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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", "Materials and Methods", "Results", "Discussion" ]	[ "voltage-gated ion channels", "death rates", "invertebrates", "medicine and health sciences", "demography", "china", "voltage-gated sodium channels", "geographical locations", "electrophysiology", "neuroscience", "animals", "mutation", "ion channels", "population biology", "insect vector...	Multi-country Survey Revealed Prevalent and Novel F1534S Mutation in Voltage-Gated Sodium Channel (VGSC) Gene in Aedes albopictus	journal.pntd.0004696	null	[ [ "Aedes albopictus , also known as Asian tiger mosquito , is notorious for its ability to transmit a number of arboviruses including dengue , Chikungunya and Zika virus as well as filarial nematodes [1–11] .", "The aggressive dispersal and thus world-wide invasiveness in recent years [5 , 6] , in addition ...	[ "Aedes albopictus is an important dengue vector because of its aggressive biting behavior and rapid spread out of its native home range in Southeast Asia .", "Pyrethroids are widely used for adult mosquito control , and resistance to pyrethroids should be carefully monitored because vector control is the only eff...	[ "Aedes albopictus is a major dengue and Chikungunya vector and highly invasive .", "In the absence of effective treatment for the arbovirus infections , vector control is the only viable option .", "Pyrethroids are the most widely used insecticide for vector control programs due to low mammalian toxicity and ra...	2016
[ "Introduction", "Results and Discussion" ]	[ "biochemistry", "evolutionary biology/sexual behavior", "infectious diseases/neglected tropical diseases", "evolutionary biology/animal behavior", "molecular biology/bioinformatics", "infectious diseases/viral infections", "virology/emerging viral diseases" ]	Towards a Semen Proteome of the Dengue Vector Mosquito: Protein Identification and Potential Functions	journal.pntd.0000989	null	[ [ "Male seminal fluid proteins ( Sfps ) influence female reproductive and feeding", "behaviors in a range of insects studied to date ( reviewed in [1] , [2] ) .", "Therefore , these proteins may", "provide targets or pathways that can be manipulated to reduce pathogen transmission", "by blood-fe...	[ "No commercially licensed vaccine or treatment is available for dengue fever ,", "a potentially lethal infection that impacts millions of lives annually .", "New", "tools that target mosquito control may reduce vector populations and break", "the cycle of dengue transmission .", "Male mosquito seminal flu...	[ "Dengue is a potentially lethal infection that impacts millions of humans", "annually .", "This disease is caused by viruses transmitted by infected female", "Aedes aegypti mosquitoes during blood feeding .", "No", "commercial vaccine or treatment is available for dengue infection .", "One way to", "b...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell physiology", "cell death", "autophagic cell death", "fungal genetics", "gene regulation", "regulatory proteins", "cell processes", "dna-binding proteins", "fungal structure", "cell polarity", "fungi", "plant science", "transcription factors", "plant pathology", "appressoria", "my...	Tpc1 is an important Zn(II)2Cys6 transcriptional regulator required for polarized growth and virulence in the rice blast fungus	journal.ppat.1006516	null	[ [ "Rice blast disease is one of the most serious diseases of cultivated rice worldwide and is caused by the filamentous , ascomycete fungus Magnaporthe oryzae[1 , 2] .", "The disease is initiated when a conidium lands on the rice leaf surface .", "Here it germinates to produce a single germ tube that di...	[ "The establishment of polarity is a critical process in pathogenic fungi , mediating infection-related morphogenesis and host tissue invasion .", "Here , we report the identification of TPC1 ( Transcription factor for Polarity Control 1 ) , which regulates invasive polarized growth in the rice blast fungus Magnap...	[ "Cellular polarity is an intrinsic feature of filamentous fungal growth and pathogenesis .", "In this study , we identified a gene required for fungal polar growth and virulence in the rice blast fungus Magnaporthe oryzae .", "This gene has been named TPC1 ( Transcription factor for Polarity Control 1 ) .", "...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "bacteriology", "systems biology", "complex systems", "developmental biology", "bacterial biofilms", "mathematics", "applied mathematics", "biology", "computational biology", "microbial growth and development", "microbiology", "pattern formation" ]	Radial and Spiral Stream Formation in Proteus mirabilis Colonies	journal.pcbi.1002332	null	[ [ "A variety of spatial patterns in growing bacterial colonies are found both in nature and in the lab [1]–[10] .", "When inoculated on semi-solid agar with succinate or other TCA cycle intermediates , motile Escherichia coli cells grow , divide , and self-organize into patterns ranging from outward-moving ...	[ "The enteric bacterium Proteus mirabilis , which is a pathogen that forms biofilms in vivo , can swarm over hard surfaces and form a variety of spatial patterns in colonies .", "Colony formation involves two distinct cell types: swarmer cells that dominate near the surface and the leading edge , and swimmer cells...	[ "Bacteria frequently colonize surfaces and grow as biofilm communities embedded in a gel-like polysaccharide matrix , and when this occurs on catheters , heart valves and other medical implants , it can lead to serious , hard-to-treat infections .", "Proteus mirabilis is an enteric bacterium that forms biofilms o...	2011
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "biotechnology", "theoretical biology", "synthetic biology", "biology", "computational biology", "molecular biology" ]	Robust Signal Processing in Living Cells	journal.pcbi.1002218	null	[ [ "All living cells rely on the capacity to respond to intra- or extracellular signals and have evolved a dedicated biochemical machinery to continuously sense , transmit , and process a variety of internal and environmental cues .", "A key requisite for reliable signal processing is the capability of livin...	[ "Cellular signaling networks have evolved an astonishing ability to function reliably and with high fidelity in uncertain environments .", "A crucial prerequisite for the high precision exhibited by many signaling circuits is their ability to keep the concentrations of active signaling compounds within tightly de...	[ "Cellular signaling networks have to function reliably and with high fidelity in an uncertain environment .", "In this paper , we investigate the topological principles to achieve such robust signal processing in living cells .", "Specifically , we identify the topological organizing principles that enable a si...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "infectious diseases/fungal infections", "microbiology" ]	CO2 Acts as a Signalling Molecule in Populations of the Fungal Pathogen Candida albicans	journal.ppat.1001193	null	[ [ "Candida albicans is the predominant fungal pathogen of humans .", "In healthy individuals C . albicans resides as a commensal of the gastrointestinal , oral and vaginal tracts .", "C . albicans can cause superficial infections which , although not life threatening , provide discomfort to the individu...	[ "When colonising host-niches or non-animated medical devices , individual cells of the fungal pathogen Candida albicans expand into significant biomasses .", "Here we show that within such biomasses , fungal metabolically generated CO2 acts as a communication molecule promoting the switch from yeast to filamentou...	[ "Pathogenic microorganisms can produce a variety of secondary metabolites and signalling molecules which can affect the host , or provide them with a selective advantage against competing commensal organisms .", "We demonstrate that gaseous , metabolically generated CO2 can serve as a signalling molecule to enhan...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "computational biology/evolutionary modeling", "evolutionary biology", "genetics and genomics/population genetics" ]	Predicting the Evolution of Sex on Complex Fitness Landscapes	journal.pcbi.1000510	null	[ [ "Sexual reproduction is widespread among multi-cellular organisms [1] .", "However , the ubiquity of sex in the natural world is in stark contrast to its perceived costs , such as the recombination load [2] or the two-fold cost of producing males [3] , [4] .", "Given these disadvantages it is puzzling...	[ "Most population genetic theories on the evolution of sex or recombination are based on fairly restrictive assumptions about the nature of the underlying fitness landscapes .", "Here we use computer simulations to study the evolution of sex on fitness landscapes with different degrees of complexity and epistasis ...	[ "One of the biggest open questions in evolutionary biology is why sexual reproduction is so common despite its manifold costs .", "Many hypotheses have been proposed that can potentially explain the emergence and maintenance of sexual reproduction in nature , and currently the biggest challenge in the field is as...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "livestock", "medicine and health sciences", "vesicles", "pathology and laboratory medicine", "biological cultures", "vertebrates", "animals", "mammals", "protein expression", "microscopy", "caco-2 cells", "molecular biology techniques", "cellular structures and organelles", "digestive sys...	In Vitro Study of Taenia solium Postoncospheral Form	journal.pntd.0004396	null	[ [ "Human and porcine cysticercosis is a disease caused by the larval cestode Taenia solium which forms cysts in the muscles or the central nervous system of its intermediate host .", "Both humans and pigs can acquire cysticercosis through fecal-oral transmission by ingesting T . solium eggs released by the ...	[ "The transitional period between the oncosphere and the cysticercus of Taenia solium is the postoncospheral ( PO ) form , which has not yet been completely characterized .", "The aim of this work was to standardize a method to obtain T . solium PO forms by in vitro cultivation .", "We studied the morphology of ...	[ "Neurocysticercosis is caused by T . solium , which is a neglected disease .", "The postoncospheral ( PO ) form is an intermediate form between the oncosphere , which is the larva , and the fully developed cysticercus , which is a cyst with a scolex .", "The morphology , development , and protein and antigen ex...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology and life sciences", "agriculture" ]	A Multi-Trait, Meta-analysis for Detecting Pleiotropic Polymorphisms for Stature, Fatness and Reproduction in Beef Cattle	journal.pgen.1004198	null	[ [ "Polymorphisms that affect complex traits ( quantitative trait loci or QTL ) may affect multiple traits .", "This pleiotropy is the main cause of the genetic correlations between traits , although another possible cause of genetic correlation is linkage disequilibrium ( LD ) between the QTL for different ...	[ "Polymorphisms that affect complex traits or quantitative trait loci ( QTL ) often affect multiple traits .", "We describe two novel methods ( 1 ) for finding single nucleotide polymorphisms ( SNPs ) significantly associated with one or more traits using a multi-trait , meta-analysis , and ( 2 ) for distinguishin...	[ "We describe novel methods for finding significant associations between a genome wide panel of SNPs and multiple complex traits , and further for distinguishing between genes with effects on multiple traits and multiple linked genes affecting different traits .", "The method uses a meta-analysis based on estimate...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "tropical diseases", "geographical locations", "social sciences", "parasitic diseases", "health care", "farms", "neglected tropical diseases", "ethiopia", "africa", "public and occupational health", "infectious diseases", "zoonoses", "protozoan infections", ...	Barriers to access to visceral leishmaniasis diagnosis and care among seasonal mobile workers in Western Tigray, Northern Ethiopia: A qualitative study	journal.pntd.0006778	null	[ [ "Visceral leishmaniasis ( VL ) is a neglected tropical disease caused by the protozoan Leishmania donovani in the Indian subcontinent and East Africa , and Leishmania infantum in Latin America and the Mediterranean basin [1 , 2] .", "The bite of the sand fly transmits VL [2] .", "The World Health Orga...	[ "Ethiopia bears a high burden of visceral leishmaniasis ( VL ) .", "Early access to VL diagnosis and care improves clinical prognosis and reduces transmission from infected humans; however , significant obstacles exist .", "The approximate 250 , 000 seasonal mobile workers ( MW ) employed annually in northweste...	[ "Ethiopia bears a high burden of visceral leishmaniasis ( VL ) —a neglected tropical disease transmitted through the bite of a sand fly that disproportionately affects vulnerable populations .", "Without treatment , VL progresses , causing increasingly severe symptoms and ultimately death within two years , in mo...	2018
[ "Introduction", "Materials and methods", "Results", "Discussion", "Conclusions" ]	[ "medicine and health sciences", "diagnostic radiology", "pathology and laboratory medicine", "education", "neurocysticercosis", "sociology", "geographical locations", "tropical diseases", "social sciences", "parasitic diseases", "health care", "magnetic resonance imaging", "encephalitis", ...	Time trend of neurocysticercosis in children with seizures in a tertiary hospital of western Nepal	journal.pntd.0005605	null	[ [ "Neurocysticercosis ( NCC ) or intracerebral cysticercosis is a common parasitic ( zoonotic ) infection involving the nervous system of human beings resulting in seizure disorder worldwide [1 , 2] .", "NCC is endemic in parts of South America , Eastern Europe , the Indian subcontinent , South East Asia an...	[ "Neurocysticercosis is a common cause of seizure disorders in children of Western Nepal .", "The clinical presentation is variable .", "The incidence varies depending on the food habits and ethnicity of the population .", "The present study was undertaken with the objective of studying the mode of presentatio...	[ "Neurocysticercosis is a common parasitic infection of the central nervous system .", "It is caused by larval form of Taenia solium and it has been identified as a “Neglected Tropical Disease” endemic in south East Asia , including Nepal , by WHO .", "The clinical features in children are pleomorphic depending ...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "cancer genetics", "endocrinology", "reproductive endocrinology", "genetics", "biology" ]	Dysregulated Estrogen Receptor Signaling in the Hypothalamic-Pituitary-Ovarian Axis Leads to Ovarian Epithelial Tumorigenesis in Mice	journal.pgen.1004230	null	[ [ "Ovarian cancer is the most lethal malignancy of the female reproductive system and the fifth leading cause of cancer-related death among women [1] .", "Approximately 90% of malignant ovarian tumors are derived from either the ovarian surface epithelium ( OSE ) or fallopian tube epithelium ( FTE ) [2] .",...	[ "The etiology of ovarian epithelial cancer is poorly understood , mainly due to the lack of an appropriate experimental model for studying the onset and progression of this disease .", "We have created a mutant mouse model in which aberrant estrogen receptor alpha ( ERα ) signaling in the hypothalamic-pituitary-o...	[ "Ovarian cancer is currently the most lethal gynecological cancer in the United States .", "Multiple epidemiological studies indicate that women who take hormone replacement therapy , estrogen or estrogen with progesterone , peri- or postmenopause will have an increased chance of developing ovarian cancer .", "...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology/aging", "neuroscience/neuronal signaling mechanisms", "neuroscience/neuronal and glial cell biology", "genetics and genomics", "genetics and genomics/bioinformatics" ]	Profiling Synaptic Proteins Identifies Regulators of Insulin Secretion and Lifespan	journal.pgen.1000283	null	[ [ "Differentiation and organization of eukaryotic cells require regulated localization of specific proteins into subcellular compartments where they perform discrete functions .", "Global analysis of protein localization in yeast revealed that >40% of proteins localize to specific subcellular compartments [...	[ "Cells are organized into distinct compartments to perform specific tasks with spatial precision .", "In neurons , presynaptic specializations are biochemically complex subcellular structures dedicated to neurotransmitter secretion .", "Activity-dependent changes in the abundance of presynaptic proteins are tho...	[ "Cells are divided into multiple subcellular compartments that perform diverse functions .", "In neurons , synapses mediate transmission of information between cells and they comprise hundreds of proteins dedicated for this purpose .", "Changes in the protein composition of synapses are thought to produce chang...	2008
