Split (3)

train · 24.8k rows

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", "Methods", "Results", "Discussion", "Conclusions" ]	[ "geomorphology", "invertebrates", "typhus", "medicine and health sciences", "ixodes", "pathology and laboratory medicine", "landforms", "pathogens", "topography", "geographical locations", "microbiology", "animals", "bacterial diseases", "rickettsiales", "bacteria", "bacterial pathogen...	Human granulocytic anaplasmosis in Kinmen, an offshore island of Taiwan	journal.pntd.0007728	null	[ [ "Human granulocytic anaplasmosis ( HGA ) is an emerging rickettsial disease caused by Anaplasma phagocytophilum .", "Since it was first identified in the United States , HGA has been reported across Europe and in China , Japan , and South Korea [1–12] .", "The disease is transmitted by Ixodes ticks , ...	[ "Human granulocytic anaplasmosis , a tick-borne infection caused by Anaplasma phagocytophilum , has received scant attention , while scrub typhus , a mite-transmitted disease caused by Orientia tsutsugamushi , is the most common rickettsiosis in Taiwan .", "The clinical presentations of both diseases are characte...	[ "Human granulocytic anaplasmosis is a tick-borne rickettsial infection caused by Anaplasma phagocytophilum .", "Although most cases resolve readily , life-threatening complications can occur without prompt antibiotic treatment .", "The major difficulty in diagnosing human granulocytic anaplasmosis is due to the...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell physiology", "medicine and health sciences", "cardiovascular anatomy", "vertebrates", "animals", "endocrine physiology", "cell polarity", "animal models", "organisms", "developmental biology", "osteichthyes", "model organisms", "developmental signaling", "arteries", "growth factors...	Cyp26 Enzymes Facilitate Second Heart Field Progenitor Addition and Maintenance of Ventricular Integrity	journal.pbio.2000504	null	[ [ "The heart is the first organ to develop and function in all vertebrates .", "Improper heart development can lead to congenital heart defects ( CHDs ) , which impinge on normal embryogenesis and can result in embryonic or neonatal lethality [1 , 2] .", "Construction of a functional vertebrate heart re...	[ "Although retinoic acid ( RA ) teratogenicity has been investigated for decades , the mechanisms underlying RA-induced outflow tract ( OFT ) malformations are not understood .", "Here , we show zebrafish embryos deficient for Cyp26a1 and Cyp26c1 enzymes , which promote RA degradation , have OFT defects resulting ...	[ "Retinoic acid ( RA ) is the most active metabolic product of vitamin A . The embryonic heart is particularly sensitive to inappropriate RA levels , with cardiac outflow tract ( OFT ) defects among the most common RA-induced malformations .", "However , the mechanisms underlying these RA-induced defects are not u...	2016
[ "Introduction", "Discussion", "Materials and Methods" ]	[ "molecular biology/recombination", "genetics and genomics/chromosome biology" ]	New Insights into Human Nondisjunction of Chromosome 21 in Oocytes	journal.pgen.1000033	null	[ [ "The overwhelming majority of trisomy 21 , or Down syndrome , is caused by the failure of chromosomes to separate properly during meiosis , also known as chromosome nondisjunction .", "As nondisjunction is the leading cause of pregnancy loss , mental retardation and birth defects , it is imperative that w...	[ "Nondisjunction of chromosome 21 is the leading cause of Down syndrome .", "Two risk factors for maternal nondisjunction of chromosome 21 are increased maternal age and altered recombination .", "In order to provide further insight on mechanisms underlying nondisjunction , we examined the association between th...	[ "Nondisjunction occurs when chromosomes fail to segregate during meiosis; when this happens , gametes with an abnormal number of chromosomes are produced .", "The clinical significance is high: nondisjunction is the leading cause of pregnancy loss and birth defects .", "We have studied trisomy 21 using DNA from...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology/germ cells", "molecular biology/chromatin structure", "molecular biology/histone modification", "developmental biology/stem cells", "genetics and genomics/chromosome biology", "genetics and genomics/epigenetics", "developmental biology/developmental molecular mechanisms", "cell ...	Regulation of Heterochromatin Assembly on Unpaired Chromosomes during Caenorhabditis elegans Meiosis by Components of a Small RNA-Mediated Pathway	journal.pgen.1000624	null	[ [ "During sexual reproduction , mutations existing in the gametes will be inherited by the offspring .", "Therefore , it is essential that gametes contain accurate copies of the genetic information .", "Through evolution , multiple mechanisms have been developed to safeguard gamete quality .", "One ...	[ "Many organisms have a mechanism for down regulating the expression of non-synapsed chromosomes and chromosomal regions during meiosis .", "This phenomenon is thought to function in genome defense .", "During early meiosis in Caenorhabditis elegans , unpaired chromosomes ( e . g . , the male X chromosome ) beco...	[ "DNA within a cell's nucleus is packaged together with proteins into a higher order structure called chromatin .", "In its simplest form , chromatin consists of DNA and a set of proteins called histones , arranged so that the DNA strand is wrapped around histone protein clusters .", "This basic chromatin struct...	2009
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "soil-transmitted helminths", "trichuriasis", "hookworm infection", "neglected tropical diseases", "infectious disease control", "ascariasis", "parasitic diseases", "helminth infection" ]	Association between Response to Albendazole Treatment and β-Tubulin Genotype Frequencies in Soil-transmitted Helminths	journal.pntd.0002247	null	[ [ "Ascaris lumbricoides ( roundworm ) , Trichuris trichiura ( whipworm ) and Necator americanus/Ancylostoma duodenale ( hookworms ) are the most common species of soil-transmitted helminths infecting humans worldwide .", "More than a billion people are infected with at least one species and 300 million are ...	[ "Albendazole ( ABZ ) , a benzimidazole ( BZ ) anthelmintic ( AH ) , is commonly used for treatment of soil-transmitted helminths ( STHs ) .", "Its regular use increases the possibility that BZ resistance may develop , which , in veterinary nematodes is caused by single nucleotide polymorphisms ( SNPs ) in the β-t...	[ "The soil-transmitted helminths ( STH ) Ascaris lumbricoides , Trichuris trichiura and the hookworms Ancylostoma duodenale and Necator americanus are endemic in many tropical countries .", "Regular treatment with albendazole or mebendazole is the major means for controlling STHs .", "However , repeated treatmen...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genomics", "model organisms", "genetics", "biology", "computational biology", "evolutionary biology", "population biology", "genetics and genomics" ]	Phylogenomic Analysis Reveals Dynamic Evolutionary History of the Drosophila Heterochromatin Protein 1 (HP1) Gene Family	journal.pgen.1002729	null	[ [ "Comparative genomics has revolutionized analysis of eukaryotic genome structure , function , and evolution .", "Genome sequencing efforts that encompass both closely and distantly related species have led to the identification of protein- and RNA-coding genes as well as noncoding regulatory sequence on a...	[ "Heterochromatin is the gene-poor , satellite-rich eukaryotic genome compartment that supports many essential cellular processes .", "The functional diversity of proteins that bind and often epigenetically define heterochromatic DNA sequence reflects the diverse functions supported by this enigmatic genome compar...	[ "Our genome is comprised of two compartments .", "The euchromatin harbors abundant genes and regulatory information , while heterochromatin harbors few genes and abundant repetitive DNA .", "These characteristic features of heterochromatin challenge traditional methods of sequence assembly and molecular dissect...	2012
[ "Introduction", "Results and Discussion", "Materials and Methods" ]	[]	Survival Kinetics of Starving Bacteria Is Biphasic and Density-Dependent	journal.pcbi.1004198	null	[ [ "Under favorable growth conditions , microorganisms can grow rapidly .", "For example , E . coli cells can grow as fast as ∼ 20 min per doubling under ideal growth conditions .", "If this rate continues , a single E . coli bacterium can generate the mass of the earth in a couple of days .", "Clear...	[ "In the lifecycle of microorganisms , prolonged starvation is prevalent and sustaining life during starvation periods is a vital task .", "In the literature , it is commonly assumed that survival kinetics of starving microbes follows exponential decay .", "This assumption , however , has not been rigorously tes...	[ "Long periods of starvation are common in the lifecycle of microorganisms .", "Textbooks routinely describe that during starvation periods , cells die at a constant rate , i . e . , exponential decay .", "The exponential decay of cell survival has been commonly assumed in the literature to analyze and predict p...	2015
[ "Introduction", "Results", "Methods" ]	[ "chemical compounds", "monomers", "phosphates", "electricity", "nucleotides", "electrostatics", "materials science", "oligomers", "thermodynamics", "physical chemistry", "chemical properties", "polymer chemistry", "guanine", "dimerization", "chemistry", "adenine", "free energy", "p...	Why do G-quadruplexes dimerize through the 5’-ends? Driving forces for G4 DNA dimerization examined in atomic detail	journal.pcbi.1007383	null	[ [ "G-quadruplexes ( G4 ) are non-canonical four-stranded structures formed by guanine-rich sequences of nucleic acids , in which sets of four guanine residues associate into planar arrays ( G-tetrads ) through cyclic Hoogsteen hydrogen bonding [1–3] .", "By stacking on top of each other , G-tetrads make up ...	[ "G-quadruplexes ( G4 ) are secondary structures formed by guanine-rich nucleic acid sequences and shown to exist in living cells where they participate in regulation of gene expression and chromosome maintenance .", "G-quadruplexes with solvent-exposed guanine tetrads show the tendency to associate together throu...	[ "Native DNA usually folds to form the canonical double helix , however , under certain conditions , it can also fold into other secondary structures .", "Some of the most interesting ones are G-quadruplexes ( G4 ) —compact DNA structures in which guanines assemble into multilayered tetrads , and whose formation h...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "engineering and technology", "african trypanosomiasis", "tropical diseases", "social sciences", "neuroscience", "parasitic diseases", "optimization", "mathematics", "materials science", "neglected tropical diseases", "vision", "eyes", "macromolecules", "m...	Developing photoreceptor-based models of visual attraction in riverine tsetse, for use in the engineering of more-attractive polyester fabrics for control devices	journal.pntd.0005448	null	[ [ "There are two forms of HAT , each caused by a different subspecies of Trypanosoma brucei .", "A small minority of cases ( ca . 2% ) comprise an acute disease termed Rhodesian HAT that occurs in Eastern and Southern Africa [1] .", "These cases are caused by T . b .", "rhodesiense for which savanna...	[ "Riverine tsetse transmit the parasites that cause the most prevalent form of human African trypanosomiasis , Gambian HAT .", "In response to the imperative for cheap and efficient tsetse control , insecticide-treated ‘tiny targets’ have been developed through refinement of tsetse attractants based on blue fabric...	[ "Tsetse flies transmit the parasites that cause sleeping sickness .", "Tsetse control can contribute to disease control thanks to cheap and efficient ‘tiny targets’ that attract tsetse using a panel of blue fabric , a highly attractive colour for the flies .", "However , the modern blue polyesters employed are ...	2017
[ "Results", "Discussion", "Materials and methods" ]	[ "cell walls", "plant anatomy", "chemical compounds", "cellulose", "plant cell biology", "light microscopy", "organic compounds", "pollen", "plant cell walls", "plant science", "microscopy", "plants", "cellular structures and organelles", "research and analysis methods", "pollen tube", ...	The brown algal mode of tip growth: Keeping stress under control	journal.pbio.2005258	null	[ [ "The prostrate filaments of the alga Ectocarpus develop via tip growth [28] .", "Prior to identifying the underlying mechanisms , a series of additional biophysical information was collected .", "The cell wall dye calcofluor-white was used in pulse-chase experiments to measure the growing region more ...	[ "Tip growth has been studied in pollen tubes , root hairs , and fungal and oomycete hyphae and is the most widely distributed unidirectional growth process on the planet .", "It ensures spatial colonization , nutrient predation , fertilization , and symbiosis with growth speeds of up to 800 μm h−1 .", "Although...	[ "Tip growth is known in organisms with filament-like structures , such as fungi ( e . g . , hyphae ) , plants ( e . g . , root hairs , moss protonemata ) , and algae ( e . g . , filamentous thalli ) .", "The driving force for growth in these organisms is the difference in osmotic pressure ( turgor ) between the i...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "body weight", "medicine and health sciences", "animal diseases", "immune cells", "immunology", "tropical diseases", "vertebrates", "parasitic diseases", "animals", "mammals", "animal models", "animal prion diseases", "routes of administration", "model organisms", "physi...	A Single Subcutaneous Injection of Cellulose Ethers Administered Long before Infection Confers Sustained Protection against Prion Diseases in Rodents	journal.ppat.1006045	null	[ [ "Prion diseases or transmissible spongiform encephalopathies are fatal neurodegenerative conditions caused by prion accumulation in the brain and lymphoreticular system [1] .", "Creutzfeldt–Jakob disease is the most common human prion disease that sporadically occurs mostly in the elderly .", "The num...	[ "Prion diseases are fatal , progressive , neurodegenerative diseases caused by prion accumulation in the brain and lymphoreticular system .", "Here we report that a single subcutaneous injection of cellulose ethers ( CEs ) , which are commonly used as inactive ingredients in foods and pharmaceuticals , markedly p...	[ "Prion diseases are progressive , fatal , neurodegenerative transmissible illnesses in humans and animals caused by prion accumulation in the brain and lymphoreticular system .", "Because they are prevalent in nature , with atypical forms continuing to emerge , prion diseases are potential threats to both public ...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "neuroscience", "cell biology" ]	Bergmann Glia and the Recognition Molecule CHL1 Organize GABAergic Axons and Direct Innervation of Purkinje Cell Dendrites	journal.pbio.0060103	Subcellular synapse organization regulates the input, integration, and output of target neurons. An astroglial scaffold and an L1 family cell adhesion molecule contribute to dendritic innervation by GABA inhibitory synapses.	[ [ "Neurons are often characterized by striking polarity and extensive subcellular specialization .", "For example , large principal neurons in many vertebrate neural circuits consist of distinct anatomical and physiological compartments [1] , which allow distributed and compartmentalized signaling [2–4] , a...	[ "The geometric and subcellular organization of axon arbors distributes and regulates electrical signaling in neurons and networks , but the underlying mechanisms have remained elusive .", "In rodent cerebellar cortex , stellate interneurons elaborate characteristic axon arbors that selectively innervate Purkinje ...	[ "Large principal neurons in vertebrate neural circuits often consist of distinct anatomical and physiological compartments , which allow distributed and compartmentalized signaling and greatly increase the computational power of single neurons .", "Superimposed upon this intrinsic compartmental architecture is th...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "infectious diseases", "in vitro", "immunology", "mus (mouse)", "animals", "eubacteria" ]	Macrophage Activation Redirects Yersinia-Infected Host Cell Death from Apoptosis to Caspase-1-Dependent Pyroptosis	journal.ppat.0030161	null	[ [ "The genus Yersinia includes three species pathogenic for humans: Yersinia pestis , the causative agent of plague , and Y . entercolitica and Y . pseudotuberculosis , which cause gastroenteritis and lymphadenitis and occasionally systemic infection .", "All pathogenic Yersinia species harbor a 70 kb virul...	[ "Infection of macrophages by Yersinia species results in YopJ-dependent apoptosis , and naïve macrophages are highly susceptible to this form of cell death .", "Previous studies have demonstrated that macrophages activated with lipopolysaccharide ( LPS ) prior to infection are resistant to YopJ-dependent cell dea...	[ "Pathogenic Yersinia are bacteria capable of interacting with host immune cells and inhibiting their function .", "Macrophages are potent antimicrobial immune cells that eliminate invading microbes , and represent a major target for Yersinia during infection .", "Yersinia triggers death of resting macrophages b...	2007
