ...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/animal genetics", "physiology/sensory systems", "neuroscience/sensory systems", "nutrition", "developmental biology/aging", "physiology", "diabetes and endocrinology/obesity", "physiology/endocrinology", "nutrition/obesity", "microbiology", "neuroscience", "molecular bio...	A Neuromedin U Receptor Acts with the Sensory System to Modulate Food Type-Dependent Effects on C. elegans Lifespan	journal.pbio.1000376	Different food types modulate worm lifespan and involve the neuropeptide receptor NMUR-1, which acts with the sensory neurons in a bacterial lipopolysaccaharide structure-dependent manner.	[ [ "The sensory systems of Caenorhabditis elegans and Drosophila melanogaster have been shown to modulate the lifespan of these animals [1]–[4] .", "This sensory influence involves subsets of gustatory and olfactory neurons [2] , [3] that either shorten or lengthen lifespan , which suggests that", "( i )...	[ "The type of food source has previously been shown to be as important as the level of food intake in influencing lifespan .", "Here we report that different Escherichia coli food sources alter Caenorhabditis elegans lifespan .", "These effects are modulated by different subsets of sensory neurons , which act wi...	[ "Work on the model organisms C . elegans and D . melanogaster has contributed important and often surprising insights into the factors that determine lifespan .", "One intriguing finding is that lifespan in both animals can be extended or shortened by interfering with the function of neurons that smell or taste f...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell death", "molecular neuroscience", "neurobiology of disease and regeneration", "medicine and health sciences", "animal genetics", "cell processes", "neuroscience", "gene function", "animal models", "genetics of disease", "developmental biology", "mutation", "model organisms", "organis...	Disruption of SUMO-Specific Protease 2 Induces Mitochondria Mediated Neurodegeneration	journal.pgen.1004579	null	[ [ "Emerging evidence suggests the importance of protein modification by Small Ubiquitin-related Modifier ( SUMO ) in neural development and function [1]–[3] .", "Abnormal SUMO modification has been found in several neurodegenerative diseases , characterized by progressive loss or dysfunction of neurons [4]–...	[ "Post-translational modification of proteins by small ubiquitin-related modifier ( SUMO ) is reversible and highly evolutionarily conserved from yeasts to humans .", "Unlike ubiquitination with a well-established role in protein degradation , sumoylation may alter protein function , activity , stability and subce...	[ "Protein modification by SUMO is a reversible and evolutionarily conserved process .", "Members of the SUMO-specific protease ( SENP ) family are known to reverse SUMO-conjugation in many defined systems , but their importance in mammalian development and pathogenesis remains largely elusive .", "Although SUMO-...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry", "computational biology", "evolutionary biology", "genetics and genomics" ]	The Evolution of Combinatorial Gene Regulation in Fungi	journal.pbio.0060038	Experimental approaches combined with comparative genomics show how a large combinatorial transcription circuit has rewired over evolutionary time scales.	[ [ "The recent genome sequencing and annotation of the major model organisms established that organismal complexity does not scale in a simple way with gene count .", "This discordance is consistent with earlier proposals that “tinkering” with gene regulation may be a particularly powerful mode of evolution ...	[ "It is widely suspected that gene regulatory networks are highly plastic .", "The rapid turnover of transcription factor binding sites has been predicted on theoretical grounds and has been experimentally demonstrated in closely related species .", "We combined experimental approaches with comparative genomics ...	[ "In explaining the diversity of organisms on Earth , it is increasingly evident that evolutionary changes in when and where genes are expressed provide a crucial source of variation .", "By using genome-wide transcription factor localization experiments in S . cerevisiae , K . lactis , and C . albicans , combined...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "viral vaccines", "virology", "immunology", "biology", "microbiology", "immune response", "immunoglobulins" ]	B Cell Repertoire Analysis Identifies New Antigenic Domains on Glycoprotein B of Human Cytomegalovirus which Are Target of Neutralizing Antibodies	journal.ppat.1002172	null	[ [ "Human cytomegalovirus ( HCMV ) is an important , ubiquitously occurring , human pathogen in immunocompromised hosts .", "The virus can cause severe disease in transplant recipients [1] .", "In large parts of the world HCMV is also the most common viral infection acquired in utero .", "In the USA ...	[ "Human cytomegalovirus ( HCMV ) , a herpesvirus , is a ubiquitously distributed pathogen that causes severe disease in immunosuppressed patients and infected newborns .", "Efforts are underway to prepare effective subunit vaccines and therapies including antiviral antibodies .", "However , current vaccine effor...	[ "The development of antibodies is a major defense mechanism against viruses .", "Understanding the repertoire of antiviral antibodies induced during infection is a necessary prerequisite to defining the protective activities of an antiviral antibody response .", "The isolation of antigen specific memory B cells...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "helminths", "tropical diseases", "hookworms", "parasitic diseases", "animals", "necator americanus", "ascaris", "ascaris lumbricoides", "neglected tropical diseases", "strongyloides stercoralis", "ancylostoma", "strongyloides", "infectiou...	Expanding molecular diagnostics of helminthiasis: Piloting use of the GPLN platform for surveillance of soil transmitted helminthiasis and schistosomiasis in Ghana	journal.pntd.0006129	null	[ [ "In 1988 the WHO set out to eradicate polio after the successful development of effective polio vaccines and since then the eradication campaign has reduced the number of countries reporting endemic polio from 125 to three in 2016 .", "Control of polio has been a co-ordinated effort involving two main arm...	[ "The efforts to control and eradicate polio as a global health burden have been successful to the point where currently only three countries now report endemic polio , and the number of cases of polio continues to decrease .", "The success of the polio programme has been dependant on a well-developed network of l...	[ "The successful campaign being waged against polio has eliminated the disease from most countries where it was once endemic .", "With this success , it is anticipated that the disease will be eradicated in the coming years with only 37 cases being reported in 2016 .", "Although the efforts to control polio are ...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "immune cells", "antigen-presenting cells", "immunology", "carcinomas", "cancers and neoplasms", "oncology", "mutation", "nonsense mutation", "adenocarcinomas", "frameshift mutation", "animal cells", "somatic mutation", "point mutation", "colorectal cancer...	Exome-wide somatic mutation characterization of small bowel adenocarcinoma	journal.pgen.1007200	null	[ [ "The gastrointestinal tract , a continuous passageway , includes the main digestive organs: the stomach , the small bowel , and the large bowel .", "The small bowel makes up 75% of the length of the gastrointestinal tract , yet small bowel tumors constitute only approximately 3% of gastrointestinal tumors...	[ "Small bowel adenocarcinoma ( SBA ) is an aggressive disease with limited treatment options .", "Despite previous studies , its molecular genetic background has remained somewhat elusive .", "To comprehensively characterize the mutational landscape of this tumor type , and to identify possible targets of treatm...	[ "Small bowel adenocarcinoma is a rare but aggressive disease with limited treatment options .", "Of gastrointestinal tumors , small bowel tumors account for 3% , of which around one third are adenocarcinomas .", "Due to the scarcity of evidence-based treatment recommendations there is a dire need for knowledge ...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "oncology", "medicine", "cancer genetics", "basic cancer research", "genetics", "population genetics", "biology", "human genetics", "cancer risk factors", "genetics of disease", "genetics and genomics", "gene function" ]	Interplay between BRCA1 and RHAMM Regulates Epithelial Apicobasal Polarization and May Influence Risk of Breast Cancer	journal.pbio.1001199	Genetic analysis identifies the HMMR gene as a modifier of the breast cancer risk associated with BRCA1 gene mutation, while cell biological analysis of the protein product suggests a function in regulating development of the mammary gland.	[ [ "The mammary gland is composed of two epithelial cell lineages that form an inner apicobasal-polarized luminal layer surrounded by an outer , or basal , layer of contractile myoepithelial cells [1] .", "Epithelial cell subsets are likely maintained through a differentiation hierarchy supported by an estro...	[ "Differentiated mammary epithelium shows apicobasal polarity , and loss of tissue organization is an early hallmark of breast carcinogenesis .", "In BRCA1 mutation carriers , accumulation of stem and progenitor cells in normal breast tissue and increased risk of developing tumors of basal-like type suggest that B...	[ "Mutations in two genes that were initially identified as predisposing carriers to early-onset breast cancer , BRCA1 and BRCA2 , cause similar perturbations in cellular responses to DNA damage but predispose carriers to distinct tumor types .", "Thus , the two genes may trigger different carcinogenic processes ."