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "children", "medicine and health sciences", "pathology and laboratory medicine", "education", "sociology", "social sciences", "animals", "age groups", "signs and symptoms", "fleas", "medical risk factors", "families", "public and occupational health", "epidemiology", "...	Prevalence, intensity and risk factors of tungiasis in Kilifi County, Kenya II: Results from a school-based observational study	journal.pntd.0007326	null	[ [ "Sand flea disease ( tungiasis ) is a highly neglected parasitic skin disease which inflicts pain and suffering on millions of impoverished people in South America , the Caribbean and sub-Saharan Africa .", "Research on tungiasis is scant and most of the publications originate from South America [1] [2] ,...	[ "Awareness of the public health importance of tungiasis has been growing in East Africa in recent years , but data on epidemiological characteristics necessary for the planning and implementation of control measures do not exist .", "The work presented here was part of a larger cross-sectional study on the epidem...	[ "Tungiasis is a neglected tropical skin disease caused by penetrated sand fleas , the adult female of which burrows into the skin of the feet .", "The parasite rapidly expands its body size by a factor of 2000 .", "The growth causes immense itching , inflammation , pain and debilitation .", "The current lack ...	2019
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell death", "autophagic cell death", "lysosomes", "medicine and health sciences", "pathology and laboratory medicine", "intracellular pathogens", "dictyosteliomycota", "pathogens", "cell processes", "membrane proteins", "model organisms", "experimental organism systems", "cellular structur...	The ESCRT and autophagy machineries cooperate to repair ESX-1-dependent damage at the Mycobacterium-containing vacuole but have opposite impact on containing the infection	journal.ppat.1007501	null	[ [ "After phagocytic uptake , the closely related pathogenic bacteria Mycobacterium tuberculosis and M . marinum reside in an altered and maturation-arrested phagosome , thereby avoiding its toxic chemical environment [1] , but remaining protected from the cell-autonomous cytosolic defences [2] .", "This Myc...	[ "Phagocytic cells capture and kill most invader microbes within the bactericidal phagosome , but some pathogens subvert killing by damaging the compartment and escaping to the cytosol .", "To prevent the leakage of pathogen virulence and host defence factors , as well as bacteria escape , host cells have to conta...	[ "Upon uptake by a host cell , intracellular pathogens reside in a membranous compartment called phagosome .", "Within the phagosome , microbes are protected from the extracellular and cytosolic immune defences , whilst access to nutrients is limited .", "Some microbes gain access to the host cytosol by damaging...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell physiology", "cell death", "medicine and health sciences", "autophagic cell death", "pathology and laboratory medicine", "gene regulation", "hepacivirus", "pathogens", "cell processes", "endoplasmic reticulum", "microbiology", "viruses", "membrane fusion", "rna viruses", "cellular ...	HCV-induced autophagosomes are generated via homotypic fusion of phagophores that mediate HCV RNA replication	journal.ppat.1006609	null	[ [ "Autophagy is a catabolic process that is important for maintaining cellular homeostasis .", "It begins with the formation of membrane crescents termed phagophores or isolation membranes in the cytosol .", "The membranes of phagophores will subsequently expand to sequester part of the cytoplasm , resu...	[ "Hepatitis C virus ( HCV ) induces autophagy to promote its replication , including its RNA replication , which can take place on double-membrane vesicles known as autophagosomes .", "However , how HCV induces the biogenesis of autophagosomes and how HCV RNA replication complex may be assembled on autophagosomes ...	[ "Autophagy is a catabolic process that is important for maintaining cellular homeostasis .", "During autophagy , crescent membrane structures known as phagophores first appear in the cytoplasm , which then expand to form enclosed double-membrane vesicles known as autophagosomes .", "It has been shown that hepat...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "people and places", "organisms", "helminth infections", "medicine and health sciences", "protozoans", "parasitic intestinal diseases", "south america", "population dynamics", "biology and life sciences", "geographical locations", "population biology", "protozoan infections", "intestinal par...	Geospatial distribution of intestinal parasitic infections in Rio de Janeiro (Brazil) and its association with social determinants	journal.pntd.0005445	null	[ [ "Neglected tropical diseases , including intestinal parasitic infections , are a significant cause of morbidity and mortality in endemic countries [1] .", "Intestinal parasitic infections have particular relevance as they affect the poorest and most deprived areas in tropical and subtropical regions [1] ....	[ "Intestinal parasitic infections remain among the most common infectious diseases worldwide .", "This study aimed to estimate their prevalence and provide a detailed analysis of geographical distribution of intestinal parasites in the metropolitan region of Rio de Janeiro , considering demographic , socio-economi...	[ "Intestinal parasitic infections are considered indicators of health and socio-environmental vulnerability , and are associated with precarious sanitation and water quality of a country .", "They continue to pose a serious public health problem , especially in developing countries where sanitation is not expanded...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Polyfunctional HIV-Specific Antibody Responses Are Associated with Spontaneous HIV Control	journal.ppat.1005315	null	[ [ "Vaccine-mediated protection from HIV-1 infection has been observed in humans in association with extra-neutralizing antibody functions , including the ability to induce effector functions such as antibody-dependent cellular cytotoxicity ( ADCC ) [1] .", "Similarly , HIV-infected patients who are able to ...	[ "Elite controllers ( ECs ) represent a unique model of a functional cure for HIV-1 infection as these individuals develop HIV-specific immunity able to persistently suppress viremia .", "Because accumulating evidence suggests that HIV controllers generate antibodies with enhanced capacity to drive antibody-depend...	[ "A small fraction of HIV-infected subjects mount immune responses that are able to suppress viral replication such that virus cannot be detected in the blood .", "Understanding how these individuals , known as elite controllers , achieve this outcome may provide a model for strategies to treat or prevent HIV infe...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	A Hereditary Spastic Paraplegia Mouse Model Supports a Role of ZFYVE26/SPASTIZIN for the Endolysosomal System	journal.pgen.1003988	null	[ [ "Hereditary spastic paraplegias ( HSPs/SPGs ) are a heterogeneous group of neurodegenerative movement disorders , which present with progressive weakness and spasticity of the legs .", "The unifying neuropathology is a time- and length-dependent degeneration of cortical motoneuron axons .", "Whereas i...	[ "Hereditary spastic paraplegias ( HSPs ) are characterized by progressive weakness and spasticity of the legs because of the degeneration of cortical motoneuron axons .", "SPG15 is a recessively inherited HSP variant caused by mutations in the ZFYVE26 gene and is additionally characterized by cerebellar ataxia , ...	[ "Hereditary spastic paraplegias ( HSPs ) are inherited disorders characterized by progressive weakness and spasticity of the legs .", "In HSP patients , nerve fibers connecting cortical motoneurons with spinal cord neurons are progressively lost .", "HSP subtype 15 ( SPG15 ) is caused by mutations in ZFYVE26 , ...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "action potentials", "medicine and health sciences", "engineering and technology", "signal processing", "applied mathematics", "membrane potential", "vertebrates", "electrophysiology", "neuroscience", "animals", "jitter", "mammals", "simulation and modeling", "algorithms", "primates", ...	Unsupervised clustering of temporal patterns in high-dimensional neuronal ensembles using a novel dissimilarity measure	journal.pcbi.1006283	null	[ [ "Precisely timed spike patterns spanning multiple neurons are a ubiquitous feature of both spontaneous and stimulus-evoked brain network activity .", "Remarkably , not all patterns are generated with equal probability .", "Synaptic connectivity , shaped by development and experience , favors certain s...	[ "Temporally ordered multi-neuron patterns likely encode information in the brain .", "We introduce an unsupervised method , SPOTDisClust ( Spike Pattern Optimal Transport Dissimilarity Clustering ) , for their detection from high-dimensional neural ensembles .", "SPOTDisClust measures similarity between two ens...	[ "The brain encodes information by ensembles of neurons , and recent technological developments allow researchers to simultaneously record from over thousands of neurons .", "Neurons exhibit spontaneous activity patterns , which are constrained by experience and development , limiting the portion of state space th...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases/neglected tropical diseases", "public health and epidemiology/epidemiology", "public health and epidemiology/global health", "public health and epidemiology/infectious diseases", "infectious diseases/skin infections", "infectious diseases/protozoal infections", "infectious diseases/...	Risk Factors for Anthroponotic Cutaneous Leishmaniasis at the Household Level in Kabul, Afghanistan	journal.pntd.0000639	null	[ [ "After decades of war , Kabul , Afghanistan , became the world's largest focus of cutaneous leishmaniasis ( CL ) with an estimated annual incidence of 67 , 500 cases [1] .", "CL is a vector-borne protozoan disease that is characterized by cutaneous lesions which develop at the site of the insect bite [2] ...	[ "Kabul , Afghanistan , is the largest focus of anthroponotic cutaneous leishmaniasis ( ACL ) in the world .", "ACL is a protozoan disease transmitted to humans by the bite of phlebotomine sand flies .", "Although not fatal , ACL can lead to considerable stigmatization of affected populations .", "Using data f...	[ "Cutaneous leishmaniasis is a vector-borne protozoan disease that is characterized by cutaneous lesions which develop at the site of the insect bite .", "Lesions can vary in severity , clinical appearance , and time to cure; in a proportion of patients lesions can become chronic , leading to disfiguring mucosal l...	2010
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "neglected tropical diseases", "parasitic diseases" ]	The Transcriptome Analysis of Strongyloides stercoralis L3i Larvae Reveals Targets for Intervention in a Neglected Disease	journal.pntd.0001513	null	[ [ "Strongyloidiasis caused by Strongyloides stercoralis is a soil-transmitted helminthiasis distributed worldwide , affecting more than 100 million people , with endemic areas in Southeast Asia , Latin America , sub-Saharan Africa , and parts of the southeastern United States [1] , [2] .", "Recently , it wa...	[ "Strongyloidiasis is one of the most neglected diseases distributed worldwide with endemic areas in developed countries , where chronic infections are life threatening .", "Despite its impact , very little is known about the molecular biology of the parasite involved and its interplay with its hosts .", "Next g...	[ "Strongyloides stercoralis ( Nematoda ) is an important parasite of humans , causing Strongyloidiasis , considered as one of the most neglected diseases , affecting more than 100 million people worldwide .", "Chronic infections in endemic areas can be maintained for decades through the autoinfective cycle with th...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunology/immunomodulation", "immunology/immunity to infections", "infectious diseases/protozoal infections", "immunology/leukocyte activation" ]	CD4+ Natural Regulatory T Cells Prevent Experimental Cerebral Malaria via CTLA-4 When Expanded In Vivo	journal.ppat.1001221	null	[ [ "Severe malaria syndromes , including cerebral malaria ( CM ) , claim the lives of approximately 900 , 000 people annually , mostly children under the age of 5 living in sub-Saharan Africa [1] .", "The mechanisms of CM pathogenesis remain poorly understood , since studies in humans are often restricted to...	[ "Studies in malaria patients indicate that higher frequencies of peripheral blood CD4+ Foxp3+ CD25+ regulatory T ( Treg ) cells correlate with increased blood parasitemia .", "This observation implies that Treg cells impair pathogen clearance and thus may be detrimental to the host during infection .", "In C57B...	[ "Severe malaria can kill people via complications such as cerebral malaria .", "The number of malaria parasites in the body is a major determinant of whether a patient will develop severe disease .", "T cells are thought to help control parasite numbers , but regulatory T cells , which are known to dampen immun...	2010
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Synaptic Plasticity in Neural Networks Needs Homeostasis with a Fast Rate Detector	journal.pcbi.1003330	null	[ [ "The awake cortex is constantly active , even in the absence of external inputs .", "This baseline activity , commonly referred to as the “background state” , is characterized by low synchrony at the population level and highly irregular firing of single neurons .", "While the direct implications of t...	[ "Hebbian changes of excitatory synapses are driven by and further enhance correlations between pre- and postsynaptic activities .", "Hence , Hebbian plasticity forms a positive feedback loop that can lead to instability in simulated neural networks .", "To keep activity at healthy , low levels , plasticity must...	[ "Learning and memory in the brain are thought to be mediated through Hebbian plasticity .", "When a group of neurons is repetitively active together , their connections get strengthened .", "This can cause co-activation even in the absence of the stimulus that triggered the change .", "To avoid run-away behav...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases/bacterial infections", "infectious diseases/neglected tropical diseases", "infectious diseases" ]	Warmer Weather Linked to Tick Attack and Emergence of Severe Rickettsioses	journal.pntd.0000338	null	[ [ "The recent outbreak of Chikungunya virus in the Indian Ocean Islands and India [1] that reached Europe in 2007 [2] , has illustrated the current medical importance of globalising vector-transmitted infections [3] .", "The impact of ticks on human public health was recognised with the emergence of Lyme di...	[ "The impact of climate on the vector behaviour of the worldwide dog tick Rhipicephalus sanguineus is a cause of concern .", "This tick is a vector for life-threatening organisms including Rickettsia rickettsii , the agent of Rocky Mountain spotted fever , R . conorii , the agent of Mediterranean spotted fever , a...	[ "The impact of climate on the behaviour of the worldwide dog tick Rhipicephalus sanguineus is a cause of concern .", "This tick is a vector for life-threatening organisms including Rickettsia rickettsii , the agent of Rocky Mountain spotted fever , R . conorii , the agent of Mediterranean spotted fever , and the ...	2008