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "pharmacology/drug development" ]	A Novel Tropically Stable Oral Amphotericin B Formulation (iCo-010) Exhibits Efficacy against Visceral Leishmaniasis in a Murine Model	journal.pntd.0000913	null	[ [ "Visceral leishmaniasis ( VL ) is a systemic form of a vector-borne parasitic disease caused by obligate intra-macrophage protozoa of the genus Leishmania .", "VL is transmitted via the bite of an infected sand fly [1] , [2] .", "The parasites are then disseminated through the vascular and lymphatic s...	[ "To develop an oral formulation of amphotericin B ( AmB ) that is stable at the temperatures of WHO Climatic Zones 3 and 4 ( 30–43°C ) and to evaluate its efficacy in a murine model of visceral leishmaniasis ( VL ) .", "The stability testing of four novel oral lipid AmB formulations composed of mono- and di-glyce...	[ "Visceral leishmaniasis ( VL ) is a systemic form of a vector-borne parasitic disease caused by obligate intra-macrophage protozoa of the genus Leishmania .", "VL is always fatal in humans if left untreated and treatment options are limited .", "Amphotericin B ( AmB ) , a polyene antibiotic , is the most active...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "circadian rhythms", "chronobiology", "biology and life sciences", "proteomics", "circadian oscillators", "daylight" ]	The Proteomic Landscape of the Suprachiasmatic Nucleus Clock Reveals Large-Scale Coordination of Key Biological Processes	journal.pgen.1004695	null	[ [ "Proper temporal organization of behavioral , physiological and biochemical processes and their synchronization with the environmental light/dark cycle are fundamental features of most organisms [1] .", "In mammals , the central pacemaker that coordinates this adaptive response to temporal cues resides in...	[ "The suprachiasmatic nucleus ( SCN ) acts as the central clock to coordinate circadian oscillations in mammalian behavior , physiology and gene expression .", "Despite our knowledge of the circadian transcriptome of the SCN , how it impacts genome-wide protein expression is not well understood .", "Here , we in...	[ "The suprachiasmatic nucleus ( SCN ) serves as the master circadian pacemaker in mammals , coordinating the physiological responses of a myriad of peripheral clocks throughout the body and linking their rhythms to the environmental light-dark cycle .", "In this study , we interrogated the murine SCN proteome acro...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "blood cells", "livestock", "viral vaccines", "medicine and health sciences", "immune cells", "immune physiology", "pathology and laboratory medicine", "pathogens", "immunology", "messenger rna", "microbiology", "vertebrates", "animals", "mammals", "vaccines", "preventive medicine", ...	An mRNA Vaccine Encoding Rabies Virus Glycoprotein Induces Protection against Lethal Infection in Mice and Correlates of Protection in Adult and Newborn Pigs	journal.pntd.0004746	null	[ [ "Rabies is an invariably fatal neurological disease that affects different species of warm-blooded animals , including wild animals , pets , and humans .", "This infectious disease is caused by a strictly neurotropic virus .", "The rabies virus has a bullet-shaped , enveloped virion with a negative-se...	[ "Rabies is a zoonotic infectious disease of the central nervous system ( CNS ) .", "In unvaccinated or untreated subjects , rabies virus infection causes severe neurological symptoms and is invariably fatal .", "Despite the long-standing existence of effective vaccines , vaccine availability remains insufficien...	[ "Although first successful vaccination against rabies virus infection was performed by Louis Pasteur in the 19th century , every year about 50 , 000 patients , predominantly children , succumb to rabies infection because of insufficient availability of effective low-cost vaccines worldwide .", "The work presented...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "flow cytometry", "medicine and health sciences", "luciferase", "immune cells", "pathology and laboratory medicine", "enzymes", "pathogens", "immune activation", "immunology", "microbiology", "enzymology", "vertebrates", "animals", "mammals", "retroviruses", "viruses",...	Primate lentiviruses use at least three alternative strategies to suppress NF-κB-mediated immune activation	journal.ppat.1006598	null	[ [ "Cells are equipped with a plethora of pattern recognition receptors ( PRRs ) that induce an antiviral immune response upon sensing of patterns associated with viral infection .", "Among them are cytosolic receptors such as cGAS , PQBP1 , IFI16 , and RIG-I recognizing viral DNA or RNA species , as well as...	[ "Primate lentiviruses have evolved sophisticated strategies to suppress the immune response of their host species .", "For example , HIV-2 and most simian immunodeficiency viruses ( SIVs ) use their accessory protein Nef to prevent T cell activation and antiviral gene expression by downmodulating the T cell recep...	[ "The cellular transcription factor NF-κB plays a complex role in the lentiviral replication cycle .", "On the one hand , activation of NF-κB is required for efficient transcription of viral genes and reactivation of latent proviruses .", "On the other hand , NF-κB is also a key driver of antiviral gene expressi...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "chemical compounds", "engineering and technology", "sports and exercise medicine", "enzymology", "carbohydrates", "physical activity", "organic compounds", "glucose", "metabolites", "materials science", "enzyme metabolism", "mitochondria", "bioenergetics", ...	Systems-level computational modeling demonstrates fuel selection switching in high capacity running and low capacity running rats	journal.pcbi.1005982	null	[ [ "Fuel selection , the balancing of glucose , fatty acids , and amino acid utilization to match the ATP demand , is a hallmark of healthy metabolism [1] .", "It has been shown that endurance trained individuals can better maintain the oxidation of fatty acid ( FA ) throughout mild to moderate intensity exe...	[ "High capacity and low capacity running rats , HCR and LCR respectively , have been bred to represent two extremes of running endurance and have recently demonstrated disparities in fuel usage during transient aerobic exercise .", "HCR rats can maintain fatty acid ( FA ) utilization throughout the course of trans...	[ "Our bodies consume carbohydrates , fats , and amino acids as fuels , utilizing various catabolic pathways to transfer the energy required for normal physiological functions .", "The way these pathways function can have an important impact on overall health .", "While most catabolic pathways are known , we are ...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "diagnostic radiology", "granulomas", "immunology", "vertebrates", "animals", "mammals", "primates", "dna libraries", "dna", "bacteria", "old world monkeys", "research and analysis methods", "white blood cells", "imaging ...	Concurrent infection with Mycobacterium tuberculosis confers robust protection against secondary infection in macaques	journal.ppat.1007305	null	[ [ "There has been significant debate as to whether natural Mtb infection confers protection against reinfection .", "Epidemiologic studies from the pre-antibiotic era suggest that primary Mycobacterium tuberculosis ( Mtb ) infection provides up to 80% protection against TB disease due to secondary exposure[...	[ "For many pathogens , including most targets of effective vaccines , infection elicits an immune response that confers significant protection against reinfection .", "There has been significant debate as to whether natural Mycobacterium tuberculosis ( Mtb ) infection confers protection against reinfection .", "...	[ "Tuberculosis ( TB ) , a lung disease caused by the bacterial pathogen Mycobacterium tuberculosis , is endemic in many developing countries .", "This infection is transmitted from a person with active tuberculosis through coughing , talking , and singing .", "Exposure to this bacterium can result in a spectrum ...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular biology/post-translational regulation of gene expression", "genetics and genomics/gene discovery", "genetics and genomics/gene expression", "genetics and genomics/functional genomics", "molecular biology/rna splicing", "developmental biology/developmental molecular mechanisms" ]	PPS, a Large Multidomain Protein, Functions with Sex-Lethal to Regulate Alternative Splicing in Drosophila	journal.pgen.1000872	null	[ [ "Understanding tissue- and stage-specific gene regulation remains one of the central issues in developmental biology .", "Studies of developmentally important genes , such as those that specify and maintain cell fate , have revealed that many genes are regulated post-transcriptionally .", "The Drosoph...	[ "Alternative splicing controls the expression of many genes , including the Drosophila sex determination gene Sex-lethal ( Sxl ) .", "Sxl expression is controlled via a negative regulatory mechanism where inclusion of the translation-terminating male exon is blocked in females .", "Previous studies have shown t...	[ "In Drosophila the sex-specific ON/OFF regulation of Sex-lethal ( Sxl ) is controlled by an autoregulatory splicing mechanism that depends on the SXL protein interacting with general splicing factors .", "Here we identify PPS as a novel component of the machinery required for Sxl splicing autoregulation by showin...	2010
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "chemical compounds", "gene regulation", "metabolic processes", "pathogens", "regulatory proteins", "microbiology", "dna-binding proteins", "carbohydrates", "organic compounds", "glucose", "fungi", "regulator genes", "e...	Integration of the tricarboxylic acid (TCA) cycle with cAMP signaling and Sfl2 pathways in the regulation of CO2 sensing and hyphal development in Candida albicans	journal.pgen.1006949	null	[ [ "The ubiquitous tricarboxylic acid ( TCA ) cycle is a central pathway for the metabolism of carbon sources , lipids , and amino acids , and provides a major energy source for the cell under aerobic conditions .", "It is composed of a set of enzymes , which are required for the generation of NADH and FADH2...	[ "Morphological transitions and metabolic regulation are critical for the human fungal pathogen Candida albicans to adapt to the changing host environment .", "In this study , we generated a library of central metabolic pathway mutants in the tricarboxylic acid ( TCA ) cycle , and investigated the functional conse...	[ "Energy metabolism through the TCA cycle and mitochondrial electron transport are critical for the human fungal pathogen Candida albicans to survive and propagate in the host .", "This is , in part , due to the fact that C . albicans is a Crabtree-negative species , and thus exclusively uses respiration when oxyg...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	SmD1 Modulates the miRNA Pathway Independently of Its Pre-mRNA Splicing Function	journal.pgen.1005475	null	[ [ "miRNAs are a class of ~22–24 nt endogenous regulatory RNAs present in all cell types of multicellular organisms [1 , 2] .", "By regulating the expression of diverse target RNAs , miRNAs play a key role in myriad biological processes including development , homeostasis , and innate immunity .", "In Dr...	[ "microRNAs ( miRNAs ) are a class of endogenous regulatory RNAs that play a key role in myriad biological processes .", "Upon transcription , primary miRNA transcripts are sequentially processed by Drosha and Dicer ribonucleases into ~22–24 nt miRNAs .", "Subsequently , miRNAs are incorporated into the RNA-indu...	[ "microRNAs ( miRNAs ) are a class of small regulatory RNAs that fine-tune gene expression by reducing protein output from their target messenger RNAs and are implicated in myriad physiological and pathological processes .", "miRNAs are generated from long primary transcripts via sequential actions of the Drosha/P...	2015
[ "Introduction", "Results", "Discussion", "Materials & Methods" ]	[]	A Mechanism for the Inhibition of DNA-PK-Mediated DNA Sensing by a Virus	journal.ppat.1003649	null	[ [ "The battle between host and pathogen has driven the evolution of the immune system and of pathogens .", "The result of this on-going fight is the development of sophisticated host detection and response systems and also of elegant pathogen subversion mechanisms [1] , [2] .", "As part of the innate im...	[ "The innate immune system is critical in the response to infection by pathogens and it is activated by pattern recognition receptors ( PRRs ) binding to pathogen associated molecular patterns ( PAMPs ) .", "During viral infection , the direct recognition of the viral nucleic acids , such as the genomes of DNA vir...	[ "To mount an immune response to an invading bacterium or virus ( pathogens ) , the host must detect foreign molecules from the pathogen .", "Pathogens have conserved features called pathogen associated molecular patterns ( PAMPs ) that are distinct from host cells and which are recognised by the host using specif...	2013
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "organismal evolution", "plant anatomy", "population genetics", "variant genotypes", "microbiology", "genetic mapping", "plant science", "effective population size", "microbial evolution", "population biology", "leaves", "evolutionary genetics", "viral evolution", "genetic drift", "popul...	Estimating virus effective population size and selection without neutral markers	journal.ppat.1006702	null	[ [ "Evolution in isolated populations results from the interplay between several forces , including mutation , selection , and genetic drift .", "Mutation creates genetic diversity within a population .", "Subsequent selection and genetic drift drive the evolution of diversity within the population .", ...	[ "By combining high-throughput sequencing ( HTS ) with experimental evolution , we can observe the within-host dynamics of pathogen variants of biomedical or ecological interest .", "We studied the evolutionary dynamics of five variants of Potato virus Y ( PVY ) in 15 doubled-haploid lines of pepper .", "All pla...	[ "A growing number of experimental evolution studies are using an “evolve-and-resequence” approach to observe the within-host dynamics of pathogen variants of biomedical or ecological interest .", "The resulting data are particularly appropriate for studying the effects of evolutionary forces , such as selection a...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public health and epidemiology", "epidemiological methods", "epidemiology", "biology", "microbiology", "public health", "parasitology" ]	An In-Depth Analysis of a Piece of Shit: Distribution of Schistosoma mansoni and Hookworm Eggs in Human Stool	journal.pntd.0001969	null	[ [ "Although schistosomiasis and soil-transmitted helminthiasis affect hundreds of millions of people and account for more than 40% of the global burden due to neglected tropical diseases , parasitic worm infections are often still neglected [1]–[3] .", "An accurate diagnosis is necessary for adequate patien...	[ "An accurate diagnosis of helminth infection is important to improve patient management .", "However , there is considerable intra- and inter-specimen variation of helminth egg counts in human feces .", "Homogenization of stool samples has been suggested to improve diagnostic accuracy , but there are no detaile...	[ "An accurate diagnosis of parasitic worm ( helminth ) infections is important for adequate patient treatment and disease control programs .", "Helminth eggs in human stool samples are used as an indicator of infection intensity and morbidity .", "However , little is known about the exact distribution of helmint...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "ecology", "evolutionary biology", "rattus (rat)" ]	Generalized Reciprocity in Rats	journal.pbio.0050196	Empirical evidence from rats supports the theory of generalized reciprocity, in which individuals are more likely to cooperate with an unknown individual if they have received help in the past.	[ [ "Cooperation among unrelated individuals may be achieved by reciprocal altruism in which two or more individuals help each other in turn [1 , 2] .", "The decision to cooperate is based on expected future help , which may be judged from past interactions .", "Most theoretical models of reciprocal altru...	[ "The evolution of cooperation among nonrelatives has been explained by direct , indirect , and strong reciprocity .", "Animals should base the decision to help others on expected future help , which they may judge from past behavior of their partner .", "Although many examples of cooperative behavior exist in n...	[ "The evolution of cooperation is based on four general mechanisms: mutualism , where an action benefits all partners directly; kin selection , where related individuals are supported; “green beard” altruism that is based on a genetic correlation between altruism genes and respective markers; and reciprocal altruism...	2007