...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/protozoal infections", "immunology/antigen processing and recognition", "immunology/immunity to infections" ]	Dendritic Cells and Hepatocytes Use Distinct Pathways to Process Protective Antigen from Plasmodium in vivo	journal.ppat.1001318	null	[ [ "Immunization with irradiated Plasmodium sporozoites to induce sterile protection against live parasite challenge is a powerful model for malaria vaccination [1] .", "Protective immunity is mediated in part by CD8+ T cells specific for the circumsporozoite ( CS ) protein of Plasmodium [2] , [3] .", "P...	[ "Malaria-protective CD8+ T cells specific for the circumsporozoite ( CS ) protein are primed by dendritic cells ( DCs ) after sporozoite injection by infected mosquitoes .", "The primed cells then eliminate parasite liver stages after recognizing the CS epitopes presented by hepatocytes .", "To define the in vi...	[ "Malaria causes the deaths of 0 . 5–2 million people each year , mainly in Africa .", "A safe and effective vaccine is likely needed for the control or eradication of this disease .", "Immunization by irradiated malaria-infected mosquitoes has been shown to protect people against malaria .", "Irradiated paras...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "evolutionary ecology", "intestinal parasites", "ecology", "biology and life sciences", "evolutionary biology", "parasitology" ]	Natural Selection on Individual Variation in Tolerance of Gastrointestinal Nematode Infection	journal.pbio.1001917	A 25-year study of wild sheep shows that individuals vary in how quickly they lose weight as parasite infections increase, and that those who lose the least weight when heavily infected produce more offspring.	[ [ "Hosts of gastrointestinal nematodes vary widely in the number of parasites they harbour [1] and the severity of symptoms they experience at a given parasite burden [2] .", "Explaining such variation is a major challenge with practical implications for biomedicine and agricultural sciences , but also repr...	[ "Hosts may mitigate the impact of parasites by two broad strategies: resistance , which limits parasite burden , and tolerance , which limits the fitness or health cost of increasing parasite burden .", "The degree and causes of variation in both resistance and tolerance are expected to influence host–parasite ev...	[ "Animals can defend themselves against parasites through either resistance ( reducing parasite numbers , for example , by killing them ) or tolerance ( maintaining health as infections levels increase , for example , by repairing damage ) .", "Resistance has been well-studied in wild animals , but tolerance has b...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "arthropoda", "organisms", "invertebrates", "drosophila melanogaster", "natural selection", "biology and life sciences", "population genetics", "evolutionary theory", "evolutionary biology", "drosophila", "evolutionary processes", "animals", "genetic drift", "evolutionary genetics", "ins...	Background Selection as Baseline for Nucleotide Variation across the Drosophila Genome	journal.pgen.1004434	null	[ [ "The causes of the variation observed within natural populations have been a long-standing question in evolutionary and genetic studies .", "Particular insight into these causes can be gained by analyzing the distribution of nucleotide diversity across genomes , where species- and population-specific para...	[ "The constant removal of deleterious mutations by natural selection causes a reduction in neutral diversity and efficacy of selection at genetically linked sites ( a process called Background Selection , BGS ) .", "Population genetic studies , however , often ignore BGS effects when investigating demographic even...	[ "The removal of deleterious mutations from natural populations has potential consequences on patterns of variation across genomes .", "Population genetic analyses , however , often assume that such effects are negligible across recombining regions of species like Drosophila .", "We use simple models of purifyin...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "interaction networks", "clinical research design", "protein interaction networks", "research design", "network analysis", "pharmacology", "mood disorders", "research and analysis methods", "computer and information sciences", "drug safety", "drug marketing", ...	PathFX provides mechanistic insights into drug efficacy and safety for regulatory review and therapeutic development	journal.pcbi.1006614	null	[ [ "The drug discovery process is long , difficult , and expensive .", "Only ~10% of drugs entered in human studies make it to the market[1] because many drugs have insufficient efficacy[2] or significant safety issues[3 , 4] .", "The lack of efficacy may be related to poor bioavailability , incomplete i...	[ "Failure to demonstrate efficacy and safety issues are important reasons that drugs do not reach the market .", "An incomplete understanding of how drugs exert their effects hinders regulatory and pharmaceutical industry projections of a drug’s benefits and risks .", "Signaling pathways mediate drug response an...	[ "Many drugs fail to reach the market because they are not sufficiently efficacious for their disease indication or they cause intolerable side-effects .", "To understand drug efficacy and safety , we created an algorithm , PathFX .", "The algorithm identified relationships between drugs and diseases , and drugs...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular biology/recombination", "molecular biology/chromosome structure" ]	Pch2 Links Chromosome Axis Remodeling at Future Crossover Sites and Crossover Distribution during Yeast Meiosis	journal.pgen.1000557	null	[ [ "During meiosis , a single round of DNA replication is followed by two rounds of chromosome separation , with homologous chromosomes ( homologs ) segregating during meiosis I and sister chromatids during meiosis II .", "Homolog segregation critically depends on formation of crossovers ( COs ) between homo...	[ "Segregation of homologous chromosomes during meiosis I depends on appropriately positioned crossovers/chiasmata .", "Crossover assurance ensures at least one crossover per homolog pair , while interference reduces double crossovers .", "Here , we have investigated the interplay between chromosome axis morphoge...	[ "In the germ line of sexually reproducing organisms , haploid gametes are generated from diploid precursor cells by a specialized cell division called meiosis .", "Reduction by half of chromosome numbers during the first meiotic division depends on genetic exchange , resulting in the formation of crossovers .", ...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "toxins", "body fluids", "pathology and laboratory medicine", "engineering and technology", "enterotoxins", "toxicology", "toxic agents", "escherichia coli", "prokaryotic models", "model organisms", "infectious disease control", "agricultural production", "v...	The Molecular Basis for Control of ETEC Enterotoxin Expression in Response to Environment and Host	journal.ppat.1004605	null	[ [ "ETEC are Gram negative bacteria that cause severe diarrhoea , known as non-vibrio cholera , in humans [1] , [2] .", "First isolated in 1971 , ETEC are responsible for 210 million infections annually , mostly in developing countries , leading to 380 , 000 deaths [3] .", "Disease results primarily from...	[ "Enterotoxigenic Escherichia coli ( ETEC ) cause severe diarrhoea in humans and neonatal farm animals .", "Annually , 380 , 000 human deaths , and multi-million dollar losses in the farming industry , can be attributed to ETEC infections .", "Illness results from the action of enterotoxins , which disrupt signa...	[ "Diarrheagenic illness remains a major disease burden in the developing world .", "Enterotoxigenic Escherichia coli ( ETEC ) are the leading bacterial cause of such disease; hundreds of millions of cases occur every year .", "The severe watery diarrhoea associated with ETEC infections results from the action of...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "skin", "children", "medicine and health sciences", "integumentary system", "pathology and laboratory medicine", "chlamydia trachomatis", "pathogens", "immunology", "tropical diseases", "microbiology", "bacterial diseases", "age groups", "signs and symptoms", "eye diseases", "sexually tr...	Trachomatous scarring among children in a formerly hyper-endemic district of Tanzania	journal.pntd.0006085	null	[ [ "Trachoma results from repeated ocular infection with Chlamydia trachomatis and is the leading infectious cause of blindness worldwide .", "[1] While the conjunctival inflammation associated with active infection is predominantly seen before 10 years of age , the resultant conjunctival scarring usually pr...	[ "Associations between repeated ocular infections with Chlamydia trachomatis in childhood and conjunctival scarring in adulthood are well established .", "Trachomatous scarring ( TS ) in children has also been observed in hyper-endemic areas , but data are scant regarding childhood scarring in areas where trachoma...	[ "Trachoma is a disease in which the conjunctiva of the eye is repeatedly infected by the intracellular organism Chlamydia trachomatis .", "This can cause scarring of the eyelid’s inner surface , which in turn can cause the eyelashes to turn inwards , scratching the eye and leading to blindness .", "This scarrin...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "brain", "vertebrates", "social sciences", "neuroscience", "animals", "mammals", "animal models", "animal anatomy", "model organisms", "materials science", "zoology", "research and analysis methods", "animal cells", "touch", "texture", "animal physiolo...	Coherence between Rat Sensorimotor System and Hippocampus Is Enhanced during Tactile Discrimination	journal.pbio.1002384	In rats, the rhythms of whisking and hippocampal theta become coherent precisely when rats approach and explore a texture; higher coherence enhances the identification of texture.	