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headings list	keywords list	title stringlengths 20 281	id stringlengths 20 20	toc stringlengths 57 522 ⌀	sections list	abstract list	summary list	year stringclasses 13 values
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "children", "medicine and health sciences", "vertebrates", "parasitic diseases", "animals", "mammals", "parasitology", "dogs", "age groups", "families", "public and occupational health", "infectious diseases", "parasitic intestinal diseases", "protozoan infections", "people and places", ...	Environmental and socio-demographic individual, family and neighborhood factors associated with children intestinal parasitoses at Iguazú, in the subtropical northern border of Argentina	journal.pntd.0006098	null	[ [ "Infectious diseases associated with the gastrointestinal tract continue to be a major public health concern , especially in middle and low-income populations from tropical and subtropical areas of the developing world [1 , 2] .", "Gastrointestinal parasitoses caused by intestinal protozoan ( IP ) ( e . g...	[ "Intestinal parasitoses are a major concern for public health , especially in children from middle and low-income populations of tropical and subtropical areas .", "We examined the presence and co-infection of parasites in humans as well as parasitic environmental contamination in Puerto Iguazú , Argentina .", ...	[ "Enteroparasites are among the main issues in public health arena , especially in children of vulnerable communities from developing countries .", "We performed a combined analysis of the factors that describe parasite prevalence in children and their environment .", "Our result evidenced a combined effect of s...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases", "immunology", "homo (human)", "eubacteria" ]	Human Innate Mycobacterium tuberculosis–Reactive αβTCR+ Thymocytes	journal.ppat.0040039	null	[ [ "Approximately one-third of the world's population is infected with Mycobacterium tuberculosis ( Mtb ) .", "Tuberculosis remains a leading cause of mortality worldwide and is responsible for 2–3 million deaths per year [1] .", "Household contact studies show that over 50% of exposed individuals never ...	[ "The control of Mycobacterium tuberculosis ( Mtb ) infection is heavily dependent on the adaptive Th1 cellular immune response .", "Paradoxically , optimal priming of the Th1 response requires activation of priming dendritic cells with Th1 cytokine IFN-γ .", "At present , the innate cellular mechanisms required...	[ "Mycobacterium tuberculosis ( Mtb ) infects about one-third of the world's population .", "Most people who are exposed remain healthy , but control of this intracellular bacterium requires a robust cellular immune response .", "Production of the pro-inflammatory cytokine IFN-γ from cells in the adaptive immune ...	2008
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "plagues", "enzyme-linked immunoassays", "immune physiology", "pathology and laboratory medicine", "pathogens", "immunology", "microbiology", "vaccines", "preventive medicine", "bacterial diseases", "drug delivery system preparation", "antigen encapsulation", ...	Humoral and cellular immune responses to Yersinia pestis Pla antigen in humans immunized with live plague vaccine	journal.pntd.0006511	null	[ [ "Plague is known as a primary natural zoonosis but is an extremely deadly infection for humans .", "The disease is caused by Yersinia pestis , a gram-negative bacterium , which upon entry in the body of mammalian host is capable of establishing three major forms of plague: bubonic , septicemic , and pneum...	[ "To establish correlates of human immunity to the live plague vaccine ( LPV ) , we analyzed parameters of cellular and antibody response to the plasminogen activator Pla of Y . pestis .", "This outer membrane protease is an essential virulence factor that is steadily expressed by Y . pestis .", "PBMCs and sera ...	[ "Yersinia pestis , the causative agent of plague , has been recognized as one of the most devastating pathogen experienced by mankind .", "It remains endemic in many parts of the world , and is considered emerging pathogen .", "A live attenuated Y . pestis strain EV line NIIEG has been used for decades in the f...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular biology/histone modification", "molecular biology/chromatin structure" ]	Histone H4 Lysine 12 Acetylation Regulates Telomeric Heterochromatin Plasticity in Saccharomyces cerevisiae	journal.pgen.1001272	null	[ [ "Saccharomyces cerevisiae telomeres and mating type loci ( HMR and HML ) are well-characterized transcriptionally silenced domains .", "Heterochromatin tends to initiate at a specific DNA element and propagates along a chromatin fiber to repress the expression of nearby genes [1] .", "The major struct...	[ "Recent studies have established that the highly condensed and transcriptionally silent heterochromatic domains in budding yeast are virtually dynamic structures .", "The underlying mechanisms for heterochromatin dynamics , however , remain obscure .", "In this study , we show that histones are dynamically acet...	[ "The genetic material in eukaryotes is packaged into chromatin .", "The chromatin structure is orchestrated such that euchromatic regions are relatively uncondensed and accessible to factors that bind DNA , whereas heterochromatic regions are densely packaged into higher-order conformations .", "The compact nat...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "biology", "veterinary science" ]	Characterisation of the Wildlife Reservoir Community for Human and Animal Trypanosomiasis in the Luangwa Valley, Zambia	journal.pntd.0001211	null	[ [ "Trypanosomes are true multi-host parasites capable of infecting a wide range of wildlife species that constitute a reservoir of infection for both people and domestic animals .", "Natural infections of trypanosomes in wildlife were first identified during the Sleeping Sickness Commission in the Luangwa V...	[ "Animal and human trypanosomiasis are constraints to both animal and human health in Sub-Saharan Africa , but there is little recent evidence as to how these parasites circulate in wild hosts in natural ecosystems .", "The Luangwa Valley in Zambia supports high densities of tsetse flies ( Glossina species ) and i...	[ "Animal and human trypanosomiasis are constraints to both animal and human health in Sub-Saharan Africa , but there is little recent evidence as to how these parasites circulate in natural hosts in natural ecosystems .", "A cross-sectional survey of trypanosome prevalence in 418 wildlife hosts was conducted in th...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "shrimp", "invertebrates", "medicine and health sciences", "immune cells", "rna interference", "immune physiology", "293t cells", "immunology", "cell processes", "biological cultures", "animals", "crustaceans", "epigenetics", "antibodies", "digestive system", "research...	The polymeric immunoglobulin receptor-like protein from Marsupenaeus japonicus is a receptor for white spot syndrome virus infection	journal.ppat.1007558	null	[ [ "Viral infection process is a very complex interaction and consists of multiple steps [1] .", "It starts with virion attachment to the host cell membrane , followed by specific binding to receptors .", "Viral receptor engagement allows viruses either to release their genome into the cell directly at t...	[ "Viral entry into the host cell is the first step towards successful infection .", "Viral entry starts with virion attachment , and binding to receptors .", "Receptor binding viruses either directly release their genome into the cell , or enter cells through endocytosis .", "For DNA viruses and a few RNA viru...	[ "White Spot Syndrome Virus ( WSSV ) is one of the most virulent pathogens in shrimp farming .", "Several viral candidate receptors , or attachment factors were reported in previous studies , however , most of them are not authentic transmembrane proteins .", "In particular , the protein receptor ( s ) required ...	2019
[ "Introduction", "Material, methods, and models", "Results", "Discussion" ]	[ "plant anatomy", "buds", "computerized simulations", "mathematical models", "hormones", "plant science", "plant hormones", "microscopy", "plants", "flowering plants", "research and analysis methods", "computer and information sciences", "mathematical and statistical techniques", "scanning ...	Mathematical model studies of the comprehensive generation of major and minor phyllotactic patterns in plants with a predominant focus on orixate phyllotaxis	journal.pcbi.1007044	null	[ [ "Plants bear leaves around the stem in a regular arrangement; this is termed phyllotaxis .", "Across diverse plant species , phyllotaxis has common characteristics , which are often described mathematically and are reflected in a limited variety of phyllotactic patterns , including the distichous , decuss...	[ "Plant leaves are arranged around the stem in a beautiful geometry that is called phyllotaxis .", "In the majority of plants , phyllotaxis exhibits a distichous , Fibonacci spiral , decussate , or tricussate pattern .", "To explain the regularity and limited variety of phyllotactic patterns , many theoretical m...	[ "Phyllotaxis , the beautiful geometry of plant-leaf arrangement around the stem , has long attracted the attention of researchers of biological-pattern formation .", "Many mathematical models , as typified by those of Douady and Couder ( alternate-specific form , DC1; more generalized form , DC2 ) , have been pro...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "invertebrates", "rna interference", "microtubules", "microtubule dynamics", "cell processes", "neuroscience", "animals", "animal models", "drosophila melanogaster", "model organisms", "nerve fibers", "mitochondria", "epigenetics", "bioenergetics", "microtubule polymerization", "cellul...	Mitochondria and Caspases Tune Nmnat-Mediated Stabilization to Promote Axon Regeneration	journal.pgen.1006503	null	[ [ "The ability of neurons to survive injury , misfolded proteins , hypoxic stress and other deleterious conditions allows the nervous system to function for a lifetime without large-scale production of new neurons .", "Neuronal survival strategies buy the cells time to maintain or regain function .", "F...	[ "Axon injury can lead to several cell survival responses including increased stability and axon regeneration .", "Using an accessible Drosophila model system , we investigated the regulation of injury responses and their relationship .", "Axon injury stabilizes the rest of the cell , including the entire dendri...	[ "Unlike many other cell types , most neurons last a lifetime .", "When injured , these cells often activate survival and repair strategies rather than dying .", "One such response is regeneration of the axon after it is injured .", "Axon regeneration is a conserved process activated by the same signaling casc...	2016
[ "Introduction", "Materials and Methods", "Results and Discussion" ]	[]	Genomic and Proteomic Studies on the Mode of Action of Oxaboroles against the African Trypanosome	journal.pntd.0004299	null	[ [ "Human African trypanosomiasis ( HAT ) is caused by two subspecies of the unicellular parasite Trypanosoma brucei , an infection which is transmitted by the bite of a tsetse fly .", "HAT progresses through a haemo-lymphatic stage into a meningo-encephalitic stage [1] and has a fatality rate close to 100% ...	[ "SCYX-7158 , an oxaborole , is currently in Phase I clinical trials for the treatment of human African trypanosomiasis .", "Here we investigate possible modes of action against Trypanosoma brucei using orthogonal chemo-proteomic and genomic approaches .", "SILAC-based proteomic studies using an oxaborole analog...	[ "The mode of action of a new class of boron-containing chemicals ( the oxaboroles ) , currently under development for the treatment of human African trypanosomiasis , is unknown .", "Here we identify a number of potential candidate proteins that could be involved either in the mode of action of these compounds or...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "protein interaction networks", "mathematics", "algebra", "network analysis", "protein structure", "computer and information sciences", "proteins", "algebraic structures", "proteomics", "protein structure networks", "molecular biology", "protein structure comparison", "biochemistry", "eige...	Vicus: Exploiting local structures to improve network-based analysis of biological data	journal.pcbi.1005621	null	[ [ "Networks are a powerful paradigm for representing relations among objects from micro to macro level .", "It is no surprise that networks became a representation of choice for many problems in biology and medicine including gene-gene and protein-protein interaction networks [1] , diseases [2] and their in...	[ "Biological networks entail important topological features and patterns critical to understanding interactions within complicated biological systems .", "Despite a great progress in understanding their structure , much more can be done to improve our inference and network analysis .", "Spectral methods play a k...	[ "Networks are a representation of choice for many problems in biology and medicine including protein interactions , metabolic pathways , evolutionary biology , cancer subtyping and disease modeling to name a few .", "The key to much of network analysis lies in the spectrum decomposition represented by eigenvector...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "microbial evolution", "biology", "microbiology", "evolutionary biology", "population biology", "infectious disease control", "infectious disease modeling" ]	Pharmacodynamics, Population Dynamics, and the Evolution of Persistence in Staphylococcus aureus	journal.pgen.1003123	null	[ [ "While it is convenient to consider genetically identical populations of bacteria as collections of physiologically homogeneous cells , they are commonly composed of phenotypically different subpopulations .", "Usually by some form of stochastic switch , during the course of growth or at stationary phase ...	[ "When growing populations of bacteria are confronted with bactericidal antibiotics , the vast majority of cells are killed , but subpopulations of genetically susceptible but phenotypically resistant bacteria survive .", "In accord with the prevailing view , these “persisters” are non- or slowly dividing cells ra...	[ "Because of its importance to therapy , a great deal of effort has been devoted to understanding the mechanisms responsible for and the genetic basis of persistence in inherently susceptible but phenotypically antibiotic-resistant subpopulations of bacteria .", "Much of this research is based on the premise that ...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "lao people", "burkholderia pseudomallei", "pathology and laboratory medicine", "melioidosis", "pathogens", "microbiology", "ethnicities", "bacterial diseases", "cereal crops", "fungi", "rice", "experimental organism systems", "crops", "molecular biology t...	Utility of a Lateral Flow Immunoassay (LFI) to Detect Burkholderia pseudomallei in Soil Samples	journal.pntd.0005204	null	[ [ "The Gram-negative Burkholderia pseudomallei is a soil-dwelling organism and also the cause of melioidosis , an often fatal infectious disease [1 , 2] .", "Melioidosis can be difficult to diagnose due to its diverse clinical manifestations .", "The diagnostic confirmation relies on microbiological cul...	[ "Culture is the gold standard for the detection of environmental B . pseudomallei .", "In general , soil specimens are cultured in enrichment broth for 2 days , and then the culture broth is streaked on an agar plate and incubated further for 7 days .", "However , identifying B . pseudomallei on the agar plates...	[ "Burkholderia pseudomallei is an environmental Gram-negative bacillus and the causative agent of melioidosis .", "Culture and PCR assays are standard diagnostic tools used to detect B . pseudomallei in the environment .", "However , those tests require experienced microbiologists and are regularly conducted onl...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "neurological disorders/alzheimer disease", "neurological disorders/prion diseases", "computational biology/molecular dynamics", "biophysics/protein folding" ]	Thermodynamic Selection of Steric Zipper Patterns in the Amyloid Cross-β Spine	journal.pcbi.1000492	null	[ [ "Amyloid fibrils are hallmarks of several neurodegenerative diseases including Alzheimer's , Parkinson's , and prion diseases [1] .", "Unlike other protein quaternary structures [2] , amyloid fibrils share a sequence independent structural motif known as the cross- β spine; individual strands from constit...	[ "At the core of amyloid fibrils is the cross-β spine , a long tape of β-sheets formed by the constituent proteins .", "Recent high-resolution x-ray studies show that the unit of this filamentous structure is a β-sheet bilayer with side chains within the bilayer forming a tightly interdigitating “steric zipper” in...	[ "Accumulation of amyloid fibrils is a salient feature of various protein misfolding diseases .", "Recent advances in precision experiments have begun to reveal their atomistic structures .", "Quantitative elucidation of how the observed structures are selected over other possible filament patterns would provide...	2009