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "spectrometric identification of proteins", "rna-binding proteins", "medicine and health sciences", "pathology and laboratory medicine", "gene regulation", "protein interaction networks", "microbiology", "stable isotope labeling by amino acids in cell culture", "viruses", "rna viruses", "network...	Identification of RNA Binding Proteins Associated with Dengue Virus RNA in Infected Cells Reveals Temporally Distinct Host Factor Requirements	journal.pntd.0004921	null	[ [ "Dengue is a mosquito-borne viral disease that infects 50–100 million people annually , resulting in dengue fever that is either asymptomatic or flu-like .", "However , tens-of-thousands of people develop the more severe , and sometimes fatal , dengue hemorrhagic fever/shock syndrome ( DHF/DSS ) [1] .", ...	[ "There are currently no vaccines or antivirals available for dengue virus infection , which can cause dengue hemorrhagic fever and death .", "A better understanding of the host pathogen interaction is required to develop effective therapies to treat DENV .", "In particular , very little is known about how cellu...	[ "DENV is the most important mosquito transmitted viral disease in humans causing almost 400 million infections each year .", "Early detection is possible; however , there are no antivirals or vaccines available for this potentially lethal virus .", "Host factors that are required for viral amplification provide...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell differentiation", "animal models", "developmental biology", "drosophila melanogaster", "model organisms", "organism development", "molecular development", "morphogenesis", "pattern formation", "adhesion molecules", "biology", "morphogens", "signaling", "cell fate determination" ]	A Feed-Forward Loop Coupling Extracellular BMP Transport and Morphogenesis in Drosophila Wing	journal.pgen.1003403	null	[ [ "A key question in developmental biology is to address how tissue morphogenesis is regulated by a variety of extracellular signals .", "This includes identification of such extracellular signaling molecules and intracellular mechanisms that trigger morphogenesis .", "Since arrival of extracellular fac...	[ "A variety of extracellular factors regulate morphogenesis during development .", "However , coordination between extracellular signaling and dynamic morphogenesis is largely unexplored .", "We address the fundamental question by studying posterior crossvein ( PCV ) development in Drosophila as a model , in whi...	[ "It has been extensively studied how tissue morphogenesis is regulated by a variety of extracellular cues .", "Given that dynamic morphogenesis coincides with arrival of extracellular factors , there must be also mechanisms that coordinate extracellular signaling and intracellular morphogenesis .", "However , t...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunology/immune response", "public health and epidemiology/infectious diseases", "infectious diseases/protozoal infections", "infectious diseases/tropical and travel-associated diseases", "immunology/immunity to infections" ]	Long-Lived Antibody and B Cell Memory Responses to the Human Malaria Parasites, Plasmodium falciparum and Plasmodium vivax	journal.ppat.1000770	null	[ [ "Malaria , a parasitic disease of humans caused predominantly by two species of Plasmodium , P . falciparum and P . vivax , remains an important cause of mortality and morbidity in many parts of the world .", "Development of a vaccine against malaria has proven challenging due to the complex nature of the...	[ "Antibodies constitute a critical component of the naturally acquired immunity that develops following frequent exposure to malaria .", "However , specific antibody titres have been reported to decline rapidly in the absence of reinfection , supporting the widely perceived notion that malaria infections fail to i...	[ "It is widely perceived that immunity to malaria is short-lived , rendering people susceptible to repeated malaria infections .", "However , there have been very few studies on “memory” responses , how the human immune system recognizes previously encountered malaria parasites .", "In particular , very little i...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "mathematics", "drosophila", "developmental biology" ]	Self-organizing Mechanism for Development of Space-filling Neuronal Dendrites	journal.pcbi.0030212	null	[ [ "One of the primary interests in developmental biology is the emergence of function through morphogenesis .", "Morphological diversity of dendrites and its impact on neuronal computation perfectly represents the importance of this problem: shapes of dendrites are highly variable from one neuronal type to ...	[ "Neurons develop distinctive dendritic morphologies to receive and process information .", "Previous experiments showed that competitive dendro-dendritic interactions play critical roles in shaping dendrites of the space-filling type , which uniformly cover their receptive field .", "We incorporated this findin...	[ "Neurons elaborate two types of neuronal extensions .", "One is axon , which sends outputs to other neurons .", "Another is dendrite , which is specialized for receiving and processing synaptic or sensory inputs .", "Like elaborated branches of trees , the shape of dendrites is quite variable from one type to...	2007
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell physiology", "chemical compounds", "mitochondrial dna", "cell metabolism", "organic compounds", "forms of dna", "amino acids", "mitochondria", "dna", "epigenetics", "bioenergetics", "cellular structures and organelles", "dna methylation", "chromatin", "amino acid metabolism", "ch...	Mitochondrial nicotinamide adenine dinucleotide reduced (NADH) oxidation links the tricarboxylic acid (TCA) cycle with methionine metabolism and nuclear DNA methylation	journal.pbio.2005707	null	[ [ "Mitochondrial function is key to normal cellular physiology , given the many different biochemical process that occur in the organelle [1] .", "A tremendous amount of effort over the past several decades has been dedicated to understanding how mitochondrial dysfunction impacts the cellular environment an...	[ "Mitochondrial function affects many aspects of cellular physiology , and , most recently , its role in epigenetics has been reported .", "Mechanistically , how mitochondrial function alters DNA methylation patterns in the nucleus remains ill defined .", "Using a cell culture model of induced mitochondrial DNA ...	[ "Epigenetic changes in the nucleus play a role in the regulation of gene expression , and metabolism has been shown to affect the epigenome .", "As mitochondria are not only the powerhouses but also important metabolic hubs in cells , changes in mitochondrial metabolism are likely to affect the epigenome and , as...	2018
[ "Introduction", "Results", "Discussion", "Material and Methods" ]	[ "virology/animal models of infection", "immunology/innate immunity", "infectious diseases/viral infections", "virology/host antiviral responses", "virology/host invasion and cell entry" ]	Whole-Body Analysis of a Viral Infection: Vascular Endothelium is a Primary Target of Infectious Hematopoietic Necrosis Virus in Zebrafish Larvae	journal.ppat.1001269	null	[ [ "It is often quite difficult to locate viral infections , as viruses are invisible to the light microscope and are generally noticed by the relatively non-specific symptoms they cause .", "Specific tools such as monoclonal antibodies allow their detection with techniques that cannot be carried out at the ...	[ "The progression of viral infections is notoriously difficult to follow in whole organisms .", "The small , transparent zebrafish larva constitutes a valuable system to study how pathogens spread .", "We describe here the course of infection of zebrafish early larvae with a heat-adapted variant of the Infectiou...	[ "The zebrafish larva is uniquely amenable to imaging among vertebrate models because of its small size , transparency , and ease of anesthesia , making it a useful model to understand host-pathogen interactions .", "We have performed the first detailed analysis of a viral infection in zebrafish .", "Infection o...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "meiosis", "molecular cell biology", "chromosome biology", "nucleic acids", "centromeres", "dna recombination", "dna", "biology", "genomics", "molecular biology", "genetics and genomics" ]	Synaptonemal Complex Components Persist at Centromeres and Are Required for Homologous Centromere Pairing in Mouse Spermatocytes	journal.pgen.1002701	null	[ [ "During the first meiotic division , homologous chromosomes pair , recombine and dissociate .", "Successful completion of these processes is required for a pair of homologous chromosomes ( bivalent ) to mount the meiotic spindle .", "Organization of the chromosomes into pairs ensures orderly segregati...	[ "Recent studies in simple model organisms have shown that centromere pairing is important for ensuring high-fidelity meiotic chromosome segregation .", "However , this process and the mechanisms regulating it in higher eukaryotes are unknown .", "Here we present the first detailed study of meiotic centromere pa...	[ "Meiosis is the key developmental program of gametogenesis during which haploid gametes are generated to cope with the doubling chromosome number that occurs after fertilization .", "During the first meiotic division , homologous chromosomes pair , recombine , and dissociate .", "Errors in any of these processe...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biotechnology", "evolutionary biology", "virology" ]	Endothelial Targeting of Cowpea Mosaic Virus (CPMV) via Surface Vimentin	journal.ppat.1000417	null	[ [ "Cowpea mosaic virus ( CPMV ) is a member of the comoviridae family of plant viruses .", "The 31 nm-diameter capsid has a pseudo T = 3 symmetry composed of 3 beta-barrel domains formed from 2 capsid proteins , and is structurally related to animal picornaviruses that include such viruses as poliovirus , c...	[ "Cowpea mosaic virus ( CPMV ) is a plant comovirus in the picornavirus superfamily , and is used for a wide variety of biomedical and material science applications .", "Although its replication is restricted to plants , CPMV binds to and enters mammalian cells , including endothelial cells and particularly tumor ...	[ "Cowpea mosaic virus ( CPMV ) , a plant virus that does not replicate in animals , is extensively used in material science and nanobiotechnology .", "CPMV has been found to specifically interact with mammalian cells after oral or intravenous administration , as well as in intravital vascular imaging studies that ...	2009
[ "Introduction", "Results", "Discussion" ]	[ "medicine and health sciences", "protein metabolism", "particle physics", "mathematical models", "simulation and modeling", "atoms", "nutrition", "composite particles", "mathematical modeling", "amino acid metabolism", "research and analysis methods", "computer and information sciences", "ma...	Natural Isotopic Signatures of Variations in Body Nitrogen Fluxes: A Compartmental Model Analysis	journal.pcbi.1003865	null	[ [ "Nitrogen ( N ) metabolism in the body involves a complex network of various between- and within-tissues fluxes , consisting in the transport and/or transformation of various N compounds such as proteins ( P ) , amino acids ( AA ) , urea and ammonia .", "These various N transfers and metabolic processes a...	[ "Body tissues are generally 15N-enriched over the diet , with a discrimination factor ( Δ15N ) that varies among tissues and individuals as a function of their nutritional and physiopathological condition .", "However , both 15N bioaccumulation and intra- and inter-individual Δ15N variations are still poorly unde...	[ "Body proteins ensure vital functions , and their constancy is maintained through the tight coordination of many nitrogen metabolic fluxes , but our understanding of how this flux system is regulated , and sometimes dysregulated , remains fragmentary and incomplete .", "Besides , body tissues are generally natura...	2014
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "microbial mutation", "microbiology", "gene function", "microbial evolution", "molecular genetics", "microbial growth and development", "microbial physiology", "proteins", "biology", "microbial ecology", "biochemistry", "virology", "gene identification and analysis", "genetics", "microbi...	A Bacteriophage-Encoded J-Domain Protein Interacts with the DnaK/Hsp70 Chaperone and Stabilizes the Heat-Shock Factor σ32 of Escherichia coli	journal.pgen.1003037	null	[ [ "The universally conserved molecular chaperone machines maintain cellular protein homeostasis by acting at almost every stage in the life of proteins [1] .", "In the bacterium Escherichia coli , the multifunctional DnaK ( Hsp70 ) chaperone machine ( the DnaK/DnaJ/GrpE complex ) performs key cellular funct...	[ "The universally conserved J-domain proteins ( JDPs ) are obligate cochaperone partners of the Hsp70 ( DnaK ) chaperone .", "They stimulate Hsp70's ATPase activity , facilitate substrate delivery , and confer specific cellular localization to Hsp70 .", "In this work , we have identified and characterized the fi...	[ "Bacteriophages are the most abundant biological entities on earth .", "As a consequence , they represent the largest reservoir of unexplored genetic information .", "They control bacterial growth , mediate horizontal gene transfer , and thus exert profound influence on microbial ecology and growth .", "One o...	2012