[ [ "Fluctuations in local field potential ( LFP ) affect a neuronal population’s likelihood of spike output and its sensitivity to synaptic inputs [1–3] ) .", "When the oscillations of two brain regions are coherent , the respective neuronal populations might be functionally coupled to allow efficient transm...	[ "Rhythms with time scales of multiple cycles per second permeate the mammalian brain , yet neuroscientists are not certain of their functional roles .", "One leading idea is that coherent oscillation between two brain regions facilitates the exchange of information between them .", "In rats , the hippocampus an...	[ "Many regions of the mammalian brain exhibit oscillations in electrical activity .", "In rats , the 5–12 Hz theta rhythm is present in the hippocampus and in diverse areas of the cerebral cortex .", "What is the function of this rhythm ?", "One proposal is that the exchange of information between two brain re...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "diagnostic medicine", "clinical immunology", "immunology", "biology", "microbiology" ]	Relatively Low Level of Antigen-specific Monocytes Detected in Blood from Untreated Tuberculosis Patients Using CD4+ T-cell Receptor Tetramers	journal.ppat.1003036	null	[ [ "With approximately one-third of the world's population infected with Mycobacterium tuberculosis ( MTB ) , tuberculosis ( TB ) continues to persist as a major infectious disease that significantly contributes to global morbidity and mortality [1] .", "However , 5–10% of infected individuals will eventuall...	[ "The in vivo kinetics of antigen-presenting cells ( APCs ) in patients with advanced and convalescent tuberculosis ( TB ) is not well characterized .", "In order to target Mycobacterium tuberculosis ( MTB ) peptides- and HLA-DR-holding monocytes and macrophages , 2 MTB peptide-specific CD4+ T-cell receptor ( TCR ...	[ "Mycobacterium tuberculosis ( MTB ) is one of the most dangerous pathogens in the world .", "It is estimated that one-third of the world population contracts the bacteria during their lives .", "Approximately 5–10% of infected individuals will eventually develop an active form of the disease .", "Cellular imm...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "organismal evolution", "genomic evolution", "human evolution", "biology", "evolutionary biology", "comparative genomics", "evolutionary genetics" ]	De Novo Origin of Human Protein-Coding Genes	journal.pgen.1002379	null	[ [ "The origin of new genes has always been an intriguing evolutionary question [1] .", "New genes play significant roles in the evolution of lineage specific phenotypes and adaptive innovation [2] .", "The origin of genes can involve gene duplication , exon shuffling , retroposition , mobile elements , ...	[ "The de novo origin of a new protein-coding gene from non-coding DNA is considered to be a very rare occurrence in genomes .", "Here we identify 60 new protein-coding genes that originated de novo on the human lineage since divergence from the chimpanzee .", "The functionality of these genes is supported by bot...	[ "The origin of genes can involve mechanisms such as gene duplication , exon shuffling , retroposition , mobile elements , lateral gene transfer , gene fusion/fission , and de novo origination .", "However , de novo origin , which means genes originate from a non-coding DNA region , is considered to be a very rare...	2011
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "microbiology", "vertebrates", "cloning", "animals", "viruses", "mutation", "physiological parameters", "rna viruses", "body temperature", "molecular biology techniques", "research and analysis methods", "i...	West Nile Virus Temperature Sensitivity and Avian Virulence Are Modulated by NS1-2B Polymorphisms	journal.pntd.0004938	null	[ [ "West Nile virus ( WNV ) is the most widely distributed flavivirus in the world , occurring on all continents except Antarctica [1 , 2] .", "Recent human disease outbreaks in Europe and North America have brought increased scientific and public health attention to WNV; however , WNV may also cause signifi...	[ "West Nile virus ( WNV ) replicates in a wide variety of avian species , which serve as reservoir and amplification hosts .", "WNV strains isolated in North America , such as the prototype strain NY99 , elicit a highly pathogenic response in certain avian species , notably American crows ( AMCRs; Corvus brachyrhy...	[ "West Nile virus ( WNV ) is a mosquito-borne virus that has caused outbreaks in humans in many regions of the world .", "Birds are the natural hosts for WNV .", "However , different strains of WNV cause different disease outcomes in birds .", "Here , we compared two WNV strains , one of which causes higher mo...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "death rates", "taxonomy", "medicine and health sciences", "china", "spatial epidemiology", "geographical locations", "vertebrates", "animals", "mammals", "hemorrhagic fever with renal syndrome", "phylogenetics", "data management", "phylogenetic analysis", "population biology", "infectio...	The characteristics of current natural foci of hemorrhagic fever with renal syndrome in Shandong Province, China, 2012-2015	journal.pntd.0007148	null	[ [ "Hemorrhagic fever with renal syndrome ( HFRS ) , a global infectious disease caused by hantaviruses ( HV ) in the Bunyaviridae family , is characterized by fever , hemorrhage , kidney damage and hypotension .", "All the currently known HV genotypes can cause HFRS , including Hantaan virus ( HTNV ) , Seou...	[ "Hemorrhagic fever with renal syndrome ( HFRS ) , an infectious disease caused by hantaviruses , is endemic in China and remains a serious public health problem .", "Historically , Shandong Province has had the largest HFRS burden in China .", "However , we do not have a comprehensive and clear understanding of...	[ "Hemorrhagic fever with renal syndrome ( HFRS ) is a global infectious disease , which is still a serious public health threat in China today .", "The reported HFRS cases in Shandong Province accounted for approximate one third of total cases in the whole country .", "HFRS is a zoonosis mainly caused by Hantaan...	2019
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "learning", "medicine and health sciences", "action potentials", "decision making", "neural networks", "nervous system", "applied mathematics", "membrane potential", "social sciences", "electrophysiology", "neuroscience", "learning and memory", "simulation and modeling", "algorithms", "s...	Learning and executing goal-directed choices by internally generated sequences in spiking neural circuits	journal.pcbi.1005669	null	[ [ "Neural sequences have been widely observed in many brain areas including the cortex [1 , 2 , 3 , 4] , and the hippocampus [5 , 6 , 7 , 8 , 9 , 10 , 11] .", "Based on how sequences are initialized , they can be placed into two broad categories , namely externally and internally generated sequences [12] ."...	[ "Recent neural ensemble recordings have established a link between goal-directed spatial decision making and internally generated neural sequences in the hippocampus of rats .", "To elucidate the synaptic mechanisms of these sequences underlying spatial decision making processes , we develop and investigate a spi...	[ "Adaptive goal-directed decision making is critical for animals , robots and humans to navigate through space .", "In this study , we propose a novel neural mechanism for implementing spatial decision making in cued-choice tasks .", "We show that in a spiking neural circuit model , the interplay of network dyna...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "gene regulation", "microbiology", "dna transcription", "regulator genes", "dna replication", "gene types", "dna", "microbial genetics", "small interfering rnas", "gene expression", "viral replication", "lytic cycle", "viral genetics", "biochemistry", "rna", "nucleic acids", "virolog...	The Epstein-Barr Virus Immunoevasins BCRF1 and BPLF1 Are Expressed by a Mechanism Independent of the Canonical Late Pre-initiation Complex	journal.ppat.1006008	null	[ [ "Late genes represent more than one third of the herpesvirus genome .", "The functions of many of these genes are indispensable for the life cycle of the virus .", "Late genes encode structural proteins that form the viral capsid , and glycoproteins that mediate virus attachment , fusion and entry dur...	[ "Subversion of host immune surveillance is a crucial step in viral pathogenesis .", "Epstein-Barr virus ( EBV ) encodes two immune evasion gene products , BCRF1 ( viral IL-10 ) and BPLF1 ( deubiquitinase/deneddylase ) ; both proteins suppress antiviral immune responses during primary infection .", "The BCRF1 an...	[ "Late proteins are expressed during the productive cycle of Epstein-Barr virus ( EBV ) after the onset of viral DNA replication .", "Many late proteins serve structural functions; they form the capsid shell around the viral genome or mediate attachment and fusion of the virus to the host cell .", "EBV also enco...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "blood cells", "medicine and health sciences", "body fluids", "pathology and laboratory medicine", "blood counts", "hepatitis", "hemodynamics", "signs and symptoms", "platelets", "cardiology", "infectious diseases", "thrombocytopenia", "animal cells", "hematology", "blood plasma", "hem...	Development of standard clinical endpoints for use in dengue interventional trials	journal.pntd.0006497	null	[ [ "Dengue is a major public health problem worldwide , with an estimated 3 . 9 billion people at risk globally [1] .", "While most dengue virus ( DENV ) infections are asymptomatic or result in a self-limited acute febrile illness ( AFI ) , some are life-threatening due to severe plasma leakage , severe ble...	