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "action potentials", "medicine and health sciences", "classical mechanics", "vibration", "membrane potential", "social sciences", "vertebrates", "electrophysiology", "neuroscience", "animals", "mammals", "animal anatomy", "damage mechanics", "zoology", "mechanoreceptors", "bending", ...	Dynamic cues for whisker-based object localization: An analytical solution to vibration during active whisker touch	journal.pcbi.1006032	null	[ [ "Vibration of tactile sensors contributes to perception of surface texture and object identification in humans [1 , 2] , prosthetic devices [3 , 4] , and potentially rodents [5–8] .", "Vibration could also be an important cue for determining the distance to objects using swept sensors .", "This method...	[ "Vibrations are important cues for tactile perception across species .", "Whisker-based sensation in mice is a powerful model system for investigating mechanisms of tactile perception .", "However , the role vibration plays in whisker-based sensation remains unsettled , in part due to difficulties in modeling t...	[ "Vibrations play an important role in the sense of touch in many species , but exactly how they influence touch perception remains mysterious .", "An important reason for this mystery is the difficulty in measuring vibrations during touch .", "Mice are a powerful model system for investigating touch perception ...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "mycology", "fungal genetics", "genetics", "biology and life sciences", "molecular genetics", "molecular biology" ]	PRO40 Is a Scaffold Protein of the Cell Wall Integrity Pathway, Linking the MAP Kinase Module to the Upstream Activator Protein Kinase C	journal.pgen.1004582	null	[ [ "Mitogen-activated protein kinase ( MAPK ) cascades are central components of signaling networks in all eukaryotic organisms [1]–[3] .", "They consist of a three-tiered module containing a MAPK kinase kinase ( MAPKKK ) , a MAPK kinase ( MAPKK ) , and a MAPK , each activating the subsequent one via phospho...	[ "Mitogen-activated protein kinase ( MAPK ) pathways are crucial signaling instruments in eukaryotes .", "Most ascomycetes possess three MAPK modules that are involved in key developmental processes like sexual propagation or pathogenesis .", "However , the regulation of these modules by adapters or scaffolds is...	[ "The specific response to environmental cues is crucial for cell differentiation and is often mediated by highly conserved eukaryotic MAP kinase ( MAPK ) pathways .", "How these pathways react specifically to huge numbers of different cues is still unclear , and current literature about adapter and scaffolding pr...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases", "medicine and health sciences", "emerging infectious diseases", "pathology and laboratory medicine", "host-pathogen interactions", "medical microbiology", "microbial pathogens", "biology and life sciences", "microbiology", "pathogenesis", "bacterial pathogens" ]	Mycobacterium ulcerans Fails to Infect through Skin Abrasions in a Guinea Pig Infection Model: Implications for Transmission	journal.pntd.0002770	null	[ [ "Buruli ulcer , a severe cutaneous infection caused by the environmental pathogen Mycobacterium ulcerans is a major cause of morbidity in West and Central Africa [1] , [2] .", "The disease begins with a painless nodule that can lead to severe ulceration .", "Though mortality is low , morbidity is extr...	[ "Transmission of M . ulcerans , the etiological agent of Buruli ulcer , from the environment to humans remains an enigma despite decades of research .", "Major transmission hypotheses propose", "1 ) that M . ulcerans is acquired through an insect bite or", "2 ) that bacteria enter an existing wound through ex...	[ "Buruli ulcer , a severe skin disease in West and Central Africa results in significant disability .", "The causative bacterium , M . ulcerans has been detected in many aquatic sources , but how bacteria enter the skin is an enigma .", "Two major hypotheses for infection are", "1 ) that bacteria are injected ...	2014
[ "Introduction", "Model", "Results", "Discussion" ]	[ "ecology and environmental sciences", "predator-prey dynamics", "population dynamics", "systems science", "mathematics", "population biology", "thermodynamics", "computer and information sciences", "ecosystems", "dynamical systems", "free energy", "community ecology", "physics", "populatio...	A phase transition induces chaos in a predator-prey ecosystem with a dynamic fitness landscape	journal.pcbi.1005644	null	[ [ "In many natural ecosystems , at least one constituent species evolves quickly enough relative to its population growth that the two effects become interdependent .", "This phenomenon can occur when selection forces are tied to such sudden environmental effects as algal blooms or flooding [1] , or it can ...	[ "In many ecosystems , natural selection can occur quickly enough to influence the population dynamics and thus future selection .", "This suggests the importance of extending classical population dynamics models to include such eco-evolutionary processes .", "Here , we describe a predator-prey model in which th...	[ "Evolution is usually thought to occur very gradually , taking millennia or longer in order to appreciably affect a species' survival mechanisms .", "Conversely , demographic shifts due to predator invasion or environmental change can occur relatively quickly , creating abrupt and lasting effects on a species sur...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "neurological disorders/prion diseases" ]	Beyond PrPres Type 1/Type 2 Dichotomy in Creutzfeldt-Jakob Disease	journal.ppat.1000029	null	[ [ "Transmissible spongiform encephalopathies ( TSE ) are neurodegenerative disorders affecting a large spectrum of mammalian species that share similar characteristics , including a long incubation period ( which in man may be measured in decades ) and a progressive clinical course resulting in death [1] .", ...	[ "Sporadic Creutzfeldt-Jakob disease ( sCJD ) cases are currently subclassified according to the methionine/valine polymorphism at codon 129 of the PRNP gene and the proteinase K ( PK ) digested abnormal prion protein ( PrPres ) identified on Western blotting ( type 1 or type 2 ) .", "These biochemically distinct ...	[ "Prion diseases are transmissible neurodegenerative disorders characterized by accumulation of an abnormal isoform ( PrPSc ) of a host-encoded protein ( PrPC ) in affected tissues .", "According to the prion hypothesis , PrPSc alone constitutes the infectious agent .", "Sporadic Creutzfeldt-Jakob disease ( sCJD...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "chemical compounds", "caulobacter", "gene regulation", "messenger rna", "carbohydrates", "organic compounds", "xylose", "prokaryotic models", "model organisms", "mitochondria", "bioenergetics", "cellular structures and organelles", "bacteria", "research and analysis methods", "small int...	Human Cells Require Non-stop Ribosome Rescue Activity in Mitochondria	journal.pgen.1005964	null	[ [ "The presence of a stop codon at the end of an open reading frame signals that the nascent protein is complete .", "Decoding of the stop codon by a release factor results in peptidyl-tRNA hydrolysis , releasing the completed protein and allowing the ribosome to be recycled [1] .", "Specific contacts b...	[ "Bacteria use trans-translation and the alternative rescue factors ArfA ( P36675 ) and ArfB ( Q9A8Y3 ) to hydrolyze peptidyl-tRNA on ribosomes that stall near the 3' end of an mRNA during protein synthesis .", "The eukaryotic protein ICT1 ( Q14197 ) is homologous to ArfB .", "In vitro ribosome rescue assays of ...	[ "Ribosomes can stall during protein synthesis on truncated or damaged mRNAs that lack a stop codon .", "In bacteria , these “non-stop” ribosomes are rescued by trans-translation or by an alternative rescue factor , ArfA or ArfB .", "Most eukaryotes do not have trans-translation , but mammals have a homolog of A...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "dna-binding proteins", "genome analysis", "protein structure", "sequence motif analysis", "research and analysis methods", "sequence analysis", "sequence alignment", "bioinformatics", "proteins", "biological databases", "gene ontologies", "molecular biology", "protein structure comparison",...	Widespread position-specific conservation of synonymous rare codons within coding sequences	journal.pcbi.1005531	null	[ [ "Most amino acids are encoded by multiple codons , but these synonymous codons are not used with equal frequency .", "Rare codons generally correlate with lower levels of cognate tRNA , or weaker codon:anticodon interactions [1 , 2] .", "As a result , rare codons are generally associated with slower t...	[ "Synonymous rare codons are considered to be sub-optimal for gene expression because they are translated more slowly than common codons .", "Yet surprisingly , many protein coding sequences include large clusters of synonymous rare codons .", "Rare codons at the 5’ terminus of coding sequences have been shown t...	[ "Proteins are long linear polymers that must fold into complex three-dimensional shapes in order to carry out their cellular functions .", "Every protein is synthesized by the ribosome , which decodes each trinucleotide codon in an mRNA coding sequence in order to select the amino acid residue that will occupy ea...	2017
[ "Introduction", "Methods and materials", "Results", "Discussion" ]	[ "medicine and health sciences", "immune physiology", "enzyme-linked immunoassays", "pathology and laboratory medicine", "microbial cultures", "pathogens", "vibrio", "immunology", "tropical diseases", "microbiology", "biological cultures", "bacterial diseases", "crystals", "vibrio cholerae"...	Development of a new dipstick (Cholkit) for rapid detection of Vibrio cholerae O1 in acute watery diarrheal stools	journal.pntd.0006286	null	[ [ "Cholera is an acute watery diarrheal disease caused mainly by Vibrio cholerae serogroup O1 and less commonly by V . cholerae O139 .", "Cholera can lead to severe diarrhea and death if untreated .", "V . cholerae O1 is transmitted through fecal-oral contamination , and cholera is thus predominantly as...	[ "Recognizing cholera cases early , especially in the initial phase of an outbreak and in areas where cholera has not previously circulated , is a high public health priority .", "Laboratory capacity in such settings is often limited .", "To address this , we have developed a rapid diagnostic test ( RDT ) termed...	[ "Cholera is a severely dehydrating diarrheal disease that can lead to death if remains untreated .", "The incidence of case fatality is higher at the beginning of the outbreak .", "Diagnosis of cholera in the early stage of outbreak is a high public health priority .", "Although countries facing complex emerg...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "viral latency", "infectious diseases", "virology", "viruses and cancer", "biology", "microbiology", "viral diseases", "viral replication" ]	CTCF and Rad21 Act as Host Cell Restriction Factors for Kaposi's Sarcoma-Associated Herpesvirus (KSHV) Lytic Replication by Modulating Viral Gene Transcription	journal.ppat.1003880	null	[ [ "Infection with Kaposi's sarcoma-associated herpesvirus ( KSHV , HHV8 ) is causally associated with Kaposi's sarcoma ( KS ) , primary effusion lymphoma ( PEL ) and multicentric Castleman's disease ( for a review , see reference [1] ) .", "KSHV maintains a persistent latent infection as an episome in B lym...	[ "Kaposi's sarcoma-associated herpesvirus ( KSHV ) is a human herpesvirus that causes Kaposi's sarcoma and is associated with the development of lymphoproliferative diseases .", "KSHV reactivation from latency and virion production is dependent on efficient transcription of over eighty lytic cycle genes and viral ...	[ "Kaposi's sarcoma-associated herpesvirus ( KSHV ) is a human virus that causes Kaposi's sarcoma and lymphoma .", "KSHV establishes a lifelong infection in B lymphocytes , and persists in a latent form as circular DNA molecules .", "Reactivation and replication yield infectious virions , allowing transmission an...	2014
[ "Introduction", "Results and Discussion", "Materials and Methods" ]	[ "genome evolution", "population genetics", "microbiology", "telomeres", "model organisms", "dna", "genome complexity", "transposons", "chromosome biology", "protozoan models", "dna amplification", "biology", "molecular biology", "nucleic acids", "genetics", "genomics", "molecular cel...	The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes	journal.pbio.1001473	With more chromosomes than any other sequenced genome, the macronuclear genome of Oxytricha trifallax has a unique and complex architecture, including alternative fragmentation and predominantly single-gene chromosomes.	[ [ "Oxytricha trifallax is a distinctive ciliate [1]—an ancient lineage of protists named for their coats of cilia .", "Like all ciliates , Oxytricha has two types of nuclei: a micronucleus , a germline nucleus that is largely transcriptionally inactive during vegetative growth , and a macronucleus , which i...	[ "The macronuclear genome of the ciliate Oxytricha trifallax displays an extreme and unique eukaryotic genome architecture with extensive genomic variation .", "During sexual genome development , the expressed , somatic macronuclear genome is whittled down to the genic portion of a small fraction ( ∼5% ) of its pr...	[ "The macronuclear genome of the ciliate Oxytricha trifallax , contained in its somatic nucleus , has a unique genome architecture .", "Unlike its diploid germline genome , which is transcriptionally inactive during normal cellular growth , the macronuclear genome is fragmented into at least 16 , 000 tiny ( ∼3 . 2...	2013
[ "Introduction", "Results/Discussion", "Methods" ]	[]	Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement	journal.pcbi.1004404	null	[ [ "RNA interference ( RNAi ) is a key cellular mechanism involved in the regulation of gene expression and the defense against viruses[1 , 2] .", "As the central component of RNAi , the RNA induced silencing complex ( RISC ) mediates the sequence-specific recognition and inhibition of target mRNA[3 , 4] .",...	[ "Argonaute ( Ago ) proteins and microRNAs ( miRNAs ) are central components in RNA interference , which is a key cellular mechanism for sequence-specific gene silencing .", "Despite intensive studies , molecular mechanisms of how Ago recognizes miRNA remain largely elusive .", "In this study , we propose a two-...	[ "In RNA interference , Argonaute proteins and microRNAs together form the functional core that regulates the gene expression with high sequence specificity .", "Elucidating the detailed mechanism of molecular recognition between Argonaute proteins and microRNAs is thus important not only for the fundamental under...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "biotechnology", "medicine and health sciences", "protein interactions", "named entity recognition", "text mining", "genome analysis", "pharmacology", "information technology", "extraction techniques", "genomic medicine", "research and analysis methods", "computer and information sciences", ...	A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts	journal.pcbi.1005962	null	[ [ "Text mining has become a widespread approach to identify and extract information from unstructured text .", "Text mining is used to extract facts and relationships in a structured form that can be used to annotate specialized databases , to transfer knowledge between domains and more generally within bus...	[ "Across academia and industry , text mining has become a popular strategy for keeping up with the rapid growth of the scientific literature .", "Text mining of the scientific literature has mostly been carried out on collections of abstracts , due to their availability .", "Here we present an analysis of 15 mil...	[ "Text mining has become an integral part of all fields in science .", "Owing to the large number of articles published every day , it is necessary to employ automated systems to assist in curation , knowledge management and discovery .", "To date , most systems make use of information collected from abstracts o...	2018