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "immunodeficiency viruses", "virology", "biology", "microbiology", "viral structure" ]	Protease Cleavage Leads to Formation of Mature Trimer Interface in HIV-1 Capsid	journal.ppat.1002886	null	[ [ "The Gag polyprotein encompasses the major structural elements responsible for assembly of retroviruses , including human immunodeficiency virus type 1 ( HIV-1 ) .", "Assembly and budding involve Gag self-association and interactions with the host cell plasma membrane , the viral genomic RNA , and host ce...	[ "During retrovirus particle maturation , the assembled Gag polyprotein is cleaved by the viral protease into matrix ( MA ) , capsid ( CA ) , and nucleocapsid ( NC ) proteins .", "To form the mature viral capsid , CA rearranges , resulting in a lattice composed of hexameric and pentameric CA units .", "Recent st...	[ "HIV-1 virions assemble as immature particles that must undergo proteolytic maturation to become infectious .", "During the maturation process , the Gag polyprotein is cleaved into matrix ( MA ) , capsid ( CA ) , nucleocapsid ( NC ) , and p6 proteins , and CA assembles to form a mature viral capsid .", "Here , ...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology" ]	HIF-1 Regulates Iron Homeostasis in Caenorhabditis elegans by Activation and Inhibition of Genes Involved in Iron Uptake and Storage	journal.pgen.1002394	null	[ [ "Iron is essential due to its presence in proteins involved in DNA synthesis , mitochondrial respiration and oxygen transport .", "Regulation of cellular iron content is crucial: excess cellular iron catalyzes the generation of reactive oxygen species that damage DNA and proteins , while cellular iron def...	[ "Caenorhabditis elegans ftn-1 and ftn-2 , which encode the iron-storage protein ferritin , are transcriptionally inhibited during iron deficiency in intestine .", "Intestinal specific transcription is dependent on binding of ELT-2 to GATA binding sites in an iron-dependent enhancer ( IDE ) located in ftn-1 and ft...	[ "Due to its presence in proteins involved in hemoglobin synthesis , DNA synthesis , and mitochondrial respiration , eukaryotic cells require iron for survival .", "Excess iron can lead to oxidative damage , while iron deficiency reduces cell growth and causes cell death .", "Dysregulation of iron homeostasis in...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "cell differentiation", "developmental biology", "probability distribution", "methylation", "mathematics", "epigenetics", "dna", "mammalian genomics", "dna methylation", "chromatin", "chromosome biology", "gene expression", "chemistry", "chromatin modification", "dna modification", "ge...	Integrative single-cell omics analyses reveal epigenetic heterogeneity in mouse embryonic stem cells	journal.pcbi.1006034	null	[ [ "Embryonic stem cells ( ESCs ) have a wide range of applications in both basic research and pre-clinical drug screening .", "ESCs are characterized with the capacity to self-renew and to differentiate into multi-lineage cells [1 , 2] .", "While continuously proliferating , the undifferentiated ESCs ar...	[ "Embryonic stem cells ( ESCs ) consist of a population of self-renewing cells displaying extensive phenotypic and functional heterogeneity .", "Research towards the understanding of the epigenetic mechanisms underlying the heterogeneity among ESCs is still in its initial stage .", "Key issues , such as how to i...	[ "DNA methylation is an epigenetic mark with covalent modification that occurs directly on genetic material .", "In vertebrates , the most common form of DNA methylation is 5-methylcytosine ( 5-mC ) at which a methyl group ( CH3 ) is attached to the cytosine nucleotide , especially in the context of CpG dinucleoti...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology and life sciences", "medicine and health sciences" ]	HTLV-1 Tax-Mediated Inhibition of FOXO3a Activity Is Critical for the Persistence of Terminally Differentiated CD4+ T Cells	journal.ppat.1004575	null	[ [ "Infection with the human T cell leukemia virus type I ( HTLV-1 ) affects more than 20 million people worldwide [1] and HTLV-1-associated diseases are a major cause of mortality and morbidity in endemic areas where infection rates range from 2 to 30% .", "Chronic infection with HTLV-1 can result in a numb...	[ "The mechanisms involved in the persistence of activated CD4+ T lymphocytes following primary human T leukemia/lymphoma virus type 1 ( HTLV-1 ) infection remain unclear .", "Here , we demonstrate that the HTLV-1 Tax oncoprotein modulates phosphorylation and transcriptional activity of the FOXO3a transcription fac...	[ "HTLV- infection contributes to the development of Adult T cell Leukemia ( ATL ) or the neurological disorder HTLV-1-associated myelopathy/tropical spastic paraparesis ( HAM/TSP ) .", "HTLV-1 principally targets CD4+ T lymphocytes and causes profound changes in activation , immune function and cell death .", "T...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "parasite evolution", "pathogens", "immunology", "vertebrates", "animals", "parasitology", "clinical medicine", "molecular motors", "actin motors", "motor proteins", "contractile proteins", "major histocompatibility compl...	Evolution of major histocompatibility complex gene copy number	journal.pcbi.1007015	null	[ [ "Major histocompatibility complex ( MHC ) genes code for proteins that present pathogen-derived oligopeptides ( antigens ) to T-cells , thus initiating an adaptive immune response .", "MHC genes are highly polymorphic , with dozens to hundreds of variants typically segregating in natural populations ( rev...	[ "MHC genes , which code for proteins responsible for presenting pathogen-derived antigens to the host immune system , show remarkable copy-number variation both between and within species .", "However , the evolutionary forces driving this variation are poorly understood .", "Here , we use computer simulations ...	[ "Highly polymorphic genes of the Major Histocompatibility Complex ( MHC ) code for proteins responsible for presenting antigens to lymphocytes , thus initiating adaptive immune response .", "The polymorphism is driven by coevolution with parasites which are selected to evade recognition by MHC proteins .", "Exp...	2019
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "immunology", "dna-binding proteins", "dna damage", "fungi", "clinical medicine", "model organisms", "polymerases", "dna replication", "experimental organism systems", "sequence motif analysis", "dna", "hypersensitivity", "research and analysis methods", "...	The translesion DNA polymerases Pol ζ and Rev1 are activated independently of PCNA ubiquitination upon UV radiation in mutants of DNA polymerase δ	journal.pgen.1007119	null	[ [ "Despite the remarkable catalytic activities of replicative DNA polymerases , these enzymes cannot efficiently incorporate nucleotides opposite damaged template DNA .", "Therefore , in eukaryotes , translesion DNA synthesis ( TLS ) is carried out by specialized , low stringency damage-tolerant polymerases...	[ "Replicative DNA polymerases cannot insert efficiently nucleotides at sites of base lesions .", "This function is taken over by specialized translesion DNA synthesis ( TLS ) polymerases to allow DNA replication completion in the presence of DNA damage .", "In eukaryotes , Rad6- and Rad18-mediated PCNA ubiquitin...	[ "Replicative DNA polymerases have the essential role of replicating genomic DNA during the S phase of each cell cycle .", "DNA replication occurs smoothly and accurately if the DNA to be replicated is undamaged .", "Conversely , replicative DNA polymerases stall abruptly when they encounter a damaged base on th...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Promotion of Bone Morphogenetic Protein Signaling by Tetraspanins and Glycosphingolipids	journal.pgen.1005221	null	[ [ "Bone morphogenetic proteins ( BMPs ) belong to the transforming growth factor β ( TGFβ ) superfamily of secreted polypeptides that regulate a variety of developmental and homeostatic processes [1 , 2] .", "The TGFβ ligands are synthesized as precursor proteins that can be subsequently processed by protea...	[ "Bone morphogenetic proteins ( BMPs ) belong to the transforming growth factor β ( TGFβ ) superfamily of secreted molecules .", "BMPs play essential roles in multiple developmental and homeostatic processes in metazoans .", "Malfunction of the BMP pathway can cause a variety of diseases in humans , including ca...	[ "The bone morphogenetic protein ( BMP ) signaling pathway is required for multiple developmental processes during metazoan development .", "Various diseases , including cancer , can result from mis-regulation of the BMP pathway .", "Thus , it is critical to identify factors that ensure proper regulation of BMP ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "systems biology", "biology", "computational biology", "genetics and genomics" ]	Tuning the Mammalian Circadian Clock: Robust Synergy of Two Loops	journal.pcbi.1002309	null	[ [ "Circadian rhythms can be found in most organisms , from bacteria to humans and are a fundamental property of living cells [1] .", "These endogenous rhythms provide a way to anticipate external cues and to adapt molecular and behavioural processes to specific day-times with the advantage of temporally sep...	[ "The circadian clock is accountable for the regulation of internal rhythms in most living organisms .", "It allows the anticipation of environmental changes during the day and a better adaptation of physiological processes .", "In mammals the main clock is located in the suprachiasmatic nucleus ( SCN ) and sync...	[ "Most organisms have evolved an internal clock which allows them to anticipate and react to the light/dark daily rhythm and is able to generate oscillation with a circa 24 hour rhythm .", "A molecular network involving feedback loops is responsible for the rhythm generation .", "A large number of clock-controll...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "chemical bonding", "luciferase", "nucleic acid synthesis", "enzymes", "messenger rna", "dna-binding proteins", "nucleocapsids", "microbiology", "viral structure", "enzymology", "dna transcription", "polymerases", "rna synthesis", "microbial genetics", "hydrogen bonding", "chemical syn...	Modulation of Re-initiation of Measles Virus Transcription at Intergenic Regions by PXD to NTAIL Binding Strength	journal.ppat.1006058	null	[ [ "Measles virus ( MeV ) , a member of the Morbillivirus genus , belongs to the Paramyxoviridae family of the Mononegavirales order [1] .", "These viruses possess a non-segmented RNA genome of negative polarity that is encapsidated by the nucleoprotein ( N ) to form a helical nucleocapsid .", "Not only ...	[ "Measles virus ( MeV ) and all Paramyxoviridae members rely on a complex polymerase machinery to ensure viral transcription and replication .", "Their polymerase associates the phosphoprotein ( P ) and the L protein that is endowed with all necessary enzymatic activities .", "To be processive , the polymerase u...	[ "Three proteins , the polymerase L , the phosphoprotein P and the nucleoprotein N , interplay to ensure transcription and replication of measles virus , a member of the Paramyxoviridae family .", "A regular array of nucleoprotein shields the viral genomic RNA .", "The resulting nucleocapsid constitutes the temp...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "carbohydrate metabolism", "medicine and health sciences", "neuroscience", "developmental biology", "ganglion cells", "nerve fibers", "embryos", "embryology", "developmental neuroscience", "sensory physiology", "animal cells", "axons", "short reports", "metabolism", "biochemistry", "si...	Receptors of intermediates of carbohydrate metabolism, GPR91 and GPR99, mediate axon growth	journal.pbio.2003619	null	[ [ "GPR91 and GPR99 are G-protein-coupled receptors ( GPCRs ) activated by Krebs cycle intermediates , part of the larger class of carbohydrate metabolites—an observation that renewed interest in a biochemical pathway discovered decades ago [1 , 2] .", "GPR91 , through its activation by succinate outside the...	[ "During the development of the visual system , high levels of energy are expended propelling axons from the retina to the brain .", "However , the role of intermediates of carbohydrate metabolism in the development of the visual system has been overlooked .", "Here , we report that the carbohydrate metabolites ...	[ "Development of the visual system requires high levels of energy and tight regulation of multiple factors integrated by axon projections during navigation to their appropriate targets .", "While intermediates of carbohydrate metabolism have key roles in many biological processes , much less is known about their e...	2018
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "african trypanosomiasis", "variant genotypes", "tropical diseases", "geographical locations", "parasitic diseases", "parasitic protozoans", "alleles", "genetic mapping", "protozoans", "neglected tropical diseases", "molecular genetics", "molecular biology tec...	Association between IL1 gene polymorphism and human African trypanosomiasis in populations of sleeping sickness foci of southern Cameroon	journal.pntd.0007283	null	[ [ "Human African Trypanosomiasis ( HAT ) , or sleeping sickness , is a parasitic infection caused by flagellated parasites of the genus Trypanosoma .", "The parasites belong to Trypanosoma brucei complex which is subdivided into three subspecies: Trypanosoma brucei gambiense ( Dutton , 1902 ) is responsible...	[ "Human African Trypanosomiasis ( HAT ) is a neglected tropical disease caused by infections due to Trypanosoma brucei subspecies .", "In addition to the well-established environmental and behavioural risks of becoming infected , there is evidence for a genetic component to the response to trypanosome infection ."...	[ "Human African Trypanosomiasis ( HAT ) , or sleeping sickness , is a parasitic disease caused by flagellated parasites of the genus Trypanosoma .", "This disease has been included into the WHO roadmap for neglected tropical diseases with elimination as a public health problem targeted for 2020 and the interruptio...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "microbiology/microbial evolution and genomics", "microbiology/cellular microbiology and pathogenesis", "microbiology/medical microbiology", "microbiology" ]	The QseC Adrenergic Signaling Cascade in Enterohemorrhagic E. coli (EHEC)	journal.ppat.1000553	null	[ [ "The survival of an organism lies within its intrinsic ability to detect and efficiently respond to stress cues .", "Stress responses play a key role in adaptation to environmental , psychosocial , and physical insults .", "Hence it comes as no surprise that stress responses require synchronization an...	[ "The ability to respond to stress is at the core of an organism's survival .", "The hormones epinephrine and norepinephrine play a central role in stress responses in mammals , which require the synchronized interaction of the whole neuroendocrine system .", "Mammalian adrenergic receptors are G-coupled protein...	[ "Bacterial cells respond to the human stress hormones epinephrine ( adrenaline ) and norepinephrine ( noradrenaline ) .", "These hormones are sensed by a bacterial receptor named QseC , which is a sensor kinase in the membrane that increases its autophosphorylation upon binding to these host signals .", "In add...	2009
[ "Introduction", "Results", "Discussion", "Material and Methods" ]	[]	Receptor Polymorphism and Genomic Structure Interact to Shape Bitter Taste Perception	journal.pgen.1005530	null	[ [ "Bitter taste perception plays a fundamental role in dietary preferences and behaviours , by shaping aversions to foods and drinks .", "Indeed , averse responses to bitterness are instinctive and drive rejection and avoidance behaviours widely observed in animal models , but also in human infants [1–5] ."...	[ "The ability to taste bitterness evolved to safeguard most animals , including humans , against potentially toxic substances , thereby leading to food rejection .", "Nonetheless , bitter perception is subject to individual variations due to the presence of genetic functional polymorphisms in bitter taste receptor...	[ "Human bitter taste is believed to protect us from the ingestion of poisonous substances , thereby shaping food rejections .", "Bitter perception differs , however , across individuals , due to genetic variations in the ~25 bitter taste receptor ( TAS2R ) genes .", "A famous example known since the 1930s is the...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "developmental biology", "developmental neuroscience", "synaptic plasticity", "molecular neuroscience", "learning and memory", "neurobiology of disease and regeneration", "epilepsy", "synapses", "signaling", "molecular development", "neurology", "signaling pathways", "developme...	Reduced Juvenile Long-Term Depression in Tuberous Sclerosis Complex Is Mitigated in Adults by Compensatory Recruitment of mGluR5 and Erk Signaling	journal.pbio.1001627	A mouse model of the human genetic disorder tuberous sclerosis complex fails to undergo developmental down-regulation of mGluR5 expression and activation of Erk signaling, probably contributing to the aberrant plasticity and epilepsy in this disease.	[ [ "Tuberous sclerosis complex ( TSC ) is a multisystem autosomal dominant disorder that is characterized by the development of systemic benign hamartomas and cortical tubers , mental disability , autism , and epilepsy [1] , [2] .", "Affecting approximately 1 in 6 , 000 people , TSC is caused by mutations in...	[ "Tuberous sclerosis complex ( TSC ) is a multisystem genetic disease that manifests with mental retardation , tumor formation , autism , and epilepsy .", "Heightened signaling through the mammalian target of rapamycin ( mTOR ) pathway is involved in TSC pathology , however it remains unclear how other signaling p...	[ "Tuberous sclerosis complex ( TSC ) is a genetic disorder that afflicts around 1 in 6 , 000 people and results from a mutation in one of two genes , TSC1 or TSC2 .", "TSC patients suffer a number of neuronal symptoms including various degrees of autism , mental retardation , and epilepsy , the latter found in mor...	2013