[ "Dengue is a major public health problem worldwide .", "Although several drug candidates have been evaluated in randomized controlled trials , none has been effective and at present , early recognition of severe dengue and timely supportive care are used to reduce mortality .", "While the first dengue vaccine w...	[ "Dengue is a major public health problem worldwide .", "Although several drug candidates have been evaluated in randomized controlled trials , none has been effective , and early recognition of severe dengue and timely supportive care remain the only means to reduce mortality .", "While the first dengue vaccine...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "rabies", "clinical epidemiology", "epidemiology", "infectious disease epidemiology", "travel-associated diseases", "viral diseases" ]	Imported Human Rabies Cases Worldwide, 1990–2012	journal.pntd.0002209	null	[ [ "Rabies is readily diagnosed when it presents in the classic furious form .", "The paralytic and atypical forms can pose significant problems in diagnosis , particularly when found in rabies-free countries in travelers who acquired the disease abroad .", "The discussion of geographical and post-exposu...	[ "Sixty cases of human rabies in international travelers were reviewed from 1990–2012 .", "A significant proportion of the cases were observed in migrants or their descendants when emigrating from their country of origin or after a trip to visit friends and relatives or for other reasons ( 43 . 3% ) .", "The cas...	[ "Rabies is readily diagnosed when it presents in the classic furious form .", "The paralytic and atypical forms can pose significant problems in diagnosis , particularly when found in rabies-free countries in travelers who acquired the disease abroad .", "We systematically reviewed the existing literature and c...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "invertebrates", "medicine and health sciences", "nervous system", "gene regulation", "neuroscience", "animals", "animal models", "developmental biology", "drosophila melanogaster", "model organisms", "cell nucleus", "nuclear bodies", "embryos", "cellular structures and organelles", "dro...	Cell-Autonomous and Non-cell-autonomous Function of Hox Genes Specify Segmental Neuroblast Identity in the Gnathal Region of the Embryonic CNS in Drosophila	journal.pgen.1005961	null	[ [ "The Drosophila central nervous system ( CNS ) consists of 20 segmental units ( neuromeres ) , the sizes and composition of which are specifically adapted to the functional requirements of the respective body parts in the head , thorax and abdomen .", "Thus , neural stem cells ( called neuroblasts , NBs )...	[ "During central nervous system ( CNS ) development neural stem cells ( Neuroblasts , NBs ) have to acquire an identity appropriate to their location .", "In thoracic and abdominal segments of Drosophila , the expression pattern of Bithorax-Complex Hox genes is known to specify the segmental identity of NBs prior ...	[ "The central nervous system ( CNS ) needs to be subdivided into functionally specified regions .", "In the developing CNS of Drosophila , each neural stem cell , called neuroblasts ( NB ) , acquires a unique identity according to its anterior-posterior and dorso-ventral position to generate a specific cell lineag...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunity", "microbial pathogens", "immunology", "host-pathogen interaction", "biology", "microbiology", "bacterial pathogens", "immune response" ]	IRG and GBP Host Resistance Factors Target Aberrant, “Non-self” Vacuoles Characterized by the Missing of “Self” IRGM Proteins	journal.ppat.1003414	null	[ [ "Many intracellular pathogens including the bacterium C . trachomatis and the protozoa T . gondii co-opt the host cell endomembrane system to enclose themselves inside membrane-bound vacuoles .", "Within the confines of these remodeled PVs , microbes acquire nutrients and replicate [1] .", "To combat ...	[ "Interferon-inducible GTPases of the Immunity Related GTPase ( IRG ) and Guanylate Binding Protein ( GBP ) families provide resistance to intracellular pathogenic microbes .", "IRGs and GBPs stably associate with pathogen-containing vacuoles ( PVs ) and elicit immune pathways directed at the targeted vacuoles .",...	[ "Cell-autonomous host defense pathways directed against vacuolar pathogens constitute an essential arm of the mammalian innate immune defense system .", "Underlying most of these defense strategies is the ability of the host cell to recognize foreign or pathogen-modified structures and to deliver antimicrobial mo...	2013
[ "Introduction", "Results", "Discussion" ]	[ "systems biology", "biochemistry", "biochemical simulations", "computer and information sciences", "network analysis", "regulatory networks", "biology and life sciences", "signaling networks", "computational biology" ]	The Self-Limiting Dynamics of TGF-β Signaling In Silico and In Vitro, with Negative Feedback through PPM1A Upregulation	journal.pcbi.1003573	null	[ [ "Transforming Growth Factor-β ( TGF-β ) , a regulator of cell migration and cell fate , is a pharmaceutical target for the treatment of metastatic cancer and fibrotic diseases [1] .", "Signal transduction from extracellular TGF-β to the cell nucleus through the Smad pathway is well documented [2]–[7] .", ...	[ "The TGF-β/Smad signaling system decreases its activity through strong negative regulation .", "Several molecular mechanisms of negative regulation have been published , but the relative impact of each mechanism on the overall system is unknown .", "In this work , we used computational and experimental methods ...	[ "TGF-β signaling pathway regulates a variety of cellular responses , such as differentiation , migration and apoptosis .", "Phosphorylated R-Smad , the central signaling protein in this pathway , exhibits self-limiting behaviors: it not only decreases quickly after TGF-β is removed , but it also decreases slowly ...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "skin", "invertebrates", "medicine and health sciences", "integumentary system", "gene regulation", "dna-binding proteins", "animals", "animal models", "drosophila melanogaster", "model organisms", "physiological parameters", "body temperature", "epidermis", "epigenetics", "chromatin", ...	Phenotypic Plasticity through Transcriptional Regulation of the Evolutionary Hotspot Gene tan in Drosophila melanogaster	journal.pgen.1006218	null	[ [ "Phenotypic plasticity , “the property of a given genotype to produce different phenotypes in response to distinct environmental conditions” [1] , is a widespread phenomenon .", "Phenotypic plasticity can be adaptive if different but optimal phenotypes are produced by a given genotype in distinct environm...	[ "Phenotypic plasticity is the ability of a given genotype to produce different phenotypes in response to distinct environmental conditions .", "Phenotypic plasticity can be adaptive .", "Furthermore , it is thought to facilitate evolution .", "Although phenotypic plasticity is a widespread phenomenon , its mo...	[ "Environmental conditions can strongly modulate the phenotype produced by a particular genotype .", "This process , called phenotypic plasticity , has major implications in medicine and agricultural sciences , and is thought to facilitate evolution .", "Phenotypic plasticity is observed in many animals and plan...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Expanding the Marine Virosphere Using Metagenomics	journal.pgen.1003987	null	[ [ "Prokaryotic viruses , often referred to as phages , are one of the largest reservoirs of underexplored genetic diversity on Earth .", "They are more numerous than any other biological form on the planet , and the astronomical values put forward for their numbers are to the tune of 1030 , difficult to com...	[ "Viruses infecting prokaryotic cells ( phages ) are the most abundant entities of the biosphere and contain a largely uncharted wealth of genomic diversity .", "They play a critical role in the biology of their hosts and in ecosystem functioning at large .", "The classical approaches studying phages require iso...	[ "Prokaryotic species contain extremely large gene pools ( pan-genome ) the study of which has been constrained by the difficulties in getting enough cultivated representatives of most of them .", "The situation of their viruses , also known as phages , that provide part of this genomic diversity and preserve it ,...	2013
[ "Introduction", "Results and Discussion", "Methods" ]	[ "sequencing techniques", "rna-binding proteins", "crystal structure", "protein interactions", "condensed matter physics", "protein structure prediction", "protein structure", "sequence motif analysis", "molecular biology techniques", "protein structure databases", "crystallography", "research ...	Binding Site Identification and Flexible Docking of Single Stranded RNA to Proteins Using a Fragment-Based Approach	journal.pcbi.1004697	null	[ [ "RNA participates in most processes leading to genome expression and its regulation [1 , 2] , mainly in association with proteins [3 , 4] .", "Protein-RNA interactions are also involved in several neurodegenerative diseases [5] and cancers [6] .", "Understanding such interaction and the design of drug...	[ "Protein-RNA docking is hampered by the high flexibility of RNA , and particularly single-stranded RNA ( ssRNA ) .", "Yet , ssRNA regions typically carry the specificity of protein recognition .", "The lack of methodology for modeling such regions limits the accuracy of current protein-RNA docking methods .", ...	[ "Protein-RNA interactions fulfill a large variety of fundamental cellular functions , in particular for regulation of genome expression .", "A full understanding of these interactions requires an atomistic description of the interface in the complex .", "It can aid in silico design of new therapeutics to modula...