[ "Introduction", "Model", "Results", "Discussions" ]	[ "nucleic acid synthesis", "enzymes", "cell cycle and cell division", "cell processes", "enzymology", "dna-binding proteins", "ribozymes", "systems science", "mathematics", "polymerases", "rna amplification", "rna synthesis", "chemical synthesis", "research and analysis methods", "compute...	Horizontal transfer between loose compartments stabilizes replication of fragmented ribozymes	journal.pcbi.1007094	null	[ [ "One of the crucial questions in the origin of life is how molecules acquired the capability of undergoing open-ended Darwinian evolution [1 , 2] .", "A potential answer is offered by the template-directed self-replication of a replicase , a replicase that can replicate itself .", "To determine whethe...	[ "The emergence of replicases that can replicate themselves is a central issue in the origin of life .", "Recent experiments suggest that such replicases can be realized if an RNA polymerase ribozyme is divided into fragments short enough to be replicable by the ribozyme and if these fragments self-assemble into a...	[ "How evolution got started is a crucial question in the origin of life .", "One possibility is that RNA molecules gained the ability to catalyze self-replication .", "Researchers recently proposed how this possibility might have been realized: a long RNA catalyst was divided into short replicable fragments , an...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "death rates", "united states", "invertebrates", "medicine and health sciences", "plagues", "body fluids", "pathology and laboratory medicine", "demography", "pathogens", "geographical locations", "microbiology", "vector-borne diseases", "animals", "north america", "bacterial diseases", ...	Comparative Ability of Oropsylla montana and Xenopsylla cheopis Fleas to Transmit Yersinia pestis by Two Different Mechanisms	journal.pntd.0005276	null	[ [ "Once fleas had been implicated as important vectors of the plague bacillus , Yersinia pestis , attention quickly turned to the mechanism and dynamics of flea-borne transmission .", "The first experiments , conducted between 1904–1907 by members of the Indian Plague Research Commission and others , charac...	[ "Transmission of Yersinia pestis by flea bite can occur by two mechanisms .", "After taking a blood meal from a bacteremic mammal , fleas have the potential to transmit the very next time they feed .", "This early-phase transmission resembles mechanical transmission in some respects , but the mechanism is unkno...	[ "The ecology of plague is complex and its epidemiology is enigmatic .", "Many different flea species are able to transmit Yersinia pestis , the plague bacillus , and they can transmit in two different ways .", "Early-phase transmission can occur during the first week after a flea has fed on a diseased animal ."...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "blood cells", "phosphorylation", "cell walls", "cell physiology", "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "pathogens", "immunology", "microbiology", "cell metabolism", "monomers (chemistry)", "inflammasomes", "cellular structures and organelles...	The Listeria monocytogenes PASTA Kinase PrkA and Its Substrate YvcK Are Required for Cell Wall Homeostasis, Metabolism, and Virulence	journal.ppat.1006001	null	[ [ "Intracellular pathogens are responsible for a majority of the world’s most devastating infectious disease .", "A subset of intracellular pathogens , known as cytosolic pathogens , survive and thrive in the host cell cytoplasm .", "Recently , it has become clear that some traditionally extracellular o...	[ "Obstacles to bacterial survival and replication in the cytosol of host cells , and the mechanisms used by bacterial pathogens to adapt to this niche are not well understood .", "Listeria monocytogenes is a well-studied Gram-positive foodborne pathogen that has evolved to invade and replicate within the host cell...	[ "Infection with intracellular pathogens causes a majority of the global infectious disease associated mortality .", "A number of intracellular pathogens must directly access the host cytosol in order to cause disease; however , non-cytosol adapted bacteria do not survive or replicate upon access to the cytosol ."...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Risk Factors for Visceral Leishmaniasis among Residents and Migrants in Kafta-Humera, Ethiopia	journal.pntd.0002543	null	[ [ "Visceral leishmaniasis ( VL ) is a lethal parasitic disease transmitted by phlebotomine sand flies .", "The typical clinical picture is a chronic systemic illness with fever , weight loss , splenomegaly , hepatomegaly , and bone marrow suppression with pancytopenia .", "East Africa is second only to ...	[ "Visceral leishmaniasis is a lethal parasitic disease transmitted by phlebotomine sand flies .", "The largest focus of VL in Ethiopia is located in the lowland region bordering Sudan , where the epidemiology is complicated by the presence of thousands of seasonal agricultural workers who live under precarious con...	[ "Visceral leishmaniasis is a lethal parasitic disease transmitted by sand flies .", "The largest focus of VL in Ethiopia is located in the lowland region bordering Sudan , where hundreds of thousands of agricultural workers migrate for work every year during the planting and harvest seasons .", "We conducted tw...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biology and life sciences", "developmental biology" ]	Vangl2-Regulated Polarisation of Second Heart Field-Derived Cells Is Required for Outflow Tract Lengthening during Cardiac Development	journal.pgen.1004871	null	[ [ "Malformations affecting the outflow of the heart are a major cause of morbidity and mortality in childhood .", "While many of these malformations occur sporadically , studies of families with congenital heart defects , alongside animal studies , have revealed that phenotypically discrete heart malformati...	[ "Planar cell polarity ( PCP ) is the mechanism by which cells orient themselves in the plane of an epithelium or during directed cell migration , and is regulated by a highly conserved signalling pathway .", "Mutations in the PCP gene Vangl2 , as well as in other key components of the pathway , cause a spectrum o...	[ "Congenital heart defects are common , affecting almost 1% of all live births .", "Many of these affect the outflow region , where the aorta and pulmonary trunk connect with the main ventricular chambers .", "Congenital heart defects arise from disruption of normal developmental processes and can be modelled in...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/epigenetics", "molecular biology/chromosome structure", "molecular biology/dna replication", "genetics and genomics/chromosome biology" ]	Preferential Re-Replication of Drosophila Heterochromatin in the Absence of Geminin	journal.pgen.1001112	null	[ [ "The precise duplication of the genome is a fundamental requirement to maintain genomic integrity .", "Eukaryotic cells employ a tightly regulated origin licensing system to ensure that each origin of DNA replication is activated once and only once during S phase [1] .", "Failure to properly license r...	[ "To ensure genomic integrity , the genome must be duplicated exactly once per cell cycle .", "Disruption of replication licensing mechanisms may lead to re-replication and genomic instability .", "Cdt1 , also known as Double-parked ( Dup ) in Drosophila , is a key regulator of the assembly of the pre-replicativ...	[ "Catastrophic consequences may occur if the cell fails to either completely copy the genome or if it duplicates some regions of the genome more than once in a cell cycle .", "The cell must coordinate thousands of DNA replication start sites ( origins ) to ensure that the entire genome is copied and that no replic...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Selection on Plant Male Function Genes Identifies Candidates for Reproductive Isolation of Yellow Monkeyflowers	journal.pgen.1003965	null	[ [ "By identifying the genes underlying barriers to reproduction , we gain broad insight into the processes driving speciation and the origins of organismal diversity .", "Reproductive barriers have long been known to include multiple pre-zygotic mechanisms that function before fertilization , after which po...	[ "Understanding the genetic basis of reproductive isolation promises insight into speciation and the origins of biological diversity .", "While progress has been made in identifying genes underlying barriers to reproduction that function after fertilization ( post-zygotic isolation ) , we know much less about earl...	[ "Barriers to reproduction are necessary for generating new species .", "Little is known about the genes underlying reproductive barriers , particularly those that function prior to fertilization , but their identity is of great interest as they offer insight into the genetic mechanisms and evolutionary forces gen...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "microbiome", "chemical compounds", "disaccharides", "appetite", "microbiology", "diet", "carbohydrates", "organic compounds", "physiological processes", "fungi", "nutrition", "eating", "bacteria", "microbial genomics", "food", "medical microbiology", ...	Commensal bacteria and essential amino acids control food choice behavior and reproduction	journal.pbio.2000862	null	[ [ "The appropriate intake of nutrients has a major beneficial impact on health and lifespan [1–3] .", "The level of dietary protein intake has emerged as a key determinant of overall mortality , fecundity , and lifespan in species ranging from humans [4] to mice [5] and Drosophila [6–9] .", "Accordingly...	[ "Choosing the right nutrients to consume is essential to health and wellbeing across species .", "However , the factors that influence these decisions are poorly understood .", "This is particularly true for dietary proteins , which are important determinants of lifespan and reproduction .", "We show that in ...	[ "What animals , including humans , choose to eat has a tremendous impact on health and wellbeing .", "Though intake of dietary proteins and amino acids is essential for animals , excessive consumption of these nutrients is known to have detrimental effects .", "Many animals , therefore , execute precise control...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "cell motility", "medicine and health sciences", "body fluids", "immune physiology", "immune cells", "ears", "immunology", "sand flies", "parasitic diseases", "antibodies", "insect vectors", "neutrophils", "immune system proteins", "infectious diseases", "white blood cel...	Immunity to LuloHya and Lundep, the salivary spreading factors from Lutzomyia longipalpis, protects against Leishmania major infection	journal.ppat.1007006	null	[ [ "Leishmaniasis , a vector-borne parasitic disease , comprises several clinical manifestations ranging from skin sores to life-threating visceral diseases .", "The causative agents , Leishmania parasites , are transmitted to the vertebrate host by the bite of infected female phlebotomine sand flies ( Dipte...	[ "Salivary components from disease vectors help arthropods to acquire blood and have been shown to enhance pathogen transmission in different model systems .", "Here we show that two salivary enzymes from Lutzomyia longipalpis have a synergist effect that facilitates a more efficient blood meal intake and diffusio...	[ "Blood-feeding is key to sand flies reproductive success and an important link in Leishmania spp .", "transmission .", "While the sand flies attempt to modify the bite site to enhance blood feeding success , the host’s ability to react to injury becomes compromised and could facilitate pathogen invasion .", "...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "fungal spores", "chromosome structure and function", "molecular probe techniques", "cell cycle and cell division", "cell processes", "dna damage", "telomeres", "fungi", "model organisms", "experimental organism systems", "molecular biology techniques", "dna", "synthesis phase", "fungal re...	Rnr1, but not Rnr3, facilitates the sustained telomerase-dependent elongation of telomeres	journal.pgen.1007082	null	[ [ "Telomeres are nucleoprotein complexes that protect the linear ends of eukaryotic chromosomes from nucleolytic degradation and unwanted DNA repair activities [1–3] .", "Due to the \"end-replication-problem\" telomeres shorten with every cell division [2] .", "Once telomeres reach a critical length , w...	[ "Ribonucleotide reductase ( RNR ) provides the precursors for the generation of dNTPs , which are required for DNA synthesis and repair .", "Here , we investigated the function of the major RNR subunits Rnr1 and Rnr3 in telomere elongation in budding yeast .", "We show that Rnr1 is essential for the sustained e...	[ "Telomeres protect the ends of eukaryotic chromosomes and as such determine the replicative capacity of a cell .", "In budding yeast and approximately 80% of human tumors the enzyme telomerase maintains telomere length by adding newly synthesized repeats to telomeres using dNTPs generated by Ribonucleotide reduct...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "developmental neuroscience", "cellular neuroscience", "behavioral neuroscience", "neuronal morphology", "genetics", "biology", "neuroscience", "neural circuit formation" ]	Sensory Neuron-Derived Eph Regulates Glomerular Arbors and Modulatory Function of a Central Serotonergic Neuron	journal.pgen.1003452	null	[ [ "Serotonin , 5-hydroxytryptamine ( 5-HT ) , an evolutionarily ancient monoamine , plays diverse roles in the brain [1] , [2] , [3] .", "In the mammalian brain , serotonin is implicated in the regulation of behavioural arousal and control of motor output [4] , [5] with a proposed phylogenetically ancient f...	[ "Olfactory sensory neurons connect to the antennal lobe of the fly to create the primary units for processing odor cues , the glomeruli .", "Unique amongst antennal-lobe neurons is an identified wide-field serotonergic neuron , the contralaterally-projecting , serotonin-immunoreactive deutocerebral neuron ( CSDn ...	[ "Serotonin , a major neuromodulatory transmitter , regulates diverse behaviours .", "Serotonergic dysfunction is implicated in various neuropsychological disorders , such as anxiety and depression , as well as in neurodegenerative disorders .", "In the central nervous systems , across taxa , serotonergic neuron...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics and genomics/functional genomics", "genetics and genomics/gene expression", "computational biology/alternative splicing", "computational biology/genomics", "genetics and genomics/epigenetics", "genetics and genomics/bioinformatics" ]	Discovery and Annotation of Functional Chromatin Signatures in the Human Genome	journal.pcbi.1000566	null	[ [ "The genome sequence is a static entity defining the possible transcriptional output of every cell type in the human body [1] .", "By contrast , chromatin structure dynamically influences the transcriptional potential of each genomic loci in a particular cell .", "Over 100 different histone modificati...	[ "Transcriptional regulation in human cells is a complex process involving a multitude of regulatory elements encoded by the genome .", "Recent studies have shown that distinct chromatin signatures mark a variety of functional genomic elements and that subtle variations of these signatures mark elements with diffe...	[ "Recent studies have observed that histone tails can be modified in a variety of ways .", "Analyzing a collection of 21 histone modifications , we attempted to determine what common signatures are associated with different classes of regulatory elements and whether they mark places of distinct function .", "Ind...	2009
