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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" ]	[ "gastroenterology and hepatology/gastrointestinal infections", "microbiology/medical microbiology", "infectious diseases/antimicrobials and drug resistance" ]	The Sudden Dominance of blaCTX–M Harbouring Plasmids in Shigella spp. Circulating in Southern Vietnam	journal.pntd.0000702	null	[ [ "Enterobacteriaceae that have the capability to express CTX-M ( so named because of their hydrolytic activity against cefotaxime ) family extended spectrum beta lactamases ( ESBLs ) have emerged as a major health threat worldwide [1] , [2] .", "Most of the research in this area is conducted in industriali...	[ "Plasmid mediated antimicrobial resistance in the Enterobacteriaceae is a global problem .", "The rise of CTX-M class extended spectrum beta lactamases ( ESBLs ) has been well documented in industrialized countries .", "Vietnam is representative of a typical transitional middle income country where the spectrum...	[ "Shigellosis is a disease caused by bacteria belonging to Shigella spp .", "and is a leading cause of bacterial gastrointestinal infections in infants in unindustrialized countries .", "The Shigellae are dynamic and capable of rapid change when placed under selective pressure in a human population .", "Extend...	2010
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "body fluids", "immune physiology", "enzyme-linked immunoassays", "spleen", "melioidosis", "urine", "drug delivery system preparation", "bacterial diseases", "routes of administration", "antigen encapsulation", "pharmaceutics", "pharmacology", "kidneys", "...	In vivo Distribution and Clearance of Purified Capsular Polysaccharide from Burkholderia pseudomallei in a Murine Model	journal.pntd.0005217	null	[ [ "Burkholderia pseudomallei is a Gram-negative , soil-dwelling bacillus and the etiologic pathogen of melioidosis , a severe infection endemic in tropical areas with the highest incidence in Southeast Asia and northern Australia [1] .", "In early 2016 , it was predicted that approximately 165 , 000 individ...	[ "Burkholderia pseudomallei is the causative agent of melioidosis , a severe infection prominent in northern Australia and Southeast Asia .", "The “gold standard” for melioidosis diagnosis is bacterial isolation , which takes several days to complete .", "The resulting delay in diagnosis leads to delayed treatme...	[ "An outer membrane component , capsular polysaccharide ( CPS ) , is a virulence factor expressed by many Gram-negative bacteria including Burkholderia pseudomallei , the causative agent of melioidosis .", "Recently , B . pseudomallei CPS was identified as a useful diagnostic biomarker , leading to the development...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics", "computational biology" ]	Information Flow Analysis of Interactome Networks	journal.pcbi.1000350	null	[ [ "In the last decade , several high-throughput experimental techniques have allowed", "systematic mapping of protein-protein interaction networks , or interactome networks ,", "for model organisms [1]–[4] and human [5] , [6] .", "Interactome networks provide us with a global view of complex biologi...	[ "Recent studies of cellular networks have revealed modular organizations of genes", "and proteins .", "For example , in interactome networks , a module refers to a group", "of interacting proteins that form molecular complexes and/or biochemical", "pathways and together mediate a biological process .", "H...	[ "Protein–protein interactions mediate numerous biological processes .", "In", "the last decade , there have been efforts to comprehensively map", "protein–protein interactions occurring in an organism .", "The interaction", "data generated from these high-throughput projects can be represented as", "int...	2009
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "bacteriology", "phosphorylation", "medicine and health sciences", "gut bacteria", "protein interactions", "pathology and laboratory medicine", "chemical compounds", "clostridium", "pathogens", "bacillus", "microbiology", "marker genes", "organic compounds", "bacterial sporulation", "pro...	Flexibility and constraint: Evolutionary remodeling of the sporulation initiation pathway in Firmicutes	journal.pgen.1007470	null	[ [ "Responses to changing environmental conditions are mediated by signal transduction pathways that recognize a signal , convey that signal into the cell , and initiate an appropriate cellular response .", "In bacteria , two-component signaling systems , typically comprised of a histidine kinase ( HK ) and ...	[ "The evolution of signal transduction pathways is constrained by the requirements of signal fidelity , yet flexibility is necessary to allow pathway remodeling in response to environmental challenges .", "A detailed understanding of how flexibility and constraint shape bacterial two component signaling systems is...	[ "Survival in a changing world requires signal transduction circuitry that can evolve to sense and respond to new environmental challenges .", "The Firmicute sporulation initiation ( Spo0 ) pathway is a compelling example of a pathway with a circuit diagram that has changed over the course of evolution .", "In C...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "hiv", "vascular biology", "viral diseases", "cardiovascular" ]	Slit2/Robo4 Signaling Modulates HIV-1 gp120-Induced Lymphatic Hyperpermeability	journal.ppat.1002461	null	[ [ "HIV becomes established at mucosal sites by infecting dendritic cells , CD4+ T lymphocytes and macrophages in the lamina propria after its entry .", "From there , virus and infected cells disseminate via lymphatic endothelial channels to the draining lymph nodes , and subsequently pass into the bloodstre...	[ "Dissemination of HIV in the host involves transit of the virus and virus-infected cells across the lymphatic endothelium .", "HIV may alter lymphatic endothelial permeability to foster dissemination , but the mechanism is largely unexplored .", "Using a primary human lymphatic endothelial cell model , we found...	[ "The most common route of HIV transmission is through unprotected sexual contact .", "By this route , HIV first infects cells in the mucous membranes of the mouth , vagina or rectum .", "From the mucosa , virus and virus-infected cells move through lymphatic endothelial channels to draining lymph nodes where th...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "protein interactions", "molecular dynamics", "macromolecular assemblies", "signaling networks", "protein structure", "biophysics simulations", "sequence analysis", "biochemistry simulations", "proteins", "chemistry", "biology", "proteomics", "biophysics", "biochemistry", "biochemical si...	Dynamic Control of Selectivity in the Ubiquitination Pathway Revealed by an ASP to GLU Substitution in an Intra-Molecular Salt-Bridge Network	journal.pcbi.1002754	null	[ [ "Biological systems critically rely on selective and specific protein interactions , creating building blocks that cooperatively form the basis of functional complexity [1] .", "In particular , regulatory and signaling pathways , such as conjugation of ubiquitin ( Ub ) or similar ubiquitin-like modifiers ...	[ "Ubiquitination relies on a subtle balance between selectivity and promiscuity achieved through specific interactions between ubiquitin-conjugating enzymes ( E2s ) and ubiquitin ligases ( E3s ) .", "Here , we report how a single aspartic to glutamic acid substitution acts as a dynamic switch to tip the selectivit...	[ "During their life , proteins undergo various modifications ranging from structural marking or signaling to degradation .", "One major biochemical process involves ubiquitin , a small and evolutionary conserved protein .", "This regulatory protein serves as a tag that , when attached to a protein substrate , al...	2012