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "chromosome structure and function", "microbiology", "mitosis", "model organisms", "cell division", "chromosome biology", "proteins", "schizosaccharomyces pombe", "biology", "biochemistry", "cell biology", "nucleic acids", "genetics", "yeast and fungal models", "saccharomyces cerevisiae"...	Importance of Polη for Damage-Induced Cohesion Reveals Differential Regulation of Cohesion Establishment at the Break Site and Genome-Wide	journal.pgen.1003158	null	[ [ "Correct chromosome segregation is fundamental for genome integrity , and facilitated by the cohesin complex , that tethers sister chromatids from S phase until anaphase , a function known as cohesion [1] , [2] , [3] .", "Cohesin consists of four subunits: Smc1 , Smc3 , Scc1 ( also called Mcd1 ) , and Scc...	[ "Genome integrity depends on correct chromosome segregation , which in turn relies on cohesion between sister chromatids from S phase until anaphase .", "S phase cohesion , together with DNA double-strand break ( DSB ) recruitment of cohesin and formation of damage-induced ( DI ) cohesion , has previously been sh...	[ "Correct chromosome segregation requires that sister chromatids are held together by the protein complex cohesin , from S phase until anaphase .", "This S phase established cohesion is , together with DSB recruitment of cohesin and formation of damage-induced ( DI ) cohesion , also important for repair of DSBs ."...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "community ecology", "animal models", "drosophila melanogaster", "model organisms", "ecology", "biology", "species interactions", "microbiology", "host-pathogen interaction", "microbial ecology" ]	Bacterial Communities of Diverse Drosophila Species: Ecological Context of a Host–Microbe Model System	journal.pgen.1002272	null	[ [ "The genetic and experimental tractability of Drosophila melanogaster often overshadows the phenotypic , evolutionary and ecological diversity of its relatives .", "Over 3000 species of Drosophila and related genera inhabit all continents except Antarctica , occur in practically every type of habitat , an...	[ "Drosophila melanogaster is emerging as an important model of non-pathogenic host–microbe interactions .", "The genetic and experimental tractability of Drosophila has led to significant gains in our understanding of animal–microbial symbiosis .", "However , the full implications of these results cannot be appr...	[ "All animals are associated with large consortia of non-pathogenic microbes .", "Most of these “microbiomes” are not well characterized despite their importance for many aspects of host biology including human and animal health and the agricultural impact of pest species .", "The fruit fly Drosophila melanogast...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "bacteriology", "escherichia coli", "systems biology", "bacterial physiology", "prokaryotic models", "model organisms", "biology", "microbiology", "microbial growth and development", "genetics and genomics" ]	Pre-Disposition and Epigenetics Govern Variation in Bacterial Survival upon Stress	journal.pgen.1003148	null	[ [ "Microbial phenotypic heterogeneity , defined as variability of a given trait in a genetically identical population in a homogeneous environment , has been repeatedly observed [1] , [2] .", "It is manifest , for example , in the broad distributions of individual gene expression levels recorded in studies ...	[ "Bacteria suffer various stresses in their unpredictable environment .", "In response , clonal populations may exhibit cell-to-cell variation , hypothetically to maximize their survival .", "The origins , propagation , and consequences of this variability remain poorly understood .", "Variability persists thr...	[ "Individual organisms of identical genetic background , living in a homogeneous constant environment , may nonetheless exhibit observable differences dubbed phenotypic plasticity or variability .", "When such a population is challenged with an unforeseen stress , the disparity among individuals may increase , yie...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/protozoal infections", "infectious diseases/neglected tropical diseases", "infectious diseases", "genetics and genomics/functional genomics" ]	Retention and Loss of RNA Interference Pathways in Trypanosomatid Protozoans	journal.ppat.1001161	null	[ [ "In metazoans , RNAi interference and related pathways play many key roles including regulation of mRNA levels and translation , chromatin silencing , programmed DNA rearrangements , genome surveillance , and defense against invading viruses .", "The phylogenetic distribution of key genes required for RNA...	[ "RNA interference ( RNAi ) pathways are widespread in metaozoans but the genes required show variable occurrence or activity in eukaryotic microbes , including many pathogens .", "While some Leishmania lack RNAi activity and Argonaute or Dicer genes , we show that Leishmania braziliensis and other species within ...	[ "RNAi interference pathways play fundamental roles in eukaryotes and provide important methods for the analysis of gene function .", "Occasionally RNAi has been lost , precluding its use as a tool , as well as raising the question of what forces could lead to loss of such a key pathway .", "Genomic and function...	2010
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Simulation Predicts IGFBP2-HIF1α Interaction Drives Glioblastoma Growth	journal.pcbi.1004169	null	[ [ "A variety of multiscale modeling methods has been used to describe the growth of solid tumors , including both discrete and continuous approaches .", "A non-inclusive set of references include [25–29] , along with several recent reviews [30–36] .", "Previous mathematical models of glioma progression ...	[ "Tremendous strides have been made in improving patients’ survival from cancer with one glaring exception: brain cancer .", "Glioblastoma is the most common , aggressive and highly malignant type of primary brain tumor .", "The average overall survival remains less than 1 year .", "Notably , cancer patients w...	[ "Current treatment for glioblastoma patients is limited to nonspecific methods: surgery followed by a combination of radio- and chemotherapy .", "With these methods , glioma patient survival is less than one year post-diagnosis .", "Targeting specific protein signaling pathways offers potentially more potent th...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Type I Interferon Induced Epigenetic Regulation of Macrophages Suppresses Innate and Adaptive Immunity in Acute Respiratory Viral Infection	journal.ppat.1005338	null	[ [ "IAV is an airborne pathogen that is responsible for significant mortality in humans [1] .", "Infection with seasonal strains of IAV is typically limited to the upper respiratory tract and causes mild to moderately severe respiratory disease .", "In contrast , highly pathogenic strains of IAV can spre...	[ "Influenza A virus ( IAV ) is an airborne pathogen that causes significant morbidity and mortality each year .", "Macrophages ( Mϕ ) are the first immune population to encounter IAV virions in the lungs and are required to control infection .", "In the present study , we explored the mechanism by which cytokine...	[ "IAV causes seasonal epidemics that result in significant morbidity and mortality annually .", "Less frequently , novel viral strains emerge and are responsible for much larger outbreaks around the globe .", "In the last pandemic in 2009 , an estimated 300 , 000 people died from IAV infection or secondary compl...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunology/innate immunity", "dermatology/skin infections", "dermatology/acne-like disorders", "dermatology/dermatologic pathology" ]	Production of Superoxide Anions by Keratinocytes Initiates P. acnes-Induced Inflammation of the Skin	journal.ppat.1000527	null	[ [ "Acne vulgaris is a chronic inflammatory disorder of the sebaceous follicles .", "Acne is the most common skin disease , estimated to affect up to 80% of individuals at some point between the ages of 11 and 30 years .", "Despite its common occurrence , the pathogenesis of acne is not fully understood ...	[ "Acne vulgaris is a chronic inflammatory disorder of the sebaceous follicles .", "Propionibacterium acnes ( P . acnes ) , a gram-positive anareobic bacterium , plays a critical role in the development of these inflammatory lesions .", "This study aimed at determining whether reactive oxygen species ( ROS ) are ...	[ "Acne vulgaris is a chronic inflammatory disorder of the sebaceous follicles .", "It is the most common skin disease , affecting up to 80% of individuals at some point between the ages of 11 and 30 years .", "Propionibacterium acnes ( P . acnes ) plays a role in the development of inflammatory acne lesions , bu...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "t helper cells", "innate immune system", "medicine and health sciences", "immune cells", "immune physiology", "cytokines", "enzyme-linked immunoassays", "immunology", "vaccines", "preventive medicine", "developmental biology", "molecular development", "vaccination and immun...	A Quantitative Analysis of Complexity of Human Pathogen-Specific CD4 T Cell Responses in Healthy M. tuberculosis Infected South Africans	journal.ppat.1005760	null	[ [ "Antigen-specific CD4 T cell responses are functionally very diverse , and have been classified into several different Th subsets based on their expression of distinct chemokine receptors , secretion of effector cytokines , and different transcriptional programs and differentiation states [1 , 2] .", "The...	[ "We performed a quantitative analysis of the HLA restriction , antigen and epitope specificity of human pathogen specific responses in healthy individuals infected with M . tuberculosis ( Mtb ) , in a South African cohort as a test case .", "The results estimate the breadth of T cell responses for the first time ...	[ "Human pathogen-specific immune responses are tremendously complex and the techniques to study them ever expanding .", "There is an urgent need for a quantitative analysis and better understanding of pathogen-specific immune responses .", "Mycobacterium tuberculosis ( Mtb ) is one of the leading causes of morta...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "cell biology", "virology", "infectious diseases/hiv infection and aids", "microbiology", "immunology/immunity to infections" ]	Proteasomal Degradation of TRIM5α during Retrovirus Restriction	journal.ppat.1000074	null	[ [ "Retroviruses exhibit a restricted host range due to the requirement for specific interactions between viral and host proteins to complete the viral life cycle .", "Also limiting retroviral tropism are several recently identified intracellular antiviral factors ( [1]–[5] ) ; reviewed in [6]–[10] ) .", ...	[ "The host protein TRIM5α inhibits retroviral infection at an early post-penetration stage by targeting the incoming viral capsid .", "While the detailed mechanism of restriction remains unclear , recent studies have implicated the activity of cellular proteasomes in the restriction of retroviral reverse transcrip...	[ "Recent studies have identified several cellular proteins that restrict infection by a variety of retroviruses .", "One of these restriction factors , TRIM5α , is partially responsible for the differences in susceptibility of monkeys and humans to SIV and HIV-1 , respectively .", "TRIM5α inhibits retrovirus inf...	2008