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "dengue virus", "medicine and health sciences", "immune physiology", "enzyme-linked immunoassays", "pathology and laboratory medicine", "pathogens", "immunology", "microbiology", "vertebrates", "cloning", "animals", "mammals", "viruses", "primates", "vaccines", "animal models", "mole...	Potent neutralizing antibodies elicited by dengue vaccine in rhesus macaque target diverse epitopes	journal.ppat.1007716	null	[ [ "Dengue virus ( DENV ) , a mosquito-borne flavivirus , causes an estimated 390 million infections annually and presents a formidable burden on the global healthcare system [1] .", "DENV infection can result in common dengue fever ( DF ) and more severe illnesses such as dengue hemorrhagic fever ( DHF ) an...	[ "There is still no safe and effective vaccine against dengue virus infection .", "Epidemics of dengue virus infection are increasingly a threat to human health around the world .", "Antibodies generated in response to dengue infection have been shown to impact disease development and effectiveness of dengue vac...	[ "Dengue virus ( DENV ) is a leading cause of human illness in the tropics and subtropics , with about 40% of the world’s population living in areas at risk for infection .", "There are four DENV serotypes .", "Patients who have previously been infected by one dengue serotype may develop more severe symptoms suc...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry", "simulation and modeling", "biology and life sciences", "enzymology", "enzyme chemistry", "research and analysis methods" ]	Predicting the Functions and Specificity of Triterpenoid Synthases: A Mechanism-Based Multi-intermediate Docking Approach	journal.pcbi.1003874	null	[ [ "The terpenoids , also called isoprenoids , are one of the largest and most structurally diverse classes of natural products , and play vital roles in almost all life forms [1] , [2] .", "In the biosynthesis of terpenoids , the isoprene units ( C5 ) are assembled by polyprenyl transferases to give long ch...	[ "Terpenoid synthases construct the carbon skeletons of tens of thousands of natural products .", "To predict functions and specificity of triterpenoid synthases , a mechanism-based , multi-intermediate docking approach is proposed .", "In addition to enzyme function prediction , other potential applications of ...	[ "The rapid growth in the number of protein sequences presents challenges for enzyme function assignment .", "Computational methods , such as bioinformatics , homology modeling and docking , are becoming increasingly important for predicting of enzyme functions from protein sequences .", "Terpenoids are one of l...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	KSHV Latency Locus Cooperates with Myc to Drive Lymphoma in Mice	journal.ppat.1005135	null	[ [ "Myc encodes a multifunctional protein which is involved in many biological functions , including transcriptional control , cell cycle , signal transduction , oncogenesis , and development ( reviewed in [1] ) .", "Recurrent deregulation of c-Myc ( Myc ) is a hallmark of many lymphoma such as Burkitt lymph...	[ "Kaposi sarcoma-associated herpesvirus ( KSHV ) has been linked to Kaposi sarcoma and B-cell malignancies .", "Mechanisms of KSHV-induced oncogenesis remain elusive , however , in part due to lack of reliable in vivo models .", "Recently , we showed that transgenic mice expressing the KSHV latent genes , includ...	[ "Kaposi’s sarcoma-associated herpesvirus ( KSHV ) is associated with Kaposi sarcoma as well as the B-cell malignancies primary effusion lymphoma ( PEL ) and multicentric Castleman’s disease ( MCD ) .", "Only a few KSHV genes , including all micro RNAs , are expressed in latent infection of B cells .", "We alrea...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "gene identification and analysis", "genetics", "biology and life sciences", "molecular genetics", "zoology", "parasitology" ]	Molecular Analysis of Echinostome Metacercariae from Their Second Intermediate Host Found in a Localised Geographic Region Reveals Genetic Heterogeneity and Possible Cryptic Speciation	journal.pntd.0002778	null	[ [ "Echinostomes are intestinal trematodes of humans and animals that are endemic to Southeast Asia and the Far East , i . e . mainland China , Taiwan , India , Korea , Malaysia , Philippines , Indonesia , and Thailand , and present a public health problem [1] .", "Human echinostomiasis has been attributed t...	[ "Echinostome metacercariae are the infective stage for humans and animals .", "The identification of echinostomes has been based until recently on morphology but molecular techniques using sequences of ribosomal RNA and mitochondrial DNA have indicated major clades within the group .", "In this study we have us...	[ "Infections by food-borne trematodes are estimated to infect over 40 million people worldwide , although infections by echinostomes make up only a portion of these cases , usually in regions where their prevalence is high .", "In South East Asia and in the far east of Asia , human infection is associated with cul...	2014
[ "Introduction", "Model", "Results", "Discussion" ]	[ "epilepsy", "medicine and health sciences", "computational neuroscience", "neurology", "biology and life sciences", "computational biology" ]	Dynamic Mechanisms of Neocortical Focal Seizure Onset	journal.pcbi.1003787	null	[ [ "Neocortical focal seizures are episodes of pathological brain activity that appear to originate from spatially localised regions of the neocortex .", "The classical understanding of such seizures is that localised pathological tissue generates epileptic discharges ( epileptogenic zone [1] ) , which subse...	[ "Recent experimental and clinical studies have provided diverse insight into the mechanisms of human focal seizure initiation and propagation .", "Often these findings exist at different scales of observation , and are not reconciled into a common understanding .", "Here we develop a new , multiscale mathematic...	[ "According to the WHO fact sheet , epilepsy is a neurological disorder affecting about 50 million people worldwide .", "Even today 30% of epilepsy patients do not respond well to drug therapies .", "Neocortical focal epilepsy is a particular type of epilepsy in which drug treatments fail and surgical success ra...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biofilms", "antimicrobials", "sequencing techniques", "medicine and health sciences", "neurochemistry", "pathology and laboratory medicine", "chemical compounds", "pathogens", "drugs", "microbiology", "operons", "carbohydrates", "neuroscience", "staphylococcus aureus", "vancomycin", "...	The DUF59 Containing Protein SufT Is Involved in the Maturation of Iron-Sulfur (FeS) Proteins during Conditions of High FeS Cofactor Demand in Staphylococcus aureus	journal.pgen.1006233	null	[ [ "Iron ( Fe ) is an essential nutrient for nearly all organisms .", "Fe is acquired from the environment and is transported into cells using specific uptake systems .", "Studies have shown that ~80% of the intracellular Fe is located in inorganic cofactors , called iron-sulfur ( FeS ) clusters , and he...	[ "Proteins containing DUF59 domains have roles in iron-sulfur ( FeS ) cluster assembly and are widespread throughout Eukarya , Bacteria , and Archaea .", "However , the function ( s ) of this domain is unknown .", "Staphylococcus aureus SufT is composed solely of a DUF59 domain .", "We noted that sufT is often...	[ "Iron-sulfur ( FeS ) clusters are inorganic cofactors that are used for diverse cellular processes including cellular respiration , DNA replication and repair , antibiotic resistance , and dinitrogen fixation .", "A failure to properly assemble FeS clusters in proteins results in widespread metabolic disorders , ...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "united states", "medicine and health sciences", "body fluids", "hispanic people", "tropical diseases", "geographical locations", "parasitic diseases", "parasitic protozoans", "ethnicities", "north america", "protozoans", "neglected tropical diseases", "latin americans", "public and occupa...	Estimating the Burden of Chagas Disease in the United States	journal.pntd.0005033	null	[ [ "Chagas disease , caused by infection with the parasite Trypanosoma cruzi , affects an estimated 8–10 million people globally .", "Among those infected with the parasite , approximately 30% will develop chronic Chagas cardiac disease , including serious arrhythmias and heart failure .", "This infectio...	[ "In recent years , there has been growing awareness of the significant burden of Chagas disease in the United States ( US ) .", "However , epidemiological data on both prevalence and access to care for this disease are limited .", "The objective of this study is to provide an updated national estimate of Chagas...	[ "Chagas disease is a parasitic infection that primarily affects poor populations in Latin America .", "However , awareness of this disease in the United States has increased in recent years .", "In this study , we utilize data from the American Community Survey and the World Health Organization to estimate the ...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "respiratory medicine/respiratory infections", "microbiology/immunity to infections", "microbiology/innate immunity", "immunology/innate immunity", "infectious diseases/viral infections", "virology/host antiviral responses" ]	Type I Interferon Signaling Regulates Ly6Chi Monocytes and Neutrophils during Acute Viral Pneumonia in Mice	journal.ppat.1001304	null	[ [ "Type I interferons ( IFN-I ) are produced by different cell types including alveolar macrophages ( AM ) , plasmacytoid dendritic cells , and epithelial cells following virus infection in the lung [1] , [2] .", "These IFN-I cytokines engage a unique heterodimeric IFN-α receptor ( IFNAR ) to induce various...	[ "Type I interferon ( IFN-I ) plays a critical role in the homeostasis of hematopoietic stem cells and influences neutrophil influx to the site of inflammation .", "IFN-I receptor knockout ( Ifnar1−/− ) mice develop significant defects in the infiltration of Ly6Chi monocytes in the lung after influenza infection (...	[ "Type I interferon ( IFN-I ) was originally reported as a molecule that interferes with influenza virus replication .", "Various IFN-I inducible antiviral proteins contribute to dampening virus replication and dissemination .", "Thus , loss of IFN-I signaling attenuates antiviral response and aggravates disease...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunopathology", "immunity", "innate immunity", "immunity to infections", "immune defense", "immunology", "biology" ]	Eosinophils Are Important for Protection, Immunoregulation and Pathology during Infection with Nematode Microfilariae	journal.ppat.1003988	null	[ [ "Eosinophilia is one of the principal features of parasitic helminth infection and is also associated with asthmatic disease and many gastro-intestinal disorders .", "However , for many years the relative role of eosinophils in protection against parasites and/or pathology has been contentious .", "Eo...	[ "Eosinophil responses typify both allergic and parasitic helminth disease .", "In helminthic disease , the role of eosinophils can be both protective in immune responses and destructive in pathological responses .", "To investigate whether eosinophils are involved in both protection and pathology during filaria...	[ "Eosinophil recruitment is a classic characteristic of both allergic and parasitic helminth diseases .", "Elucidation of the role of eosinophils in these diseases is of pivotal importance for understanding the mechanisms of protection and the development of pathology .", "In the last few years , the part played...	2014
[ "Introduction", "Results and Discussion", "Materials and Methods" ]	[ "biogeography", "geologic time", "ecology and environmental sciences", "population genetics", "paleoecology", "biodiversity", "fossil record", "geology", "speciation", "paleontology", "population biology", "ecological metrics", "geography", "paleogeography", "phylogeography", "species ...	Near-Stasis in the Long-Term Diversification of Mesozoic Tetrapods	journal.pbio.1002359	A large-scale examination of the fossil record reveals slow diversification rates in tetrapods across the 190-million-year Mesozoic era, followed by a possible rapid and abrupt 4-fold increase in species richness after the Cretaceous-Paleogene mass extinction event.	[ [ "Tetrapods , the limbed vertebrates , include mammals , amphibians , and reptiles ( including birds ) , and today comprise more than 30 , 000 species .", "Alongside plants and insects , they are key components of the non-marine biota and play a diverse range of ecological roles .", "Patterns of tetrap...	[ "How did evolution generate the extraordinary diversity of vertebrates on land ?", "Zero species are known prior to ~380 million years ago , and more than 30 , 000 are present today .", "An expansionist model suggests this was achieved by large and unbounded increases , leading to substantially greater diversit...	[ "Vertebrates invaded the land more than 360 million years ago .", "Since then , they diversified to more than 30 , 000 tetrapod species today , including birds , mammals , squamates , and amphibians .", "The fossil record provides our best window onto diversification across such long spans of time , but is unev...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Phenylbutyrate Is Bacteriostatic against Mycobacterium tuberculosis and Regulates the Macrophage Response to Infection, Synergistically with 25-Hydroxy-Vitamin D₃	journal.ppat.1005007	null	[ [ "Tuberculosis ( TB ) is the world’s leading bacterial cause of death , with 9 million new cases and 1 . 5 million deaths in 2013 [1] .", "Despite the availability of antimicrobials , effective treatment regimes require long-term administration of multiple drugs , which can lead to toxicity , problems with...	[ "Adjunctive vitamin D treatment for pulmonary tuberculosis enhances resolution of inflammation but has modest effects on bacterial clearance .", "Sodium 4-phenylbutyrate ( PBA ) is in clinical use for a range of conditions and has been shown to synergise with vitamin D metabolites to upregulate cathelicidin antim...	[ "Tuberculosis ( TB ) is the world’s leading bacterial cause of death .", "Effective treatment currently requires a minimum of 4 drugs taken for at least 6 months .", "While these drugs kill the TB causing bacteria ( Mtb ) , they do not directly resolve the inmmunopathology associated with morbidity .", "Immun...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "antimicrobials", "urology", "medicine and health sciences", "enzyme-linked immunoassays", "pathology and laboratory medicine", "maternal health", "obstetrics and gynecology", "pathogens", "drugs", "tropical diseases", "geographical locations", "microbiology", "retroviruses", "viruses", ...	The Global Epidemiology of Syphilis in the Past Century – A Systematic Review Based on Antenatal Syphilis Prevalence	journal.pntd.0004711	null	[ [ "Can a meaningful pattern be discerned in the large variations in syphilis rates over the last century ?", "A first step toward answering this question is the mapping of syphilis rates across time and place followed by correlation analyses with possible explanatory variables [1] .", "Numerous papers h...	[ "How can we explain the uneven decline of syphilis around the world following the introduction of penicillin ?", "In this paper we use antenatal syphilis prevalence ( ASP ) to investigate how syphilis prevalence varied worldwide in the past century , and what risk factors correlate with this variance .", "1 ) A...	[ "Syphilis rates have varied tremendously between different populations around the world .", "We conducted a systematic review of syphilis prevalence in pregnant women in 13 populations with available data for the last 100 years .", "Our findings were that in most populations syphilis prevalence dropped to under...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biotechnology", "group-specific staining", "innate immune system", "medicine and health sciences", "luciferase", "immune physiology", "cytokines", "chemical compounds", "pathology and laboratory medicine", "protein interactions", "electrophoretic mobility shift assay", "small molecules", "e...	Development of novel NEMO-binding domain mimetics for inhibiting IKK/NF-κB activation	journal.pbio.2004663	null	[ [ "Nuclear factor κB ( NF-κB ) is a transcription factor essential for regulating immune responses , cell proliferation , apoptosis , embryonic development , senescence , and cancer [1] .", "In mammalian cells , the NF-κB family is composed of 5 subunits , RelA/p65 , RelB , C-Rel , p50 ( p105/NF-κB1 ) , and...	[ "Nuclear factor κB ( NF-κB ) is a transcription factor important for regulating innate and adaptive immunity , cellular proliferation , apoptosis , and senescence .", "Dysregulation of NF-κB and its upstream regulator IκB kinase ( IKK ) contributes to the pathogenesis of multiple inflammatory and degenerative dis...	[ "Aberrant up-regulation of the transcription factor nuclear factor κB ( NF-κB ) and the IκB kinase ( IKK ) that regulates NF-κB is associated with a variety of inflammatory and degenerative diseases in humans , including aging .", "Thus , development of effective and specific drugs able to decrease IKK/NF-κB acti...	2018