[ "Introduction", "Methods" ]	[ "dermatology", "invertebrates", "typhus", "medicine and health sciences", "pathology and laboratory medicine", "japan", "pathogens", "geographical locations", "microbiology", "animals", "bacterial diseases", "signs and symptoms", "infectious disease control", "bacterial pathogens", "orie...	A review of the global epidemiology of scrub typhus	journal.pntd.0006062	null	[ [ "The traditional endemic area of scrub typhus is known as the “tsutsugamushi triangle” .", "It is a region covering more than 8 million km2 , from the Russian Far East in the north , to Pakistan in the west , Australia in the south , and the Japan in the east [23 , 48 , 49] .", "There are one billion ...	[ "Scrub typhus is a serious public health problem in the Asia-Pacific area .", "It threatens one billion people globally , and causes illness in one million people each year .", "Caused by Orientia tsutsugamushi , scrub typhus can result in severe multiorgan failure with a case fatality rate up to 70% without ap...	[ "Scrub typhus is a serious public health problem in the Asia-Pacific area .", "There is an estimated one million new scrub typhus infections each year , and over one billion people around the world are at risk .", "Without appropriate treatment , the case fatality rate of scrub typhus can reach 30% or even high...	2017
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "computational biology/systems biology", "genetics and genomics/gene expression" ]	Context-Specific Metabolic Networks Are Consistent with Experiments	journal.pcbi.1000082	null	[ [ "Commonly , genome-scale metabolic networks are reconstructed to contain all known metabolic genes and reactions in a particular organism [1] .", "These reconstructions are thus a superset of the metabolic reactions that are functioning in the organism at any one time .", "The processes that determine...	[ "Reconstructions of cellular metabolism are publicly available for a variety of different microorganisms and some mammalian genomes .", "To date , these reconstructions are “genome-scale” and strive to include all reactions implied by the genome annotation , as well as those with direct experimental evidence .", ...	[ "Systems biology aims to characterize cells and organisms as systems through the careful curation of all components .", "Large models that account for all known metabolism in microorganisms have been created by our group and by others around the world .", "Furthermore , models are available for human cells .", ...	2008
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "myocardial infarction", "clinical genetics", "genetics and genomics", "cardiovascular" ]	Genome-Wide Association of Pericardial Fat Identifies a Unique Locus for Ectopic Fat	journal.pgen.1002705	null	[ [ "Obesity is a heterogeneous condition , and its attendant metabolic sequelae may not be adequately captured by using traditional metrics of generalized adiposity [1] .", "In part , this is because different fat depots may be associated with differential metabolic risk .", "For example , visceral abdom...	[ "Pericardial fat is a localized fat depot associated with coronary artery calcium and myocardial infarction .", "We hypothesized that genetic loci would be associated with pericardial fat independent of other body fat depots .", "Pericardial fat was quantified in 5 , 487 individuals of European ancestry from th...	[ "Pericardial fat is a localized fat depot associated with coronary artery calcium and myocardial infarction .", "To test whether genetic loci are associated with pericardial fat independent of other body fat depots , we measured pericardial fat in 5 , 487 individuals of European ancestry .", "After performing a...	2012
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "flow cytometry", "innate immune system", "medicine and health sciences", "immune cells", "immune physiology", "cytokines", "immunology", "messenger rna", "vertebrates", "animals", "mammals", "organisms", "developmental biology", "molecular development", "research and an...	Humoral immune response to adenovirus induce tolerogenic bystander dendritic cells that promote generation of regulatory T cells	journal.ppat.1007127	null	[ [ "Human adenoviruses ( HAdVs ) , of which there may be 85 types ( based on serology and genome analyses ) , typically cause self-limiting respiratory , ocular , and gastro-intestinal tract infections in immunocompetent individuals .", "After repeated encounters , most young adults generally harbor cross-re...	[ "Following repeated encounters with adenoviruses most of us develop robust humoral and cellular immune responses that are thought to act together to combat ongoing and subsequent infections .", "Yet in spite of robust immune responses , adenoviruses establish subclinical persistent infections that can last for de...	[ "While numerous studies have addressed the cellular and humoral response to primary virus encounters , relatively little is known about the interplay between persistent infections , neutralizing antibodies , antigen-presenting cells , and T-cell responses .", "Our studies suggests that if adenovirus–antibody comp...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Morphological and Molecular Descriptors of the Developmental Cycle of Babesia divergens Parasites in Human Erythrocytes	journal.pntd.0003711	null	[ [ "Human babesiosis is a rapidly emerging , zoonotic , infectious disease causing potentially life-threatening malaria-like symptoms in humans .", "It is caused by intra-erythrocytic protozoan parasites of the genus Babesia [1] and it is transmitted to humans via an ixodid tick vector or through a blood tra...	[ "Human babesiosis , especially caused by the cattle derived Babesia divergens parasite , is on the increase , resulting in renewed attentiveness to this potentially life threatening emerging zoonotic disease .", "The molecular mechanisms underlying the pathophysiology and intra-erythrocytic development of these p...	[ "Vector-borne parasitic diseases are still the major cause of morbidity and mortality in both humans as animals .", "Some of these parasites have been well studied , including the malaria parasite , Plasmodium falciparum , since these cause major fatalities in humans .", "However , other parasites like Babesia ...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "fish", "morphogenic segmentation", "immunology", "parathyroid", "vertebrates", "animals", "epithelial cells", "animal models", "osteichthyes", "developmental biology", "model organisms", "experimental organism systems", "embryos", "morphogenesis", "rese...	Tbx1 and Foxi3 genetically interact in the pharyngeal pouch endoderm in a mouse model for 22q11.2 deletion syndrome	journal.pgen.1008301	null	[ [ "The pharyngeal apparatus ( PA ) is an evolutionarily conserved structure that forms early in vertebrate embryos .", "The PA develops as a series of bulges , termed arches , found on the lateral surface of the head region of the embryo .", "During mammalian development , five pairs of pharyngeal arche...	[ "We investigated whether Tbx1 , the gene for 22q11 . 2 deletion syndrome ( 22q11 . 2DS ) and Foxi3 , both required for segmentation of the pharyngeal apparatus ( PA ) to individual arches , genetically interact .", "We found that all Tbx1+/-;Foxi3+/- double heterozygous mouse embryos had thymus and parathyroid gl...	[ "The mechanisms required for segmentation of the pharyngeal apparatus ( PA ) to individual arches are not precisely delineated in mammalian species .", "Using mouse models , we found that two transcription factor genes , Tbx1 , the gene for 22q11 . 2 deletion syndrome and Foxi3 , genetically interact in the third...