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "virology/emerging viral diseases", "virology" ]	Isolation of Genetically Diverse Marburg Viruses from Egyptian Fruit Bats	journal.ppat.1000536	null	[ [ "Viruses of the Marburgvirus and Ebolavirus genera ( family Filoviridae ) cause outbreaks of hemorrhagic fever in Africa characterized by person-to-person spread and high case fatality .", "Humans have on occasion acquired infection from contact with tissues of diseased nonhuman primates and perhaps herbi...	[ "In July and September 2007 , miners working in Kitaka Cave , Uganda , were diagnosed with Marburg hemorrhagic fever .", "The likely source of infection in the cave was Egyptian fruit bats ( Rousettus aegyptiacus ) based on detection of Marburg virus RNA in 31/611 ( 5 . 1% ) bats , virus-specific antibody in bat ...	[ "Marburg virus , similar to its close cousin Ebola virus , can cause large outbreaks of hemorrhagic fever ( HF ) in rural Africa with case fatalities approaching 90% .", "For decades , a long-standing enigma has been the identity of the natural reservoir of this deadly virus .", "In this report , we identify th...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "evolutionary biology/animal genetics", "cardiovascular disorders/myopathies", "infectious diseases/neglected tropical diseases", "evolutionary biology", "molecular biology", "immunology/autoimmunity", "cardiovascular disorders/heart failure" ]	Trypanosoma cruzi in the Chicken Model: Chagas-Like Heart Disease in the Absence of Parasitism	journal.pntd.0001000	null	[ [ "Trypanosoma cruzi infection ( American Trypanosomiasis ) is an endemic ailment transmitted by hematophagous ( Reduviid:Triatominae ) bugs , by blood transfusion and transplacentally from the mother to offspring [1] .", "In pregnant women T . cruzi infections may lead to fetal complications , with desorpt...	[ "The administration of anti-trypanosome nitroderivatives curtails Trypanosoma cruzi infection in Chagas disease patients , but does not prevent destructive lesions in the heart .", "This observation suggests that an effective treatment for the disease requires understanding its pathogenesis .", "To understand t...	[ "The Trypanosoma cruzi acute infections can be asymptomatic but approximately one third of the chronically infected cases may present Chagas disease .", "Parasite persistence and autoimmunity are theories trying to explain the clinical and pathological manifestations of Chagas disease in the heart and the digesti...	2011
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "blood cells", "white blood cells", "immune cells", "cell biology", "animal cells", "t cells", "biology and life sciences", "cellular types", "immunology" ]	Quantification of HTLV-1 Clonality and TCR Diversity	journal.pcbi.1003646	null	[ [ "How can we estimate diversity from a population sample ?", "In viral infections , the number of viral variants and their population structure inform our understanding of disease pathogenesis , and can suggest treatment strategies [1] , [2] .", "In immunology , the repertoire and population structure ...	[ "Estimation of immunological and microbiological diversity is vital to our understanding of infection and the immune response .", "For instance , what is the diversity of the T cell repertoire ?", "These questions are partially addressed by high-throughput sequencing techniques that enable identification of imm...	[ "The “unseen species problem” is ubiquitous in biology and is frequently encountered outside its original setting in population ecology .", "For example , the human retrovirus HTLV-1 persists within hosts in multiple , genetically identical clones of infected cells .", "However , the number of clones in one hos...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "animal models of infection", "virulence factors and mechanisms", "viral immune evasion", "virology", "biology", "microbiology" ]	Norovirus Regulation of the Innate Immune Response and Apoptosis Occurs via the Product of the Alternative Open Reading Frame 4	journal.ppat.1002413	null	[ [ "Collectively , the innate and adaptive immune systems result in a strong evolutionary pressure on pathogens to develop countermeasures to allow their continued existence .", "Therefore pathogens , including viruses , have evolved a multitude of mechanisms for evading the host response to infection , ofte...	[ "Small RNA viruses have evolved many mechanisms to increase the capacity of their short genomes .", "Here we describe the identification and characterization of a novel open reading frame ( ORF4 ) encoded by the murine norovirus ( MNV ) subgenomic RNA , in an alternative reading frame overlapping the VP1 coding r...	[ "This report describes the identification and characterization of a novel protein of unknown function encoded by a mouse virus genetically similar to human noroviruses .", "This gene is unique to the mouse virus and occupies the same part of the genome that codes for the major capsid protein .", "The protein th...	2011
[ "Introduction", "Results/Discussion", "Methods" ]	[ "medicine", "public health and epidemiology", "infectious disease epidemiology", "population dynamics", "population genetics", "hepatitis", "effective population size", "population biology", "epidemiological methods", "hepatitis c", "infectious diseases", "epidemiology", "biology", "diseas...	Integrating Phylodynamics and Epidemiology to Estimate Transmission Diversity in Viral Epidemics	journal.pcbi.1002876	null	[ [ "Mathematical epidemiology describes the spread of infectious diseases and aims to aid in the design of effective public health interventions [1]–[3] .", "Central to this endeavour is the basic reproductive number ( R0 ) of an infectious disease , the mean number of secondary infections per primary infect...	[ "The epidemiology of chronic viral infections , such as those caused by Hepatitis C Virus ( HCV ) and Human Immunodeficiency Virus ( HIV ) , is affected by the risk group structure of the infected population .", "Risk groups are defined by each of their members having acquired infection through a specific behavio...	[ "To design strategies that efficiently mitigate an epidemic requires estimates of how many people each carrier is likely to infect , what is the variation of this number among infections , and what is the time needed for these transmissions to take place .", "The disciplines of epidemiology and population genetic...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medical microbiology", "biology", "microbiology" ]	Unique Cell Adhesion and Invasion Properties of Yersinia enterocolitica O:3, the Most Frequent Cause of Human Yersiniosis	journal.ppat.1002117	null	[ [ "Yersinia enterocolitica is a common gram-negative zoonotic pathogen that is able to grow in the environment and cause enteric diseases ( Yersiniosis ) , ranging from enteritis , severe diarrhea , mesenteric lymphadenitis , hepatic or splenic abscesses to postinfectious extraintestinal sequelae such as reacti...	[ "Many enteric pathogens are equipped with multiple cell adhesion factors which are important for host tissue colonization and virulence .", "Y . enterocolitica , a common food-borne pathogen with invasive properties , uses the surface proteins invasin and YadA for host cell binding and entry .", "In this study ...	[ "Bacterial infections are generally initiated by molecular interactions that occur between the pathogen and its host cell .", "These interactions are usually mediated by adhesion and invasion factors exposed from the surface of the bacteria which are necessary for the colonization of host tissues and fundamental ...	2011
[ "Introduction", "Results", "Discussion", "Material and methods" ]	[ "enzymes", "metabolic networks", "enzymology", "simulation and modeling", "metabolites", "network analysis", "enzyme metabolism", "molecular biology techniques", "enzyme chemistry", "research and analysis methods", "secondary metabolites", "sequence analysis", "computer and information scien...	RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor	journal.pcbi.1006541	null	[ [ "Genome-scale metabolic models ( GEMs ) are comprehensive in silico representations of the complete set of metabolic reactions that take place in a cell [1] .", "GEMs can be used to understand and predict how organisms react to variations on genetic and environmental parameters [2] .", "Recent studies...	[ "RAVEN is a commonly used MATLAB toolbox for genome-scale metabolic model ( GEM ) reconstruction , curation and constraint-based modelling and simulation .", "Here we present RAVEN Toolbox 2 . 0 with major enhancements , including:", "( i ) de novo reconstruction of GEMs based on the MetaCyc pathway database;",...	[ "Cellular metabolism is a large and complex network .", "Hence , investigations of metabolic networks are aided by in silico modelling and simulations .", "Metabolic networks can be derived from whole-genome sequences , through identifying what enzymes are present and connecting these to formalized chemical rea...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Identification of a Novel Regulatory Mechanism of Nutrient Transport Controlled by TORC1-Npr1-Amu1/Par32	journal.pgen.1005382	null	[ [ "Proteins of the Mep-Amt-Rh superfamily including the human Rhesus factors mediate the transmembrane transport of ammonium from bacteria to mammals [1–4] .", "Ammonium , hereafter referring to the sum of NH4+ and NH3 , is a key nitrogen source for microorganisms and plants whereas it is mainly documented ...	[ "Fine-tuning the plasma-membrane permeability to essential nutrients is fundamental to cell growth optimization .", "Nutritional signals including nitrogen availability are integrated by the TORC1 complex which notably regulates arrestin-mediated endocytosis of amino-acid transporters .", "Ammonium is a ubiquit...	[ "Cells have evolved a variety of mechanisms to control the permeability of the plasma membrane to face environmental perturbations .", "Transcriptional regulation , endocytosis , gating and activity control of channels and transporters enable global or specific responses to stressful conditions and focused variat...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "kala-azar", "biogeography", "medicine and health sciences", "ecology and environmental sciences", "population genetics", "tropical diseases", "geographical locations", "parasitic diseases", "parasitic protozoans", "protozoans", "leishmania", "neglected tropical diseases", "molecular biology...	Single locus genotyping to track Leishmania donovani in the Indian subcontinent: Application in Nepal	journal.pntd.0005420	null	[ [ "Visceral Leishmaniasis ( VL ) is a neglected tropical disease caused by parasites of the Leishmania donovani species complex , which are transmitted by the bite of phlebotomine sand flies .", "WHO estimates that annually , 300 million people worldwide are at risk of VL [1] .", "In the Indian subconti...	[ "We designed a straightforward method for discriminating circulating Leishmania populations in the Indian subcontinent ( ISC ) .", "Research on transmission dynamics of visceral leishmaniasis ( VL , or Kala-azar ) was recently identified as one of the key research priorities for elimination of the disease in the ...	[ "Visceral Leishmaniasis ( VL ) or Kala-azar is a life-threatening neglected tropical disease that annually affects half a million people worldwide .", "In the Indian subcontinent ( India , Nepal , Bangladesh ) , the disease is caused by infection with the protozoan parasite Leishmania donovani , which is transmit...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public health and epidemiology", "environmental health", "epidemiology", "environmental epidemiology", "public health" ]	Podoconiosis in East and West Gojam Zones, Northern Ethiopia	journal.pntd.0001744	null	[ [ "Podoconiosis is a non- infectious elephantiasis distinct from lymphatic filariasis that affects barefoot individuals exposed to red clay soil of volcanic origin .", "In particular , podoconiosis is prevalent among barefoot subsistence farmers that live and work in these areas [1] .", "Even though the...	[ "Podoconiosis is a neglected tropical disease ( NTD ) that is prevalent in red clay soil-covered highlands of tropical Africa , Central and South America , and northern India .", "It is estimated that up to one million cases exist in Ethiopia .", "This study aimed to estimate the prevalence of podoconiosis in E...	[ "Podoconiosis is non-infectious elephantiasis that affects barefoot people that have prolonged exposure to red clay soil .", "It is common in tropical Africa , central America and northern India .", "Podoconiosis presents as bilateral below knee swelling .", "Podoconiosis can be both prevented and controlled ...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "bacteriology", "bacterial physiology", "molecular cell biology", "cell division", "virology", "cytokinesis", "genetics", "host-pathogen interaction", "microbiology", "biology", "microbial growth and development", "viral replication", "gene function" ]	The Kil Peptide of Bacteriophage λ Blocks Escherichia coli Cytokinesis via ZipA-Dependent Inhibition of FtsZ Assembly	journal.pgen.1004217	null	[ [ "The replication and lytic functions of bacteriophage λ rapidly diminish Escherichia coli viability and lead to ultimate host death by lysis [1] .", "Decades-old research uncovered a secondary mode of λ-induced host cell death using a defective prophage containing only the immunity region and the PL opero...	[ "Assembly of the essential , tubulin-like FtsZ protein into a ring-shaped structure at the nascent division site determines the timing and position of cytokinesis in most bacteria and serves as a scaffold for recruitment of the cell division machinery .", "Here we report that expression of bacteriophage λ kil , e...	[ "Bacterial antibiotic resistance is a serious concern , particularly its role in hospital-acquired infection .", "Viruses that infect bacteria ( bacteriophage ) can kill their host , and some prevent the bacterial cell from reproducing during that process .", "Since their discovery , phage have been considered ...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Prolyl Oligopeptidase from the Blood Fluke Schistosoma mansoni: From Functional Analysis to Anti-schistosomal Inhibitors	journal.pntd.0003827	null	[ [ "Schistosomiasis , also known as bilharzia , is caused by blood flukes of the genus Schistosoma with approximately 240 million people infected [1] .", "Three species of schistosome principally infect humans: Schistosoma haematobium , which causes urinary schistosomiasis , and S . japonicum and S . mansoni...	[ "Blood flukes of the genus Schistosoma cause schistosomiasis , a parasitic disease that infects over 240 million people worldwide , and for which there is a need to identify new targets for chemotherapeutic interventions .", "Our research is focused on Schistosoma mansoni prolyl oligopeptidase ( SmPOP ) from the ...	[ "Schistosomiasis ( bilharzia ) is a major global health problem caused by the schistosome flatworm which lives in the bloodstream .", "Treatment and control of the disease relies on a single drug , and should resistance emerge , there would be increased pressure to discover new drug targets .", "Proteolytic enz...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "developmental biology/germ cells", "molecular biology/histone modification", "developmental biology/developmental evolution", "cell biology/developmental molecular mechanisms", "genetics and genomics/epigenetics", "genetics and genomics/chromosome biology", "evolutionary biology/developmental molecular...	Female Meiotic Sex Chromosome Inactivation in Chicken	journal.pgen.1000466	null	[ [ "During meiotic prophase , homologous chromosomes pair and are held together by the synaptonemal complex ( reviewed in [1] ) .", "In spermatocytes of male mammals , the heterologous X and Y chromosomes pair and synapse only in small pseudoautosomal regions ( PARs ) .", "The presence of the largely uns...	[ "During meiotic prophase in male mammals , the heterologous X and Y chromosomes remain largely unsynapsed , and meiotic sex chromosome inactivation ( MSCI ) leads to formation of the transcriptionally silenced XY body .", "In birds , the heterogametic sex is female , carrying Z and W chromosomes ( ZW ) , whereas ...	[ "Meiosis is a sequence of two specialized cell divisions during which haploid gametes are generated .", "During meiotic prophase , homologous chromosomes pair and recombine to allow proper separation of chromosomes during the first meiotic division .", "The pairing mechanism is challenged by the presence of the...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/gene expression", "genetics and genomics/bioinformatics", "pharmacology/drug development", "cardiovascular disorders/cardiovascular pharmacology", "genetics and genomics/genetics of disease", "pharmacology/personalized medicine", "physiology/renal, fluid, and electrolyte physiolog...	Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model	journal.pcbi.1000938	null	[ [ "Despite the advantages gained from drug therapy in medicine , drug development has historically presented an expensive and frequently perplexing challenge for researchers .", "Identifying useful drug targets for treating disease and matching them to chemical compounds that can elicit the desired effect t...	[ "Recent advances in structural bioinformatics have enabled the prediction of protein-drug off-targets based on their ligand binding sites .", "Concurrent developments in systems biology allow for prediction of the functional effects of system perturbations using large-scale network models .", "Integration of th...	[ "Pharmaceutical science is only beginning to scratch the surface on the exact mechanisms of drug action that lead to a drug's breadth of patient responses , both intended and side effects .", "Decades of clinical trials , molecular studies , and more recent computational analysis have sought to characterize the i...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm	journal.pcbi.1004470	null	[ [ "Mutations in protein sequences that lead to altered functions have been found to drive or participate in many human diseases [1 , 2] .", "An important goal of molecular biology is to understand functional changes upon single-point mutations in proteins .", "This is a challenging task for both wet and...	[ "An important goal in molecular biology is to understand functional changes upon single-point mutations in proteins .", "Doing so through a detailed characterization of structure spaces and underlying energy landscapes is desirable but continues to challenge methods based on Molecular Dynamics .", "In this pape...	[ "Important human diseases are linked to mutations in proteins .", "One such protein , Ras , undergoes mutations in over 25% of human cancers .", "Its biological activity involves switching between two distinct states , and several oncogenic mutations affect this switching .", "Despite significant investigatio...	2015