[ "Introduction", "Model", "Results", "Discussion" ]	[ "immune cells", "antigen-presenting cells", "immunology", "host-pathogen interaction", "microbiology", "mathematics", "population modeling", "bacterial pathogens", "theoretical biology", "t cells", "infectious disease modeling", "biology", "pathogenesis", "nonlinear dynamics", "immune re...	Competition for Antigen between Th1 and Th2 Responses Determines the Timing of the Immune Response Switch during Mycobaterium avium Subspecies paratuberulosis Infection in Ruminants	journal.pcbi.1003414	null	[ [ "Mycobacterium avim subsp .", "paratuberculosis ( MAP ) infects intestine of ruminants ( e . g . , cattle and sheep ) and causes a chronic inflammatory disease called Johne's disease ( JD ) [1] , [2] .", "Due to reduction of milk production and early culling of diseased animals , JD causes a significa...	[ "Johne's disease ( JD ) , a persistent and slow progressing infection of ruminants such as cows and sheep , is caused by slow replicating bacilli Mycobacterium avium subspecies paratuberculosis ( MAP ) infecting macrophages in the gut .", "Infected animals initially mount a cell-mediated CD4 T cell response again...	[ "Mycobacterium avium subsp .", "paratuberculosis ( MAP ) is the causative agent of Johne's disease , a chronic enteric disease of ruminants such as sheep and cows .", "Due to early culling and reduction in milk production of affected animals , MAP inflicts high economic cost to diary farms .", "MAP infection ...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology", "microbiology", "molecular cell biology" ]	Digoxin Suppresses HIV-1 Replication by Altering Viral RNA Processing	journal.ppat.1003241	null	[ [ "Current highly active anti-retroviral therapies ( HAARTs ) have successfully delayed the progression of HIV-1-infected individuals to AIDS by targeting viral entry and all HIV-1 enzymes [1] , [2] .", "However , the clinical application of ARTs is being affected by the spread of drug resistant viral strai...	[ "To develop new approaches to control HIV-1 replication , we examined the capacity of recently described small molecular modulators of RNA splicing for their effects on viral RNA metabolism .", "Of the drugs tested , digoxin was found to induce a dramatic inhibition of HIV-1 structural protein synthesis , a respo...	[ "Antiretroviral therapies ( ART ) for HIV/AIDS are successful in slowing disease progression by inhibiting viral proteins .", "However , the ability of HIV to adapt to ARTs has given rise to drug-resistant virus strains that now represent ≥16% of newly infected people .", "This development calls for the generat...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The Genetic Basis of Escherichia coli Pathoadaptation to Macrophages	journal.ppat.1003802	null	[ [ "Bacteria can be used to study evolution in real time in controlled environments , i . e . experimental evolution [1] .", "Different studies have demonstrated that bacterial populations have an enormous potential to adapt to relatively simple abiotic challenges under laboratory environments [2] , [3] .", ...	[ "Antagonistic interactions are likely important driving forces of the evolutionary process underlying bacterial genome complexity and diversity .", "We hypothesized that the ability of evolved bacteria to escape specific components of host innate immunity , such as phagocytosis and killing by macrophages ( MΦ ) ,...	[ "The selective pressure imposed by the host immune system is an important component of microbial adaptation from commensalism to pathogenicity .", "We used experimental evolution to study the initial steps of the adaptation of Escherichia coli to cells of the innate immune system , i . e . , macrophages .", "Ou...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "evidence-based healthcare/methods for diagnostic and therapeutic studies", "infectious diseases/epidemiology and control of infectious diseases" ]	LAMP for Human African Trypanosomiasis: A Comparative Study of Detection Formats	journal.pntd.0000865	null	[ [ "Loop-mediated isothermal amplification ( LAMP ) [1] is a DNA amplification technique whose advantages over traditional PCR have put it at the forefront of the search for innovative new diagnostics for infectious diseases such as human African trypanosomiasis ( HAT ) [2] .", "Rapid and unambiguous visual ...	[ "Loop-mediated isothermal amplification ( LAMP ) is at the forefront of the search for innovative diagnostics for human African trypanosomiasis ( HAT ) .", "Several simple endpoint detection methods have been developed for LAMP and here we compare four of these:", "( i ) visualization of turbidity;", "( ii ) ...	[ "Human African trypanosomiasis ( HAT ) is a disease of the rural poor in sub-Saharan Africa where diagnostic laboratories are scarce and often ill equipped .", "Specific LAMP ( loop-mediated isothermal amplification ) tests for HAT have been developed and represent a significant step forward in the search for sim...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Evolutionary Signatures amongst Disease Genes Permit Novel Methods for Gene Prioritization and Construction of Informative Gene-Based Networks	journal.pgen.1004967	null	[ [ "Advances in sequencing technologies and collaborative , large-scale—omics and genome-wide association projects are providing investigators with overwhelming lists of candidate disease gene associations .", "In the past decade , nearly 2 , 000 genomic regions have been associated with over 300 complex tra...	[ "Genes involved in the same function tend to have similar evolutionary histories , in that their rates of evolution covary over time .", "This coevolutionary signature , termed Evolutionary Rate Covariation ( ERC ) , is calculated using only gene sequences from a set of closely related species and has demonstrate...	[ "Molecular evolution has informed our understanding of gene function; however , classical methods have largely been static in their implementation , focusing on single genes .", "Here , we present and prove the utility of a dynamic , network-based understanding of molecular evolution to infer relationships betwee...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "cancer detection and diagnosis", "invertebrates", "medicine and health sciences", "lymphatic mapping", "education", "sociology", "geographical locations", "tropical diseases", "social sciences", "parasitic diseases", "animals", "parasitology", "oncology", "filariasis", "neglected tropic...	Progress towards lymphatic filariasis elimination in Ghana from 2000-2016: Analysis of microfilaria prevalence data from 430 communities	journal.pntd.0007115	null	[ [ "Lymphatic filariasis ( LF ) , commonly known as elephantiasis , is a debilitating and disfiguring tropical disease caused by lymphatic-dwelling filarial parasites Wuchereria bancrofti , Brugia malayi and Brugia timori .", "The disease is transmitted by different species of mosquitoes depending on the geo...	[ "Ghana started its national programme to eliminate lymphatic filariasis ( LF ) in 2000 , with mass drug administration ( MDA ) with ivermectin and albendazole as main strategy .", "We review the progress towards elimination that was made by 2016 for all endemic districts of Ghana and analyze microfilaria ( mf ) p...	[ "Lymphatic filariasis ( LF ) control in Ghana has relied on ivermectin and albendazole since the year 2000 when the Ghana Filariasis Elimination Programme started .", "We analyzed trends in microfilaraemia prevalence during MDA , reported coverage , and transmission assessment survey using data obtained from the ...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "mathematics", "yeast and fungi", "biophysics", "genetics and genomics" ]	Heritable Stochastic Switching Revealed by Single-Cell Genealogy	journal.pbio.0050239	When cells divide, each daughter cell inherits a share of the contents of the mother. If the contents include a regulatory system with a feedback loop, sister cells switch states in synchrony.	[ [ "Inheritance is more than the faithful copying and partitioning of genomic information .", "When cells divide , the mother cell passes numerous other cellular components to the freshly born daughter , including nucleosomes , transcription factors , mitochondria , and substantial fractions of its proteome ...	[ "The partitioning and subsequent inheritance of cellular factors like proteins and RNAs is a ubiquitous feature of cell division .", "However , direct quantitative measures of how such nongenetic inheritance affects subsequent changes in gene expression have been lacking .", "We tracked families of the yeast Sa...	[ "When cells divide , not only DNA but an entire pattern of gene expression can be passed from mother to daughter cell .", "Once cell division is complete , random processes cause this pattern to change , with closely related cells growing less similar over time .", "We measured inheritance of a dynamic gene-exp...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "dna metabolism", "cancer genetics", "genetic networks", "drugs and devices", "enzymes", "microbiology", "chemical biology", "genome analysis tools", "genome databases", "model organisms", "dna replication", "nuclease", "dna", "mutation databases", "genetics and genomics", ...	An Evolutionarily Conserved Synthetic Lethal Interaction Network Identifies FEN1 as a Broad-Spectrum Target for Anticancer Therapeutic Development	journal.pgen.1003254	null	[ [ "Cancerous cells carry somatic mutations that genotypically distinguish them from surrounding noncancerous cells , and this provides an opportunity that can be exploited for therapeutic development .", "One strategy for the specific targeting of cancer genotypes relative to nonmutated somatic cells is to ...	[ "Harnessing genetic differences between cancerous and noncancerous cells offers a strategy for the development of new therapies .", "Extrapolating from yeast genetic interaction data , we used cultured human cells and siRNA to construct and evaluate a synthetic lethal interaction network comprised of chromosome i...	[ "Anticancer therapeutic discovery is a major challenge in cancer research .", "Because cancer is a disease caused by somatic genetic mutations , the search for anticancer therapeutics is often driven by the ability to exploit genetic differences specific to tumor cells .", "Recently , cancer therapeutic develop...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "condensation", "chromosome structure and function", "molecular probe techniques", "enzymes", "condensed matter physics", "enzymology", "phosphatases", "sequence motif analysis", "molecular biology techniques", "epigenetics", "chromatin", "research and analysis methods", "sequence analysis",...	Condensin ATPase motifs contribute differentially to the maintenance of chromosome morphology and genome stability	journal.pbio.2003980	null	[ [ "Chromosomes must undergo a major structural reorganization to allow the efficient and error-free segregation of genetic information during mitosis .", "This process is known as chromosome condensation and is promoted by the condensin complex [1–3] .", "The condensation of chromosomes has been describ...	[ "Effective transfer of genetic information during cell division requires a major reorganization of chromosome structure .", "This process is triggered by condensin , a conserved pentameric ATPase essential for chromosome condensation .", "How condensin harnesses the energy of ATP hydrolysis to promote chromatin...	[ "In eukaryotes , the deletion of a single copy of most genes shows little or no detectable phenotype under standard proliferative conditions .", "This implies that a large reduction in the level of a gene product can be tolerated by eukaryotic organisms and that a “reserve capacity” is built in the protein machin...	2018
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "ecology", "biology and life sciences", "sensory perception", "neuroscience", "parasitology", "behavioral ecology" ]	Diverse Host-Seeking Behaviors of Skin-Penetrating Nematodes	journal.ppat.1004305	null	[ [ "Skin-penetrating nematodes such as the threadworm Str .", "stercoralis and the hookworms Ancylostoma duodenale and Necator americanus ( Figure 1A ) are intestinal parasites that infect approximately 1 billion people worldwide .", "Infection with skin-penetrating worms can cause chronic gastrointestin...	[ "Skin-penetrating parasitic nematodes infect approximately one billion people worldwide and are responsible for some of the most common neglected tropical diseases .", "The infective larvae of skin-penetrating nematodes are thought to search for hosts using sensory cues , yet their host-seeking behavior is poorly...	[ "Parasitic worms are a significant public health problem .", "Skin-penetrating worms such as hookworms and the human threadworm Strongyloides stercoralis dwell in the soil before infecting their host .", "However , how they locate and identify appropriate hosts is not understood .", "Here we investigated the ...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "ecology/evolutionary ecology", "ecology/behavioral ecology", "evolutionary biology/evolutionary ecology", "ecology", "evolutionary biology/animal behavior", "ecology/community ecology and biodiversity", "evolutionary biology" ]	Host Niches and Defensive Extended Phenotypes Structure Parasitoid Wasp Communities	journal.pbio.1000179	null	[ [ "Identifying the processes that structure communities remains one of the fundamental challenges facing ecology [1]–[5] and greatly influences our ability to predict the effects of species invasions and extinctions [6]–[8] .", "However , the issues are complex , and recent reviews have emphasised the need ...	[ "Oak galls are spectacular extended phenotypes of gallwasp genes in host oak tissues and have evolved complex morphologies that serve , in part , to exclude parasitoid natural enemies .", "Parasitoids and their insect herbivore hosts have coevolved to produce diverse communities comprising about a third of all an...	[ "Herbivorous insects , such as the wasps that induce trees to make galls , and the parasitoids that attack ( and ultimately kill ) the wasps comprise about a third of all animal species , but it remains unclear what determines the structure of these complex coevolving communities .", "Here , we analyzed 48 parasi...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "bacterial diseases", "infectious diseases", "infectious disease epidemiology", "epidemiology", "infectious disease control", "gastrointestinal infections", "salmonella" ]	Differential Epidemiology of Salmonella Typhi and Paratyphi A in Kathmandu, Nepal: A Matched Case Control Investigation in a Highly Endemic Enteric Fever Setting	journal.pntd.0002391	null	[ [ "The human systemic disease enteric fever is most commonly caused by the Salmonella enterica serovars Typhi ( S . Typhi ) and Paratyphi A ( S . Paratyphi A ) [1] , [2] .", "The disease is found in areas with poor sanitation and hygiene [3] , and has an estimated global burden of 27 million new cases and 2...	[ "Enteric fever , a systemic infection caused by the bacteria Salmonella Typhi and Salmonella Paratyphi A , is endemic in Kathmandu , Nepal .", "Previous work identified proximity to poor quality water sources as a community-level risk for infection .", "Here , we sought to examine individual-level risk factors ...	[ "Enteric fever , caused by ingestion of bacteria Salmonella Typhi or Salmonella Paratyphi A , is common in regions with poor water quality and sanitation .", "We sought to identify individual-level risks for infection in Kathmandu , Nepal , a region endemic for enteric fever .", "In this study , we enrolled pat...