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "neglected tropical diseases", "vectors and hosts" ]	Genetic Characterization of Zika Virus Strains: Geographic Expansion of the Asian Lineage	journal.pntd.0001477	null	[ [ "Zika virus ( ZIKV ) is a member of the Spondweni serocomplex within the genus Flavivirus , family Flaviviridae [1] .", "Other mosquito-borne flaviviruses of public health importance include yellow fever , dengue , St . Louis encephalitis , West Nile and Japanese encephalitis viruses .", "Although res...	[ "Zika virus ( ZIKV ) is a mosquito-borne flavivirus distributed throughout much of Africa and Asia .", "Infection with the virus may cause acute febrile illness that clinically resembles dengue fever .", "A recent study indicated the existence of three geographically distinct viral lineages; however this analys...	[ "Zika virus ( ZIKV ) is a mosquito-transmitted flavivirus found in both Africa and Asia .", "Human infection with the virus may result in a febrile illness similar to dengue fever and many other tropical infections found in these regions .", "Previously , little was known about the genetic relationships between...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "cell biology", "genetics", "biology and life sciences", "molecular cell biology" ]	TIF-IA-Dependent Regulation of Ribosome Synthesis in Drosophila Muscle Is Required to Maintain Systemic Insulin Signaling and Larval Growth	journal.pgen.1004750	null	[ [ "Nutrient availability is a critical determinant of cell , tissue and body growth in developing animals .", "Nearly two decades of research has identified the Target-of-Rapamycin ( TOR ) kinase signaling pathway as a major nutrient-responsive growth pathway in eukaryotes [1] , [2] .", "TOR functions i...	[ "The conserved TOR kinase signaling network links nutrient availability to cell , tissue and body growth in animals .", "One important growth-regulatory target of TOR signaling is ribosome biogenesis .", "Studies in yeast and mammalian cell culture have described how TOR controls rRNA synthesis—a limiting step ...	[ "All animals need adequate nutrition to grow and develop .", "Studies in tissue culture and model organisms have identified the TOR kinase signaling pathway as a key nutrient-dependent regulator of growth .", "Under nutrient rich conditions , TOR kinase is active and stimulates metabolic processes that drive gr...	2014
[ "Introduction", "Results", "Discussion" ]	[ "medicine", "immune cells", "immune activation", "immunology", "host-pathogen interaction", "microbiology", "fungi", "immune defense", "fungal diseases", "infectious diseases", "mycology", "biology", "infectious disease modeling", "pathogenesis", "immune response", "yeast", "computer...	A Virtual Infection Model Quantifies Innate Effector Mechanisms and Candida albicans Immune Escape in Human Blood	journal.pcbi.1003479	null	[ [ "Sepsis is a systemic inflammatory response triggered by infection and a major cause of death worldwide [1]–[3] .", "In recent years , fungal pathogens have caused an increasing number of sepsis cases with high mortality rates [4] , [5] .", "The major fungal pathogen Candida albicans is a common human...	[ "Candida albicans bloodstream infection is increasingly frequent and can result in disseminated candidiasis associated with high mortality rates .", "To analyze the innate immune response against C . albicans , fungal cells were added to human whole-blood samples .", "After inoculation , C . albicans started to...	[ "Candida albicans is the most important fungal pathogen in nosocomial bloodstream infections .", "So far little is known about the interplay of different cellular and non-cellular immune mechanisms mediating the protective response against C . albicans in blood .", "The in vivo scenario of C . albicans infectio...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "bacteriology", "gram negative bacteria", "organismal evolution", "medical microbiology", "microbial evolution", "gene identification and analysis", "gene expression", "genetics", "gene regulation", "biology and life sciences", "molecular genetics", "microbiology", "microbial pathogens", "...	Transcriptional Frameshifting Rescues Citrobacter rodentium Type VI Secretion by the Production of Two Length Variants from the Prematurely Interrupted tssM Gene	journal.pgen.1004869	null	[ [ "The Type VI secretion system ( T6SS ) is a macromolecular machine widespread in proteobacteria that delivers protein toxins into either eukaryotic or bacterial cells [1]–[5] .", "The Vibrio cholerae T6SS has been shown to inject an effector domain carrying actin cross-linking activity into eukaryotic cel...	[ "The Type VI secretion system ( T6SS ) mediates toxin delivery into both eukaryotic and prokaryotic cells .", "It is composed of a cytoplasmic structure resembling the tail of contractile bacteriophages anchored to the cell envelope through a membrane complex composed of the TssL and TssM inner membrane proteins ...	[ "Nonstandard decoding mechanisms lead to the synthesis of different protein variants from a single DNA sequence .", "These mechanisms are particularly important when the genome length has to be limited such as viral genomes , limited by the available space in the capsid , or to synthesize two different polypeptid...	2014
[ "Introduction", "Material and methods", "Results", "Discussion", "Conclusions" ]	[ "medicine and health sciences", "tropical diseases", "vertebrates", "parasitic diseases", "animals", "mammals", "health care", "sanitation", "neglected tropical diseases", "infectious disease control", "public and occupational health", "infectious diseases", "swine", "zoonoses", "hygiene...	Animal influence on water, sanitation and hygiene measures for zoonosis control at the household level: A systematic literature review	journal.pntd.0006619	null	[ [ "Neglected tropical diseases ( NTDs ) are a group of communicable diseases estimated to affect over a billion people globally , particularly those with least economic resources , access to health care , good nutrition , clean water and sanitation facilities; the weak political influence of affected groups as ...	[ "Neglected zoonotic diseases ( NZDs ) have a significant impact on the livelihoods of the world’s poorest populations , which often lack access to basic services .", "Water , sanitation and hygiene ( WASH ) programmes are included among the key strategies for achieving the World Health Organization’s 2020 Roadmap...	[ "Neglected Tropical Diseases ( NTDs ) affect the health and economies of populations globally .", "Many of these diseases are zoonotic , occurring as a consequence of the interaction between humans and animals , particularly at the household level in low- and middle-income countries .", "Based on the WHO Global...	2018
[ "Introduction", "Materials and methods", "Results and discussion" ]	[ "cell physiology", "medicine and health sciences", "pathology and laboratory medicine", "chemical compounds", "biological cultures", "metabolic networks", "cell processes", "cell metabolism", "toxicology", "physiological processes", "toxicity", "metabolites", "network analysis", "cell grow...	Characterizing steady states of genome-scale metabolic networks in continuous cell cultures	journal.pcbi.1005835	null	[ [ "Biotechnological products are obtained by treating cells as little factories that transform substrates into products of interest .", "There are three major modes of cell culture: batch , fed-batch and continuous .", "In batch , cells are grown with a fixed initial pool of nutrients until they starve ...	[ "In the continuous mode of cell culture , a constant flow carrying fresh media replaces culture fluid , cells , nutrients and secreted metabolites .", "Here we present a model for continuous cell culture coupling intra-cellular metabolism to extracellular variables describing the state of the bioreactor , taking ...	