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "computational biology/systems biology" ]	Integrative Features of the Yeast Phosphoproteome and Protein–Protein Interaction Map	journal.pcbi.1001064	null	[ [ "Protein phosphorylation is a reversible , ubiquitous , and fundamentally post-translational modification ( PTM ) that regulates a variety of biological processes; one of its critical roles is the control of protein signaling [1]–[3] .", "Recent advances in mass-spectrometry ( MS ) –based technologies and...	[ "Following recent advances in high-throughput mass spectrometry ( MS ) –based proteomics , the numbers of identified phosphoproteins and their phosphosites have greatly increased in a wide variety of organisms .", "Although a critical role of phosphorylation is control of protein signaling , our understanding of ...	[ "To date , high-throughput proteome technologies have revealed that hundreds to thousands of proteins in each of many organisms are phosphorylated under the appropriate environmental conditions .", "A critical role of phosphorylation is control of protein signaling .", "However , only a fraction of the identifi...	2011
[ "Introduction", "Results", "Discussion", "Material and methods" ]	[ "biotechnology", "plant anatomy", "nuclear staining", "cell cycle and cell division", "cell processes", "brassica", "hormones", "pollen", "plant science", "model organisms", "plant hormones", "genetically modified plants", "experimental organism systems", "plants", "flowering plants", ...	Auxin production in diploid microsporocytes is necessary and sufficient for early stages of pollen development	journal.pgen.1007397	null	[ [ "Life cycle of eukaryotes alternates between haploid and diploid generations .", "The alternation of generations is initiated by meiosis ( 2n to 1n ) and gamete fusion ( 1n to 2n ) [1] .", "In land plants , the multicellular diploid generation is called sporophyte , whereas the multicellular haploid o...	[ "Gametophytic development in Arabidopsis depends on nutrients and cell wall materials from sporophytic cells .", "However , it is not clear whether hormones and signaling molecules from sporophytic tissues are also required for gametophytic development .", "Herein , we show that auxin produced by the flavin mon...	[ "Plant life cycle alternates between the diploid sporophyte generation and the haploid gametophyte generation .", "Understanding the molecular mechanisms governing the generation alternation impacts fundamental plant biology and plant breeding .", "It is known that the development of haploid generation in vascu...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	A Voltage-Gated Calcium Channel Regulates Lysosomal Fusion with Endosomes and Autophagosomes and Is Required for Neuronal Homeostasis	journal.pbio.1002103	A voltage-gated calcium channel required for neurotransmitter release also regulates the fusion of neuronal lysosomes with endosomes and autophagosomes, thereby helping to maintain cellular homeostasis.	[ [ "Autophagy is an evolutionarily conserved , lysosome-mediated degradation process required to maintain cellular homeostasis [1 , 2] .", "In eukaryotic cells , autophagy is a ubiquitous process that is important for several physiological processes .", "It occurs at a basal level in most cells to remove...	[ "Autophagy helps deliver sequestered intracellular cargo to lysosomes for proteolytic degradation and thereby maintains cellular homeostasis by preventing accumulation of toxic substances in cells .", "In a forward mosaic screen in Drosophila designed to identify genes required for neuronal function and maintenan...	[ "Autophagy is a cellular process used by cells to prevent the accumulation of toxic substances .", "It delivers misfolded proteins and damaged organelles by fusing autophagosomes—organelles formed by a double membrane that surrounds the “debris” to be eliminated—with lysosomes .", "How this fusion process is re...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "phosphorylation", "vesicles", "enzyme-linked immunoassays", "gene regulation", "cell processes", "egfr signaling", "immunologic techniques", "cellular structures and organelles", "research and analysis methods", "small interfering rnas", "proteins", "gene expression", "immunoassays", "glu...	The alpha-1 subunit of the Na+,K+-ATPase (ATP1A1) is required for macropinocytic entry of respiratory syncytial virus (RSV) in human respiratory epithelial cells	journal.ppat.1007963	null	[ [ "Human respiratory syncytial virus ( RSV ) is the leading viral cause of severe lower respiratory tract infections in infants and young children worldwide [1] .", "RSV-associated acute lower respiratory infection of children younger than 5 years of age causes ~118 , 000 deaths worldwide annually [2] .", ...	[ "Human respiratory syncytial virus ( RSV ) is the leading viral cause of acute pediatric lower respiratory tract infections worldwide , with no available vaccine or effective antiviral drug .", "To gain insight into virus-host interactions , we performed a genome-wide siRNA screen .", "The expression of over 20...	[ "RSV continues to be the most important viral cause of severe bronchiolitis and pneumonia in infants and young children , and also has a substantial impact in the elderly .", "It is estimated to claim the lives of ~118 , 000 children under five years of age annually .", "No vaccine or antiviral drug suitable fo...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/genomics", "infectious diseases/tropical and travel-associated diseases", "genetics and genomics/comparative genomics" ]	The Genome of Borrelia recurrentis, the Agent of Deadly Louse-Borne Relapsing Fever, Is a Degraded Subset of Tick-Borne Borrelia duttonii	journal.pgen.1000185	null	[ [ "Spirochetes of the genus Borrelia are bacterial pathogens responsible for relapsing fever and Lyme borreliosis .", "Whereas the Lyme disease agents Borrelia burgdorferi [1] , [2] , Borrelia garinii [3] , and Borrelia afzelii [4] are transmitted by hard ticks , the numerous relapsing fever borreliae are t...	[ "In an effort to understand how a tick-borne pathogen adapts to the body louse , we sequenced and compared the genomes of the recurrent fever agents Borrelia recurrentis and B . duttonii .", "The 1 , 242 , 163–1 , 574 , 910-bp fragmented genomes of B . recurrentis and B . duttonii contain a unique 23-kb linear pl...	[ "Borreliae are vector-borne spirochetes that are responsible for Lyme disease and recurrent fevers .", "We completed the genome sequences of the tick-borne Borrelia duttonii and the louse-borne B . recurrentis .", "The former of these is responsible for emerging infections that mimic malaria in Africa and in tr...	2008
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "gastroenterology and hepatology/hepatology", "public health and epidemiology/epidemiology", "infectious diseases/helminth infections", "public health and epidemiology/infectious diseases", "radiology and medical imaging/ultrasonography" ]	The Impact of Schistosoma japonicum Infection and Treatment on Ultrasound-Detectable Morbidity: A Five-Year Cohort Study in Southwest China	journal.pntd.0000685	null	[ [ "Schistosomiasis causes morbidity in the human host through the schistosome egg , which triggers inflammation and fibrosis that can lead to anemia , impaired growth and in severe cases , gastrointestinal bleeding and death [1]–[4] .", "The major intestinal schistosomes , Schistosoma japonicum , found in A...	[ "Ultrasonography allows for non-invasive examination of the liver and spleen and can further our understanding of schistosomiasis morbidity .", "We followed 578 people in Southwest China for up to five years .", "Participants were tested for Schistosoma japonicum infection in stool and seven standard measures o...	[ "Schistosomiasis is a water-borne parasite that infects approximately 200 million people worldwide .", "Schistosoma japonicum , found in Asia , causes disease by releasing eggs in the liver , leading to fibrosis , anemia , and , in children , impaired growth .", "Ultrasound can assess liver pathology from schis...	2010
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "public health and epidemiology", "microbiology/parasitology" ]	Prevalence and Risk Factors of Intestinal Parasitism in Rural and Remote West Malaysia	journal.pntd.0000974	null	[ [ "Globally , the neglected intestinal parasitic infections ( IPIs ) such as soil-transmitted helminth ( STH ) and protozoa infections have been recognized as one of the most significant causes of illnesses and diseases especially among disadvantaged communities .", "With an average prevalence rate of 50% i...	[ "Intestinal parasitic infections ( IPIs ) have a worldwide distribution and have been identified as one of the most significant causes of illnesses and diseases among the disadvantaged population .", "In Malaysia , IPIs still persist in some rural areas , and this study was conducted to determine the current epid...	[ "Intestinal parasitic infections ( IPIs ) are among the most prevalent human afflictions; these infections still have major impact on the socioeconomic and public health of the bottom billion of the world's poorest people .", "Although Malaysia has a thriving economy , IPIs are still very much prevalent and causi...	2011
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "infectious disease epidemiology", "african trypanosomiasis", "tropical diseases", "parasitic diseases", "health care", "mathematics", "forecasting", "statistics (mathematics)", "screening guidelines", "neglected tropical diseases", "infectious disease control",...	Forecasting Human African Trypanosomiasis Prevalences from Population Screening Data Using Continuous Time Models	journal.pcbi.1005103	null	[ [ "Human African trypanosomiasis ( HAT ) , also known as sleeping sickness , is a parasitic disease that is caused by two sub-species of the protozoa Trypanosoma brucei: Trypanosoma brucei gambiense ( gambiense HAT ) and Trypanosoma brucei rhodesiense ( rhodiense HAT ) .", "The infection causing the disease...	[ "To eliminate and eradicate gambiense human African trypanosomiasis ( HAT ) , maximizing the effectiveness of active case finding is of key importance .", "The progression of the epidemic is largely influenced by the planning of these operations .", "This paper introduces and analyzes five models for predicting...	[ "The primary strategy to fight gambiense human African trypanosomiasis ( HAT ) is to perform extensive population screening operations among endemic villages .", "Since the progression of the epidemic is largely influenced by the planning of these operations , it is crucial to develop adequate models on this rela...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "microbial metabolism", "microbial physiology", "microbial pathogens", "biology", "microbiology", "host-pathogen interaction", "bacterial pathogens", "microbial ecology" ]	Metabolite Cross-Feeding Enhances Virulence in a Model Polymicrobial Infection	journal.ppat.1002012	null	[ [ "The survival of pathogens in the human body has been rigorously studied for well over a century .", "The ability of bacteria to colonize , persist and thrive in vivo is due to an array of capabilities including the ability to attach to host tissues , produce extracellular virulence factors , and evade th...	[ "Microbes within polymicrobial infections often display synergistic interactions resulting in enhanced pathogenesis; however , the molecular mechanisms governing these interactions are not well understood .", "Development of model systems that allow detailed mechanistic studies of polymicrobial synergy is a criti...	[ "Many bacterial infections are not the result of colonization and persistence of a single pathogenic microbe in an infection site but instead the result of colonization by several .", "Although the importance of polymicrobial interactions and pathogenesis has been noted by many prominent microbiologists including...	2011
[ "Introduction", "Results/Discussion", "Methods" ]	[]	Target Prediction for an Open Access Set of Compounds Active against Mycobacterium tuberculosis	journal.pcbi.1003253	null	[ [ "One third of the world's population is infected with Mycobacterium tuberculosis ( MTB ) , the causative agent of tuberculosis [1] .", "Approximately 95% of infected individuals are thought to have persistent , latent MTB infections that remain dormant until activated by specific environmental and host re...	[ "Mycobacterium tuberculosis , the causative agent of tuberculosis ( TB ) , infects an estimated two billion people worldwide and is the leading cause of mortality due to infectious disease .", "The development of new anti-TB therapeutics is required , because of the emergence of multi-drug resistance strains as w...	[ "Mycobacterium tuberculosis is a major worldwide pathogen infecting millions individuals every year .", "Additionally , the number of antibiotic resistant strains has dramatically increased over the last decades .", "Trying to address this challenge , the pharmaceutical company GlaxoSmithKline has recently publ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "bacteriology", "genome expression analysis", "gene regulation", "microbiology", "ribozymes", "rna stability", "gene function", "staphylococci", "molecular genetics", "bacterial pathogens", "biology", "gram positive", "biochemistry", "rna", "bacterial physiology", "rna processing", "...	Transcriptome-Wide Analyses of 5′-Ends in RNase J Mutants of a Gram-Positive Pathogen Reveal a Role in RNA Maturation, Regulation and Degradation	journal.pgen.1004207	null	[ [ "RNA decay is an important regulatory process in bacteria and is thought to be a major factor in post-transcriptional control [1] .", "Some bacterial mRNAs have halflives of only seconds , most mRNAs have halflives of minutes , and a few especially stable RNAs can last for hours [2] , however the signals ...	[ "RNA decay and maturation have in recent years been recognised as major regulatory mechanisms in bacteria .", "In contrast to Escherichia coli , the Firmicute ( Gram-positive ) bacteria often do not encode the well-studied endonuclease RNase E , but instead rely on the endonucleases RNase Y , RNase J1 and RNase J...	[ "The long RNA ( ribonucleic acid ) chains are key intermediates in the transfer of information from the genes on chromosomes to the production of protein .", "An RNA copy ( mRNA ) is transcribed from the gene , and this copy is then translated into protein by a complex molecular machine called the ribosome .", ...	2014