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "invertebrates", "dengue virus", "morocco", "medicine and health sciences", "body fluids", "pathology and laboratory medicine", "togaviruses", "chikungunya infection", "viral transmission and infection", "pathogens", "geographical locations", "microbiology", "tropical diseases", "saliva", ...	Potential of Aedes albopictus to cause the emergence of arboviruses in Morocco	journal.pntd.0006997	null	[ [ "Over the past decades , arboviruses caused acute emergences leading to global pandemics .", "Dengue viruses ( DENV; family Flaviviridae , genus Flavivirus ) are responsible for 390 million infections per year including 96 million symptomatic cases [1] .", "In 2005 , chikungunya virus ( CHIKV; family ...	[ "In 2015 , the mosquito Aedes albopictus was detected in Rabat , Morocco .", "This invasive species can be involved in the transmission of more than 25 arboviruses .", "It is known that each combination of mosquito population and virus genotype leads to a specific interaction that can shape the outcome of infec...	[ "The Asian tiger mosquito Aedes albopictus is responsible for the transmission of several arboviruses such as dengue and chikungunya viruses .", "In 30 to 40 years , it has extended its geographical distribution in both tropical and temperate regions of all continents .", "The species was first detected in Sept...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "invertebrates", "rna interference", "microbiology", "animals", "animal models", "drosophila melanogaster", "model organisms", "epigenetics", "drosophila", "research and analysis methods", "viral immune evasion", "insects", "arthropoda", "biochemistry", "rna", "cell biology", "nuclei...	Novel Drosophila Viruses Encode Host-Specific Suppressors of RNAi	journal.ppat.1004256	null	[ [ "As obligate intracellular parasites , viruses modulate and exploit the host cellular environment for their replication .", "The host antiviral defense system restricts virus infections , and in turn , viruses dedicate a significant fraction of their coding capacity to produce factors that antagonize the ...	[ "The ongoing conflict between viruses and their hosts can drive the co-evolution between host immune genes and viral suppressors of immunity .", "It has been suggested that an evolutionary ‘arms race’ may occur between rapidly evolving components of the antiviral RNAi pathway of Drosophila and viral genes that an...	[ "Viruses and their hosts can engage in an evolutionary arms race .", "Viruses may select for hosts with more effective immune responses , whereas the immune response of the host may select for viruses that evade the immune system .", "These viral counter-defenses may in turn drive adaptations in host immune gen...	2014
[ "Introduction", "Results and Discussion", "Materials and Methods" ]	[ "organismal evolution", "ecology and environmental sciences", "medicine and health sciences", "microbial physiology", "ecology", "medical microbiology", "microbial evolution", "epidemiology", "disease dynamics", "microbial pathogens", "population dynamics", "biology and life sciences", "popu...	Bistable Expression of Virulence Genes in Salmonella Leads to the Formation of an Antibiotic-Tolerant Subpopulation	journal.pbio.1001928	The bistable expression of virulence genes in Salmonella allows a clonal population to hedge its bets: one subpopulation suffers a growth cost, but is tolerant to antibiotics.	[ [ "Genetically identical bacterial cells can exhibit remarkable phenotypic differences even when grown in homogeneous environments [1] , [2] .", "These differences can arise from stochastic fluctuations in the expression of individual genes [3] .", "Although there is evidence that the majority of genes ...	[ "Phenotypic heterogeneity can confer clonal groups of organisms with new functionality .", "A paradigmatic example is the bistable expression of virulence genes in Salmonella typhimurium , which leads to phenotypically virulent and phenotypically avirulent subpopulations .", "The two subpopulations have been sh...	[ "Scientists have recently realized that nature and nurture are not the only determinants of an individual's traits; some organisms also use random molecular processes to generate phenotypic variation among genetically identical individuals .", "This raises the question of whether such phenotypic variation could b...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "vector biology", "tsetse fly", "biology", "microbiology" ]	Optimizing the Colour and Fabric of Targets for the Control of the Tsetse Fly Glossina fuscipes fuscipes	journal.pntd.0001661	null	[ [ "Tsetse flies ( Glossina spp . ) are restricted to sub-Saharan Africa where they transmit the trypanosomes causing the diseases of nagana in livestock and sleeping sickness , also known as human African trypanosomiasis ( HAT ) , in humans .", "Tsetse are commonly divided into three groups:", "i ) the ...	[ "Most cases of human African trypanosomiasis ( HAT ) start with a bite from one of the subspecies of Glossina fuscipes .", "Tsetse use a range of olfactory and visual stimuli to locate their hosts and this response can be exploited to lure tsetse to insecticide-treated targets thereby reducing transmission .", ...	[ "Efforts to control human African trypanosomiasis ( HAT ) would be strengthened by the development and application of more cost-effective methods of controlling the various species of tsetse fly vector .", "Among the most promising approaches is the use of insecticide-treated targets which use various olfactory a...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "public and occupational health", "infectious diseases", "medicine and health sciences" ]	Impact of ASHA Training on Active Case Detection of Visceral Leishmaniasis in Bihar, India	journal.pntd.0002774	null	[ [ "There are estimated 200 , 000 to 400 , 000 new cases of visceral leishmaniasis ( VL ) , also known as kala-azar [1] every year worldwide .", "Bihar state in India contributes the majority of the disease burden of VL which is most prevalent in poorest populations [1] , [2] .", "The major risk factor f...	[ "One of the major challenges for management of visceral leishmaniasis ( VL ) is early diagnosis of cases to improve treatment outcome and reduce transmission .", "We have therefore investigated active case detection of VL with the help of accredited social health activists ( ASHA ) .", "ASHAs are women who live...	[ "Visceral leishmaniasis ( VL ) is a potentially deadly parasitic disease that affects over 20 , 000 people in Bihar , India annually .", "Accredited social health activists ( ASHA ) are women who live in the community and render their services towards maternal and other health concerns in the villages where VL is...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "soil-transmitted helminths", "trichuriasis", "hookworm infection", "parasitic diseases", "helminth infection" ]	In Vitro and In Vivo Efficacy of Monepantel (AAD 1566) against Laboratory Models of Human Intestinal Nematode Infections	journal.pntd.0001457	null	[ [ "The hookworm species Ancylostoma duodenale and Necator americanus , the whipworm Trichuris trichiura , the threadworm Strongyloides stercoralis , and the roundworm Ascaris lumbricoides are soil-transmitted helminths ( STH ) of great public health importance .", "Cumulatively , these parasites affect more...	[ "Few effective drugs are available for soil-transmitted helminthiases and drug resistance is of concern .", "In the present work , we tested the efficacy of the veterinary drug monepantel , a potential drug development candidate compared to standard drugs in vitro and in parasite-rodent models of relevance to hum...	[ "Soil-transmitted helminthiases affect more than one billion people among the most vulnerable populations in developing countries .", "Currently , control of these infections primarily relies on chemotherapy .", "Only five drugs are available , all of which have been in use for decades .", "None of the drugs ...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "genetics", "biology", "evolutionary biology", "zoology" ]	Developmental Link between Sex and Nutrition; doublesex Regulates Sex-Specific Mandible Growth via Juvenile Hormone Signaling in Stag Beetles	journal.pgen.1004098	null	[ [ "The evolution of sex-specific traits in animals has long fascinated biologists .", "How is growth regulated so that it differs dramatically between males and females ?", "Sexual dimorphisms are widespread across diverse animal taxa and include exaggerated sexually selected traits like the antlers of ...	[ "Sexual dimorphisms in trait expression are widespread among animals and are especially pronounced in ornaments and weapons of sexual selection , which can attain exaggerated sizes .", "Expression of exaggerated traits is usually male-specific and nutrition sensitive .", "Consequently , the developmental mechan...	[ "Sexual dimorphisms such as the exaggerated antlers of deer , the enormous clawed chelae of crabs , and the horns and mandibles of beetles , are widespread across animal taxa and have fascinated biologists for centuries .", "Much recent work has uncovered the importance of the role of the sex-determination pathwa...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "oncology", "infectious diseases", "medicine and health sciences", "clinical immunology", "biology and life sciences", "immunology", "microbiology" ]	Exploitation of the Complement System by Oncogenic Kaposi's Sarcoma-Associated Herpesvirus for Cell Survival and Persistent Infection	journal.ppat.1004412	null	[ [ "Kaposi's sarcoma-associated herpesvirus ( KSHV ) , also known as human herpesvirus 8 ( HHV8 ) , is a DNA tumor virus associated with the development of Kaposi's sarcoma ( KS ) , primary effusion lymphoma ( PEL ) , and a subset of multicentric Castleman's disease [1]–[3] .", "KS is a vascular tumor of pro...	[ "During evolution , herpesviruses have developed numerous , and often very ingenious , strategies to counteract efficient host immunity .", "Specifically , Kaposi's sarcoma-associated herpesvirus ( KSHV ) eludes host immunity by undergoing a dormant stage , called latency wherein it expresses a minimal number of ...	[ "The complement system is an important part of the innate immune system .", "Pathogens have evolved diverse strategies to evade host immune responses including attack of the complement system .", "Kaposi's sarcoma-associated herpesvirus ( KSHV ) is associated with Kaposi's sarcoma ( KS ) , primary effusion lymp...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "public health and epidemiology", "chagas disease", "molecular epidemiology", "epidemiology", "genetics", "molecular genetics", "biology", "evolutionary biology", "parasitic diseases", "evolutionary systematics", "genetics and genomics" ]	Molecular Epidemiology of Human Oral Chagas Disease Outbreaks in Colombia	journal.pntd.0002041	null	[ [ "Chagas disease caused by Trypanosoma cruzi is considered a zoonotic and neglected disease that represents an important public health problem in the Americas .", "This parasite is mainly transmitted by the faeces of triatomine insects and shows tremendous genetic variability reflected in at least six Disc...	[ "Trypanosoma cruzi , the causative agent of Chagas disease , displays significant genetic variability revealed by six Discrete Typing Units ( TcI-TcVI ) .", "In this pathology , oral transmission represents an emerging epidemiological scenario where different outbreaks associated to food/beverages consumption hav...	[ "Chagas disease represents a serious health problem affecting more than 10 million people in the Americas .", "The oral transmission route has emerged as a new epidemiological scenario that needs to be considered in prevention and control strategies .", "Herein was developed a high-resolution molecular characte...	2013
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "genetics", "biology", "microbiology", "genetics and genomics" ]	Cellular Levels and Binding of c-di-GMP Control Subcellular Localization and Activity of the Vibrio cholerae Transcriptional Regulator VpsT	journal.ppat.1002719	null	[ [ "Second messengers are small diffusible signaling molecules that are produced or degraded in response to external stimuli and relay information to a receptor to elicit a specific cellular response [1] .", "The cyclic nucleotide cyclic diguanylate ( c-di-GMP ) is a bacterial second messenger that controls ...	[ "The second messenger , cyclic diguanylate ( c-di-GMP ) , regulates diverse cellular processes in bacteria .", "C-di-GMP is produced by diguanylate cyclases ( DGCs ) , degraded by phosphodiesterases ( PDEs ) , and receptors couple c-di-GMP production to cellular responses .", "In many bacteria , including Vibri...	[ "C-di-GMP is a ubiquitous intracellular signaling molecule in bacteria and controls diverse cellular processes including biofilm formation , motility and virulence .", "The genomes of many bacteria often contain numerous genes encoding proteins predicted to produce and degrade c-di-GMP .", "However , it is curr...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "genomics", "genetics", "biology and life sciences", "epigenomics", "computational biology" ]	Histone Modifications Are Associated with Transcript Isoform Diversity in Normal and Cancer Cells	journal.pcbi.1003611	null	[ [ "Molecular processes such as alternative splicing and transcription start-site switching are primary drivers of transcript diversity .", "About 95% of the ∼23 , 000 human genes are estimated to produce more than one mRNA isoform [1] .", "Beyond the genes with protein-coding potential , recent discover...	[ "Mechanisms that generate transcript diversity are of fundamental importance in eukaryotes .", "Although a large fraction of human protein-coding genes and lincRNAs produce more than one mRNA isoform each , the regulation of this phenomenon is still incompletely understood .", "Much progress has been made in de...	[ "Traditionally , the regulation of gene expression was thought to be largely based on DNA and RNA sequence motifs .", "However , this dogma has recently been challenged as other factors , such as epigenetic patterning of the genome , have become better understood .", "Sparse but convincing experimental evidence...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "viral vaccines", "medicine and health sciences", "immune physiology", "enzyme-linked immunoassays", "china", "immunology", "geographical locations", "microbiology", "pediatrics", "vaccines", "preventive medicine", "pediatric infections", "antibodies", "immunologic techniques", "vaccinat...	Low Protective Efficacy of the Current Japanese Encephalitis Vaccine against the Emerging Genotype 5 Japanese Encephalitis Virus	journal.pntd.0004686	null	[ [ "Japanese encephalitis ( JE ) , probably the world’s most frequently occurring viral encephalitis , is a neurological infectious disease caused by Japanese encephalitis virus ( JEV ) , transmitted via mosquito bite [1] .", "The mortality rate of JE patients is 30–35% and 50% of JE survivors live with neur...	[ "The current Japanese encephalitis ( JE ) vaccine derived from G3 JE virus ( JEV ) can induce protective immunity against G1–G4 JEV genotypes .", "However , protective efficacy against the emerging G5 genotype has not been reported .", "Using in vitro and in vivo tests , biological phenotype and cross-immunorea...	[ "The human disease Japanese encephalitis ( JE ) can be prevented by vaccination , although it is not entirely clear if the emerging JEV G5 genotype can be controlled using the vaccine based on the G3 genotype .", "Consequently , we systematically compared G3 and G5 cross-neutralizing immune responses in vaccinate...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "biology", "metabolism" ]	Tri6 Is a Global Transcription Regulator in the Phytopathogen Fusarium graminearum	journal.ppat.1002266	null	[ [ "Fusarium graminearum Schwabe [telemorph Gibberella zeae ( Schwein . ) Petch] is the causal agent of Fusarium head blight ( FHB ) , one of the most destructive crop diseases in temperate climes throughout the world .", "In addition to yield reduction , FHB is often associated with the accumulation of the ...	[ "In F . graminearum , the transcriptional regulator Tri6 is encoded within the trichothecene gene cluster and regulates genes involved in the biosynthesis of the secondary metabolite deoxynivalenol ( DON ) .", "The Tri6 protein with its Cys2His2 zinc-finger may also conform to the class of global transcription re...	[ "Our knowledge of mechanisms involved in the activation and biosynthesis of DON comes largely from in vitro culture studies .", "Cumulated knowledge suggests that the physiological status of the fungus and the availability of nutrients are the main determining factors for DON production .", "Integration of vari...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "clinical research design", "vomiting", "geographical locations", "tropical diseases", "india", "parasitic diseases", "research design", "physiological processes", "phase iii clinical investigation", "clinical medicine", "s...	Safety and efficacy of short course combination regimens with AmBisome, miltefosine and paromomycin for the treatment of visceral leishmaniasis (VL) in Bangladesh	journal.pntd.0005635	null	[ [ "World-wide , 200 , 000–400 , 000 new cases of visceral leishmaniasis ( VL ) occur annually [1] .", "The majority of these cases occur in South Asia; mainly in Bihar , India and neighbouring regions of Nepal , and in the highly endemic Mymensingh province of Bangladesh .", "Before the introduction of ...	[ "AmBisome therapy for VL has an excellent efficacy and safety profile and has been adopted as a first-line regimen in Bangladesh .", "Second-line treatment options are limited and should preferably be given in short course combinations in order to prevent the development of resistant strains .", "Combination re...	[ "Treatment is one of the key strategies for visceral leishmaniasis control and elimination .", "Historically a number of monotherapy drugs for VL treatment were used in Bangladesh , including pentavalent antimonials , amphotericin B deoxycholate ( AmB ) , and miltefosine ( MF ) .", "With the limited number of d...	2017