[ "While at present most biotechnology industrial facilities adopt batch or fed-batch processes , continuous processing has been vigorously defended in the literature and many predict its adoption in the near future .", "However , identical cultures may lead to distinct steady states and the lack of comprehension o...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases/helminth infections", "infectious diseases/antimicrobials and drug resistance", "infectious diseases/neglected tropical diseases" ]	Comparison of Microscopy and Alamar Blue Reduction in a Larval Based Assay for Schistosome Drug Screening	journal.pntd.0000795	null	[ [ "Schistosomiasis is the most important helminth infection and the second most important parasitic disease next to malaria .", "It continues to spread in parts of the world due to water management and irrigation projects [1] .", "The major current strategy for control of schistosomiasis is chemotherapy...	[ "In view of the current widespread use of and reliance on a single schistosomicide , praziquantel , there is a pressing need to discover and develop alternative drugs for schistosomiasis .", "One approach to this is to develop High Throughput in vitro whole organism screens ( HTS ) to identify hits amongst large ...	[ "Only one drug , praziquantel , is widely available for treating schistosomiasis , a disease affecting an estimated 200 million people .", "Because of increasing usage there is concern about development of praziquantel drug resistance and a perceived need to develop new schistosomicides .", "Possible sources of...	2010
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "markov models", "computational biology", "social sciences", "anthropology", "genetic mapping", "simulation and modeling", "neanderthals", "mathematics", "paleontology", "population biology", "paleoanthropology", "research and analysis methods", "population density", "hidden markov models"...	Detecting archaic introgression using an unadmixed outgroup	journal.pgen.1007641	null	[ [ "An archaic genomic segment introgressed into a population is expected to have a high density of variants not found in populations without the introgression .", "We use a Hidden Markov Model ( HMM ) to classify genomic segments into states with varying density of such variants .", "We focus on a scena...	[ "Human populations outside of Africa have experienced at least two bouts of introgression from archaic humans , from Neanderthals and Denisovans .", "In Papuans there is prior evidence of both these introgressions .", "Here we present a new approach to detect segments of individual genomes of archaic origin wit...	[ "The genetic history of present-day individuals includes episodes of mating between divergent groups , which have led to 'introgressed' genetic material persisting in modern genome sequences .", "Perhaps the most notable examples of such events in humans are the introgressions from Neanderthals into non-Africans ...	2018
[ "Introduction", "Methods", "Results", "Discussion", "Conclusions" ]	[ "death rates", "invertebrates", "medicine and health sciences", "body fluids", "engineering and technology", "animals", "reproductive physiology", "developmental biology", "pupae", "population biology", "insect vectors", "prototypes", "infectious diseases", "aedes aegypti", "technology d...	Reducing the cost and assessing the performance of a novel adult mass-rearing cage for the dengue, chikungunya, yellow fever and Zika vector, Aedes aegypti (Linnaeus)	journal.pntd.0007775	null	[ [ "Aedes aegypti ( Linnaeus ) is a highly invasive , medically important mosquito species which has received a considerable increase in attention after being linked to the Zika outbreak in Brazil in 2015 [1] .", "Together with Aedes albopictus ( Skuse ) , the species also transmits several arboviral disease...	[ "The widespread emergence of resistance to insecticides used to control adult Aedes mosquitoes has made traditional control strategies inadequate for the reduction of various vector populations .", "Therefore , complementary vector control methods , such as the Sterile Insect Technique , are needed to enhance exi...	[ "Dengue , among other arboviral infections , is a neglected disease and a major health issue that is re-emerging in tropical countries due to the poor efficacy of conventional vector control methods .", "Therefore , there is a growing need for more sustainable techniques to control Aedes mosquito species , while ...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics and genomics/genetics of disease", "mathematics/statistics", "genetics and genomics/population genetics" ]	Simultaneous Analysis of All SNPs in Genome-Wide and Re-Sequencing Association Studies	journal.pgen.1000130	null	[ [ "The ideal analysis of a genome-wide association ( GWA ) study for a complex disease would involve analysing all the SNP genotypes simultaneously to find a set of SNPs most associated with disease risk .", "Such an analysis can improve performance over single-SNP tests , since a weak effect may be more ap...	[ "Testing one SNP at a time does not fully realise the potential of genome-wide association studies to identify multiple causal variants , which is a plausible scenario for many complex diseases .", "We show that simultaneous analysis of the entire set of SNPs from a genome-wide study to identify the subset that b...	[ "Tests of association with disease status are normally conducted one SNP at a time , ignoring the effects of all other genotyped SNPs .", "We developed a computationally efficient method to simultaneously analyse all SNPs , either in a genome-wide association ( GWA ) study , or a fine-mapping study based on re-se...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology and life sciences", "medicine and health sciences", "research and analysis methods" ]	The Association of the Vanin-1 N131S Variant with Blood Pressure Is Mediated by Endoplasmic Reticulum-Associated Degradation and Loss of Function	journal.pgen.1004641	null	[ [ "Hypertension ( HTN ) or high blood pressure ( BP ) is common in populations worldwide and a major risk factor for cardiovascular disease ( CVD ) and all-cause mortality [1] .", "Although it is observed across ethnically diverse populations , the prevalence of HTN in the US varies from 27% in persons of E...	[ "High blood pressure ( BP ) is the most common cardiovascular risk factor worldwide and a major contributor to heart disease and stroke .", "We previously discovered a BP-associated missense SNP ( single nucleotide polymorphism ) –rs2272996–in the gene encoding vanin-1 , a glycosylphosphatidylinositol ( GPI ) -an...	[ "Hypertension ( HTN ) or high blood pressure ( BP ) is common worldwide and a major risk factor for cardiovascular disease and all-cause mortality .", "Identification of genetic variants of consequence for HTN serves as the molecular basis for its treatment .", "Using admixture mapping analysis of the Family Bl...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "periplasm", "fluorescence imaging", "oxidative stress", "metabolic processes", "microbiology", "fermentation", "deletion mutagenesis", "molecular biology techniques", "mutagenesis and gene deletion techniques", "cellular structures and organelles", "research and analysis methods", "stress sig...	Oxidative stress induced in E. coli by the human antimicrobial peptide LL-37	journal.ppat.1006481	null	[ [ "Antimicrobial peptides ( AMPs , also called host-defense peptides ) play a number of important roles in the innate immune response of plants and animals [1] .", "Important human AMPs include the cathelidicin LL-37 and the defensins [2] .", "In humans , AMPs are constitutively expressed in phagocytes ...	[ "Antimicrobial peptides ( AMPs ) are thought to kill bacterial cells by permeabilizing their membranes .", "However , some antimicrobial peptides inhibit E . coli growth more efficiently in aerobic than in anaerobic conditions .", "In the attack of the human cathelicidin LL-37 on E . coli , real-time , single-c...	