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "biology" ]	EMT Inducers Catalyze Malignant Transformation of Mammary Epithelial Cells and Drive Tumorigenesis towards Claudin-Low Tumors in Transgenic Mice	journal.pgen.1002723	null	[ [ "While the disruption of embryonic processes has been acknowledged as a cause of the outgrowth of paediatric neoplasms , more recent observations suggest that the aberrant reactivation of developmental regulatory programs might also contribute to progression in the advanced stages of cancers in adults [1] .",...	[ "The epithelial-mesenchymal transition ( EMT ) is an embryonic transdifferentiation process consisting of conversion of polarized epithelial cells to motile mesenchymal ones .", "EMT–inducing transcription factors are aberrantly expressed in multiple tumor types and are known to favor the metastatic dissemination...	[ "The epithelial-mesenchymal transition ( EMT ) is essential to germ layer formation and cell migration in the early vertebrate embryo .", "EMT is aberrantly reactivated under pathological conditions , including fibrotic disease and cancer progression .", "In the latter process , EMT is known to promote invasion...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "mathematics", "theoretical biology", "applied mathematics", "biology", "population biology" ]	Evolutionary Game Theory and Social Learning Can Determine How Vaccine Scares Unfold	journal.pcbi.1002452	null	[ [ "Vaccine coverage in England & Wales during the whole cell pertussis vaccine scare in the 1970s and the measles-mumps-rubella ( MMR ) vaccine scare in the 1990s share a common pattern of decline and recovery over many years ( Figure 1 ) .", "For pertussis , the decline resulted in large-scale outbreaks ."...	[ "Immunization programs have often been impeded by vaccine scares , as evidenced by the measles-mumps-rubella ( MMR ) autism vaccine scare in Britain .", "A “free rider” effect may be partly responsible: vaccine-generated herd immunity can reduce disease incidence to such low levels that real or imagined vaccine r...	[ "“Herd immunity” is a phenomenon whereby an entire population—including unvaccinated individuals—can be protected from infection by vaccinating only a certain percentage of the population .", "This suggests that immunization programs can be victims of their own success: past vaccinations can drive disease inciden...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Rheumatic Heart Disease-Attributable Mortality at Ages 5–69 Years in Fiji: A Five-Year, National, Population-Based Record-Linkage Cohort Study	journal.pntd.0004033	null	[ [ "Rheumatic heart disease ( RHD ) is the chronic consequence of an aberrant immune response to infection by the bacterial pathogen Streptococcus pyogenes that results in permanent scarring of the heart valves .", "[1] This process , which may manifest clinically as heart failure , stroke and early death , ...	[ "Rheumatic heart disease ( RHD ) is considered a major public health problem in developing countries , although scarce data are available to substantiate this .", "Here we quantify mortality from RHD in Fiji during 2008–2012 in people aged 5–69 years .", "Using 1 , 773 , 999 records derived from multiple source...	[ "Rheumatic heart disease is the result of an abnormal immune response to the bacteria Streptococcus pyogenes .", "The disease causes permanent scarring of the heart values , which results in heart failure , stroke and early death .", "It primarily affects the world’s poorest and most disadvantaged populations a...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "genetics and genomics/genetics of disease", "mathematics/statistics", "genetics and genomics/bioinformatics", "genetics and genomics/population genetics" ]	Sensitive Detection of Chromosomal Segments of Distinct Ancestry in Admixed Populations	journal.pgen.1000519	null	[ [ "The identification of chromosomal segments of distinct continental ancestry in admixed populations is an important problem , with a wide range of applications from disease mapping to understanding human history .", "Early efforts to solve this problem used coarse sets of unlinked markers [1]–[3] and most...	[ "Identifying the ancestry of chromosomal segments of distinct ancestry has a wide range of applications from disease mapping to learning about history .", "Most methods require the use of unlinked markers; but , using all markers from genome-wide scanning arrays , it should in principle be possible to infer the a...	[ "The genomes of individuals from admixed populations consist of chromosomal segments of distinct ancestry .", "For example , the genomes of African American individuals contain segments of both African and European ancestry , so that a specific location in the genome may inherit 0 , 1 , or 2 copies of European an...	2009
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "cell biology/cell growth and division", "gastroenterology and hepatology/hepatology", "developmental biology/stem cells" ]	Ploidy Reductions in Murine Fusion-Derived Hepatocytes	journal.pgen.1000385	null	[ [ "Cell divisions in mitosis are thought to always produce daughter cells with the same chromosome content as the parental cell .", "Our recent studies with fusion-derived polyploid hepatocytes challenge that ideology .", "We propose that polyploid hepatocytes can undergo ploidy reductions , leading to ...	[ "We previously showed that fusion between hepatocytes lacking a crucial liver enzyme , fumarylacetoacetate hydrolase ( FAH ) , and wild-type blood cells resulted in hepatocyte reprogramming .", "FAH expression was restored in hybrid hepatocytes and , upon in vivo expansion , ameliorated the effects of FAH deficie...	[ "The liver comprises many different types of cells , including hepatocytes .", "Hepatocytes perform numerous physiological functions , such as detoxification , metabolism , and protein synthesis .", "Hepatocytes have the ability to fuse with blood cells , generating hybrid hepatocytes that contain nuclei from b...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "tropical diseases", "geographical locations", "social sciences", "neuroscience", "surgical and invasive medical procedures", "bacterial diseases", "tanzania", "eye diseases", "neglected tropical diseases", "vision", "eyes", "africa", "blindness", "infecti...	Identifying Patient Perceived Barriers to Trichiasis Surgery in Kongwa District, Tanzania	journal.pntd.0005211	null	[ [ "Trachomatous trichiasis ( TT ) , a complication of trachoma , is the leading infectious cause of preventable blindness in the world today [1] .", "Repeated infection of children with Chlamydia trachomatis can lead to scarring of the conjunctiva , causing entropion in adults as the eyelid turns inward , a...	[ "Trachomatous trichiasis ( TT ) , inturned eyelashes from repeated infection with Chlamydia trachomatis , is the leading infectious cause of blindness in the world .", "Though surgery will correct entropion caused by trachoma , uptake of TT surgery remains low .", "In this case-control study , we identify barri...	[ "The burden of trachomatis trichiasis ( TT ) , a complication of trachoma , is largest in the poorest societies of our world .", "One part of the World Health Organization ( WHO ) strategy to eliminate blinding trachoma is surgery for patients with TT , and trachoma programs in endemic countries have worked to in...	2017
[ "Introduction", "Methods", "Results", "Discussion", "Conclusions" ]	[ "humoral immunity", "mycobacterium leprae", "medicine and health sciences", "immunology", "tropical diseases", "geographical locations", "bacterial diseases", "neglected tropical diseases", "infectious disease control", "bacteria", "bangladesh", "infectious diseases", "epidemiology", "acti...	Minimum requirements and optimal testing strategies of a diagnostic test for leprosy as a tool towards zero transmission: A modeling study	journal.pntd.0006529	null	[ [ "Leprosy is an infectious disease caused by Mycobacterium leprae , affecting the skin , peripheral nerves , the mucosa of the upper respiratory tract and the eyes [1] .", "The most likely route of transmission of M . leprae is via the aerosolic route [2] .", "Individuals , who have close and frequent ...	[ "The availability of a diagnostic test to detect subclinical leprosy cases is crucial to interrupt the transmission of M . leprae .", "In this study we assessed the minimum sensitivity level of such a ( hypothetical ) diagnostic test and the optimal testing strategy in order to effectively reduce the new case det...	[ "The annual number of new leprosy cases has been stable in the past decade , indicating that transmission has not been yet been interrupted .", "As current control seems to be insufficient to bring down the number of cases , there is a need for novel tools to interrupt transmission .", "A diagnostic that permit...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/complex traits", "genetics and genomics/genetics of disease", "genetics and genomics/population genetics", "diabetes and endocrinology", "genetics and genomics", "diabetes and endocrinology/type 2 diabetes" ]	A Genome-Wide Association Study Identifies Susceptibility Variants for Type 2 Diabetes in Han Chinese	journal.pgen.1000847	null	[ [ "Type 2 diabetes ( T2D ) affects at least 6% of the world's population; the worldwide prevalence is expected to double by 2025 [1] .", "T2D is a complex disorder that is characterized by hyperglycemia , which results from impaired pancreatic β cell function , decreased insulin action at target tissues , a...	[ "To investigate the underlying mechanisms of T2D pathogenesis , we looked for diabetes susceptibility genes that increase the risk of type 2 diabetes ( T2D ) in a Han Chinese population .", "A two-stage genome-wide association ( GWA ) study was conducted , in which 995 patients and 894 controls were genotyped usi...	[ "Type 2 diabetes ( T2D ) is a complex disease that involves many genes and environmental factors .", "Genome-wide and candidate-gene association studies have thus far identified at least 19 regions containing genes that may confer a risk for T2D .", "However , most of these studies were conducted with patients ...	2010
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "physics", "biophysic al simulations", "macromolecular assemblies", "biology", "computational biology", "biophysics simulations", "biophysics" ]	Role of Histone Tails in Structural Stability of the Nucleosome	journal.pcbi.1002279	null	[ [ "Eukaryotic DNA is organized into nucleosomes [1] , in which about 150 bp of DNA are wrapped in left-handed superhelical turns around an octameric histone protein complex [2] .", "The histone octamer has a tripartite structure composed of a tetramer flanked by two H2A–H2B dimers .", "The Å resolution ...	[ "Histone tails play an important role in nucleosome structure and dynamics .", "Here we investigate the effect of truncation of histone tails H3 , H4 , H2A and H2B on nucleosome structure with 100 ns all-atom molecular dynamics simulations .", "Tail domains of H3 and H2B show propensity of -helics formation dur...	[ "Histone tails are the most common sites of post-translational modifications .", "Tail modifications alter both inter and intra nucleosomal interactions to disrupt the condensed chromatin structure , thereby playing crucial role in gene access .", "Here we investigated histone tail functions on the stability of...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Haemophilus Responses to Nutritional Immunity: Epigenetic and Morphological Contribution to Biofilm Architecture, Invasion, Persistence and Disease Severity	journal.ppat.1003709	null	[ [ "Nontypeable Haemophilus influenzae ( NTHI ) is an obligate commensal that asymptomatically colonizes the human nasopharynx .", "Permissive risk factors , which include upper respiratory tract viral infection and Eustachian tube dysfunction , influence NTHI migration from the nasopharynx to sterile sites ...	[ "In an effort to suppress microbial outgrowth , the host sequesters essential nutrients in a process termed nutritional immunity .", "However , inflammatory responses to bacterial insult can restore nutritional resources .", "Given that nutrient availability modulates virulence factor production and biofilm for...	[ "Clinical management of upper and lower respiratory tract diseases caused by nontypeable Haemophilus influenzae ( NTHI ) is a significant socioeconomic burden .", "Therapies targeting the pathogenic lifestyle of NTHI remain non-existent due to a lack of understanding of host microenvironmental cues and bacterial ...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	The Elementary Operations of Human Vision Are Not Reducible to Template-Matching	journal.pcbi.1004499	null	[ [ "Animals constantly submit environmental signals to neural operations designed to extract useful information for guiding behaviour .", "Whether their sensory apparatus is considered in its entirety as a behavioural machine or in relation to hardware components like individual nerve cells , it can be descr...	[ "It is generally acknowledged that biological vision presents nonlinear characteristics , yet linear filtering accounts of visual processing are ubiquitous .", "The template-matching operation implemented by the linear-nonlinear cascade ( linear filter followed by static nonlinearity ) is the most widely adopted ...	[ "Any attempt to model human vision must first ask: can it be approximated by a process that linearly matches the visual stimulus with an internal template ?", "We often take this approximation for granted without properly checking its validity .", "Even if we assume that the approximation is valid under specifi...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/helminth infections", "infectious diseases/neglected tropical diseases" ]	The Nicotinic Acetylcholine Receptors of the Parasitic Nematode Ascaris suum: Formation of Two Distinct Drug Targets by Varying the Relative Expression Levels of Two Subunits	journal.ppat.1000517	null	[ [ "Nematodes of the genus Ascaris are large ( ∼30 cm ) gastrointestinal parasites of swine ( Ascaris suum ) and humans ( Ascaris lumbricoides ) .", "Ascaris lumbricoides infects ∼1 . 4 billion people globally , and is particularly prevalent in conditions of poor sanitation and poverty [1] , [2] .", "In ...	[ "Parasitic nematodes are of medical and veterinary importance , adversely affecting human health and animal welfare .", "Ascaris suum is a gastrointestinal parasite of pigs; in addition to its veterinary significance it is a good model of the human parasite Ascaris lumbricoides , estimated to infect ∼1 . 4 billio...	[ "Ascarid nematodes are major pathogens of humans and livestock .", "The major method of control is by the use of anthelmintic drugs , many of which target the nervous system .", "Drugs such as levamisole , pyrantel and oxantel target the nicotinic acetylcholine receptors present on muscle .", "Nematodes have ...	2009