[ "Introduction", "Model", "Results and discussion" ]	[ "cell physiology", "cell motility", "medicine and health sciences", "classical mechanics", "cell cycle and cell division", "cell processes", "cell polarity", "simulation and modeling", "physiological processes", "developmental biology", "embryos", "wound healing", "research and analysis meth...	Active Vertex Model for cell-resolution description of epithelial tissue mechanics	journal.pcbi.1005569	null	[ [ "Owing to its origins in the physics of foams [62] , in the VM cells are modelled as two-dimensional convex polygons that cover the plane with no holes and overlaps , i . e . , the epithelial tissue is represented as a convex polygonal partitioning of the plane ( Fig 1 ) .", "The main simplification compa...	[ "We introduce an Active Vertex Model ( AVM ) for cell-resolution studies of the mechanics of confluent epithelial tissues consisting of tens of thousands of cells , with a level of detail inaccessible to similar methods .", "The AVM combines the Vertex Model for confluent epithelial tissues with active matter dyn...	[ "We present a detailed analysis of the Active Vertex Model to study the mechanics of confluent epithelial tissues and cell monolayers .", "The model combines the commonly used Vertex Model for describing epithelial tissue mechanics with the active matter dynamics extensively studied in soft matter physics .", "...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "engineering and technology", "signal processing", "social sciences", "neuroscience", "signal filtering", "perception", "cognitive psychology", "white noise", "vision", "eyes", "head", "psychology", "bandpass filters", "anatomy", "psychophysics", "biol...	Dynamic properties of internal noise probed by modulating binocular rivalry	journal.pcbi.1007071	null	[ [ "Despite appearing constant , our sensory perception fluctuates from moment to moment because of the non-deterministic nature of biological neurons .", "This ‘internal noise’ operates at multiple timescales , and affects our decisions about sensory information .", "Internal noise is particularly appar...	[ "Neural systems are inherently noisy , and this noise can affect our perception from moment to moment .", "This is particularly apparent in binocular rivalry , where perception of competing stimuli shown to the left and right eyes alternates over time .", "We modulated rivalling stimuli using dynamic sequences ...	[ "Although our perception of the world appears constant , sensory representations are variable because of the ‘noisy’ nature of biological neurons .", "Here we used a binocular rivalry paradigm , in which conflicting images are shown to the two eyes , to probe the properties of this internal variability .", "Usi...	2019
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "phosphorylation", "medicine and health sciences", "molecular probe techniques", "endothelial cells", "permeability", "immunoblotting", "plasmid construction", "epithelial cells", "health care", "materials science", "dna construction", "molecular biology techniques", "research and analysis m...	A streptococcal Fic domain-containing protein disrupts blood-brain barrier integrity by activating moesin in endothelial cells	journal.ppat.1007737	null	[ [ "Streptococcus equi subsp .", "zooepidemicus ( SEZ ) is a Lancefield Group C opportunistic pathogen capable of infecting a broad range of animal species , including humans [1] .", "The most significant burden of disease caused by SEZ is in farmed animals , including horses , cows and pigs [2] .", ...	[ "Streptococcus equi subsp .", "zooepidemicus ( SEZ ) is a zoonotic pathogen capable of causing meningitis in humans .", "The mechanisms that enable pathogens to traverse the blood-brain barrier ( BBB ) are incompletely understood .", "Here , we investigated the role of a newly identified Fic domain-containing...	[ "Streptococcus equi subsp .", "zooepidemicus ( SEZ ) is an important animal pathogen and can cause meningitis in humans .", "Little is known about how this Group C streptococcal species penetrates the blood-brain barrier ( BBB ) .", "We identified bifA , a gene that is critical for SEZ to cause meningitis in ...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	A Cytosine Methytransferase Modulates the Cell Envelope Stress Response in the Cholera Pathogen	journal.pgen.1005666	null	[ [ "DNA methylation—the covalent attachment of methyl moieties to specific nucleotides in the genome by DNA methyltransferases ( MTases ) —is a fundamental mechanism for epigenetic regulation in all domains of life ( reviewed in [1 , 2] ) .", "Bacterial DNA MTases principally generate three modified DNA base...	[ "DNA methylation is a key epigenetic regulator in all domains of life , yet the effects of most bacterial DNA methyltransferases on cellular processes are largely undefined .", "Here , we used diverse techniques , including bisulfite sequencing , transcriptomics , and transposon insertion site sequencing to exten...	[ "Methylation of DNA is used by numerous organisms to regulate a wide variety of cellular processes , but specific roles for most DNA methyltransferases have not been defined .", "We studied one such enzyme in Vibrio cholerae , the cholera pathogen , using genome-wide approaches to compare DNA methylation , gene e...	2015
[ "Introduction", "Results and discussion", "Materials and methods" ]	[ "ecology and environmental sciences", "bacteriophages", "oceans", "microbiology", "sequence assembly tools", "viruses", "genomic databases", "metagenomics", "mediterranean sea", "aquatic environments", "genome analysis", "bodies of water", "marine environments", "sea water", "microbial g...	Genome diversity of marine phages recovered from Mediterranean metagenomes: Size matters	journal.pgen.1007018	null	[ [ "Bacteriophages ( viruses that infect bacteria ) , often referred to as phages , are considered the most abundant and diverse biological entities in aquatic systems [1] with an estimated population density of 107 per ml of seawater [2] .", "They are not only abundant but also important players in the ener...	[ "Marine viruses play a critical role not only in the global geochemical cycles but also in the biology and evolution of their hosts .", "Despite their importance , viral diversity remains underexplored mostly due to sampling and cultivation challenges .", "Direct sequencing approaches such as viromics has provi...	[ "These data provided a glimpse of the genetic diversity and variability of viral sequences without introducing the amplification biases produced when studying viromes .", "Metagenomes contain abundant viral material due to cells retrieved while undergoing viral lysis or as temperate viruses inserted in the chromo...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "fluorescence imaging", "medicine and health sciences", "muscle tissue", "fluorophotometry", "developmental biology", "muscle proteins", "pupae", "bioassays and physiological analysis", "muscle biochemistry", "muscle analysis", "research and analysis methods", "muscle physiology", "fluoresce...	A small proportion of Talin molecules transmit forces at developing muscle attachments in vivo	journal.pbio.3000057	The protein Talin links the transmembrane cell adhesion molecule integrin to the actin cytoskeleton. Quantitative FRET-based force measurements across Talin in vivo reveal that only few Talin molecules are under force during the development of muscle attachment sites.	[ [ "The shape of multicellular organisms critically depends on the presence of mechanical forces during development [1 , 2] .", "Forces not only generate form and flows within tissues [3 , 4] but can also control cell fate decisions [5 , 6] and trigger mitosis [7] .", "There are various ways to quantify ...	[ "Cells in developing organisms are subjected to particular mechanical forces that shape tissues and instruct cell fate decisions .", "How these forces are sensed and transmitted at the molecular level is therefore an important question , one that has mainly been investigated in cultured cells in vitro .", "Here...	[ "Cells in our body are constantly exposed to mechanical forces , which they need to sense and react to .", "In previous studies , fluorescent force sensors were developed to demonstrate that individual proteins in adhesion structures of a cell experience forces in the piconewton ( pN ) range .", "However , thes...	2019
[ "Introduction", "Results", "Discussion", "Materials & Methods" ]	[ "learning", "medicine and health sciences", "diagnostic radiology", "functional magnetic resonance imaging", "sleep", "brain", "social sciences", "neuroscience", "learning and memory", "magnetic resonance imaging", "physiological processes", "cognitive psychology", "cognition", "brain mapp...	Cued Reactivation of Motor Learning during Sleep Leads to Overnight Changes in Functional Brain Activity and Connectivity	journal.pbio.1002451	Slow-wave sleep and rapid eye movement sleep are associated with the reactivation and consolidation of a motor skill within distinct brain networks.	[ [ "Memory consolidation begins the moment new information is encoded and is a process where initially fragile memories are stabilised , strengthened , and reorganised in the brain [1] .", "Learning a new motor skill , for example , requires episodes of repeated practice , and is also supported by offline co...	[ "Sleep plays a role in memory consolidation .", "This is demonstrated by improved performance and neural plasticity underlying that improvement after sleep .", "Targeted memory reactivation ( TMR ) allows the manipulation of sleep-dependent consolidation through intentionally biasing the replay of specific memo...	[ "After a motor skill is learned , the memory undergoes \"offline\" processing so that improvement occurs even without further practice .", "Sleep has been shown to enhance this consolidation and , in the process , to reorganize the brain regions involved .", "However , it remains unclear how sleep does this , a...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "evolutionary biology", "saccharomyces", "computational biology" ]	The Importance of Bottlenecks in Protein Networks: Correlation with Gene Essentiality and Expression Dynamics	journal.pcbi.0030059	null	[ [ "Protein networks are a topic of great current interest , particularly after a growing number of large-scale protein networks have been determined [1–6] .", "Protein–protein interaction networks and regulatory networks are the key representatives for biological networks with undirected and directed edges ...	[ "It has been a long-standing goal in systems biology to find relations between the topological properties and functional features of protein networks .", "However , most of the focus in network studies has been on highly connected proteins ( “hubs” ) .", "As a complementary notion , it is possible to define bot...	[ "A network is a graph consisting of a number of nodes with edges connecting them .", "Recently , network models have been widely applied to biological systems .", "Here , we are mainly interested in two types of biological networks: the interaction network , where nodes are proteins and edges connect interactin...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Simulations" ]	[ "evolutionary biology/human evolution", "genetics and genomics" ]	Inferring Human Colonization History Using a Copying Model	journal.pgen.1000078	null	[ [ "According to current models , modern humans arose in Africa and spread around the world , with little or no genetic contribution from the hominid populations that they displaced [1] , [2] , [3] .", "Genetic diversity decreases progressively with land distance from East Africa [4] providing support for a ...	[ "Genome-wide scans of genetic variation can potentially provide detailed information on how modern humans colonized the world but require new methods of analysis .", "We introduce a statistical approach that uses Single Nucleotide Polymorphism ( SNP ) data to identify sharing of chromosomal segments between popul...	[ "Humans like to tell stories .", "Amongst the most captivating is the story of the global spread of modern humans from their original homeland in Africa .", "Traditionally this has been the preserve of anthropologists , but geneticists are starting to make an important contribution .", "However , genetic evid...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	A Highly Conserved Bacterial D-Serine Uptake System Links Host Metabolism and Virulence	journal.ppat.1005359	null	[ [ "Escherichia coli is an extremely diverse Gram-negative bacterial species , commonly establishing itself as a commensal member of the microbiota early after birth in healthy humans and animals [1] .", "However , owing to a large degree of genome plasticity , numerous pathogenic forms of E . coli dubbed ‘p...	[ "The ability of any organism to sense and respond to challenges presented in the environment is critically important for promoting or restricting colonization of specific sites .", "Recent work has demonstrated that the host metabolite D-serine has the ability to markedly influence the outcome of infection by rep...	[ "The host intestinal tract is a challenging environment for any foreign organisms not usually found within the microbiota .", "Intruding pathogens must survive physical barriers and readily compete with the local micro flora for limited nutrients within their preferred niche .", "In order to do this , intestina...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "public health and epidemiology/epidemiology", "infectious diseases/viral infections", "ecology/spatial and landscape ecology", "mathematics/statistics", "infectious diseases/epidemiology and control of infectious diseases" ]	Quantifying the Spatial Dimension of Dengue Virus Epidemic Spread within a Tropical Urban Environment	journal.pntd.0000920	null	[ [ "Dengue is a mosquito-borne infection that has re-emerged as a major international public health concern over the last four decades [1] , [2] , [3] .", "Caused by four closely related yet antigenically distinct single-stranded RNA viruses ( genus Flavivirus , family Flaviridae ) , dengue viruses persist i...	[ "Dengue infection spread in naive populations occurs in an explosive and widespread fashion primarily due to the absence of population herd immunity , the population dynamics and dispersal of Ae .", "aegypti , and the movement of individuals within the urban space .", "Knowledge on the relative contribution of ...	[ "Global trends in population growth and human redistribution and movement have reshaped the map of dengue transmission risk , exposing a significant proportion of the world's population to the threat of dengue epidemics .", "Knowledge on the relative contribution of vector and human movement to the widespread and...