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "livestock", "medicine and health sciences", "pathology and laboratory medicine", "ruminants", "viral transmission and infection", "pathogens", "applied mathematics", "vector-borne diseases", "microbiology", "vertebrates", "bluetongue virus", "reoviruses", "animals", "mammals", "simulati...	Quantifying the roles of host movement and vector dispersal in the transmission of vector-borne diseases of livestock	journal.pcbi.1005470	null	[ [ "The role of host movements in the transmission of vector-borne diseases has largely been ignored [1 , 2] .", "Recently , however , several studies have quantified the importance of human movements for the spread of vector-borne diseases .", "Mobile phone data were used to infer mobility patterns and ...	[ "The role of host movement in the spread of vector-borne diseases of livestock has been little studied .", "Here we develop a mathematical framework that allows us to disentangle and quantify the roles of vector dispersal and livestock movement in transmission between farms .", "We apply this framework to outbr...	[ "Diseases which are transmitted by the bites of insects can be spread to new locations through the movement of both infected insects and infected hosts .", "The importance of these routes has implications for disease control , because we can often restrict host movement , and so potentially reduce spread , but ca...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "genome engineering", "control theory", "medicine and health sciences", "gene therapy", "mitochondrial dna", "engineering and technology", "nucleases", "enzymes", "synthetic biology", "dna-binding proteins", "enzymology", "plant energy production", "synthetic bioengineering", "control engi...	Energetic costs of cellular and therapeutic control of stochastic mitochondrial DNA populations	journal.pcbi.1007023	null	[ [ "Most human cells contain 100-10 , 000 copies of mitochondrial DNA ( mtDNA ) which are situated inside the mitochondria .", "The proteins encoded by mtDNA are crucial for mitochondrial functionality , and mutations in mtDNA can cause devastating diseases [1–6] .", "Heteroplasmy , the proportion of mut...	[ "The dynamics of the cellular proportion of mutant mtDNA molecules is crucial for mitochondrial diseases .", "Cellular populations of mitochondria are under homeostatic control , but the details of the control mechanisms involved remain elusive .", "Here , we use stochastic modelling to derive general results f...	[ "Mitochondria , best known for their role in energy production , are crucial to the survival of most of our cells .", "To respond to energetic demands and mitigate against mutational damage , cells control the mitochondrial populations within them .", "However , the character of these control mechanisms remains...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "antimicrobials", "medicine and health sciences", "pathology and laboratory medicine", "gene regulation", "melioidosis", "drugs", "immunology", "microbiology", "bacterial diseases", "sepsis", "signs and symptoms", "antibiotics", "epigenetics", "pharmacology", "immune system proteins", ...	Host gene expression analysis in Sri Lankan melioidosis patients	journal.pntd.0005643	null	[ [ "Melioidosis , an emerging infectious disease of public health importance in many tropical countries , is caused by the gram negative bacterium Burkholderia pseudomallei and is commonly reported in southeast Asia and northern Australia [1] .", "B . pseudomallei is an intracellular facultative pathogen , w...	[ "Melioidosis is a life threatening infectious disease caused by the gram-negative bacillus Burkholderia pseudomallei predominantly found in southeast Asia and northern Australia .", "Studying the host transcription profiles in response to infection is crucial for understanding disease pathogenesis and correlates ...	[ "Melioidosis is a life threatening infectious disease caused by a soil-associated gram-negative bacterium , B . pseudomallei .", "Melioidosis is endemic in southeast Asia and northern Australia; however , the global distribution of B . pseudomallei and the disease burden of melioidosis is still poorly understood ...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell death", "autophagic cell death", "medicine and health sciences", "pathology and laboratory medicine", "cell processes", "light microscopy", "fungal structure", "cereal crops", "rice", "model organisms", "microscopy", "crops", "mitochondria", "appressoria", "bioenergetics", "molec...	MoDnm1 Dynamin Mediating Peroxisomal and Mitochondrial Fission in Complex with MoFis1 and MoMdv1 Is Important for Development of Functional Appressorium in Magnaporthe oryzae	journal.ppat.1005823	null	[ [ "Dynamins are large GTPase superfamily proteins that are involved in scission ( cleavage of the vesicle from the parent membrane ) of nascent vesicles from parent membranes in eukaryotic cells [1] .", "Dynamins interact directly with the lipid bilayer at the necks of clathrin-coated pits to sever and rele...	[ "Dynamins are large superfamily GTPase proteins that are involved in various cellular processes including budding of transport vesicles , division of organelles , cytokinesis , and pathogen resistance .", "Here , we characterized several dynamin-related proteins from the rice blast fungus Magnaporthe oryzae and f...	[ "Dynamin superfamily members are involved in budding of transport vesicles and division of organelles in eukaryotic cells .", "To further understand how dynamins function in phytopathogenic fungi , we characterized several dynamin-related proteins from the rice blast fungus M . oryzae .", "In addition to reveal...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "fungal genetics", "computational biology", "fungi", "genome analysis", "genetic elements", "research and analysis methods", "genomic libraries", "mycology", "gene expression", "biological databases", "fungal genomics", "database and informatics methods", "genetics", "transposable elements...	Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles	journal.pgen.1006108	null	[ [ "Transposable elements ( TEs ) are mobile genetic units that colonize prokaryotic and eukaryotic genomes and generate intra- and inter-specific variability .", "Despite the ubiquity of TEs in the eukaryotic domain , the genome fraction occupied by these elements is highly diverse , accounting for approxim...	[ "Transposable elements ( TEs ) are exceptional contributors to eukaryotic genome diversity .", "Their ubiquitous presence impacts the genomes of nearly all species and mediates genome evolution by causing mutations and chromosomal rearrangements and by modulating gene expression .", "We performed an exhaustive ...	[ "Transposable elements ( TEs ) are enigmatic genetic units that have played important roles in the evolution of eukaryotic genomes .", "Since their discovery in the 1950s , they have gained increasing attention and are known today as active genome modelers in multiple species .", "Although these elements have b...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "plant anatomy", "medicine and health sciences", "pathology and laboratory medicine", "apoplastic space", "enzymes", "pathogens", "enzymology", "microbiology", "plant science", "crops", "cysteine proteases", "plant pathology", "plants", "bacteria", "bacterial pathogens", "pseudomonas",...	Screen of Non-annotated Small Secreted Proteins of Pseudomonas syringae Reveals a Virulence Factor That Inhibits Tomato Immune Proteases	journal.ppat.1005874	null	[ [ "Pseudomonas syringae is an important model system for plant-pathogen interactions .", "Different pathovars of this Gram-negative bacterium can cause disease on a broad variety of plants .", "Most intensively studied is pathovar tomato DC3000 ( PtoDC3000 ) , which causes bacterial speck disease on tom...	[ "Pseudomonas syringae pv .", "tomato DC3000 ( PtoDC3000 ) is an extracellular model plant pathogen , yet its potential to produce secreted effectors that manipulate the apoplast has been under investigated .", "Here we identified 131 candidate small , secreted , non-annotated proteins from the PtoDC3000 genome ...	[ "The extracellular space in the leaf ( the apoplast ) is colonized by a diversity of microbes that will have to deal with host-secreted hydrolytic enzymes , many of which accumulate during defence responses .", "We hypothesize that in addition to fungal and oomycete pathogens , the bacterial model plant pathogen ...