[ "Antimicrobial peptides play a significant role in the innate immune response of plants and animals , including humans .", "While it is well known that AMPs can permeabilize bacterial cell membranes , a growing body of evidence indicates that they cause a variety of additional deleterious effects .", "Here we u...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "body weight", "medicine and health sciences", "forkhead box", "diabetic endocrinology", "gene regulation", "regulatory proteins", "dna-binding proteins", "hormones", "endocrine physiology", "circadian oscillators", "physiological parameters", "obesity", "transcription factors", "chronobio...	Insulin signaling and reduced glucocorticoid receptor activity attenuate postprandial gene expression in liver	journal.pbio.2006249	null	[ [ "Precise temporal expression of hepatic enzymes is crucial for metabolic homeostasis , and a major part of hepatic circadian protein synthesis is regulated by precisely timed gene transcription and mRNA translation [1] .", "This is controlled by complex interactions between rhythmic endocrine signaling , ...	[ "Hepatic circadian gene transcription is tightly coupled to feeding behavior , which has a profound impact on metabolic disorders associated with diet-induced obesity .", "Here , we describe a genomics approach to uncover mechanisms controlling hepatic postprandial gene expression .", "Combined transcriptomic a...	[ "The liver is an essential organ regulating metabolic homeostasis in response to fluctuations of metabolites induced by daily rhythms of food intake .", "Homeostasis is maintained by precise dynamic regulation of signaling pathways controlling a wealth of enzymatic reactions involving lipid , bile acid , amino ac...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/bacterial infections", "microbiology/microbial physiology and metabolism", "biochemistry/small molecule chemistry", "urology/urological infections" ]	Quantitative Metabolomics Reveals an Epigenetic Blueprint for Iron Acquisition in Uropathogenic Escherichia coli	journal.ppat.1000305	null	[ [ "Urinary tract infection ( UTI ) is a highly prevalent infectious disease with a well-known female predilection and a high incidence of recurrence [1] .", "E . coli is responsible for up to 85% of community-acquired UTI , and previous studies suggest that the same E . coli strain can cause recurrent UTI's...	[ "Bacterial pathogens are frequently distinguished by the presence of acquired genes associated with iron acquisition .", "The presence of specific siderophore receptor genes , however , does not reliably predict activity of the complex protein assemblies involved in synthesis and transport of these secondary meta...	[ "Urinary tract infections ( UTIs ) are among the most common bacterial infections treated by physicians worldwide .", "Although symptoms of acute infection are often resolved with a course of antibiotics , the same bacterial strain often causes subsequent bouts of symptomatic infection .", "Escherichia coli are...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	African Glucose-6-Phosphate Dehydrogenase Alleles Associated with Protection from Severe Malaria in Heterozygous Females in Tanzania	journal.pgen.1004960	null	[ [ "Amongst the approximately 190 genetic variants causing clinical deficiency of Glucose-6-phosphate dehydrogenase ( G6PD ) that have been characterised [1] , the A- deficiency is the most common in sub-Saharan Africa populations , and is associated with protection from severe malaria [2 , 3] .", "An unders...	[ "X-linked Glucose-6-phosphate dehydrogenase ( G6PD ) A- deficiency is prevalent in sub-Saharan Africa populations , and has been associated with protection from severe malaria .", "Whether females and/or males are protected by G6PD deficiency is uncertain , due in part to G6PD and malaria phenotypic complexity an...	[ "Glucose-6-phosphate dehydrogenase ( G6PD ) is an essential enzyme that protects red blood cells from oxidative damage .", "Numerous genetic variants of G6PD , residing in the X chromosome , are found among African populations: mutations causing A- deficiency can lead to serious clinical outcomes ( including hemo...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "statistical mechanics", "applied mathematics", "bayes theorem", "marine biology", "animal behavior", "mathematics", "theoretical ecology", "stochastic processes", "zoology", "freshwater ecology", "complex systems", "theoretical biology", "probability density", "biology", "probability th...	Multi-scale Inference of Interaction Rules in Animal Groups Using Bayesian Model Selection	journal.pcbi.1002961	null	[ [ "The most striking features of the collective motion of animal groups are the large-scale patterns produced by flocks , schools and other groups .", "These patterns can extend over scales that exceed the interaction ranges of the individuals within the group [1]–[4] .", "For most flocking animals , th...	[ "Inference of interaction rules of animals moving in groups usually relies on an analysis of large scale system behaviour .", "Models are tuned through repeated simulation until they match the observed behaviour .", "More recent work has used the fine scale motions of animals to validate and fit the rules of in...	[ "The collective movement of animals in a group is an impressive phenomenon whereby large scale spatio-temporal patterns emerge from simple interactions between individuals .", "Theoretically , much of our understanding of animal group motion comes from models inspired by statistical physics .", "In these models...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "classical mechanics", "protein interactions", "molecular dynamics", "potential energy", "protein folding", "protein structure", "thermodynamics", "reaction dynamics", "physical chemistry", "proteins", "chemistry", "molecular biology", "free energy", "physics", "biochemistry", "biochem...	Molecular recognition and packing frustration in a helical protein	journal.pcbi.1005909	null	[ [ "Molecular recognition is the basis of biological function .", "For different parts of the same molecule or different molecules to recognize one another , a target set of interactions need to be favored while other potential interactions are disfavored .", "Biomolecules accomplish these simultaneous t...	[ "Biomolecular recognition entails attractive forces for the functional native states and discrimination against potential nonnative interactions that favor alternate stable configurations .", "The challenge posed by the competition of nonnative stabilization against native-centric forces is conceptualized as frus...	[ "Biomolecules need to recognize one another with high specificity: promoting “native” functional intermolecular binding events while avoiding detrimental “nonnative” bound configurations; i . e . , “frustration”—the tendency for nonnative interactions—has to be minimized .", "Folding of globular proteins entails ...	2017