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry/molecular evolution", "evolutionary biology/evolutionary and comparative genetics", "evolutionary biology/sexual behavior", "molecular biology/molecular evolution", "evolutionary biology", "genetics and genomics", "genetics and genomics/population genetics" ]	Coevolution of Interacting Fertilization Proteins	journal.pgen.1000570	null	[ [ "Given the importance of reproduction for evolutionary fitness , one might predict that reproductive proteins would be highly conserved , especially those required for interaction between sperm and egg .", "The requirement of molecular recognition between interacting proteins should result in sequence con...	[ "Reproductive proteins are among the fastest evolving in the proteome , often due to the consequences of positive selection , and their rapid evolution is frequently attributed to a coevolutionary process between interacting female and male proteins .", "Such a process could leave characteristic signatures at coe...	[ "When a sperm meets an egg , it must display the correct recognition proteins to achieve fertilization .", "Given the importance of fertilization one would think these proteins are perfected and do not change over time; however , recent studies show that they do change and quite rapidly .", "Thus , the sperm an...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "viruses and cancer", "virology", "biology", "microbiology" ]	The EBV Latent Antigen 3C Inhibits Apoptosis through Targeted Regulation of Interferon Regulatory Factors 4 and 8	journal.ppat.1003314	null	[ [ "Tumor viruses have evolved multiple strategies for modulating the expression of an array of cellular genes to enhance persistence , latency and survival of infected cells .", "Studies into these strategies have provided several lines of evidence as to the mechanisms of differential gene expression and th...	[ "Epstein-Barr virus ( EBV ) is linked to a broad spectrum of B-cell malignancies .", "EBV nuclear antigen 3C ( EBNA3C ) is an encoded latent antigen required for growth transformation of primary human B-lymphocytes .", "Interferon regulatory factor 4 ( IRF4 ) and 8 ( IRF8 ) are transcription factors of the IRF ...	[ "Interferon regulatory factor ( IRF ) family members have different roles in context of pathogen response , signal transduction , cell proliferation and hematopoietic development .", "IRF4 and IRF8 are members of the IRF family and are critical mediators of B-cell development .", "Enhanced expression of IRF4 is...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Phenotype Specific Analyses Reveal Distinct Regulatory Mechanism for Chronically Activated p53	journal.pgen.1005053	null	[ [ "The TP53 ( p53 ) tumor suppressor , a stress-responsive transcription factor ( TF ) , is somatically mutated in more than 50% of human cancers , with a range between 10% and nearly 100% depending on the tumor type .", "Furthermore , germ line mutations of p53 , in both humans and mice , predispose indivi...	[ "The downstream functions of the DNA binding tumor suppressor p53 vary depending on the cellular context , and persistent p53 activation has recently been implicated in tumor suppression and senescence .", "However , genome-wide information about p53-target gene regulation has been derived mostly from acute genot...	[ "The p53 transcription factor is a frequently mutated tumour suppressor that contributes to repairing or eliminating damaged cells .", "Levels of p53 are typically regulated through its stability; it is constantly produced and degraded , so that upon stress , p53 is up-regulated quickly .", "This acutely induce...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "plant science", "plant biology", "genetics", "biology", "genetics and genomics" ]	Ehd4 Encodes a Novel and Oryza-Genus-Specific Regulator of Photoperiodic Flowering in Rice	journal.pgen.1003281	null	[ [ "Flowering is a profound transition from vegetative to reproductive development in plants , and is largely determined by genetic pathways that integrate endogenous and environmental signals [1] .", "Plants control flowering by perceiving their surroundings , such as day-length ( photoperiod ) and temperat...	[ "Land plants have evolved increasingly complex regulatory modes of their flowering time ( or heading date in crops ) .", "Rice ( Oryza sativa L . ) is a short-day plant that flowers more rapidly in short-day but delays under long-day conditions .", "Previous studies have shown that the CO-FT module initially id...	[ "Rice is an important source of calories for mankind .", "Flowering time determines cropping seasons and regional adaptability of crops .", "Rice is originated from its wild progenitor , O . rufipogon , which is mainly distributed at tropical latitudes with a northern limit about 28 °N , more than 10 , 000 year...	2013
[ "Introduction", "Results and Discussion", "Materials and Methods" ]	[]	The Genomic Aftermath of Hybridization in the Opportunistic Pathogen Candida metapsilosis	journal.pgen.1005626	null	[ [ "Hybridization between species is an important evolutionary mechanism that can drive the origin of novel lineages and adaptation to new environments .", "Hybridization results in the combination of two diverged genomes , which are subsequently shaped by processes of recombination , deletion , and other ge...	[ "Candida metapsilosis is a rarely-isolated , opportunistic pathogen that belongs to a clade of pathogenic yeasts known as the C . parapsilosis sensu lato species complex .", "To gain insight into the recent evolution of C . metapsilosis and the genetic basis of its virulence , we sequenced the genome of 11 clinic...	[ "Human pathogens belong to different phylogenetic clades and it is clear that the ability to infect humans emerged several times independently .", "The sequencing and comparison of genomes from pathogenic and non-pathogenic species and strains paves the way to identify what genomic changes underlie the emergence ...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell physiology", "carbohydrate metabolism", "chemical compounds", "monomers", "phosphates", "enzymology", "carbohydrates", "glucose metabolism", "organic compounds", "parasitic protozoans", "glucose", "cell metabolism", "oxygen metabolism", "protozoans", "enzyme metabolism", "enzyme ...	Glycerol supports growth of the Trypanosoma brucei bloodstream forms in the absence of glucose: Analysis of metabolic adaptations on glycerol-rich conditions	journal.ppat.1007412	null	[ [ "Trypanosoma brucei is an extracellular protist parasite that causes Human African Trypanosomiasis ( HAT ) or sleeping sickness , a neglected tropical disease in Sub-Saharan Africa [1] .", "This parasite undergoes a complex life cycle from the bloodstream of a mammalian host ( bloodstream forms—BSF ) to t...	[ "The bloodstream forms of Trypanosoma brucei ( BSF ) , the parasite protist causing sleeping sickness , primarily proliferate in the blood of their mammalian hosts .", "The skin and adipose tissues were recently identified as additional major sites for parasite development .", "Glucose was the only carbon sourc...	[ "Until very recently , the bloodstream forms ( BSF ) of the Trypanosoma brucei group species have been considered to propagate exclusively in the mammalian fluids , including the blood , the lymphatic network and the cerebrospinal fluid .", "All these fluids are rich in glucose , which is widely considered by the...	2018
[ "Introduction", "Results", "Materials and Methods" ]	[ "computational biology/metabolic networks", "computational biology/systems biology" ]	Spontaneous Reaction Silencing in Metabolic Optimization	journal.pcbi.1000236	null	[ [ "A fundamental problem in systems biology is to understand how living cells adjust the usage pattern of their components to respond and adapt to specific genetic , epigenetic , and environmental conditions .", "In complex metabolic networks of single-cell organisms , there is mounting evidence in the expe...	[ "Metabolic reactions of single-cell organisms are routinely observed to become dispensable or even incapable of carrying activity under certain circumstances .", "Yet , the mechanisms as well as the range of conditions and phenotypes associated with this behavior remain very poorly understood .", "Here we predi...	[ "Cellular growth and other integrated metabolic functions are manifestations of the coordinated interconversion of a large number of chemical compounds .", "But what is the relation between such whole-cell behaviors and the activity pattern of the individual biochemical reactions ?", "In this study , we have us...	2008
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "cognitive science", "medicine and health sciences", "pathology and laboratory medicine", "decision making", "tropical diseases", "geographical locations", "vertebrates", "neuroscience", "animals", "epidemiological methods and statistics", "signs and symptoms", "reptiles", "cognition", "ne...	Mapping the Risk of Snakebite in Sri Lanka - A National Survey with Geospatial Analysis	journal.pntd.0004813	null	[ [ "Bites of venomous snakes cause significant morbidity and mortality in the rural tropics .", "Despite this , snakebite did not , until very recently , receive the attention it deserves as an important public health problem .", "The main reason for this was the paucity of robust epidemiological data on...	[ "There is a paucity of robust epidemiological data on snakebite , and data available from hospitals and localized or time-limited surveys have major limitations .", "No study has investigated the incidence of snakebite across a whole country .", "We undertook a community-based national survey and model based ge...	[ "Snakebite is a neglected tropical disease which mainly affects the rural poor in tropical countries .", "There is little reliable data on snakebite , which makes it difficult to estimate the true disease burden .", "Hospital statistics underestimate numbers of snakebites because a significant proportion of vic...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Mitochondrial Dysfunction Reveals the Role of mRNA Poly(A) Tail Regulation in Oculopharyngeal Muscular Dystrophy Pathogenesis	journal.pgen.1005092	null	[ [ "Many neurodegenerative disorders are due to expansions of trinucleotide repeats in the associated genes .", "In many cases , the pathology is thought to involve protein misfolding and accumulation in insoluble aggregates [1] .", "However , more recent data have also implicated RNA toxicity and RNA gr...	[ "Oculopharyngeal muscular dystrophy ( OPMD ) , a late-onset disorder characterized by progressive degeneration of specific muscles , results from the extension of a polyalanine tract in poly ( A ) binding protein nuclear 1 ( PABPN1 ) .", "While the roles of PABPN1 in nuclear polyadenylation and regulation of alte...	[ "Oculopharyngeal muscular dystrophy is a genetic disease characterized by progressive degeneration of specific muscles , leading to ptosis ( eyelid drooping ) , dysphagia ( swallowing difficulties ) and proximal limb weakness .", "The disease results from mutations in a nuclear protein called poly ( A ) binding p...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "gene regulation", "pathogens", "bacillus", "microbiology", "staphylococcus aureus", "dna transcription", "prokaryotic models", "regulator genes", "model organisms", "gene types", "bacteria", "bacterial pathogens", "res...	Staphylococcus aureus Transcriptome Architecture: From Laboratory to Infection-Mimicking Conditions	journal.pgen.1005962	null	[ [ "The Gram-positive bacterium Staphylococcus aureus causes human infections that range from superficial skin infections to life-threatening diseases such as pneumonia , endocarditis , osteomyelitis , bacteremia and sepsis [1] .", "This major human pathogen is also a common component of skin and mucosal flo...	[ "Staphylococcus aureus is a major pathogen that colonizes about 20% of the human population .", "Intriguingly , this Gram-positive bacterium can survive and thrive under a wide range of different conditions , both inside and outside the human body .", "Here , we investigated the transcriptional adaptation of S ...	[ "The major human pathogen Staphylococcus aureus can survive under a wide range of conditions , both inside and outside the human body .", "The goal of this study was to determine how S . aureus adapts to such different conditions and , additionally , we wanted to identify general factors governing the staphylococ...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases/infectious diseases of the nervous system", "infectious diseases/neglected tropical diseases", "neurological disorders/infectious diseases of the nervous system", "immunology/immune response", "pediatrics and child health", "public health and epidemiology/infectious diseases", "infe...	Immunogenicity of Fractional Doses of Tetravalent A/C/Y/W135 Meningococcal Polysaccharide Vaccine: Results from a Randomized Non-Inferiority Controlled Trial in Uganda	journal.pntd.0000342	null	[ [ "Sub-Saharan African countries in the “Meningitis Belt , ” situated between Ethiopia and Senegal , face epidemics of meningococcal meningitis almost every year [1] .", "Following the current World Health Organization ( WHO ) recommendation , mass vaccination campaigns with polysaccharide meningococcal vac...	[ "Neisseria meningitidis serogroup A is the main causative pathogen of meningitis epidemics in sub-Saharan Africa .", "In recent years , serogroup W135 has also been the cause of epidemics .", "Mass vaccination campaigns with polysaccharide vaccines are key elements in controlling these epidemics .", "Facing g...	[ "Meningitis are infections of the lining of the brain and spinal cord and can cause high fever , blood poisoning , and brain damage , as well as result in death in up to 10% of cases .", "Epidemics of meningitis occur almost every year in parts of sub-Saharan Africa , throughout a high-burden area spanning Senega...	2008