[ "Introduction", "Results", "Discussion", "Methods and materials" ]	[ "nucleic acid synthesis", "chemical compounds", "nucleobases", "nucleotides", "organic compounds", "dna transcription", "dna damage", "mutation", "fungi", "dna replication", "uracils", "pyrimidines", "dna", "dna synthesis", "chemical synthesis", "research and analysis methods", "gene...	Unscheduled DNA synthesis leads to elevated uracil residues at highly transcribed genomic loci in Saccharomyces cerevisiae	journal.pgen.1007516	null	[ [ "Transcription , a fundamental cellular process , can incongruously pose a serious threat to genome stability .", "Highly transcribed genomic regions have been reported to be hotspots for mutagenesis and recombination , phenomena referred to as transcription-associated mutagenesis ( TAM ) and transcriptio...	[ "Recombination and mutagenesis are elevated by active transcription .", "The correlation between transcription and genome instability is largely explained by the topological and structural changes in DNA and the associated physical obstacles generated by the transcription machinery .", "However , such explanati...	[ "Uracil in DNA , a major source of spontaneous mutations , can occur through the deamination of cytosine residues or through the direct incorporation of dUTP by DNA polymerases .", "Recent studies in yeast have shown that the uracil-associated mutations occur more frequently at highly transcribed regions .", "B...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/bacterial infections", "infectious diseases/urological infections", "microbiology/cellular microbiology and pathogenesis" ]	Escherichia coli Global Gene Expression in Urine from Women with Urinary Tract Infection	journal.ppat.1001187	null	[ [ "Animal models of infection have provided valuable insight into diverse mechanisms of bacterial pathogenesis .", "Application of microarray technology to these models has further enabled analysis of bacterial global gene expression during infection of a specific host .", "These studies have included t...	[ "Murine models of urinary tract infection ( UTI ) have provided substantial data identifying uropathogenic E . coli ( UPEC ) virulence factors and assessing their expression in vivo .", "However , it is unclear how gene expression in these animal models compares to UPEC gene expression during UTI in humans .", ...	[ "Animal models of infection have been used extensively to study how bacteria and other pathogens cause disease .", "These models provide valuable information and have led to the development of numerous vaccines and antimicrobial therapies .", "However , it is important to recognize how these animal models compa...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "immunology", "microbiology", "parasitic diseases", "protozoan life cycles", "parasitic protozoans", "developmental biology", "protozoans", "leishmania", "membrane receptor signaling", "hormone receptor signaling", "promastigot...	Leishmania amazonensis Engages CD36 to Drive Parasitophorous Vacuole Maturation	journal.ppat.1005669	null	[ [ "Leishmaniasis affects 12 million people in over 98 tropical and subtropical countries or territories [1 , 2] .", "The disease is caused by protozoan parasites of the genus Leishmania , which are transmitted by sandflies .", "In humans , an infection starts with the interaction between promastigote fo...	[ "Leishmania amastigotes manipulate the activity of macrophages to favor their own success .", "However , very little is known about the role of innate recognition and signaling triggered by amastigotes in this host-parasite interaction .", "In this work we developed a new infection model in adult Drosophila to ...	[ "Leishmaniasis is caused by Leishmania parasites and transmitted to humans by sandflies .", "After the establishment of infection , the intracellular parasite form , known as an amastigote , preferentially infects and replicates in macrophages , cells otherwise specialized for killing microbes .", "To overcome ...	2016
[ "Introduction", "Results/Discussion", "Methods" ]	[ "oncology", "medicine" ]	Aberration in DNA Methylation in B-Cell Lymphomas Has a Complex Origin and Increases with Disease Severity	journal.pgen.1003137	null	[ [ "Follicular lymphomas ( FLs ) and diffuse large B-cell lymphomas ( DLBCLs ) are the most common non-Hodgkin lymphomas [1] .", "Follicular lymphomas represent a spectrum from low- to high-grade tumors and , while predominantly diagnosed as indolent tumors , progress to more aggressive lymphomas like DLBCL ...	[ "Despite mounting evidence that epigenetic abnormalities play a key role in cancer biology , their contributions to the malignant phenotype remain poorly understood .", "Here we studied genome-wide DNA methylation in normal B-cell populations and subtypes of B-cell non-Hodgkin lymphoma: follicular lymphoma and di...	[ "Follicular lymphomas and diffuse large B-cell lymphomas are the most common non-Hodgkin lymphomas .", "Although these diseases share many mutant alleles , the underlying cause of the different phenotypes remains unclear .", "We show that direct comparison of DNA methylation patterning provides insights about g...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Understanding Voltage Gating of Providencia stuartii Porins at Atomic Level	journal.pcbi.1004255	null	[ [ "The outer membrane of Gram-negative bacteria is sprinkled of homotrimeric channels comprised of three 16-stranded β-barrels .", "They are the principal conduits for the passive penetration of hydrophilic molecules into the periplasm , and are often referred to as the general diffusion porins .", "Cla...	[ "Bacterial porins are water-filled β-barrel channels that allow translocation of solutes across the outer membrane .", "They feature a constriction zone , contributed by the plunging of extracellular loop 3 ( L3 ) into the channel lumen .", "Porins are generally in the open state , but undergo gating in respons...	[ "Porins are the main conduits for hydrophilic nutrients and ions uptake into the periplasm of Gram-negative bacteria .", "Their translocation permeability is determined by the amino-acid distribution on their extracellular loop L3 .", "Bacterial porin channels have long been known to undergo step-wise gating , ...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "chromosome structure and function", "centromeres", "fungi", "model organisms", "immunoprecipitation", "fungal evolution", "experimental organism systems", "epigenetics", "chromatin", "schizosaccharomyces", "research and analysis methods", "heterochromatin", "saccharomyces", "mycology", ...	Heterochromatin and RNAi regulate centromeres by protecting CENP-A from ubiquitin-mediated degradation	journal.pgen.1007572	null	[ [ "Chromatin is organized into different chromatin domains .", "Centromere is a specialized chromatin domain that plays a vital role in chromosome segregation [1–3] .", "In most eukaryotes , centromere is surrounded by the epigenetically distinct heterochromatin domains .", "Peri-centromeric heteroc...	[ "Centromere is a specialized chromatin domain that plays a vital role in chromosome segregation .", "In most eukaryotes , centromere is surrounded by the epigenetically distinct heterochromatin domain .", "Heterochromatin has been shown to contribute to centromere function , but the precise role of heterochroma...	[ "Centromere is a specialized chromosomal domain that is essential for faithful chromosome segregation during mitosis and meiosis .", "In most eukaryotes , centromeres are surrounded by the densely packed heterochromatin .", "The exact role of heterochromatin in centromere assembly remains elusive .", "Centrom...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "taxonomy", "invertebrates", "biliary system", "medicine and health sciences", "liver", "body fluids", "chemical compounds", "helminths", "bile", "animals", "invertebrate genomics", "trematodes", "phylogenetics", "data management", "phylogenetic analysis", "research and analysis method...	Identification and characterization of the Fasciola hepatica sodium- and chloride-dependent taurine transporter	journal.pntd.0006428	null	[ [ "Liver flukes of the genus Fasciola are parasitic trematodes , which infest mammals all over the world .", "The two most prominent representatives of the genus Fasciola are Fasciola hepatica and Fasciola gigantica , which predominates in the temperate zones and tropical Africa and Asia , respectively [1] ...	[ "The parasitic liver fluke Fasciola hepatica infests mainly ruminants , but it can also cause fasciolosis in people , who ingest the metacercariae encysted on plants .", "The drug of choice to treat fasciolosis is triclabendazole ( TBZ ) , which has been on the market for several decades .", "This is also true ...	[ "The liver fluke F . hepatica imposes an economic burden by infesting domestic ruminants .", "In addition , the WHO classified human fasciolosis as a disease of vital global public health importance , because several million people worldwide are infested by this trematode .", "Because it is currently not possib...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "phosphorylation", "flow cytometry", "cellular stress responses", "cell cycle and cell division", "cell processes", "fungi", "model organisms", "dna replication", "experimental organism systems", "dna", "synthesis phase", "research and analysis methods", "saccharomyces", "spectrum analysis...	Mutations in the Non-Catalytic Subunit Dpb2 of DNA Polymerase Epsilon Affect the Nrm1 Branch of the DNA Replication Checkpoint	journal.pgen.1006572	null	[ [ "DNA integrity of living organisms is affected by perturbations that induce replication stress including nucleotide depletion or collision with lesions encountered in DNA exposed to alkylating agents [1] .", "Therefore , each cell must constantly monitor its genome integrity and coordinate DNA replication...	[ "To preserve genome integrity , the S-phase checkpoint senses damaged DNA or nucleotide depletion and when necessary , arrests replication progression and delays cell division .", "Previous studies , based on two pol2 mutants have suggested the involvement of DNA polymerase epsilon ( Pol ε ) in sensing DNA replic...	[ "The viability of living organisms depends on the integrity of their genomes .", "Each cell has to constantly monitor DNA replication and coordinate it with cell division to avoid genomic instability .", "This is achieved through pathways known as cell cycle checkpoints .", "Therefore , upon replication pertu...	2017
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "cytology", "pathology and laboratory medicine", "biopsy", "mycetoma", "pathogens", "tropical diseases", "microbiology", "surgical and invasive medical procedures", "actinomadura", "histology", "nocardia", "neglected tropical diseases", "fungal diseases", ...	The Accuracy of Histopathological and Cytopathological Techniques in the Identification of the Mycetoma Causative Agents	journal.pntd.0007056	null	[ [ "Mycetoma is a chronic granulomatous subcutaneous inflammatory infection , endemic in subtropical and tropical regions , but it is reported globally [1 , 2] .", "It is characterised by a painless subcutaneous swelling , multiple sinuses formation and a discharge that contain grains [3 , 4] .", "The cl...	[ "Mycetoma is a devastating neglected tropical disease , caused by various fungal and bacterial pathogens .", "Correct diagnosis to the species level is mandatory for proper treatment .", "In endemic areas , various diagnostic tests and techniques are in use to achieve that , and that includes grain culture , su...	[ "In mycetoma endemic regions , the medical and health settings are commonly suboptimal , and only a few diagnostic tests and techniques are available .", "That had badly affected the patients’ proper diagnosis and management and thus the late presentation of patients with advanced disease .", "In this retrospec...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Gene Expression Switching of Receptor Subunits in Human Brain Development	journal.pcbi.1004559	null	[ [ "Chemical synapses are complex molecular structures allowing neurons to communicate and process information .", "In mammals , the molecular composition of most post-synaptic receptors has been characterized , together with their downstream signal transduction pathway [1–3] .", "Interestingly , many of...	[ "Synaptic receptors in the human brain consist of multiple protein subunits , many of which have multiple variants , coded by different genes , and are differentially expressed across brain regions and developmental stages .", "The brain can tune the electrophysiological properties of synapses to regulate plastic...	[ "Synapses change their properties during development affecting information processing and learning .", "Most synaptic receptors consist of several proteins , each having several variants coded by closely related genes .", "These protein variants are similar in structure , yet often differ slightly in their biop...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/hiv infection and aids", "immunology/antigen processing and recognition", "biochemistry/biomacromolecule-ligand interactions", "virology/antivirals, including modes of action and resistance" ]	Crystal Structure and Size-Dependent Neutralization Properties of HK20, a Human Monoclonal Antibody Binding to the Highly Conserved Heptad Repeat 1 of gp41	journal.ppat.1001195	null	[ [ "The HIV-1 envelope ( Env ) glycoprotein is the main target for neutralizing antibodies .", "Thus a successful HIV-1 vaccine must induce broadly cross-clade neutralizing antibodies as an essential correlate of protection against infection [1] .", "The HIV-1 genome and especially its env gene is highly...	[ "The human monoclonal antibody ( mAb ) HK20 neutralizes a broad spectrum of primary HIV-1 isolates by targeting the highly conserved heptad repeat 1 ( HR1 ) of gp41 , which is transiently exposed during HIV-1 entry .", "Here we present the crystal structure of the HK20 Fab in complex with a gp41 mimetic 5-Helix a...	[ "The HIV-1 envelope glycoprotein composed of the receptor binding subunit gp120 and the fusion protein gp41 is the prime target for neutralizing antibodies .", "Receptor binding induces a conformational change in gp41 that transiently exposes the conserved heptad repeat 1 ( HR1 ) region .", "We have previously ...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immune cells", "cytokines", "immune activation", "immunity to infections", "immunology", "microbiology", "host-pathogen interaction", "bacterial pathogens", "biology", "immune response", "gram positive", "immune system", "nk cells", "immunity", "innate immunity" ]	Mechanisms of NK Cell-Macrophage Bacillus anthracis Crosstalk: A Balance between Stimulation by Spores and Differential Disruption by Toxins	journal.ppat.1002481	null	[ [ "NK cells are immune cells that do not need prior exposure to antigen to exert their functions .", "Their receptors are germline encoded and do not require somatic gene rearrangements .", "These receptors recognise an array of self-molecules through highly specific mechanisms .", "The functions of...	[ "NK cells are important immune effectors for preventing microbial invasion and dissemination , through natural cytotoxicity and cytokine secretion .", "Bacillus anthracis spores can efficiently drive IFN-γ production by NK cells .", "The present study provides insights into the mechanisms of cytokine and cellul...	[ "NK cells are important immune effectors that perform a surveillance task and react to transformed , stressed , and virally infected cells .", "They represent a first-line defence against cancer and pathogen invasion .", "Different pathogens trigger distinct NK-cell activation pathways .", "The Bacillus anthr...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Peptide-MHC-I from Endogenous Antigen Outnumber Those from Exogenous Antigen, Irrespective of APC Phenotype or Activation	journal.ppat.1004941	null	[ [ "In the fight against virus invasion , TCD8+ play an essential role by killing virus-infected cells .", "Activation of these cells by professional antigen presenting cells ( pAPC ) is a vital step in generation of an effective adaptive immune response .", "pAPC are a heterogeneous population comprised...	[ "Naïve anti-viral CD8+ T cells ( TCD8+ ) are activated by the presence of peptide-MHC Class I complexes ( pMHC-I ) on the surface of professional antigen presenting cells ( pAPC ) .", "Increasing the number of pMHC-I in vivo can increase the number of responding TCD8+ .", "Antigen can be presented directly or i...	[ "To induce a protective cell type ( CD8+ T cells ) following virus infection , it is necessary to present degraded fragments of viral protein in complex with self molecules on the surface of so-called antigen presenting cells ( APC ) .", "This process can occur in infected or uninfected APC and has been studied a...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "luciferase assay", "luciferase", "enzymes", "enzymology", "vertebrates", "animals", "mammals", "biochemical analysis", "enzyme assays", "amniotes", "bioassays and physiological analysis", "calcium signaling", "g protein coupled receptors", "research and analysis methods", "erk signaling...	Constitutively active BRS3 is a genuinely orphan GPCR in placental mammals	journal.pbio.3000175	“Orphan” G protein–coupled receptors (GPCRs) are membrane-bound receptors for which a natural ligand has yet to be identified. This study shows that the mammalian GPCR BRS3 represents a new group of GPCRs that will never be deorphanized, as they function constitutively in a ligand-independent manner.	[ [ "G protein–coupled receptors ( GPCRs ) , also known as seven-transmembrane ( 7TM ) receptors , represent the largest superfamily of more than 800 vertebrate transmembrane proteins , and the main characteristic feature of these proteins is that they share a common 7TM configuration [1 , 2] .", "GPCRs have ...	[ "G protein–coupled receptors ( GPCRs ) play an important role in physiology and disease and represent the most productive drug targets .", "Orphan GPCRs , with their endogenous ligands unknown , were considered a source of drug targets and consequently attract great interest to identify their endogenous cognate l...	[ "The current model on G protein–coupled receptors ( GPCRs ) is that they have at least one endogenous ligand for the activation of the heterotrimeric G proteins that controls lots of physiological functions .", "Currently , 140 out of approximately 800 GPCRs are referred to as orphan because of a lack of knowledg...	2019