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "biology and life sciences", "veterinary science" ]	Gentamicin-Attenuated Leishmania infantum Vaccine: Protection of Dogs against Canine Visceral Leishmaniosis in Endemic Area of Southeast of Iran	journal.pntd.0002757	null	[ [ "Leishmania infantum ( L . infantum ) is a causative agent of visceral leishmaniasis ( VL ) , which is a severe and frequently lethal protozoan disease of humans and dogs .", "Canine visceral leishmaniosis ( CVL ) is widely distributed in large areas of Europe , South America , the Middle-East , Central A...	[ "An attenuated line of Leishmania infantum ( L . infantum H-line ) has been established by culturing promastigotes in vitro under gentamicin pressure .", "A vaccine trial was conducted using 103 naive dogs from a leishmaniosis non-endemic area ( 55 vaccinated and 48 unvaccinated ) brought into an endemic area of ...	[ "A 24 month vaccine trial was conducted using 103 leishmania free dogs in an area of southeast Iran endemic for visceral leishmaniosis .", "The dogs were vaccinated with gentamicin-attenuated line of Leishmania infantum .", "No local and/or general indications of disease were observed in the vaccinated dogs imm...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Surveillance of Human Echinococcosis in Castilla-Leon (Spain) between 2000-2012	journal.pntd.0004154	null	[ [ "Human echinococcosis is a zoonotic infection caused by cestodes of the genus Echinococcus sp .", "Four species infect humans: cystic echinococcosis ( CE ) is caused by Echinococcus granulosus , alveolar echinococcosis ( AE ) is caused by E . multilocularis , and polycystic forms are caused by either E . ...	[ "Cystic echinococcosis ( CE ) is an important health problem in many areas of the world including the Mediterranean region .", "However , the real CE epidemiological situation is not well established .", "In fact , it is possible that CE is a re-emerging disease due to the weakness of current control programs ....	[ "The incidence of CE in our region is still high; however , in this period of study , a slow decrease was observed .", "The sharp decline of incidence in pediatric population highlights the importance of long-term control of CE .", "The systematic search of HDR may be a more accurate method than other methods i...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "animal models", "developmental biology", "model organisms", "skeletal development", "dna", "morphogenesis", "birth defects", "biology", "mouse", "molecular biology", "nucleic acids", "dna repair", "molecular cell biology" ]	Essential Developmental, Genomic Stability, and Tumour Suppressor Functions of the Mouse Orthologue of hSSB1/NABP2	journal.pgen.1003298	null	[ [ "Appropriate and timely repair of damaged DNA is critical for maintaining genomic integrity and tumour suppression [1] , [2] .", "DNA double-strand breaks ( DSBs ) are the most cytotoxic genomic lesions , and can arise from exogenous genotoxic insult , stalled replication forks , or during physiological p...	[ "Single-stranded DNA binding proteins ( SSBs ) regulate multiple DNA transactions , including replication , transcription , and repair .", "We recently identified SSB1 as a novel protein critical for the initiation of ATM signaling and DNA double-strand break repair by homologous recombination .", "Here we repo...	[ "Single-stranded DNA binding proteins ( SSBs ) play a variety of roles in the cell , regulating transcription , replication , and DNA repair .", "We recently identified and described a novel SSB , designated SSB1 , which was shown to be critical for DNA repair in the cell .", "In this study we have used a mouse...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "humoral immunity", "medicine", "vaccination", "clinical immunology", "immunity", "virology", "biology", "microbiology" ]	Dissection of Antibody Specificities Induced by Yellow Fever Vaccination	journal.ppat.1003458	null	[ [ "The live-attenuated yellow fever ( YF ) vaccine based on the 17D virus strain is considered to be one of the most successful vaccines ever produced [1] , [2] .", "Since its development in the 1930s by Max Theiler , several hundred million doses have been administered and its effectiveness in protecting f...	[ "The live attenuated yellow fever ( YF ) vaccine has an excellent record of efficacy and one dose provides long-lasting immunity , which in many cases may last a lifetime .", "Vaccination stimulates strong innate and adaptive immune responses , and neutralizing antibodies are considered to be the major effectors ...	[ "The live-attenuated yellow fever vaccine has been administered to more than 600 million people worldwide and is considered to be one of the most successful viral vaccines ever produced .", "Following injection , the apathogenic vaccine virus replicates in the vaccinee and induces antibodies that mediate virus ne...	2013
[ "Introduction", "Methods", "Results", "Discussion", "Acknowledgments" ]	[ "infectious diseases/neglected tropical diseases", "public health and epidemiology/infectious diseases", "evidence-based healthcare/statistical methodologies and health informatics", "ecology/population ecology", "infectious diseases/epidemiology and control of infectious diseases" ]	Modeling Disease Vector Occurrence when Detection Is Imperfect: Infestation of Amazonian Palm Trees by Triatomine Bugs at Three Spatial Scales	journal.pntd.0000620	null	[ [ "Chagas disease is caused by Trypanosoma cruzi ( Kinetoplastida: Trypanosomatidae ) , a parasitic protozoan transmitted through the feces of infected blood-sucking hemipterans ( Reduviidae: Triatominae ) [1] , [2] .", "Human infection is endemic throughout Latin America , where it causes loses of more tha...	[ "Failure to detect a disease agent or vector where it actually occurs constitutes a serious drawback in epidemiology .", "In the pervasive situation where no sampling technique is perfect , the explicit analytical treatment of detection failure becomes a key step in the estimation of epidemiological parameters ."...	[ "Blood-sucking bugs of the genus Rhodnius are major vectors of Chagas disease .", "Control and surveillance of Chagas disease transmission critically depend on ascertaining whether households and nearby ecotopes ( such as palm trees ) are infested by these vectors .", "However , no bug detection technique works...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "cell biology" ]	Enzymatic Blockade of the Ubiquitin-Proteasome Pathway	journal.pbio.1000605	A viral ubiquitin-specific protease domain blocks cellular protein turnover by preemptive removal of ubiquitin chains and establishes an essential role for deubiquitylation in the removal of unfolded proteins from the endoplasmic reticulum.	[ [ "Protein quality control and ubiquitin-dependent degradation are essential for cellular homeostasis and survival [1] .", "The ubiquitin-proteasome-system ( UPS ) is responsible for the turnover of most cytosolic proteins .", "Likewise , secreted and membrane proteins that do not fold properly or fail ...	[ "Ubiquitin-dependent processes control much of cellular physiology .", "We show that expression of a highly active , Epstein-Barr virus-derived deubiquitylating enzyme ( EBV-DUB ) blocks proteasomal degradation of cytosolic and ER-derived proteins by preemptive removal of ubiquitin from proteasome substrates , a ...	[ "Constant turnover of proteins is part of normal cellular physiology .", "Newly synthesized proteins that fail to fold are recognized by dedicated receptors and tagged for immediate degradation .", "The tag usually consists of a chain of a small protein , ubiquitin , and is recognized by the proteasome .", "W...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Drosophila TIM Binds Importin α1, and Acts as an Adapter to Transport PER to the Nucleus	journal.pgen.1004974	null	[ [ "The mechanisms that generate a circadian ( ~24 h ) clock within organisms have been a subject of investigation for many years .", "In Drosophila , the core clock mechanism consists of a negative feedback loop comprised of the period ( per ) and timeless ( tim ) genes [1] .", "Transcription of the per...	[ "Regulated nuclear entry of clock proteins is a conserved feature of eukaryotic circadian clocks and serves to separate the phase of mRNA activation from mRNA repression in the molecular feedback loop .", "In Drosophila , nuclear entry of the clock proteins , PERIOD ( PER ) and TIMELESS ( TIM ) , is tightly contr...	[ "In Drosophila , circadian rhythms are driven by a negative feedback loop that includes the key regulators , period ( per ) and timeless ( tim ) .", "To generate this feedback loop , PER and TIM proteins first accumulate in the cytoplasm and then translocate to the nucleus where PER represses transcription .", ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "sequence analysis", "genomics", "functional genomics", "evolutionary biology", "evolutionary modeling", "biology", "computational biology", "comparative genomics", "macromolecular structure analysis" ]	The FGGY Carbohydrate Kinase Family: Insights into the Evolution of Functional Specificities	journal.pcbi.1002318	null	[ [ "The large and functionally heterogeneous protein families that we see today result from long evolutionary processes with multiple duplications , gene losses , lateral gene transfers , and speciation events .", "The gene duplications usually leads to functional diversification within the family , for exam...	[ "Function diversification in large protein families is a major mechanism driving expansion of cellular networks , providing organisms with new metabolic capabilities and thus adding to their evolutionary success .", "However , our understanding of the evolutionary mechanisms of functional diversity in such famili...	