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "genome sequencing", "medicine", "genomics", "genetic mutation", "genetics", "molecular genetics", "biology", "human genetics", "genetics and genomics", "clinical genetics" ]	Whole-Exome Re-Sequencing in a Family Quartet Identifies POP1 Mutations As the Cause of a Novel Skeletal Dysplasia	journal.pgen.1002027	null	[ [ "Skeletal dysplasias ( SD ) are a group of genetic disorders affecting skeletal development that cause deficiencies and deformities of the limbs and spine , dwarfism , or abnormal bone strength .", "SDs are usually inherited as dominant or recessive monogenic Mendelian traits or occur as a result of de no...	[ "Recent advances in DNA sequencing have enabled mapping of genes for monogenic traits in families with small pedigrees and even in unrelated cases .", "We report the identification of disease-causing mutations in a rare , severe , skeletal dysplasia , studying a family of two healthy unrelated parents and two aff...	[ "Skeletal dysplasias are a group of genetic disorders affecting skeletal development that cause deficiencies and deformities of the limbs and spine , dwarfism , or abnormal bone strength .", "Skeletal dysplasias are usually inherited as monogenic Mendelian traits or occur as a result of de novo mutations .", "W...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "blood cells", "innate immune system", "medicine and health sciences", "immune cells", "immune physiology", "pathology and laboratory medicine", "cytokines", "pathogens", "antigen-presenting cells", "immunology", "microbiology", "retroviruses", "viruses", "immunodeficiency viruses", "phy...	The HTLV-1 gp21 fusion peptide inhibits antigen specific T-cell activation in-vitro and in mice	journal.ppat.1007044	null	[ [ "The mutual evolutionary pressure between viruses and their hosts has driven viruses to adopt various immune evasion mechanisms [1–4] .", "Many evasion strategies of enveloped viruses , such as antigen presentation antagonism and glycan shielding , can be mediated by their fusion glycoproteins ( reviewed ...	[ "The ability of the Lentivirus HIV-1 to inhibit T-cell activation by its gp41 fusion protein is well documented , yet limited data exists regarding other viral fusion proteins .", "HIV-1 utilizes membrane binding region of gp41 to inhibit T-cell receptor ( TCR ) complex activation .", "Here we examined whether ...	[ "In order to successfully infect and persist in their hosts , viruses utilize multiple strategies to evade the immune system .", "HIV utilizes membrane interacting regions of its envelope protein , primarily used to fuse with its target cells , to inhibit T-cell activation .", "Yet , it is unknown whether this ...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunology/immunomodulation", "infectious diseases/neglected tropical diseases", "immunology/immune response", "public health and epidemiology/infectious diseases", "infectious diseases/protozoal infections", "immunology/immunity to infections" ]	Sand Fly Salivary Proteins Induce Strong Cellular Immunity in a Natural Reservoir of Visceral Leishmaniasis with Adverse Consequences for Leishmania	journal.ppat.1000441	null	[ [ "Leishmaniasis is a vector-borne neglected disease transmitted exclusively by the bite of infected phlebotomine sand flies .", "An estimated 350 million people are at risk for leishmaniasis with an annual incidence of 2 million cases and a loss of 2 , 357 , 000 disability-adjusted life years [1] , [2] , [...	[ "Immunity to a sand fly salivary protein protects against visceral leishmaniasis ( VL ) in hamsters .", "This protection was associated with the development of cellular immunity in the form of a delayed-type hypersensitivity response and the presence of IFN-γ at the site of sand fly bites .", "To date , there a...	[ "Leishmaniasis is a neglected infectious disease with a global distribution encompassing 88 countries , 350 million people at risk , and an annual incidence of 2 million cases .", "Leishmaniasis is a vector-borne disease transmitted by sand fly bites where parasites are co-deposited with saliva into the wound .",...	2009
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "animal models", "drosophila melanogaster", "model organisms", "reproductive system", "molecular cell biology", "coevolution", "evolutionary biology", "physiology", "biology", "anatomy and physiology", "evolutionary processes", "reproductive physiology" ]	Sperm-Storage Defects and Live Birth in Drosophila Females Lacking Spermathecal Secretory Cells	journal.pbio.1001192	Transgenic Drosophila are used to identify the functions of a small set of secretory cells that are typically associated with the sperm-storage organs of female insects.	[ [ "Females of many animal species store sperm after mating , in specialized organs of the reproductive tract [1] , [2] .", "In addition to sperm , seminal proteins are transferred to females during mating .", "In Drosophila , seminal proteins perform multiple functions that advance the male's reproducti...	[ "Male Drosophila flies secrete seminal-fluid proteins that mediate proper sperm storage and fertilization , and that induce changes in female behavior .", "Females also produce reproductive-tract secretions , yet their contributions to postmating physiology are poorly understood .", "Large secretory cells line ...	[ "Females of many animal species store sperm after mating , but the molecular and cellular mechanisms of sperm storage and maintenance are largely unknown .", "D . melanogaster females store sperm in the seminal receptacle and the paired spermathecae .", "Each spermathecal cap is lined with large secretory cells...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "classical mechanics", "chemical compounds", "enzymes", "enzymology", "organic compounds", "simulation and modeling", "mathematics", "algebra", "damage mechanics", "protein structure", "research and analysis methods", "proteins", "protein kinases", "deformation", "chemistry", "molecula...	On identifying collective displacements in apo-proteins that reveal eventual binding pathways	journal.pcbi.1006665	null	[ [ "Modern drug discovery operates around the principle of molecular recognition in the context of protein-ligand binding .", "In the preliminary stages , drug discovery programs often invest in quantifying the binding affinity of suitable drug candidates towards a well-established protein target .", "Ho...	[ "Binding of small molecules to proteins often involves large conformational changes in the latter , which open up pathways to the binding site .", "Observing and pinpointing these rare events in large scale , all-atom , computations of specific protein-ligand complexes , is expensive and to a great extent serendi...	[ "Designing drugs which target specific proteins involved in diseases consumes a lot of time and effort in the pharmaceutical industry .", "In recent times , in silico design of drugs using all-atom molecular modelling has started to provide crucial inputs .", "Even so , discovery of binding pathways of small mo...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infographics", "medicine and health sciences", "diagnostic radiology", "functional magnetic resonance imaging", "neural networks", "nervous system", "neuroscience", "magnetic resonance imaging", "scale-free networks", "brain mapping", "network analysis", "neuroimaging", "research and analys...	A Topological Criterion for Filtering Information in Complex Brain Networks	journal.pcbi.1005305	null	[ [ "Network science has provided a breakthrough in the analysis and modeling of biological systems with the aim to unlock molecular mechanisms behind human disease [1–3] and quantify brain ( re ) organization underlying behavior , cognition and mental disorders [4–6] .", "In part , this has been made possibl...	[ "In many biological systems , the network of interactions between the elements can only be inferred from experimental measurements .", "In neuroscience , non-invasive imaging tools are extensively used to derive either structural or functional brain networks in-vivo .", "As a result of the inference process , w...	[ "Complex brain networks are mainly estimated from empirical measurements .", "As a result , we obtain networks where everything is connected to everything else through different strengths of interaction .", "Filtering procedures are typically adopted to prune weakest connections .", "However , network propert...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "bacteriology", "medicine and health sciences", "immune physiology", "enzyme-linked immunoassays", "pathology and laboratory medicine", "pathogens", "immunology", "microbiology", "salmonella typhi", "bacterial diseases", "secretion systems", "enterobacteriaceae", "antibodies", "immunologic...	Role of T3SS-1 SipD Protein in Protecting Mice against Non-typhoidal Salmonella Typhimurium	journal.pntd.0005207	null	[ [ "Salmonellae are members of the Enterobacteriaceae family , a large group of Gram-negative bacteria [1] .", "While consisting of only two species ( enterica and bongori ) , there are a multiplicity of subspecies among which enterica spp .", "represent 99% of Salmonella infections in warm-blooded anima...	[ "Salmonella enterica species are enteric pathogens that cause severe diseases ranging from self-limiting gastroenteritis to enteric fever and sepsis in humans .", "These infectious diseases are still the major cause of morbidity and mortality in low-income countries , especially in children younger than 5 years a...	[ "Salmonella are bacteria responsible for a high global burden of invasive diseases , especially in South and South-East Asia ( mainly enteric fever due to Salmonella Typhi ) and sub-Saharan Africa ( mainly invasive Non-Typhoidal Salmonella , iNTS ) .", "This iNTS disease has emerged as a prominent cause of system...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "behavioral and social aspects of health", "tropical diseases", "social sciences", "parasitic diseases", "health care", "preventive medicine", "research design", "neglected tropical diseases", "surveys", "sanitation", "research and analysis methods", "public a...	Knowledge, attitudes and practices with regard to schistosomiasis prevention and control: Two cross-sectional household surveys before and after a Community Dialogue intervention in Nampula province, Mozambique	journal.pntd.0007138	null	[ [ "Schistosomiasis is one of the most common parasitic diseases , with approximately 190 million people infected worldwide [1] , causing over 100 , 000 deaths [2] and the loss of over 1 . 8 million disability-adjusted life years every year [3] .", "The disease is caused by worms of the Schistosoma ( S . ) g...	[ "The Community Dialogue Approach is a promising social and behaviour change intervention , which has shown potential for improving health seeking behaviour .", "To test if this approach can strengthen prevention and control of schistosomiasis at community level , Malaria Consortium implemented a Community Dialogu...	[ "Schistosomiasis is a parasitic neglected tropical disease that affects around 190 million people worldwide , causing chronic ill health and disability .", "Central to its prevention and control are the acceptance of health interventions such as the distribution of drugs on a mass scale and the adoption of good h...	2019
[ "Introduction", "Methods", "Discussion" ]	[ "death rates", "invertebrates", "dengue virus", "medicine and health sciences", "classical mechanics", "pathology and laboratory medicine", "fluid mechanics", "demography", "atmospheric science", "pathogens", "vector-borne diseases", "microbiology", "animals", "viruses", "age groups", ...	Climate and the Timing of Imported Cases as Determinants of the Dengue Outbreak in Guangzhou, 2014: Evidence from a Mathematical Model	journal.pntd.0004417	null	[ [ "Dengue is a febrile illness caused by the dengue virus which is further classified into 4 serotypes ( DENV 1–4 ) , and transmitted by Aedes aegypti and Aedes albopictus mosquitoes .", "Classically , dengue virus infection produces mild flu-like fevers but can also result in lethal dengue hemorrhagic feve...	[ "As the world’s fastest spreading vector-borne disease , dengue was estimated to infect more than 390 million people in 2010 , a 30-fold increase in the past half century .", "Although considered to be a non-endemic country , mainland China had 55 , 114 reported dengue cases from 2005 to 2014 , of which 47 , 056 ...	[ "Dengue has not been considered to be a major problem in China since it is recognized as an imported disease and only 8 , 058 cases were reported from 2005 to 2013 .", "However , in 2014 alone , 47 , 056 new cases were reported .", "In this study , a mathematical model was developed to determine the possible ca...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "animal models", "developmental biology", "cell fate determination", "model organisms", "xenopus laevis", "molecular development", "genetics", "gene expression", "epigenetics", "biology", "gene networks", "genetics and genomics", "cell differentiation" ]	Suv4-20h Histone Methyltransferases Promote Neuroectodermal Differentiation by Silencing the Pluripotency-Associated Oct-25 Gene	journal.pgen.1003188	null	[ [ "Embryonic development is controlled by fine-tuned differential gene expression .", "A succession of regulatory protein networks unfolds the zygotic gene expression program along a hierarchy of decisions , leading from the embryonic ground state to the epiblast and then to germ layers , which become patte...	[ "Post-translational modifications ( PTMs ) of histones exert fundamental roles in regulating gene expression .", "During development , groups of PTMs are constrained by unknown mechanisms into combinatorial patterns , which facilitate transitions from uncommitted embryonic cells into differentiated somatic cell l...	[ "The quest of modern developmental biology is a detailed molecular description of the process that leads from the fertilized egg to the complex and highly differentiated adult organism .", "This process is controlled largely on the level of gene expression .", "While early embryonic cells are pluripotent and ca...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Removal of Misincorporated Ribonucleotides from Prokaryotic Genomes: An Unexpected Role for Nucleotide Excision Repair	journal.pgen.1003878	null	[ [ "In order to preserve the properties and functions of a living organism , the genetic information encoded in its DNA should be kept essentially unchanged .", "In reality , DNA is constantly subjected to numerous attacks from endogenous and exogenous sources changing its chemical composition and structure ...	[ "Stringent steric exclusion mechanisms limit the misincorporation of ribonucleotides by high-fidelity DNA polymerases into genomic DNA .", "In contrast , low-fidelity Escherichia coli DNA polymerase V ( pol V ) has relatively poor sugar discrimination and frequently misincorporates ribonucleotides .", "Substitu...	[ "Most DNA polymerases differentiate between ribo- and deoxyribonucleotides quite effectively , thereby deterring insertion of nucleotides with the “wrong” sugar into chromosomes .", "Nevertheless , a significant number of ribonucleotides still get stably incorporated into genomic DNA .", "E . coli pol V is amon...	2013
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "enzyme-linked immunoassays", "immune physiology", "immunology", "animal models", "preventive medicine", "vaccines", "model organisms", "experimental organism systems", "infectious disease control", "antibodies", "immunologic techniques", "vaccination and immu...	A DNA vaccine for Crimean-Congo hemorrhagic fever protects against disease and death in two lethal mouse models	journal.pntd.0005908	null	[ [ "Crimean-Congo hemorrhagic fever virus ( CCHFV ) is a tick-borne virus with a wide geographical distribution , including Africa , the Balkans , the Middle East , Russia and western Asia [1] .", "CCHFV , a member of the Nairoviridae family in the Bunyavirales order , has a tripartite , negative-sense RNA g...	[ "Crimean-Congo hemorrhagic fever virus ( CCHFV ) is a tick-borne virus capable of causing a severe hemorrhagic fever disease in humans .", "There are currently no licensed vaccines to prevent CCHFV-associated disease .", "We developed a DNA vaccine expressing the M-segment glycoprotein precursor gene of CCHFV a...	[ "Crimean-Congo hemorrhagic Fever Virus ( CCHFV ) is a tick-borne virus capable of causing lethal human disease against which there are currently no approved vaccines .", "In this study , we compared the immunogenicity and protective efficacy of a candidate DNA vaccine expressing the glycoprotein precursor gene of...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Sex Pheromones of C. elegans Males Prime the Female Reproductive System and Ameliorate the Effects of Heat Stress	journal.pgen.1005729	null	[ [ "Comprehensive understanding of any organism requires bridging the knowledge of laboratory biology and natural history [1] .", "These two approaches to the study of life are complementary and mutually reinforcing , since one offers a powerful methodology for detailed mechanistic investigation , while the ...	[ "Pheromones are secreted molecules that mediate animal communications .", "These olfactory signals can have substantial effects on physiology and likely play important roles in organismal survival in natural habitats .", "Here we show that a blend of two ascaroside pheromones produced by C . elegans males prime...	[ "The Caenorhabditis elegans metabolome contains over a hundred ascaroside molecules .", "Most of them have no known function , or no function at all , but some act as pheromones .", "Two of these molecules , ascr#10 and ascr#3 , are produced in different proportions by males and hermaphrodites .", "We report ...	2015