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "spectrometric identification of proteins", "cellular stress responses", "giardia", "enzymes", "cell processes", "enzymology", "microbiology", "parasitic protozoans", "protozoans", "chaperone proteins", "enzyme kinetics", "giardia lamblia", "proteins", "proteomics", "biochemistry", "ce...	Trans-spliced Heat Shock Protein 90 Modulates Encystation in Giardia lamblia	journal.pntd.0002829	null	[ [ "Heat Shock Protein 90 ( Hsp90 ) , is a versatile molecular chaperone , involved in diverse cellular processes .", "It is an essential and evolutionarily conserved chaperone present in both prokaryotes and eukaryotes .", "Hsp90 have selective set of proteins to chaperone called as clients , which majo...	[ "Hsp90 from Giardia lamblia is expressed by splicing of two independently transcribed RNA molecules , coded by genes named HspN and HspC located 777 kb apart .", "The reasons underlying such unique trans-splicing based generation of GlHsp90 remain unclear .", "In this study using mass-spectrometry we identify t...	[ "Giardia lamblia is one of the most common causes of diarrhoea across the globe .", "The disease can result in fatalities especially in small children .", "The parasite is transmitted by contaminated food through faeco-oral route due to unhygienic habits .", "The parasite exhibits two stages during its lifecy...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cancer genomics", "taxonomy", "medicine and health sciences", "genetic networks", "chromosome structure and function", "basic cancer research", "cloning", "oncology", "mutation", "phylogenetics", "data management", "phylogenetic analysis", "network analysis", "genome analysis", "molecul...	Pan-cancer inference of intra-tumor heterogeneity reveals associations with different forms of genomic instability	journal.pgen.1007669	null	[ [ "Cancer is a dynamic and ever-changing disease that mutates and evolves during its progression [1] .", "While the transformation from healthy to malignant cell is characterized by a few selected oncogenic alterations [2] , genomic instability is frequently observed in formed tumors , where it fuels the ac...	[ "Genomic instability is a major driver of intra-tumor heterogeneity .", "However , unstable genomes often exhibit different molecular and clinical phenotypes , which are associated with distinct mutational processes .", "Here , we algorithmically inferred the clonal phylogenies of ~6 , 000 human tumors from 32 ...	[ "Cancer is characterized by cells accumulating molecular alterations promoting specific phenotypic features , such as uncontrolled proliferation and survival .", "Cancer cells sometimes exhibit a high number of such alterations , often driven by defects of the DNA repair pathway or by external mutagens , such as ...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "neuroscience/behavioral neuroscience", "genetics and genomics/gene function" ]	A Neuronal Acetylcholine Receptor Regulates the Balance of Muscle Excitation and Inhibition in Caenorhabditis elegans	journal.pbio.1000265	The role of a heterotrimeric neuronal acetylcholine receptor in regulating a Caenorhabditis elegans locomotion circuit are revealed down to the level of identifying all five subunits involved.	[ [ "Acetylcholine activates ligand-gated ion channels in muscles and is a major neurotransmitter in the brain , modulating a variety of cognitive and addictive behaviors [1] .", "Ionotropic acetylcholine channels result from the assembly of five individual subunits .", "Each subunit has four membrane-spa...	[ "In the nematode Caenorhabditis elegans , cholinergic motor neurons stimulate muscle contraction as well as activate GABAergic motor neurons that inhibit contraction of the contralateral muscles .", "Here , we describe the composition of an ionotropic acetylcholine receptor that is required to maintain excitation...	[ "Neuronal acetylcholine receptors modulate a wide range of activities in vertebrates and invertebrates .", "The activity and sensitivity of these receptors to particular pharmacological agents is determined by the subunit composition of the receptors .", "A rich diversity of acetylcholine receptors are expresse...	2009
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "genetics", "immunology", "biology", "microbiology", "molecular cell biology" ]	Dengue Virus Type 2 (DENV2)-Induced Oxidative Responses in Monocytes from Glucose-6-Phosphate Dehydrogenase (G6PD)-Deficient and G6PD Normal Subjects	journal.pntd.0002711	null	[ [ "Dengue infection is among the leading causes of morbidity and mortality in the tropics and subtropics where as many as 100 million people are infected with 22 , 000 deaths yearly [1] .", "Dengue infection is caused by dengue virus ( DENV ) , an RNA virus of the family Flaviviridae .", "There are four...	[ "Dengue virus is endemic in peninsular Malaysia .", "The clinical manifestations vary depending on the incubation period of the virus as well as the immunity of the patients .", "Glucose-6-phosphate dehydrogenase ( G6PD ) deficiency is prevalent in Malaysia where the incidence is 3 . 2% .", "It has been noted...	[ "An estimated 50 to 100 million cases of dengue fever occur each year worldwide .", "Among these , there are 200 , 000 to 500 , 000 cases of life-threatening dengue hemorrhagic fever ( DHF ) and dengue shock syndrome ( DSS ) .", "Factors contributing to the development of DHF/DSS are not yet fully identified ."...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunopathology", "medicine", "infectious diseases", "lymphocytic choriomeningitis", "immunology", "biology", "viral diseases" ]	IL-21 Restricts Virus-driven Treg Cell Expansion in Chronic LCMV Infection	journal.ppat.1003362	null	[ [ "The immune system has to efficiently eliminate pathogens but simultaneously needs to avoid the potential self-damage and immunopathology caused by excessive immune activation .", "Therefore , a tight regulation of immune responses is critical for host survival .", "The subset of CD4+CD25+ regulatory ...	[ "Foxp3+ regulatory T ( Treg ) cells are essential for the maintenance of immune homeostasis and tolerance .", "During viral infections , Treg cells can limit the immunopathology resulting from excessive inflammation , yet potentially inhibit effective antiviral T cell responses and promote virus persistence .", ...	[ "T cell exhaustion represents a state of T cell dysfunction associated with clinically relevant diseases , such as persistent viral infections or cancer .", "Although the molecular signature of exhausted T cells has been characterized in detail at the functional and transcriptional level , the immunological mecha...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "rna", "rna structure", "molecular cell biology", "nucleic acids", "biology", "evolutionary biology", "ribozymes" ]	Evolutionary Evidence for Alternative Structure in RNA Sequence Co-variation	journal.pcbi.1003152	null	[ [ "RNA is unique in that it is both a messenger of genetic information and it can fold to adopt highly specific functional conformations that carry out catalysis in the cell [1]–[4] .", "Large RNAs have a high propensity to misfold , requiring chaperones and in many cases protein co-factors to achieve an ac...	[ "Sequence conservation and co-variation of base pairs are hallmarks of structured RNAs .", "For certain RNAs ( e . g . riboswitches ) , a single sequence must adopt at least two alternative secondary structures to effectively regulate the message .", "If alternative secondary structures are important to the fun...	[ "RNA ( Ribonucleic Acid ) is a messenger of genetic information , master regulator , and catalyst in the cell .", "To carry out its function , RNA can fold into complex three-dimensional structures .", "Certain classes of RNAs , called riboswitches , adopt at least two alternative structures to act as a switch ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "bacterial diseases", "infectious diseases", "biology", "microbiology" ]	Capsule Type of Streptococcus pneumoniae Determines Growth Phenotype	journal.ppat.1002574	null	[ [ "Streptococcus pneumoniae is a major pathogen causing several serious human diseases including pneumonia , meningitis and sepsis as well as being a common cause of otitis media .", "The bacteria are usually surrounded by one of at least 92 known varieties of polysaccharide capsule [1] , [2] which acts as ...	[ "The polysaccharide capsule of Streptococcus pneumoniae defines over ninety serotypes , which differ in their carriage prevalence and invasiveness for poorly understood reasons .", "Recently , an inverse correlation between carriage prevalence and oligosaccharide structure of a given capsule has been described ."...	[ "Streptococcus pneumoniae bacteria are responsible for serious human infections including meningitis , pneumonia and bacteraemia and are a common cause of otitis media ( ear infection ) in children .", "However , they most often reside harmlessly in the infant nasopharynx .", "An association has long been obser...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public health and epidemiology", "social and behavioral sciences", "preventive medicine", "non-clinical medicine", "population modeling", "global health", "neglected tropical diseases", "cost effectiveness", "infectious disease control", "lymphatic filariasis", "infectious disease...	Modeling the Impact and Costs of Semiannual Mass Drug Administration for Accelerated Elimination of Lymphatic Filariasis	journal.pntd.0001984	null	[ [ "The Global Program to Eliminate Lymphatic Filariasis ( GPELF ) was launched in 2000 with the aim of eliminating lymphatic filariasis ( LF ) as a public health problem by 2020 [1] .", "The recommended strategy is to treat entire at-risk populations annually with a single dose of ivermectin and albendazole...	[ "The Global Program to Eliminate Lymphatic Filariasis ( LF ) has a target date of 2020 .", "This program is progressing well in many countries .", "However , progress has been slow in some countries , and others have not yet started their mass drug administration ( MDA ) programs .", "Acceleration is needed ....	[ "The Global Program to Eliminate Lymphatic Filariasis ( LF ) employs annual mass drug administration ( MDA ) of antifilarial drugs to reduce infection rates in populations and interrupt transmission .", "While this program is working well in many countries , progress has been slow in others , and some countries h...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "glycolipids", "medicine and health sciences", "immune physiology", "immune cells", "sphingolipids", "antigen-presenting cells", "biological cultures", "immunology", "dendritic cells", "hybridomas", "research and analysis methods", "immune system proteins", "lipids", "animal cells", "pro...	TLR9-mediated dendritic cell activation uncovers mammalian ganglioside species with specific ceramide backbones that activate invariant natural killer T cells	journal.pbio.3000169	Although the existence of self-antigens for invariant Natural Killer T (iNKT) cells is widely accepted, their precise nature remains a matter of debate. This study shows that two mammalian ganglioside species activate iNKT cells in a CD1d-dependent manner.	[ [ "Type I or invariant natural killer T ( iNKT ) cells are a subset of “innate-like” αβ T lymphocytes that rapidly produce large amounts of cytokines and chemokines and orchestrate the ensuing innate and adaptive immune responses during infection , inflammatory disorders , and cancer [1] .", "iNKT cells rec...	[ "CD1d-restricted invariant natural killer T ( iNKT ) cells represent a heterogeneous population of lipid-reactive T cells that are involved in many immune responses , mediated through T-cell receptor ( TCR ) –dependent and/or independent activation .", "Although numerous microbial lipid antigens ( Ags ) have been...	[ "Invariant natural killer T ( iNKT ) cells are a population of unconventional T lymphocytes that activate rapidly during inflammation due to their innate-like features .", "They are unconventional since they do not react to peptidic antigens ( Ags ) presented by classical major histocompatibility complex ( MHC ) ...	2019
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "phosphorylation", "medicine and health sciences", "pathology and laboratory medicine", "hela cells", "pathogens", "biological cultures", "microbiology", "plasmid construction", "viruses", "immunoprecipitation", "dna viruses", "cell cultures", "dna construction", "molecular biology techniq...	Bclaf1 critically regulates the type I interferon response and is degraded by alphaherpesvirus US3	journal.ppat.1007559	null	[ [ "Herpesviridae is a family of large DNA viruses with an ability to establish persistent infection in hosts .", "The viruses have evolved multiple strategies to establish persistent infection and combat host defenses; among these , the interferon ( IFN ) antiviral response is most prominent .", "Member...	[ "Type I interferon response plays a prominent role against viral infection , which is frequently disrupted by viruses .", "Here , we report Bcl-2 associated transcription factor 1 ( Bclaf1 ) is degraded during the alphaherpesvirus Pseudorabies virus ( PRV ) and Herpes simplex virus type 1 ( HSV-1 ) infections thr...	[ "Alphaherpesvirus , such as Pseudorabies virus ( PRV ) and Herpes simplex virus type 1 ( HSV-1 ) , can establish persistent infection and cause various diseases in hosts .", "Interferon ( IFN ) response is hosts’ first defense system against viral infection .", "Here , we report alphaherpesvirus induces degrada...	2019