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "biotechnology", "traumatic injury", "medicine and health sciences", "engineering and technology", "lasers", "animal models", "muscle proteins", "model organisms", "experimental organism systems", "optical equipment", "genetic engineering", "research and analysis methods", "proteins", "mus...	Genetic modifiers of muscular dystrophy act on sarcolemmal resealing and recovery from injury	journal.pgen.1007070	null	[ [ "Muscular dystrophies are inherited diseases that cause progressive muscle wasting [1] .", "Many muscular dystrophies are caused by mutations in genes encoding for components of the dystrophin glycoprotein complex , which anchors the actin cytoskeleton of myofibers to their cell membrane , the sarcolemma ...	[ "Genetic disruption of the dystrophin complex produces muscular dystrophy characterized by a fragile muscle plasma membrane leading to excessive muscle degeneration .", "Two genetic modifiers of Duchenne Muscular Dystrophy implicate the transforming growth factor β ( TGFβ ) pathway , osteopontin encoded by the SP...	[ "Genetic modifiers for muscular dystrophy have been identified through transcriptomic and genomic profiling in humans and mouse models .", "Two modifiers , Ltbp4 and Spp1 , encode extracellular proteins while a third modifier , Anxa6 , specifies a membrane-associated protein .", "Using a model of muscle injury ...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "ecology", "infectious diseases/epidemiology and control of infectious diseases" ]	Molecular Epidemiology of Cross-Species Giardia duodenalis Transmission in Western Uganda	journal.pntd.0000683	null	[ [ "Giardia is a genus of parasitic protozoan that infects the small and large intestines of a broad range of vertebrate hosts [1] .", "Considered among the most common human intestinal protozoa , especially in the tropics [2] , G . duodenalis ranges in clinical severity from asymptomatic to highly pathogeni...	[ "Giardia duodenalis is prevalent in tropical settings where diverse opportunities exist for transmission between people and animals .", "We conducted a cross-sectional study of G . duodenalis in people , livestock , and wild primates near Kibale National Park , Uganda , where human-livestock-wildlife interaction ...	[ "Giardia duodenalis is a common protozoan parasite that infects multiple mammalian species , including humans .", "We analyzed G . duodenalis from people , livestock , and wild non-human primates in forest fragments near Kibale National Park , western Uganda , where habitat disturbance and human-animal interactio...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biotechnology", "medicine", "model organisms", "pediatrics and child health", "neurology", "genetics", "neurological disorders", "biology", "genomics", "molecular cell biology", "neuroscience", "genetics and genomics", "pediatrics", "clinical genetics" ]	Recessive Mutations in SPTBN2 Implicate β-III Spectrin in Both Cognitive and Motor Development	journal.pgen.1003074	null	[ [ "Spectrins are a diverse family of membrane scaffold proteins .", "They were originally found in erythrocytes where mutations result in various haemolytic anemias [1] , [2] .", "Spectrins have been identified in the brain [3] but until recently little was known of the effects in humans of brain spectr...	[ "β-III spectrin is present in the brain and is known to be important in the function of the cerebellum .", "Heterozygous mutations in SPTBN2 , the gene encoding β-III spectrin , cause Spinocerebellar Ataxia Type 5 ( SCA5 ) , an adult-onset , slowly progressive , autosomal-dominant pure cerebellar ataxia .", "SC...	[ "β-III spectrin is present in the brain and is known to be important in the function of the cerebellum .", "Mutations in β-III spectrin cause spinocerebellar ataxia type 5 ( SCA5 ) , sometimes called Lincoln ataxia because it was first described in the relatives of United States President Abraham Lincoln .", "T...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/hiv infection and aids", "immunology/immunity to infections", "immunology/immune response" ]	Perforin Expression Directly Ex Vivo by HIV-Specific CD8+ T-Cells Is a Correlate of HIV Elite Control	journal.ppat.1000917	null	[ [ "Approximately 35–40 million people are currently infected with HIV worldwide .", "Most of these individuals fail to control HIV replication , and ultimately progress to acquired immune deficiency syndrome ( AIDS ) if left untreated .", "However , a subset ( <1% ) of the HIV-infected population , term...	[ "Many immune correlates of CD8+ T-cell-mediated control of HIV replication , including polyfunctionality , proliferative ability , and inhibitory receptor expression , have been discovered .", "However , no functional correlates using ex vivo cells have been identified with the known ability to cause the direct e...	[ "While the majority HIV-infected individuals progress to AIDS , a fraction of these individuals—for reasons not completely understood—do not develop AIDS and also display sustained control over viral replication; these subjects are sometimes referred to as elite controllers ( EC ) .", "Prior evidence has shown th...	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "employment", "pathology and laboratory medicine", "togaviruses", "chikungunya infection", "pathogens", "tropical diseases", "microbiology", "social sciences", "indirect costs", "alphaviruses", "health care", "viruses", "chikungunya virus", "rna viruses", ...	Estimating the cost of illness and burden of disease associated with the 2014–2015 chikungunya outbreak in the U.S. Virgin Islands	journal.pntd.0007563	null	[ [ "Chikungunya virus ( CHIKV ) , an alphavirus transmitted by Aedes ( Stegomyia ) species mosquitoes , was introduced into the Americas in December of 2013 [1] .", "By April 2016 , almost 2 million suspected or confirmed cases were reported in 45 countries and territories in the Caribbean , Central , South ...	[ "Chikungunya virus ( CHIKV ) , an alphavirus that causes fever and severe polyarthralgia , swept through the Americas in 2014 with almost 2 million suspected or confirmed cases reported by April 2016 .", "In this study , we estimate the direct medical costs , cost of lost wages due to absenteeism , and years live...	[ "Chikungunya , a virus carried and transmitted by mosquitoes , causes fever , headache , and severe joint pain in humans that often resolves within 7–10 days .", "However , a proportion of cases , up to 79% in some outbreaks , report persistent joint pain and chronic inflammatory rheumatism , resulting in decreas...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "organismal evolution", "medicine and health sciences", "pathology and laboratory medicine", "microbiology", "gene function", "developmental biology", "mutation", "molecular cell biology", "speciation", "microbial evolution", "microbial growth and development", "bacterial pathogens", "microb...	Ras GTPase-Like Protein MglA, a Controller of Bacterial Social-Motility in Myxobacteria, Has Evolved to Control Bacterial Predation by Bdellovibrio	journal.pgen.1004253	null	[ [ "Bdellovibrio bacteriovorus is a small , predatory deltaproteobacterium which invades other Gram-negative bacteria wherein it replicates .", "Bdellovibrio can encounter their prey by fast motility , driven by rotation of a single flagellum in liquid environments [1] , [2] , or by slow gliding motility on ...	[ "Bdellovibrio bacteriovorus invade Gram-negative bacteria in a predatory process requiring Type IV pili ( T4P ) at a single invasive pole , and also glide on surfaces to locate prey .", "Ras-like G-protein MglA , working with MglB and RomR in the deltaproteobacterium Myxococcus xanthus , regulates adventurous gli...	[ "Bacterial cell polarity control is important for maintaining asymmetry of polar components such as flagella and pili .", "Bdellovibrio bacteriovorus is a predatory deltaproteobacterium which attaches to , and invades , other bacteria using Type IV pili ( T4P ) extruded from the specialised , invasive , non-flage...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "blood cells", "invertebrates", "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "helminths", "immunology", "tropical diseases", "geographical locations", "fascioliasis", "parasitic diseases", "animals", "trematodes", "signs and symptoms", "neglected t...	Evaluation of nitazoxanide treatment following triclabendazole failure in an outbreak of human fascioliasis in Upper Egypt	journal.pntd.0007779	null	[ [ "Fascioliasis has emerged as a notable zoonotic disease with considerable impact on veterinary and public health .", "This prompted the World Health Organization ( WHO ) to include human fascioliasis among the important neglected tropical diseases ( NTDs ) [1] .", "It is a foodborne disease caused by ...	[ "Fascioliasis is a neglected zoonosis with major public health implications in humans .", "Although triclabendazole ( TCBZ ) is the drug of choice , there are records of TCBZ failure worldwide .", "TCBZ-resistant fascioliasis is treated with alternative approved drugs including nitazoxanide ( NTZ ) , with varyi...	[ "Fascioliasis is a neglected zoonosis with major public health implications in humans .", "Triclabendazole ( TCBZ ) is the drug of choice , but alternative approved drugs are necessary in cases of TCBZ failure .", "Nitazoxanide ( NTZ ) is an alternative used in such cases .", "However , the efficacy of NTZ in...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	THY-1 Cell Surface Antigen (CD90) Has an Important Role in the Initial Stage of Human Cytomegalovirus Infection	journal.ppat.1004999	null	[ [ "Human cytomegalovirus ( HCMV ) infects about 50% of the US population and is the leading infectious cause of birth defects and the most important infectious agent in transplant recipients .", "In vivo , HCMV predominantly infects epithelial , endothelial , fibroblast , smooth muscle , and mononuclear cel...	[ "Human cytomegalovirus ( HCMV ) infects about 50% of the US population , is the leading infectious cause of birth defects , and is considered the most important infectious agent in transplant recipients .", "The virus infects many cell types in vivo and in vitro .", "While previous studies have identified sever...	[ "Human cytomegalovirus ( HCMV ) is an important human pathogen that infects about half the US population and is a major cause of birth defects and morbidity in transplant recipients .", "Despite extensive research , much is still unknown regarding how the virus enters cells .", "We identified THY-1 , a protein ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology" ]	Parallel Evolutionary Dynamics of Adaptive Diversification in Escherichia coli	journal.pbio.1001490	The divergence of Escherichia coli bacteria into metabolically distinct ecotypes has a similar genetic basis and similar evolutionary dynamics across independently evolved populations.	[ [ "The causes and mechanisms of diversification are central issues in evolutionary biology .", "Explanations that involve the splitting of an ancestral population into geographically or otherwise isolated populations ( allopatric diversification ) have historically been favored because of theoretical diffic...	[ "The causes and mechanisms of evolutionary diversification are central issues in biology .", "Geographic isolation is the traditional explanation for diversification , but recent theoretical and empirical studies have shown that frequency-dependent selection can drive diversification without isolation and that ad...	[ "The causes and mechanisms of evolutionary diversification are central issues in biology .", "There is well-established theory that predicts that adaptive diversification can arise because of ecological interactions between individuals , such as competition or predation , but there are no empirical examples in wh...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "computational biology/macromolecular structure analysis", "biophysics/macromolecular assemblies and machines", "molecular biology/rna-protein interactions", "biochemistry/experimental biophysical methods", "biophysics/biomacromolecule-ligand interactions", "molecular biology/mrna transport and localizati...	Structural Basis for the Recognition of Cellular mRNA Export Factor REF by Herpes Viral Proteins HSV-1 ICP27 and HVS ORF57	journal.ppat.1001244	null	[ [ "All herpesviruses replicate in the host cell nucleus and therefore utilise the host cell's protein transcription and translation apparatus , while at the same time suppressing the correspondent cellular processes [1]–[5] .", "Crucially , non-spliced viral mRNA is directed into the cellular mRNA export ma...	[ "The herpesvirus proteins HSV-1 ICP27 and HVS ORF57 promote viral mRNA export by utilizing the cellular mRNA export machinery .", "This function is triggered by binding to proteins of the transcription-export ( TREX ) complex , in particular to REF/Aly which directs viral mRNA to the TAP/NFX1 pathway and , subseq...	[ "When invading host cells , herpes viruses highjack cellular components to allow them to replicate .", "It has been long recognized that each herpes virus has a specific signature adaptor protein which , among other functions , inserts viral mRNA into the cellular mRNA nuclear export pathway , enabling production...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biofilms", "medicine and health sciences", "pathology and laboratory medicine", "gene regulation", "pathogens", "microbiology", "mutation", "fungi", "experimental organism systems", "molecular biology techniques", "fungal pathogens", "research and analysis methods", "mycology", "mutant st...	Circuit diversification in a biofilm regulatory network	journal.ppat.1007787	null	[ [ "Each species has broad properties that define its members , yet individuals present diversity that reflects the events of their lineage .", "Although some phenotypic differences between individuals arise from single allelic differences or gene acquisitions , the vast majority represent the interplay of m...	[ "Genotype-phenotype relationships can vary extensively among members of a species .", "One cause of this variation is circuit diversification , the alteration of gene regulatory relationships among members of a species .", "Circuit diversification is thought to be a starting point for the circuit divergence or ...	[ "Much of what we know about microbial pathogens is derived from in-depth analysis of one or a few standard laboratory strains .", "This statement is especially true for the fungal pathogen Candida albicans , because most studies have centered on strain SC5314 and its genetically marked derivatives .", "Here we ...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "medicine and health sciences", "helminths", "tropical diseases", "parasitic diseases", "neuroscience", "animals", "data mining", "artificial neural networks", "mathematics", "forecasting", "statistics (mathematics)", "artificial intelligence", "gastroente...	Comparison of three data mining models for prediction of advanced schistosomiasis prognosis in the Hubei province	journal.pntd.0006262	null	[ [ "Approximately 240 million individuals are infected worldwide by schistosomiasis , with an estimated 3 . 31 million disability-adjusted life years lost as a result of the disease [1–4] .", "Further , one meta-analysis and several scientific reports have suggested that global burden caused by schistosomias...	[ "In order to better assist medical professionals , this study aimed to develop and compare the performance of three models—a multivariate logistic regression ( LR ) model , an artificial neural network ( ANN ) model , and a decision tree ( DT ) model—to predict the prognosis of patients with advanced schistosomiasi...	[ "Worldwide , approximately 240 million individuals are infected with schistosomiasis , a parasitic neglected tropical disease that continues to be a significant cause of morbidity and mortality , especially in China .", "Effective tools that can accurately predict the prognosis of patients with advanced schistoso...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "bacteriology", "escherichia coli", "gram negative bacteria", "medical microbiology", "microbial pathogens", "biology and life sciences", "microbiology", "bacterial pathogens" ]	A Large Family of Antivirulence Regulators Modulates the Effects of Transcriptional Activators in Gram-negative Pathogenic Bacteria	journal.ppat.1004153	null	[ [ "Enteroaggregative Escherichia coli ( EAEC ) is a diarrheagenic pathotype linked to traveler's diarrhea , foodborne outbreaks and sporadic diarrhea in industrialized and developing countries [1]–[4] .", "A Shiga toxin-lysogenized EAEC caused a large and highly lethal European outbreak in 2011 , highlighti...	[ "We have reported that transcription of a hypothetical small open reading frame ( orf60 ) in enteroaggregative E . coli ( EAEC ) strain 042 is impaired after mutation of aggR , which encodes a global virulence activator .", "We have also reported that the cryptic orf60 locus was linked to protection against EAEC ...	[ "We report here the identification and characterization of a new family of negative regulators in Gram-negative bacteria , including many pathotypes of diarrheagenic Enterobacteriaceae and members of the Pasteurellaceae .", "Members of this regulator family in enteroaggregative ( EAEC ) and enterotoxigenic E . co...	2014
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma mansoni", "medicine and health sciences", "body fluids", "helminths", "tropical diseases", "parasitic diseases", "animals", "parasitology", "urine", "neglected tropical diseases", "parasitic intestinal diseases", "protozoan infections", "intes...	Evaluation of diagnostic methods for the detection of intestinal schistosomiasis in endemic areas with low parasite loads: Saline gradient, Helmintex, Kato-Katz and rapid urine test	journal.pntd.0006232	null	[ [ "Recent estimates of helminth infections indicate the existence of more than one billion infected individuals in underdeveloped areas of Africa , Asia , and in Central and South America [1] .", "Among the different trematode species infecting humans , schistosome species are the parasites with the highest...	[ "In some tropical countries , such as Brazil , schistosomiasis control programs have led to a significant reduction in the prevalence and parasite burden of endemic populations .", "In this setting , the Kato-Katz technique , as the standard diagnostic method for the diagnosis of Schistosoma mansoni infections , ...	[ "Human infection with the flatworm Schistosoma mansoni continues to be a public health problem in many tropical countries , including Brazil .", "The parasitological method recommended by the World Health Organization for the detection of intestinal schistosomiasis , the Kato-Katz method ( KK ) , underestimates t...	2018

Subsets and Splits

No community queries yet

The top public SQL queries from the community will appear here once available.