[ "Introduction", "Results", "Discussion" ]	[ "parasite groups", "medicine and health sciences", "plasmodium", "parasite evolution", "geographical locations", "tropical diseases", "human genomics", "parasitic diseases", "parasitology", "genetic mapping", "apicomplexa", "paleontology", "paleogenetics", "africa", "people and places", ...	Population genetic analysis of the DARC locus (Duffy) reveals adaptation from standing variation associated with malaria resistance in humans	journal.pgen.1006560	null	[ [ "Infectious diseases have played a crucial part in shaping current and past human demography and genetics .", "Among all infectious diseases affecting humans , malaria has long been recognized as one of the strongest selective pressures in recent human history [1 , 2] .", "The Duffy antigen , also kno...	[ "The human DARC ( Duffy antigen receptor for chemokines ) gene encodes a membrane-bound chemokine receptor crucial for the infection of red blood cells by Plasmodium vivax , a major causative agent of malaria .", "Of the three major allelic classes segregating in human populations , the FY*O allele has been shown...	[ "Infectious diseases have undoubtedly played an important role in ancient and modern human history .", "Yet , there are relatively few regions of the genome involved in resistance to pathogens that show a strong selection signal in current genome-wide searches for this kind of signal .", "We revisit the evoluti...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "antimicrobials", "medicine and health sciences", "drugs", "tropical diseases", "geographical locations", "australia", "microbiology", "census", "health care", "bacterial diseases", "research design", "pharmaceutics", "antibiotics", "eye diseases", "screening guidelines", "drug adminis...	Relationship between Community Drug Administration Strategy and Changes in Trachoma Prevalence, 2007 to 2013	journal.pntd.0004810	null	[ [ "Trachoma , caused by serotypes of Chlamydia trachomatis is a major cause of blindness globally . [1]", "In 1997 The Alliance for the Global Elimination of Blinding Trachoma by 2020 ( GET 2020 ) initiative was launched .", "Supported by the World Health Organization ( WHO ) , the alliance promotes its...	[ "Australia is the only high income country with persisting endemic trachoma .", "A national control program involving mass drug administration with oral azithromycin , in place since 2006 , has some characteristics which differ from programs in low income settings , particularly in regard to the use of a wider ra...	[ "Australia is the only high income country with persisting endemic trachoma and a national control program has been in place since 2006 .", "The program involves annual screening of children for trachoma in communities designated to be at high risk of disease and treatment of those affected with the antibiotic az...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases", "plant science", "medicine and health sciences", "theoretical biology", "population modeling", "infectious disease epidemiology", "epidemiology", "disease dynamics", "population dynamics", "plant pathology", "biology and life sciences", "population biology", "viral dis...	The 2012 Madeira Dengue Outbreak: Epidemiological Determinants and Future Epidemic Potential	journal.pntd.0003083	null	[ [ "The ongoing spread of dengue , the most important mosquito-borne flavivirus affecting humans , from predominantly tropical and sub-tropical regions into higher latitudes , such as the United States of America , Australia and Europe , is a major public health concern [1] .", "Globalisation and climate cha...	[ "Dengue , a vector-borne viral disease of increasing global importance , is classically associated with tropical and sub-tropical regions around the world .", "Urbanisation , globalisation and climate trends , however , are facilitating the geographic spread of its mosquito vectors , thereby increasing the risk o...	[ "In 2012 , Europe saw its first dengue epidemic taking place on the Atlantic island of Madeira .", "Due to strong tourism links , 81 cases were introduced into continental Europe in a short period of three months .", "Although Aedes aegypti , the mosquito-vector responsible for this particular outbreak , is ext...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "genetics and genomics/complex traits" ]	A Novel Statistic for Genome-Wide Interaction Analysis	journal.pgen.1001131	null	[ [ "In the past three years , about 400 genome-wide association studies ( GWAS ) that", "focused largely on individually testing the associations of single SNP with diseases", "have been conducted [1] .", "These studies have identified more than 531 SNPs associated with different traits or", "dis...	[ "Although great progress in genome-wide association studies ( GWAS ) has been made ,", "the significant SNP associations identified by GWAS account for only a few", "percent of the genetic variance , leading many to question where and how we can", "find the missing heritability .", "There is increasing inte...	[ "It is expected that genome-wide interaction analysis can be a possible source of", "finding heritability unexplained by current GWAS .", "However , the existing", "statistics for testing interaction have low power for genome-wide interaction", "analysis .", "To meet challenges raised by genome-wide inter...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "corals", "infectious diseases", "public health and epidemiology", "cnidaria (jellyfish", "ecology", "etc.)", "hydra" ]	Thermal Stress and Coral Cover as Drivers of Coral Disease Outbreaks	journal.pbio.0050124	High-resolution satellite data of ocean temperature across the Great Barrier Reef reveal that warm temperature anomalies can drive outbreaks of coral disease under conditions of high coral cover.	[ [ "Climatic and oceanographic conditions can modify a wide variety of ecological processes .", "For example , ocean temperature can control species ranges , the strength of species interactions , the dispersal and survival of marine larvae , and the rates of metabolism and speciation [1–6] .", "Addition...	[ "Very little is known about how environmental changes such as increasing temperature affect disease dynamics in the ocean , especially at large spatial scales .", "We asked whether the frequency of warm temperature anomalies is positively related to the frequency of coral disease across 1 , 500 km of Australia's ...	[ "Coral reefs have been decimated over the last several decades .", "The global decline of reef-building corals is of particular concern .", "Infectious diseases are thought to be key to this mass coral mortality , and many reef ecologists suspect that anomalously high ocean temperatures contribute to the increa...	2007
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "animal types", "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "immunology", "tropical diseases", "geographical locations", "vertebrates", "microbiology", "pets and companion animals", "dogs", "animals", "mammals", "viruses", "preventive medicine", "r...	Insights and efforts to control rabies in Zambia: Evaluation of determinants and barriers to dog vaccination in Nyimba district	journal.pntd.0005946	null	[ [ "Rabies has been a public health concern and has plagued both humans and animals since around 2000 BC [1] .", "The disease is endemic on all continents except Antarctica [2] and it is believed to cause approximately 59 , 000 human deaths annually [3] .", "Rabies is more prevalent in developing countri...	[ "The current rabies control strategy in Zambia is based on dog vaccination , dog population control and dog movement restrictions .", "In Nyimba district of Zambia , dog vaccination coverage is low but the incidence of dog bites is high which places the community at risk of rabies infection .", "The renewed glo...	[ "Dog vaccination against rabies is the main method of rabies control in Zambia and it is mainly conducted by the Department of Veterinary Services under the Ministry of Fisheries and Livestock .", "This study explores the factors influencing dog vaccination against rabies and the local barriers to rabies control ...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "biotechnology", "cell motility", "medicine and health sciences", "actin filaments", "cell processes", "brassica", "parasitic diseases", "nematode infections", "plant science", "model organisms", "genetically modified plants", "experimental organism systems", "plants", "genetic engineering...	