[ "The protein universe is under constant expansion and is reshaping through multiple duplication , gene losses , lateral gene transfers , and speciation events .", "Large and functionally heterogeneous protein families that evolve through these processes contain conserved motifs and structural scaffolds , yet thei...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "animal models", "physiological processes", "developmental biology", "osteoblasts", "model organisms", "organism development", "bone", "homeostasis", "connective tissue cells", "experimental organism systems", "skeleton", "bone development", "research and an...	Conditional mouse models support the role of SLC39A14 (ZIP14) in Hyperostosis Cranialis Interna and in bone homeostasis	journal.pgen.1007321	null	[ [ "Hyperostosis Cranialis Interna ( HCI , OMIM 144755 ) is a rare bone disorder characterized by endosteal hyperostosis and osteosclerosis of the calvaria and the skull base .", "This results in the entrapment and dysfunction of cranial nerves I , II , V , VII and VIII , causing disturbances in smell , visi...	[ "Hyperostosis Cranialis Interna ( HCI ) is a rare bone disorder characterized by progressive intracranial bone overgrowth at the skull .", "Here we identified by whole-exome sequencing a dominant mutation ( L441R ) in SLC39A14 ( ZIP14 ) .", "We show that L441R ZIP14 is no longer trafficked towards the plasma me...	[ "Osteoporosis is a skeletal disorder affecting hundreds of millions of people , and is characterized by a low bone mineral density ( BMD ) and increased susceptibility to fracture .", "Genetic factors are the greatest determinants of BMD , but only a small fraction of these have been identified through genome-wid...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "helminths", "animals", "invertebrate genomics", "microsatellite loci", "genome analysis", "gene types", "molecular biology techniques", "research and analysis methods", "schistosoma japonicum", "genomic libraries", "genomics", "artificial gene amplification...	Whole Genome Amplification and Reduced-Representation Genome Sequencing of Schistosoma japonicum Miracidia	journal.pntd.0005292	null	[ [ "In China , schistosomiasis has been reduced from approximately 12 million cases in the 1950s to approximately 100 , 000 cases in 2014 , and public health officials are attempting to interrupt transmission of schistosomiasis nationwide [1–3] .", "The success of such programs has important implications for...	[ "In areas where schistosomiasis control programs have been implemented , morbidity and prevalence have been greatly reduced .", "However , to sustain these reductions and move towards interruption of transmission , new tools for disease surveillance are needed .", "Genomic methods have the potential to help tra...	[ "Schistosomiasis is a devastating tropical disease that affects more than 200 million people worldwide .", "Over the past several decades , transmission control strategies implemented in China have reduced the prevalence and morbidity of Schistosoma japonicum in many areas .", "Infections still persist , howeve...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "vesicles", "toxins", "pathology and laboratory medicine", "toxicology", "toxic agents", "materials science", "partial disruption of cell membrane", "oligomers", "cellular structures and organelles", "bacteria", "materials by structure", "research and analysis...	Listeriolysin O Membrane Damaging Activity Involves Arc Formation and Lineaction -- Implication for Listeria monocytogenes Escape from Phagocytic Vacuole	journal.ppat.1005597	null	[ [ "Listeriolysin-O ( LLO ) is Listeria monocytogenes powerful molecular weapon in host cell invasion , which is the first step of the disease listeriosis [1] .", "Following accidental ingestion of Listeria-contaminated food , healthy humans suffer from gastroenteritis , while immunocompromised individuals a...	[ "Listeriolysin-O ( LLO ) plays a crucial role during infection by Listeria monocytogenes .", "It enables escape of bacteria from phagocytic vacuole , which is the basis for its spread to other cells and tissues .", "It is not clear how LLO acts at phagosomal membranes to allow bacterial escape .", "The mechan...	[ "Listeriolysin-O ( LLO ) plays a crucial role in Listeria monocytogenes infection by allowing bacteria to escape from intracellular phagosomes and cells via an unknown molecular mechanism .", "We used high-speed atomic force microscopy ( HS-AFM ) supported with giant unilamellar vesicles imaging ( GUVs ) to chara...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "methods and resources", "cell viability testing", "pathology and laboratory medicine", "chemical compounds", "cell processes", "social sciences", "habits", "toxicology", "toxicity", "monomers (chemistry)", "materials science", "cell growth", "bioassays and ...	Evaluation of e-liquid toxicity using an open-source high-throughput screening assay	journal.pbio.2003904	null	[ [ "Electronic cigarettes ( E-cigs ) , also known as electronic nicotine delivery systems ( ENDS ) , are devices that deliver nicotine to the lung without combustion in a process known as “vaping” [1] .", "They differ from traditional cigarettes in that they do not contain tobacco , and—instead—they produce ...	[ "The e-liquids used in electronic cigarettes ( E-cigs ) consist of propylene glycol ( PG ) , vegetable glycerin ( VG ) , nicotine , and chemical additives for flavoring .", "There are currently over 7 , 700 e-liquid flavors available , and while some have been tested for toxicity in the laboratory , most have not...	[ "The e-liquids used in electronic cigarettes ( E-cigs ) typically consist of a mixture of propylene glycol ( PG ) , vegetable glycerin ( VG ) , and nicotine , as well as numerous chemical additives that are used for flavoring .", "There are currently over 7 , 700 different flavored e-liquids that are commercially...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The Ribosome Biogenesis Protein Nol9 Is Essential for Definitive Hematopoiesis and Pancreas Morphogenesis in Zebrafish	journal.pgen.1005677	null	[ [ "Ribosome biogenesis is a highly conserved and remarkably complex process that is essential for cell growth and proliferation .", "It utilizes 60% of total cellular transcription in a growing yeast cell , with 2 , 000 ribosomes synthesized every minute [1] .", "It requires the coordinated action of al...	[ "Ribosome biogenesis is a ubiquitous and essential process in cells .", "Defects in ribosome biogenesis and function result in a group of human disorders , collectively known as ribosomopathies .", "In this study , we describe a zebrafish mutant with a loss-of-function mutation in nol9 , a gene that encodes a n...	[ "The production of ribosomes , the protein-synthesizing machines , is fundamental in all cells .", "It is a very complex process that requires the coordinated actions of ribosomal and non-ribosomal proteins .", "Impairment of ribosome formation and function leads to a class of disorders known as “ribosomopathie...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "ecology/marine and freshwater ecology", "computational biology/ecosystem modeling", "ecology/community ecology and biodiversity", "mathematics/mathematical computing", "ecology/theoretical ecology", "ecology/population ecology" ]	How Microbial Community Composition Regulates Coral Disease Development	journal.pbio.1000345	Modeling reveals how rapid overgrowth by pathogenic microbes in the mucus layer surrounding corals, which often occurs under temporary stressful conditions, can persist long after environmental conditions return to normal.	[ [ "It appears that antibiotic activity and the competition between beneficial and potentially pathogenic microbes such as Vibrio spp .", "are key to understanding community dynamics within the SMC .", "In this paper , we develop models for how these interactions affect the outcome of competition within ...	[ "Reef coral cover is in rapid decline worldwide , in part due to bleaching ( expulsion of photosynthetic symbionts ) and outbreaks of infectious disease .", "One important factor associated with bleaching and in disease transmission is a shift in the composition of the microbial community in the mucus layer surro...	[ "An important correlate in bleaching and disease in reef-building corals is a shift in the makeup of the microbial community in the mucus layer surrounding the coral .", "Resident microbes critical to the healthy functioning of the coral organism are outcompeted by pathogenic microbes , often species of the Vibri...	2010
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "medicine and health sciences", "rna interference", "social sciences", "light", "animals", "electromagnetic radiation", "hormones", "animal models", "physiological processes", "developmental biology", "drosophila melanogaster", "model organisms", "animal behavior", "pupa...	Hormonal signaling cascades required for phototaxis switch in wandering Leptinotarsa decemlineata larvae	journal.pgen.1007423	null	[ [ "Movements to stage-dependent resources , i . e . , ontogenetic niche shifts ( hereafter ONS ) , occur in nearly 80% of animal taxa .", "The shifts enable animals to exploit several niches sequentially during their life cycles to meet stage-dependent nutritional requirements , to overcome stage-specific p...	[ "Many animals exploit several niches sequentially during their life cycles , a fitness referred to as ontogenetic niche shift ( ONS ) .", "To successfully accomplish ONS , transition between development stages is often coupled with changes in one or more primitive , instinctive behaviors .", "Yet , the underlin...	[ "Many animals occupy distinct niches and utilize diverse resources at different development stages in order to meet stage-dependent requirements and overcome stage-specific limitations .", "This fitness is referred to as ontogenetic niche shift ( ONS ) .", "During the preparation for ONS , animals often change ...	2019

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