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "biology", "veterinary science", "agriculture" ]	Clonal Differences between Non-Typhoidal Salmonella (NTS) Recovered from Children and Animals Living in Close Contact in The Gambia	journal.pntd.0001148	null	[ [ "Non-Typhoidal Salmonella ( NTS ) are important causes of invasive bacterial diseases and are associated with substantial mortality .", "In rural Gambia , NTS was the second most important blood culture isolate after Streptococcus pneumoniae in children with invasive bacterial disease [1] .", "Similar...	[ "Non-Typhoidal Salmonella ( NTS ) is an important cause of invasive bacterial disease and associated with mortality in Africa .", "However , little is known about the environmental reservoirs and predominant modes of transmission .", "Our study aimed to study the role of domestic animals in the transmission of ...	[ "Salmonellosis is a neglected tropical disease causing serious dysentery and septicaemia particularly in young infants , elderly and immunocompromised individuals such as HIV patients and associated with substantial mortality in developing countries .", "Salmonellosis also constitutes a major public health proble...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "animal models", "immune system", "invertebrates", "caenorhabditis elegans", "infectious disease immunology", "model organisms", "innate immune system", "clinical immunology", "immunity", "caenorhabditis", "nematoda", "biology and life sciences", "immunology", "animals", "organisms", "...	Recovery from an Acute Infection in C. elegans Requires the GATA Transcription Factor ELT-2	journal.pgen.1004609	null	[ [ "The course of human bacterial infections is controlled by a combination of immune responses , physiological changes , and , if necessary , antibiotic treatment .", "To recover from an infection and return to homeostasis , the host must activate mechanisms capable of controlling the damage caused by patho...	[ "The mechanisms involved in the recognition of microbial pathogens and activation of the immune system have been extensively studied .", "However , the mechanisms involved in the recovery phase of an infection are incompletely characterized at both the cellular and physiological levels .", "Here , we establish ...	[ "Infections by bacterial pathogens often produce substantial tissue damage and alter metabolism in the host that , if left unchecked , could be detrimental to overall fitness .", "The cellular and systemic responses that resolve these alterations in the host are not well defined .", "Here , we examine transcrip...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology", "biology and life sciences", "developmental biology" ]	Variable Combinations of Specific Ephrin Ligand/Eph Receptor Pairs Control Embryonic Tissue Separation	journal.pbio.1001955	Vertebrate embryonic cells recognize self from non-self, thus restricting repulsion at tissue boundaries, through a combination of multiple ephrins and Eph receptors, simply based on binding selectivity and asymmetric expression.	[ [ "In vertebrates , ephrins and Eph receptors have emerged as major players in the formation of cleft-like tissue boundaries .", "They control segmentation of rhombomeres [1] and somites [2] , [3] and the separation of embryonic germ layers [4]–[6] .", "Ephrins as well as Eph receptors are divided into ...	[ "Ephrins and Eph receptors are involved in the establishment of vertebrate tissue boundaries .", "The complexity of the system is puzzling , however in many instances , tissues express multiple ephrins and Ephs on both sides of the boundary , a situation that should in principle cause repulsion between cells with...	[ "How embryonic tissues separate from each other to shape the developing organism is a fundamental question in developmental biology .", "In vertebrates , this process relies on local repulsive reactions specifically generated at contacts between cells of different types .", "These reactions are triggered by typ...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "livestock", "medicine and health sciences", "immune physiology", "pathology and laboratory medicine", "pathogens", "immunology", "tropical diseases", "microbiology", "geographical locations", "brucellosis", "bacterial diseases", "veterinary diagnostics", "neglected tropical diseases", "an...	Poor performance of the rapid test for human brucellosis in health facilities in Kenya	journal.pntd.0005508	null	[ [ "Brucellosis is a zoonotic disease with a global distribution that can cause severe illness in people and important economic losses in livestock [1–4] .", "Brucella abortus and B . melitensis are the most important zoonotic pathogens , and both species are likely to be endemic in cattle and small ruminant...	[ "Human brucellosis is considered to be an important but typically under-diagnosed cause of febrile illness in many low and middle-income countries .", "In Kenya , and throughout East Africa , laboratory diagnosis for the disease is based primarily on the febrile antigen Brucella agglutination test ( FBAT ) , yet ...	[ "Brucellosis is a debilitating disease of people caused by infection with one of a number of different Brucella species .", "In almost all cases , people acquire the infection through exposure to infected animals or contaminated animal products .", "Human brucellosis is well known for its wide range of symptoms...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "parastic protozoans", "medicine", "infectious diseases", "leishmania", "leishmaniasis", "neglected tropical diseases", "protozoology", "biology", "microbiology", "parasitic diseases" ]	Appraisal of a Leishmania major Strain Stably Expressing mCherry Fluorescent Protein for Both In Vitro and In Vivo Studies of Potential Drugs and Vaccine against Cutaneous Leishmaniasis	journal.pntd.0001927	null	[ [ "Leishmania major is the main cause of cutaneous leishmaniasis ( CL ) in the Old World .", "Parasites are transmitted by Phlebotominae sandflies whilst blood feeding on infected mammalian hosts .", "CL is widely spread in the developing world , affecting people in 88 countries with 1 . 5 million new c...	[ "Leishmania major cutaneous leishmaniasis is an infectious zoonotic disease .", "It is produced by a digenetic parasite , which resides in the phagolysosomal compartment of different mammalian macrophage populations .", "There is an urgent need to develop new therapies ( drugs ) against this neglected disease t...	[ "Leishmaniasis is a parasitic disease that is far from eradication .", "The lack of an efficacious vaccine and treatment failures are major factors in its intractable worldwide prevalence .", "A non-invasive imaging technique using genetically engineered parasites that expressed fluorescent proteins could give ...	2012
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "fluorescence imaging", "cluster analysis", "neurochemistry", "statistical noise", "statistics", "hierarchical clustering", "neuroscience", "kernel functions", "mathematics", "nerve fibers", "neurotransmitters", "calcium signaling", "research and analysis methods", "gaussian noise", "ope...	Bayesian hypothesis testing and experimental design for two-photon imaging data	journal.pcbi.1007205	null	[ [ "Over the last two decades , two-photon ( 2P ) imaging has become one of the premier tools for studying coding in neural systems from the population level down to individual neural compartments [1] .", "The resulting data is highly variable due to the inherent variability of neurons and technical sources ...	[ "Variability , stochastic or otherwise , is a central feature of neural activity .", "Yet the means by which estimates of variation and uncertainty are derived from noisy observations of neural activity is often heuristic , with more weight given to numerical convenience than statistical rigour .", "For two-pho...	[ "There are many sources of noise in recordings of neural activity , and the first challenge in neural data analysis is to separate this noise from experimentally relevant variation .", "This is particularly problematic for two-photon imaging data .", "Two-photon imaging uses fluorescent indicators to measure ch...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "taxonomy", "medicine and health sciences", "pathology and laboratory medicine", "statistics", "pathogens", "microbiology", "retroviruses", "viruses", "immunodeficiency viruses", "multivariate analysis", "phylogenetics", "data management", "mathematics", "rna viruses", "phylogenetic anal...	Phylogenies from dynamic networks	journal.pcbi.1006761	null	[ [ "Understanding whether and how the transmission patterns of a pathogen are revealed by branching patterns in pathogen phylogenetic trees remains a challenging research question .", "Alongside the stochastic diversification of the pathogen on the short time scales of an infectious disease outbreak , branch...	[ "The relationship between the underlying contact network over which a pathogen spreads and the pathogen phylogenetic trees that are obtained presents an opportunity to use sequence data to learn about contact networks that are difficult to study empirically .", "However , this relationship is not explicitly known...	[ "Understanding whether and how transmission patterns are revealed by branching patterns in phylogenetic trees for pathogens remains a challenging research question .", "Besides the diversification of the pathogen , branching patterns depend strongly on the host contact structure as it shapes opportunities for the...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "sequencing techniques", "crystal structure", "condensed matter physics", "enzymology", "nucleotides", "amino acid sequence analysis", "sequence motif analysis", "dna", "dna structure", "crystallography", "molecular biology techniques", "research and analysis methods", "sequence analysis", ...	Structure of Type IIL Restriction-Modification Enzyme MmeI in Complex with DNA Has Implications for Engineering New Specificities	journal.pbio.1002442	The structure of the bifunctional Type IIL restriction-and-modification enzyme MmeI provides a basis for understanding how such enzymes recognize their substrates and a framework for manipulating their specificities.	[ [ "Due to their exquisite selectivity , Type II restriction endonucleases ( REases ) are paradigms in the study of protein-DNA sequence recognition [1 , 2] .", "Approximately 4 , 000 have now been discovered [3] , specific for a remarkable 365 different DNA sequences .", "Impressive as this number is , ...	[ "The creation of restriction enzymes with programmable DNA-binding and -cleavage specificities has long been a goal of modern biology .", "The recently discovered Type IIL MmeI family of restriction-and-modification ( RM ) enzymes that possess a shared target recognition domain provides a framework for engineerin...	[ "Type II restriction endonucleases ( REases ) are the bedrock of modern biotechnology .", "Type II REases were essential for the recombinant DNA revolution and the development of gene technology .", "However , despite the discovery of more than 4 , 000 REases , the DNA recognition specificities are limited to o...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "blood cells", "cell physiology", "junctional complexes", "spectrins", "simulation and modeling", "red blood cells", "materials science", "cellular structures and organelles", "macromolecules", "cytoskeleton", "materials by structure", "research and analysis methods", "polymers", "polymer ...	Image-based model of the spectrin cytoskeleton for red blood cell simulation	journal.pcbi.1005790	null	[ [ "Red cells possess a lipid membrane and cytoskeleton that together enclose a viscous cytoplasm characterized by a high concentration of hemoglobin .", "The elastic properties of the cell can be separated into contributions from the lipid bilayer , which supplies bending rigidity and resistance to local ch...	[ "We simulate deformable red blood cells in the microcirculation using the immersed boundary method with a cytoskeletal model that incorporates structural details revealed by tomographic images .", "The elasticity of red blood cells is known to be supplied by both their lipid bilayer membranes , which resist bendi...	[ "Red blood cells are responsible for delivering oxygen to tissues throughout the body .", "These terminally differentiated cells have developed a fascinating flexibility and resiliency that is critical to navigating the circulatory system .", "Far from being rigid bodies , red blood cells adopt biconcave disk s...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "geomorphology", "dengue virus", "medicine and health sciences", "pathology and laboratory medicine", "landforms", "pathogens", "topography", "geographical locations", "microbiology", "vertebrates", "animals", "mammals", "viruses", "rna viruses", "islands", "medical microbiology", "m...	Serological evidence of infection with dengue and Zika viruses in horses on French Pacific Islands	journal.pntd.0007162	null	[ [ "French overseas territories located in the South Pacific include New Caledonia , French Polynesia and Wallis and Futuna .", "New Caledonia is composed of one main island and several archipelagoes , and French Polynesia is composed of five archipelagoes ( Society , Marquesas , Tuamotu , Gambier and Austra...	[ "New Caledonia and French Polynesia are areas in which arboviruses circulate extensively .", "A large serological survey among horses from New Caledonia and French Polynesia was carried out to investigate the seroprevalence of flaviviruses in the horse population .", "Here , 293 equine sera samples were screene...	[ "New Caledonia and French Polynesia , located in the South Pacific , are facing circulation of dengue virus ( DENV ) for a long time and emergence of Zika virus ( ZIKV ) since 2013 .", "A large serosurvey among horses’ population from these two islands was carried out to investigate the seroprevalence of the main...	2019
[ "Introduction", "Results", "Discussion", "Material and Methods" ]	[]	Dynamic Allostery of the Catabolite Activator Protein Revealed by Interatomic Forces	journal.pcbi.1004358	null	[ [ "The regulation of DNA transcription is one of the key factors for the control of cell functions , a classic example of which is the lac-operon model .", "In this gene regulatory mechanism , the catabolite activator protein ( CAP ) promotes DNA transcription initiation .", "The homodimeric protein CAP...	[ "The Catabolite Activator Protein ( CAP ) is a showcase example for entropic allostery .", "For full activation and DNA binding , the homodimeric protein requires the binding of two cyclic AMP ( cAMP ) molecules in an anti-cooperative manner , the source of which appears to be largely of entropic nature according...	[ "The Catabolite Activator Protein ( CAP ) is a well-studied example for how cellular catabolite levels are integrated into the gene regulation .", "Its affinity for a specific stretch of DNA can be switched on by the binding of two nucleotide molecules termed cAMP to its two protomers .", "Even though the nucle...	2015
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "genetics and genomics" ]	Synthesis-Dependent Strand Annealing in Meiosis	journal.pbio.0050299	New evidence suggests that meiotic noncrossover recombination can occur without a Holliday junction intermediate.	[ [ "Homologous recombination is essential for meiosis , the cellular division process specific to gametogenesis .", "The reduction in ploidy that occurs during meiosis is necessary for sexual reproduction and is achieved by a single round of DNA replication followed by two rounds of chromosome segregation ."...	[ "Recent studies led to the proposal that meiotic gene conversion can result after transient engagement of the donor chromatid and subsequent DNA synthesis-dependent strand annealing ( SDSA ) .", "Double Holliday junction ( dHJ ) intermediates were previously proposed to form both reciprocal crossover recombinants...	[ "In organisms that reproduce sexually , sex cells ( gametes ) are produced by the specialized cell division called meiosis , which halves the number of chromosomes from two sets ( diploid ) to one ( haploid ) .", "During meiosis , homologous DNA molecules exchange genetic material in a process called homologous r...	2007
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Dynamical Adaptation in Photoreceptors	journal.pcbi.1003289	null	[ [ "The ability of neurons to modulate their response as a function of the environment or the task is at once a staple of neural information processing and an achievement of neural biophysics .", "Adaptation is at play throughout sensory systems .", "In peripheral sensory cells , one expects significant ...	[ "Adaptation is at the heart of sensation and nowhere is it more salient than in early visual processing .", "Light adaptation in photoreceptors is doubly dynamical: it depends upon the temporal structure of the input and it affects the temporal structure of the response .", "We introduce a non-linear dynamical ...	[ "Photoreceptors constitute the interface between the visual world and the cerebral world , as they convert light inputs into neural signals .", "This conversion is subject to continuous adaptation: response gain and time scale vary as a function of input history .", "This adaptation is ‘dynamical’ both because ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "invertebrates", "medicine and health sciences", "caenorhabditis", "neurodegenerative diseases", "animals", "animal models", "caenorhabditis elegans", "model organisms", "glucose signaling", "epigenetics", "motor neuron diseases", "research and analysis methods", "signal transduction", "ce...	Heritable Transmission of Stress Resistance by High Dietary Glucose in Caenorhabditis elegans	journal.pgen.1004346	null	[ [ "Aging is an inevitable process that affects all organisms and a better understanding of the underlying biological mechanisms is relevant to human health [1] .", "In nature , organisms struggle against environmental conditions to survive and hopefully reproduce .", "This is an energetically costly and...	[ "Glucose is a major energy source and is a key regulator of metabolism but excessive dietary glucose is linked to several disorders including type 2 diabetes , obesity and cardiac dysfunction .", "Dietary intake greatly influences organismal survival but whether the effects of nutritional status are transmitted t...	[ "Nutritional state has major effects on health and longevity , and investigations into the mechanisms of dietary restriction have taken the lion's share of recent genetic discoveries .", "We used Caenorhabditis elegans to investigate the role of diet on nematode physiology and report the surprising finding that e...	2014

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