The root-knot nematode effector MiPFN3 disrupts plant actin filaments and promotes parasitism	journal.ppat.1006947	null	[ [ "Root-knot nematodes ( Meloidogyne spp ) are small endoparasites with a host range that includes most flowering plants [1] .", "During the compatible interaction , the motile second stage juveniles ( J2 ) enter the host roots and migrate intercellularly to the plant vasculature [2] .", "The primary ne...	[ "Root-knot nematodes secrete effectors that manipulate their host plant cells so that the nematode can successfully establish feeding sites and complete its lifecycle .", "The root-knot nematode feeding structures , their “giant cells , ” undergo extensive cytoskeletal remodeling .", "Previous cytological studi...	[ "Root-knot nematodes are microscopic plant pests that infect plant roots and significantly reduce yields of many crop plants .", "The nematodes enter the plant roots and modify plant cells into complex , multinuclear feeding sites called giant cells .", "The formation and maintenance of giant cells is critical ...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "genome-wide association studies", "body weight", "medicine and health sciences", "statistics", "metaanalysis", "computational biology", "cancers and neoplasms", "oncology", "mathematics", "physiological parameters", "genome analysis", "polycystic ovary syndrome", "research and analysis meth...	Large-scale genome-wide meta-analysis of polycystic ovary syndrome suggests shared genetic architecture for different diagnosis criteria	journal.pgen.1007813	null	[ [ "Polycystic ovary syndrome ( PCOS ) is the most common endocrine disorder in reproductive aged women , with a complex pattern of inheritance [1–5] .", "Two different diagnostic criteria based on expert opinion have been utilized: The National Institutes of Health ( NIH ) criteria require hyperandrogenism ...	[ "Polycystic ovary syndrome ( PCOS ) is a disorder characterized by hyperandrogenism , ovulatory dysfunction and polycystic ovarian morphology .", "Affected women frequently have metabolic disturbances including insulin resistance and dysregulation of glucose homeostasis .", "PCOS is diagnosed with two different...	[ "We performed an international meta-analysis of genome-wide association studies combining over 10 , 000 , 000 genetic markers in more than 10 , 000 European women with polycystic ovary syndrome ( PCOS ) and 100 , 000 controls .", "We found three new risk variants associated with PCOS .", "Our data demonstrate t...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "zoology", "ecology", "genetics", "biology", "genomics", "evolutionary biology", "population biology", "genetics and genomics" ]	Diversification of Schistosoma japonicum in Mainland China Revealed by Mitochondrial DNA	journal.pntd.0001503	null	[ [ "Schistosomiasis is one of the most neglected tropical diseases , with six species in the Schistosoma still infecting more than 200 million people in the world [1]–[3] .", "Schistosomiasis japonica is distributed in Indonesia , Philippines , and China .", "In mainland China , this parasitic disease is...	[ "Schistosoma japonicum still causes severe parasitic disease in mainland China , but mainly in areas along the Yangtze River .", "However , the genetic diversity in populations of S . japonicum has not been well understood across its geographical distribution , and such data may provide insights into the epidemio...	[ "Despite the existing threat of schistosomiasis in some rural areas along the Yangtze River , the genetic diversity of Schistosoma japonicum has not been investigated across its wide geographical distribution in China , and such information may provide insight into the disease epidemiology and the development of it...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "regulatory networks", "biology", "computational biology" ]	Inference of Gene Regulatory Networks with Sparse Structural Equation Models Exploiting Genetic Perturbations	journal.pcbi.1003068	null	[ [ "Genes in living organisms do not function in isolation , but may interact with each other and act together forming intricate networks [1] .", "Deciphering the structure of gene regulatory networks is crucial for understanding gene functions and cellular dynamics , as well as for system-level modeling of ...	[ "Integrating genetic perturbations with gene expression data not only improves accuracy of regulatory network topology inference , but also enables learning of causal regulatory relations between genes .", "Although a number of methods have been developed to integrate both types of data , the desiderata of effici...	[ "Deciphering the structure of gene regulatory networks is crucial for understanding gene functions and cellular dynamics , as well as system-level modeling of individual genes and cellular functions .", "Computational methods exploiting gene expression and other types of data generated from high-throughput experi...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The Interaction between a Sexually Transferred Steroid Hormone and a Female Protein Regulates Oogenesis in the Malaria Mosquito Anopheles gambiae	journal.pbio.1001695	Steroid hormones transferred by the male during sex trigger a molecular cascade of events that increases the reproductive success of females in Anopheles gambiae mosquitoes.	[ [ "In many organisms , male–female molecular interactions occurring during sex shape reproductive success and may drive the rapid evolution of reproductive phenotypes [1] .", "While in species where females mate multiple times these reproductive interactions are often antagonistic due to the different repro...	[ "Molecular interactions between male and female factors during mating profoundly affect the reproductive behavior and physiology of female insects .", "In natural populations of the malaria mosquito Anopheles gambiae , blood-fed females direct nutritional resources towards oogenesis only when inseminated .", "H...	[ "Anopheles gambiae mosquitoes are the most deadly vectors of human malaria .", "The reproductive ability of these mosquitoes contributes to their role as disease vectors as it ensures high population densities for malaria transmission .", "The number of eggs developed by females after blood feeding depends on w...	2013
[ "Introduction", "Results", "Discussion", "Material and Methods" ]	[]	Absence of Maternal Methylation in Biparental Hydatidiform Moles from Women with NLRP7 Maternal-Effect Mutations Reveals Widespread Placenta-Specific Imprinting	journal.pgen.1005644	null	[ [ "The most common form of complete hydatidiform mole ( CHM ) is sporadic and androgenetic diploid in origin .", "These products of conception frequently result from the fertilization of an oocyte from which the maternal chromosomes are lost and endoreduplication of a single sperm genome , or the fertilizat...	[ "Familial recurrent hydatidiform mole ( RHM ) is a maternal-effect autosomal recessive disorder usually associated with mutations of the NLRP7 gene .", "It is characterized by HM with excessive trophoblastic proliferation , which mimics the appearance of androgenetic molar conceptuses despite their diploid bipare...	[ "Complete hydatidiform moles ( CHMs ) are abnormal human conceptsus characterized by excessive trophoblast proliferation that commonly result from the absence of a maternal genetic contribution compensated by two copies of the paternal genome .", "In a few rare cases HMs maybe recurrent ( RHM ) , characterized by...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases/neglected tropical diseases", "infectious diseases/protozoal infections" ]	Factors Associated with Acquisition of Human Infective and Animal Infective Trypanosome Infections in Domestic Livestock in Western Kenya	journal.pntd.0000941	null	[ [ "Tsetse transmitted African trypanosomiasis poses a severe socio-economic impact throughout sub-Saharan Africa with losses to production estimated at over US$ 1 . 3 billion annually in terms of meat and milk yield in cattle [1] .", "Animal trypanosomiasis , is a serious constraint to productivity in Busia...	