[ "Introduction", "Methodology", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "database searching", "animals", "age groups", "adults", "infectious disease control", "insect vectors", "research and analysis methods", "infectious diseases", "agrochemicals", "aedes aegypti", "disease vectors", "insects", "agriculture",...	Community effectiveness of indoor spraying as a dengue vector control method: A systematic review	journal.pntd.0005837	null	[ [ "Dengue is the most prevalent arthropod-borne viral disease , infecting 300 to 500 million individuals each year .", "Approximately 100 million infections are symptomatic , which can range from mild to severe disease [1 , 2 , 3] .", "An estimated 500 000 people suffer from the severe forms , nearly 90...	[ "The prevention and control of dengue rely mainly on vector control methods , including indoor residual spraying ( IRS ) and indoor space spraying ( ISS ) .", "This study aimed to systematically review the available evidence on community effectiveness of indoor spraying .", "A systematic review was conducted us...	[ "The effectiveness of indoor residual spraying ( IRS ) and indoor space spraying ( ISS ) as dengue vector control methods depends on many factors .", "This study aims to systematically review the evidence on the community effectiveness of indoor spraying of insecticides to reduce Aedes mosquito populations and th...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "biomacromolecule-ligand interactions", "medicine", "medicinal chemistry", "molecular dynamics", "drugs and devices", "enzymes", "chemical biology", "molecular mechanics", "histone modification", "protein structure", "epigenetics", "biophysics simulations", "computer graphics", "biochemist...	Expanding the Druggable Space of the LSD1/CoREST Epigenetic Target: New Potential Binding Regions for Drug-Like Molecules, Peptides, Protein Partners, and Chromatin	journal.pcbi.1003158	null	[ [ "Lysine specific demethylase-1 with its corepressor protein CoREST ( LSD1/CoREST ) has emerged as one of the most promising epigenetic targets in drug discovery and design [1] .", "LSD1/CoREST is widely investigated for its expanding biological roles in cancer , neurodegeneration , and viral infection [2]...	[ "Lysine specific demethylase-1 ( LSD1/KDM1A ) in complex with its corepressor protein CoREST is a promising target for epigenetic drugs .", "No therapeutic that targets LSD1/CoREST , however , has been reported to date .", "Recently , extended molecular dynamics ( MD ) simulations indicated that LSD1/CoREST nan...	[ "Protein dynamics plays a major role in determining the molecular interactions available to molecular binding partners , including druggable hot spots .", "The LSD1/CoREST complex is one of the most relevant epigenetic targets discovered and was shown to be a highly dynamic nanoscale clamp using molecular dynamic...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Zinc Finger Independent Genome-Wide Binding of Sp2 Potentiates Recruitment of Histone-Fold Protein Nf-y Distinguishing It from Sp1 and Sp3	journal.pgen.1005102	null	[ [ "Eukaryotic transcription factors are grouped into families based on their common structural features .", "Prototypical zinc finger-containing transcription factors are the evolutionary conserved Specificity proteins/Krüppel-like factors ( Sps/Klfs ) ( reviewed in [1 , 2 , 3 , 4] ) that share three consec...	[ "Transcription factors are grouped into families based on sequence similarity within functional domains , particularly DNA-binding domains .", "The Specificity proteins Sp1 , Sp2 and Sp3 are paradigmatic of closely related transcription factors .", "They share amino-terminal glutamine-rich regions and a conserv...	[ "A major question in eukaryotic gene regulation is how transcription factors with similar structural features elicit specific biological responses .", "We used the three transcription factors Sp1 , Sp2 and Sp3 as a paradigm for investigating this question .", "All three proteins are ubiquitously expressed , and...	2015
[ "Introduction", "Methods", "Results", "Distance Modulates Firing Synchrony and Subthreshold Correlations", "Effects of Rate, Membrane Potential Distribution and Coupling on Synchrony", "Discussion" ]	[ "circuit models", "theoretical biology", "computational neuroscience", "single neuron function", "biology and life sciences", "computational biology", "neuroscience" ]	Interplay of Intrinsic and Synaptic Conductances in the Generation of High-Frequency Oscillations in Interneuronal Networks with Irregular Spiking	journal.pcbi.1003574	null	[ [ "Fast oscillations ( 30–100 Hz and higher ) have been observed in several brain areas , and have been proposed as a general substrate of neural computation [1]–[4] .", "Several decades of intense investigations , using both experimental [5] , [6] and theoretical [7]–[13] approaches , have provided a detai...	[ "High-frequency oscillations ( above 30 Hz ) have been observed in sensory and higher-order brain areas , and are believed to constitute a general hallmark of functional neuronal activation .", "Fast inhibition in interneuronal networks has been suggested as a general mechanism for the generation of high-frequenc...	[ "Neurons in the brain engage in collective oscillations at different frequencies .", "Gamma and high-gamma oscillations ( 30–100 Hz and higher ) have been associated with cognitive functions , and are altered in psychiatric disorders such as schizophrenia and autism .", "Our understanding of how high-frequency ...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/gene discovery", "neuroscience/motor systems", "physiology/neurodevelopment", "cell biology/neuronal signaling mechanisms", "genetics and genomics/genetics of disease", "neuroscience/neurodevelopment", "developmental biology/neurodevelopment", "neuroscience/neuronal signaling me...	Negative Regulation of Active Zone Assembly by a Newly Identified SR Protein Kinase	journal.pbio.1000193	A neuronal serine-arginine protein kinase that localizes to the presynaptic active zone is required for kinase-dependent repression of active zone assembly.	[ [ "The majority of stimulus-dependent synaptic vesicle fusion occurs at presynaptic specializations called active zones ( AZs ) .", "Ultrastructurally , AZs consist of at least two components;", "1 ) a presynaptic membrane of high electron density , reflecting the presence of proteins such as Ca2+ chann...	[ "Presynaptic , electron-dense , cytoplasmic protrusions such as the T-bar ( Drosophila ) or ribbon ( vertebrates ) are believed to facilitate vesicle movement to the active zone ( AZ ) of synapses throughout the nervous system .", "The molecular composition of these structures including the T-bar and ribbon are l...	[ "Neurons communicate with each other through electrochemical impulses transmitted primarily at specialized intercellular junctions termed synapses .", "At each synapse , the primary site of synaptic vesicle fusion occurs at the active zone , an electron-dense presynaptic membrane with associated fibrillary matrix...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "toxoplasma gondii", "immune activation", "antigen-presenting cells", "immunity to infections", "immunology", "immune suppression", "microbiology", "parasitic diseases", "parasitic protozoans"...	Parasite Fate and Involvement of Infected Cells in the Induction of CD4+ and CD8+ T Cell Responses to Toxoplasma gondii	journal.ppat.1004047	null	[ [ "Toxoplasma gondii is an intracellular protozoan parasite of medical and veterinary significance that can induce acute disease in its host and is an important opportunistic pathogen in immunocompromised individuals [1] , [2] .", "Successful control of this pathogen requires a rapid TH1 immune response , c...	[ "During infection with the intracellular parasite Toxoplasma gondii , the presentation of parasite-derived antigens to CD4+ and CD8+ T cells is essential for long-term resistance to this pathogen .", "Fundamental questions remain regarding the roles of phagocytosis and active invasion in the events that lead to t...	[ "CD4+ and CD8+ T cells are critical for controlling many infections .", "To generate a T cell response during infection , T cells must encounter the microbial peptides that they recognize bound to MHC molecules on the surfaces of other cells , such as dendritic cells .", "It is currently unclear how dendritic c...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biomacromolecule-ligand interactions", "biochemistry", "macromolecular structure analysis", "plant science", "plant microbiology", "biology and life sciences", "microbiology", "bacteria", "molecular biology", "organisms", "agrobacteria" ]	Agrobacterium Uses a Unique Ligand-Binding Mode for Trapping Opines and Acquiring A Competitive Advantage in the Niche Construction on Plant Host	journal.ppat.1004444	null	[ [ "The widespread pathogen Agrobacterium tumefaciens evolved a unique process of niche construction inside the host plant: it transfers a portion ( T-DNA ) of its tumour-inducing ( Ti ) plasmid into the nuclear genome of the infected plant cells [1] , [2] .", "In the stably transformed host cells , the expr...	[ "By modifying the nuclear genome of its host , the plant pathogen Agrobacterium tumefaciens induces the development of plant tumours in which it proliferates .", "The transformed plant tissues accumulate uncommon low molecular weight compounds called opines that are growth substrates for A . tumefaciens .", "In...	[ "An ecological niche is defined , in a given environment , by the availability of nutritive resources , which can be specifically assimilated by certain living organisms to promote their proliferation .", "The bacterial pathogen Agrobacterium tumefaciens is able to engineer an ecological niche in the infected hos...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "infectious diseases of the nervous system", "protozoan infections", "parasitic diseases", "toxoplasmosis" ]	Toxoplasma Co-opts Host Cells It Does Not Invade	journal.ppat.1002825	null	[ [ "Obligate intracellular organisms , from viruses to eukaryotic pathogens , modify the microenvironment of the infected host cell to avoid clearance by host-cell-intrinsic mechanisms ( e . g . , autophagy , phago-lysosomal fusion ) as well as to block the immune system from recognizing the host cell as infecte...	[ "Like many intracellular microbes , the protozoan parasite Toxoplasma gondii injects effector proteins into cells it invades .", "One group of these effector proteins is injected from specialized organelles called the rhoptries , which have previously been described to discharge their contents only during success...	[ "Toxoplasma gondii is an intracellular parasite that infects warm blooded animals , including humans .", "In these hosts , Toxoplasma establishes a chronic infection in the brain , which the parasite accomplishes in part by injecting effector proteins , which manipulate many cellular processes , into cells it inv...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Effects of Spring Temperatures on the Strength of Selection on Timing of Reproduction in a Long-Distance Migratory Bird	journal.pbio.1002120	A 31-year study of pied flycatchers shows that it is the temperature at arrival when the offspring return to breed up to two years later that drives selection on breeding time.	[ [ "Global climate change has led to shifts in phenology , i . e . , the seasonal timing of life history events , such as budburst , flowering , hibernation , migration , or reproduction , in many species .", "Over the past three decades , plants and animals have shifted their timing , on average , three to ...	[ "Climate change has differentially affected the timing of seasonal events for interacting trophic levels , and this has often led to increased selection on seasonal timing .", "Yet , the environmental variables driving this selection have rarely been identified , limiting our ability to predict future ecological ...	[ "Pied flycatchers are long-distance migrant birds that have advanced their timing of reproduction over the past decades in response to climate change .", "We studied selection on egg-laying date using a 31-year-long population study and found that in the first 20 years , early-reproducing birds had increasingly h...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "eye lens", "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "ocular anatomy", "microbiology", "toxicology", "plasmid construction", "epithelial cells", "mutation", "enterobacteriaceae", "dna construction", "molecular biology techniques", "serratia", "bac...	Blowing epithelial cell bubbles with GumB: ShlA-family pore-forming toxins induce blebbing and rapid cellular death in corneal epithelial cells	journal.ppat.1007825	null	[ [ "Some bacteria induce changes in human cell architecture through expression of virulence factors , which aid in bacterial internalization into cells and provide a more favorable niche for microbial colonization .", "Cell alterations include the formation of pedestals on intestinal cells by enteropathogeni...	[ "Medical devices , such as contact lenses , bring bacteria in direct contact with human cells .", "Consequences of these host-pathogen interactions include the alteration of mammalian cell surface architecture and induction of cellular death that renders tissues more susceptible to infection .", "Gram-negative ...	[ "Bacteria must overcome host defenses to cause infection .", "This is especially true for corneal infections where bacteria must penetrate the epithelium in order to gain access to the stroma where bacteria can rapidly multiply , induce inflammation , and cause vision loss .", "Members of the Enterobacteriaceae...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "genomics", "biology", "computational biology", "evolutionary biology", "genetics and genomics" ]	The Vast, Conserved Mammalian lincRNome	journal.pcbi.1002917	null	[ [ "The great majority of mammalian genome sequences are transcribed , at least occasionally , a phenomenon known as pervasive transcription [1]–[4] .", "More specifically , tiling array analyses of several human chromosomes have shown that over 90% of the bases are transcribed in at least one cell type [1] ...	[ "We compare the sets of experimentally validated long intergenic non-coding ( linc ) RNAs from human and mouse and apply a maximum likelihood approach to estimate the total number of lincRNA genes as well as the size of the conserved part of the lincRNome .", "Under the assumption that the sets of experimentally ...	[ "Genome analysis of humans and other mammals reveals a surprisingly small number of protein-coding genes , only slightly over 20 , 000 ( although the diversity of actual proteins is substantially augmented by alternative transcription and alternative splicing ) .", "Recent analysis of the mammalian genomes and tr...	2013
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "ecology and environmental sciences", "china", "atmospheric science", "grasslands", "geographical locations", "vertebrates", "plant communities", "random variables", "animals", "mammals", "covariance", "geoinformatics", "hemorrhagic fever with renal syndrome...	Spatiotemporal variation of the association between climate dynamics and HFRS outbreaks in Eastern China during 2005-2016 and its geographic determinants	journal.pntd.0006554	null	[ [ "Hantaviruses are RNA viruses that belong to the Hantaviridae family .", "Hantavirus infection causes hemorrhagic fever with renal syndrome ( HFRS ) to humans .", "As a rodent-borne infectious disease , the main domestic animals in China carrying hantavirus ( including Hantaan virus , HTNV , and Seoul...	[ "Hemorrhagic fever with renal syndrome ( HFRS ) is a rodent-associated zoonosis caused by hantavirus .", "The HFRS was initially detected in northeast China in 1931 , and since 1955 it has been detected in many regions of the country .", "Global climate dynamics influences HFRS spread in a complex nonlinear way...	[ "China has the largest number of HFRS infections in the world ( 9045 cases in 2016 ) .", "Previous studies have found that HFRS infections are related to climate .", "However , the spatiotemporal distribution of the association between HFRS outbreaks at a large scale and global climate dynamics ( i . e . , over...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cellular neuroscience", "neuronal morphology", "synapses", "computational neuroscience", "electrophysiology", "single neuron function", "physiology", "biology", "anatomy and physiology", "neuroscience", "neurophysiology" ]	Location-Dependent Excitatory Synaptic Interactions in Pyramidal Neuron Dendrites	journal.pcbi.1002599	null	[ [ "Pyramidal neurons , the principal cells of the neocortex , receive at least two broad classes of excitatory inputs .", "Classical driver inputs , which give rise to the neuron's basic receptive field properties , are generally associated with vertical connections from other cortical layers [1]–[3] .", ...	[ "Neocortical pyramidal neurons ( PNs ) receive thousands of excitatory synaptic contacts on their basal dendrites .", "Some act as classical driver inputs while others are thought to modulate PN responses based on sensory or behavioral context , but the biophysical mechanisms that mediate classical-contextual int...	[ "Pyramidal neurons ( PNs ) are the principal neurons of the cerebral cortex and therefore lie at the heart of the brain's higher sensory , motor , affective , memory , and executive functions .", "But how do they work ?", "In particular , how do they manage interactions between the classical “driver” inputs tha...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "parasite groups", "oocysts", "pathology and laboratory medicine", "cryptosporidium", "parasitic diseases", "parasitic protozoans", "parasitology", "diarrhea", "physiological processes", "apicomplexa", "protozoans", "signs and symptoms", "pharmaceutics", "...	Clinical and microbiologic efficacy of the piperazine-based drug lead MMV665917 in the dairy calf cryptosporidiosis model	journal.pntd.0006183	null	[ [ "Diarrhea still causes over 10% of childhood deaths [1] .", "Although cryptosporidiosis was previously recognized as a major contributor to diarrhea in endemic areas , a recent multicenter study in Africa and Asia found that Cryptosporidium infections , mostly due to Cryptosporidium hominis or Cryptospori...	[ "Cryptosporidiosis causes life-threatening diarrhea in infants , but the best available treatment is only modestly efficacious .", "Rodents infected with relevant Cryptosporidium species do not develop diarrhea , which complicates drug development .", "Cryptosporidium parvum infection of dairy calves , however ...	[ "Cryptosporidiosis is an important cause of life-threatening diarrhea for young children and immunocompromised people , and Cryptosporidium parvum , one of the two main human Cryptosporidium pathogens , is also an important cause of diarrhea in dairy calves .", "Yet , there are no reliably effective drugs for tre...	2018
[ "Introduction", "Discussion", "Materials and Methods" ]	[ "people and places", "haplotypes", "social sciences", "demography", "genetics", "anthropology", "biology and life sciences", "population genetics", "gene flow", "genomics", "evolutionary biology", "human genomics", "indigenous populations", "evolutionary processes", "genetic drift" ]	Patterns of Admixture and Population Structure in Native Populations of Northwest North America	journal.pgen.1004530	null	[ [ "The population history of indigenous peoples of the Americas is of perennial interest to scholars studying human migrations .", "The Americas were the last continents historically peopled by modern humans , with recent evidence supporting an initial human entry via Beringia after the last glacial maximum...	[ "The initial contact of European populations with indigenous populations of the Americas produced diverse admixture processes across North , Central , and South America .", "Recent studies have examined the genetic structure of indigenous populations of Latin America and the Caribbean and their admixed descendant...	[ "We collaborated with six indigenous communities in British Columbia and Southeast Alaska to generate and analyze genome-wide data for over 100 individuals .", "We then combined this dataset with existing data from populations worldwide , performing an investigation of the genetic structure of indigenous populati...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "invertebrates", "molecular neuroscience", "neuroscience", "animals", "gene function", "animal models", "cell signaling", "drosophila melanogaster", "model organisms", "drosophila", "research and analysis methods", "gene expression", "insects", "arthropoda", "biochemistry", "signal tra...	Translational Regulation of the DOUBLETIME/CKIδ/ε Kinase by LARK Contributes to Circadian Period Modulation	journal.pgen.1004536	null	[ [ "The Drosophila doubletime ( dbt , a . k . a . discs overgrown , dco ) gene encodes a protein homologous to human casein kinase I isoforms ( CKI ) [1] , [2] , in particular CKIδ and CKIε [3] .", "It is known that the DOUBLETIME ( DBT/CKIδ/ε , hereafter referred to as “DBT” ) kinase regulates cell prolifer...	[ "The Drosophila homolog of Casein Kinase I δ/ε , DOUBLETIME ( DBT ) , is required for Wnt , Hedgehog , Fat and Hippo signaling as well as circadian clock function .", "Extensive studies have established a critical role of DBT in circadian period determination .", "However , how DBT expression is regulated remai...	[ "The CKI family of serine/threonine kinase regulates diverse cellular processes , through binding to and phosphorylation of a variety of protein substrates .", "In mammals , mutations in two members of the family , CKIε and CKIδ were found to affect circadian period length , causing phenotypes such as altered cir...	2014
[ "Introduction", "Results", "Discussion", "Materials & methods" ]	[ "antimicrobials", "cell walls", "cellular stress responses", "medicine and health sciences", "pathology and laboratory medicine", "gene regulation", "pathogens", "drugs", "cell processes", "bacillus", "microbiology", "metabolic processes", "vancomycin", "dna transcription", "prokaryotic ...	Stabilization of Bacillus subtilis Spx under cell wall stress requires the anti-adaptor protein YirB	journal.pgen.1007531	null	[ [ "In its natural habitat , the soil-dwelling bacterium Bacillus subtilis is continuously exposed to stressful conditions that can compromise its survival .", "To adapt , bacteria must be able to sense the stress and respond accordingly .", "Adaptation to stress often requires the interplay of multiple ...	[ "Spx is a global transcriptional regulator present in low-GC Gram-positive bacteria , including the model bacterium Bacillus subtilis and various human pathogens .", "In B . subtilis , activation of Spx occurs in response to disulfide stress .", "We recently reported , however , that induction of Spx also occur...	[ "Bacillus subtilis Spx is the founding member of a large family of redox-stress sensing transcriptional regulatory proteins , and Spx orthologs are important for oxidative stress and virulence in several Gram-positive pathogens .", "Spx controls a large regulon in response to disulfide stress .", "Disulfide str...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	SLO BK Potassium Channels Couple Gap Junctions to Inhibition of Calcium Signaling in Olfactory Neuron Diversification	journal.pgen.1005654	null	[ [ "The nervous system generates a tremendous diversity of cell types that enable formation of functional neural circuits for information processing and mediating behaviors .", "Cellular diversity is especially important in the developing sensory system as it allows animals to detect different cues in the en...	[ "The C . elegans AWC olfactory neuron pair communicates to specify asymmetric subtypes AWCOFF and AWCON in a stochastic manner .", "Intercellular communication between AWC and other neurons in a transient NSY-5 gap junction network antagonizes voltage-activated calcium channels , UNC-2 ( CaV2 ) and EGL-19 ( CaV1 ...	[ "Cell type diversity is important for the nervous system to function properly .", "Asymmetric differentiation of neurons along the left-right axis is one way to achieve diversity; however , the molecular mechanisms used to establish neuronal asymmetry are only partly understood .", "In the nematode C . elegans ...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology and life sciences" ]	Hypoxia Adaptations in the Grey Wolf (Canis lupus chanco) from Qinghai-Tibet Plateau	journal.pgen.1004466	null	[ [ "Species inhabiting the Qinghai-Tibet Plateau exist in low oxygen tension environments and must adapt to low oxygen tension [1] .", "Documenting the genetic mechanisms for adaptation to hypoxia can provide insights into the process of evolution under extreme conditions and hypoxia-related disease in human...	[ "The Tibetan grey wolf ( Canis lupus chanco ) occupies habitats on the Qinghai-Tibet Plateau , a high altitude ( >3000 m ) environment where low oxygen tension exerts unique selection pressure on individuals to adapt to hypoxic conditions .", "To identify genes involved in hypoxia adaptation , we generated comple...	[ "Understanding the genetic mechanisms that allow some individuals to live at high altitudes under hypoxic conditions can provide insight into the evolutionary constraints of adaptation to extreme conditions and the development of hypoxia-related disease in humans .", "The Tibetan grey wolf ( Canis lupus chanco ) ...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology/cell differentiation", "developmental biology", "developmental biology/developmental molecular mechanisms" ]	A Key Commitment Step in Erythropoiesis Is Synchronized with the Cell Cycle Clock through Mutual Inhibition between PU.1 and S-Phase Progression	journal.pbio.1000484	During red blood cell development, differentiation and cell cycle progression are intimately and uniquely linked through interdependent mechanisms involving the erythroid transcriptional suppressor PU.1 and the cyclin-dependent kinase inhibitor p57KIP2.	[ [ "Hematopoietic progenitors execute a cell division program in parallel with a differentiation program in which lineage choice is followed by lineage-specific gene expression .", "In many differentiation models , cell cycle exit , driven by cyclin-dependent kinase inhibitors ( CDKI ) , is a prerequisite fo...	[ "Hematopoietic progenitors undergo differentiation while navigating several cell division cycles , but it is unknown whether these two processes are coupled .", "We addressed this question by studying erythropoiesis in mouse fetal liver in vivo .", "We found that the initial upregulation of cell surface CD71 id...	[ "Hematopoietic progenitors that give rise to mature blood cell types execute simultaneous programs of differentiation and proliferation .", "One well-established link between the cell cycle and differentiation programs takes place at the end of terminal differentiation , when cell cycle exit is brought about by t...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	3-OST-7 Regulates BMP-Dependent Cardiac Contraction	journal.pbio.1001727	During zebrafish cardiac development, 3-OST-7 constrains BMP signaling to the atrioventricular junction and precludes it from contractile myocardium, allowing tropomyosin-dependent sarcomere assembly and contraction.	[ [ "Vertebrate heart development requires an accurate integration of patterning and morphogenetic events , leading eventually to the formation of a fully functional heart .", "It initiates with the specification of the different tissue lineages that will compose the mature heart , followed by an intricate se...	[ "The 3-O-sulfotransferase ( 3-OST ) family catalyzes rare modifications of glycosaminoglycan chains on heparan sulfate proteoglycans , yet their biological functions are largely unknown .", "Knockdown of 3-OST-7 in zebrafish uncouples cardiac ventricular contraction from normal calcium cycling and electrophysiolo...	[ "A highly complex environment at the cell surface and in the space between cells is thought to modulate cell behavior .", "Heparan sulfate proteoglycans are cell surface and extracellular matrix molecules that are covalently linked to long chains of repeating sugar units called glycosaminoglycan chains .", "The...	2013
[ "Introduction", "Results", "Discussion", "Materials & Methods" ]	[ "microbial metabolism", "microbial pathogens", "host-pathogen interaction", "biology", "microbiology" ]	Mycobacterium tuberculosis Exploits Asparagine to Assimilate Nitrogen and Resist Acid Stress during Infection	journal.ppat.1003928	null	[ [ "With nearly 1 . 3 million lives claimed in 2012 , as reported by the World Health Organization , tuberculosis ( TB ) remains the major cause of death due to a single bacterial pathogen .", "A better understanding of the interactions between Mycobacterium tuberculosis , the etiologic agent of TB , and its...	[ "Mycobacterium tuberculosis is an intracellular pathogen .", "Within macrophages , M . tuberculosis thrives in a specialized membrane-bound vacuole , the phagosome , whose pH is slightly acidic , and where access to nutrients is limited .", "Understanding how the bacillus extracts and incorporates nutrients fro...	[ "Tuberculosis ( TB ) is still responsible for nearly 1 . 3 million deaths annually .", "There is an urgent need to identify novel drug targets in the tubercle bacillus , Mycobacterium tuberculosis , in order to develop novel therapeutics .", "To proliferate inside its human host , and ensure its spreading , M ....	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "immunology/cellular microbiology and pathogenesis", "immunology/antigen processing and recognition", "immunology/immunity to infections", "pathology/immunology" ]	Dynamic Imaging of Experimental Leishmania donovani-Induced Hepatic Granulomas Detects Kupffer Cell-Restricted Antigen Presentation to Antigen-Specific CD8+ T Cells	journal.ppat.1000805	null	[ [ "Kupffer cells ( KCs ) , first identified in 1876 , are now recognised as the major population of mononuclear phagocytes to inhabit the resting liver .", "Lining the sinusoids , KCs express a wide range of phagocytic and innate recognition receptors , including CD32 [1] , lectin receptors [2] and TLRs ( n...	[ "Kupffer cells ( KCs ) represent the major phagocytic population within the liver and provide an intracellular niche for the survival of a number of important human pathogens .", "Although KCs have been extensively studied in vitro , little is known of their in vivo response to infection and their capacity to dir...	[ "Leishmania donovani is a protozoan parasite that causes severe disease in humans with associated pathology in the spleen and liver .", "In experimental models of L . donovani infection , the hepatic response to infection is characterised by the presence of a focal mononuclear cell-rich inflammatory response ( a ...	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "mathematics/statistics", "pharmacology/drug interactions" ]	The Effect of Azithromycin on Ivermectin Pharmacokinetics—A Population Pharmacokinetic Model Analysis	journal.pntd.0000236	null	[ [ "The operational efficiency of disease elimination programs in developing countries could be improved by integrating delivery of several interventions at local ( village and district ) levels [1]–[3] .", "In areas endemic for co-infection with filarial nematodes and Chlamydia trachomatis , one such integr...	[ "A recent drug interaction study reported that when azithromycin was administered with the combination of ivermectin and albendazole , there were modest increases in ivermectin pharmacokinetic parameters .", "Data from this study were reanalyzed to further explore this observation .", "A compartmental model was...	[ "This paper describes the use of a modeling and simulation approach to explore a reported pharmacokinetic interaction between two drugs ( ivermectin and azithromycin ) , which along with albendazole , are being developed for combination use in neglected tropical diseases .", "This approach is complementary to mor...	2008

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