[ "Trypanosomiasis is regarded as a constraint on livestock production in Western Kenya where the responsibility for tsetse and trypanosomiasis control has increasingly shifted from the state to the individual livestock owner .", "To assess the sustainability of these localised control efforts , this study investig...	[ "Rhodesian sleeping sickness caused by Trypanosome brucei rhodesiense is a parasitic disease transmitted by tsetse flies which is fatal in humans if it is not treated .", "The parasites also infect a range of animal species in which they do not cause acute disease and may co-exist with other non human infective p...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "fluorescence imaging", "gene regulation", "cell cycle and cell division", "cell processes", "microbiology", "dna damage", "dna", "immunologic techniques", "research and analysis methods", "small interfering rnas", "imaging techniques", "gene expression", "immunoassays", "viral replication...	Oncogenic Herpesvirus Utilizes Stress-Induced Cell Cycle Checkpoints for Efficient Lytic Replication	journal.ppat.1005424	null	[ [ "Kaposi’s sarcoma-associated herpesvirus ( KSHV ) is a human tumor virus in the family of gamma2-herpesviruses .", "KSHV is the etiologic agent of Kaposi’s sarcoma ( KS ) and other KSHV-associated lymphoproliferative diseases such as primary effusion lymphoma ( PEL ) [1 , 2] .", "KSHV genome consists ...	[ "Kaposi’s sarcoma herpesvirus ( KSHV ) causes Kaposi’s sarcoma and certain lymphoproliferative malignancies .", "Latent infection is established in the majority of tumor cells , whereas lytic replication is reactivated in a small fraction of cells , which is important for both virus spread and disease progression...	[ "Herpesviruses are known to wake up and reactivate in response to different kinds of stress .", "Our study now highlights the key molecular host cell events that KSHV has evolved to utilize for efficient viral lytic replication: the activation of p53 and upregulation of p21 , which slows down the cell cycle , but...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "neural networks", "database searching", "neuroscience", "artificial neural networks", "optimization", "mathematics", "artificial intelligence", "computational neuroscience", "convolution", "research and analysis methods", "sequence analysis", "computer and information sciences", "mathematic...	DeepPep: Deep proteome inference from peptide profiles	journal.pcbi.1005661	null	[ [ "The accurate identification of proteins in a proteomics sample is a key challenge in life sciences .", "Proteins , the final gene product and the fundamental blocks of all cellular processes , are elusive to detect .", "The standard technology that provides fast , high-throughput characterization of ...	[ "Protein inference , the identification of the protein set that is the origin of a given peptide profile , is a fundamental challenge in proteomics .", "We present DeepPep , a deep-convolutional neural network framework that predicts the protein set from a proteomics mixture , given the sequence universe of possi...	[ "The accurate identification of proteins in a proteomics sample , called the protein inference problem , is a fundamental challenge in biomedical sciences .", "Current approaches are based on applications of traditional neural networks , linear optimization and Bayesian techniques .", "We here present DeepPep ,...	2017
[ "Introduction", "Materials and methods", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "insemination", "animals", "glossina", "insect pests", "developmental biology", "pupae", "pest control", "tsetse fly", "population biology", "insect vectors", "pests", "fecundity", "infectious diseases", "fertilization", "life cycles",...	Evaluation of radiation sensitivity and mating performance of Glossina brevipalpis males	journal.pntd.0005473	null	[ [ "Tsetse flies ( Diptera; Glossinidae ) , the cyclical vectors of trypanosome parasites that cause human African trypanosomosis ( HAT ) and African animal trypanosomosis ( AAT ) , infest 10 million km² of sub-Saharan Africa [1–3] .", "In South Africa , Glossina brevipalpis Newstead and Glossina austeni New...	[ "Area-wide integrated pest management strategies that include a sterile insect technique component have been successfully used to eradicate tsetse fly populations in the past .", "To ensure the success of the sterile insect technique , the released males must be adequately sterile and be able to compete with thei...	[ "The radiation sensitivity and mating performance of colonised G . brevipalis adult and pupae were evaluated .", "It was showed that G . brevipalpis males were highly sensitive to irradiation and could be sterilised at a much lower dose , between 40 Gy and 80 Gy , than some other tsetse fly species .", "As a re...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Global Gene Expression Profiling through the Complete Life Cycle of Trypanosoma vivax	journal.pntd.0003975	null	[ [ "African trypanosomes are unicellular vector-borne hemoparasites of humans , domestic livestock and wild animals .", "They cause African trypanosomiasis , an endemic disease of sub-Saharan Africa otherwise known as sleeping sickness in humans and nagana in animals , and are transmitted between vertebrate ...	[ "The parasitic flagellate Trypanosoma vivax is a cause of animal trypanosomiasis across Africa and South America .", "The parasite has a digenetic life cycle , passing between mammalian hosts and insect vectors , and a series of developmental forms adapted to each life cycle stage .", "Each point in the life cy...	[ "Trypanosoma vivax is a single-celled parasite that infects cattle and non-domesticated animals through the bite of the tsetse fly .", "The parasite causes animal trypanosomiasis , a chronic condition resulting in severe anemia , muscle wastage and ultimately death if untreated .", "This disease is endemic acro...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "neuroethology", "auditory system", "behavioral neuroscience", "psychology", "social and behavioral sciences", "psychophysics", "biology", "sensory perception", "sensory systems", "neuroscience", "animal cognition" ]	Monkeys and Humans Share a Common Computation for Face/Voice Integration	journal.pcbi.1002165	null	[ [ "When we speak , our face moves and deforms the mouth and other regions [1] , [2] , [3] , [4] , [5] .", "These dynamics and deformations lead to a variety of visual motion cues ( “visual speech” ) related to the auditory components of speech and are integral to face-to-face communication .", "In noisy...	[ "Speech production involves the movement of the mouth and other regions of the face resulting in visual motion cues .", "These visual cues enhance intelligibility and detection of auditory speech .", "As such , face-to-face speech is fundamentally a multisensory phenomenon .", "If speech is fundamentally mult...	[ "The evolution of speech is one of our most fascinating and enduring mysteries—enduring partly because all the critical features of speech ( brains , vocal tracts , ancestral speech-like sounds ) do not fossilize .", "Furthermore , it is becoming increasingly clear that speech is , by default , a multimodal pheno...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "model organisms", "immunology", "biology", "microbiology" ]	ADCC Develops Over Time during Persistent Infection with Live-Attenuated SIV and Is Associated with Complete Protection against SIVmac251 Challenge	journal.ppat.1002890	null	[ [ "The development of a vaccine against HIV-1 continues to be hampered by our limited understanding of the types of immune responses needed for protection .", "Although safety considerations preclude the use of live-attenuated HIV-1 in people [1]–[5] , live-attenuated strains of simian immunodeficiency viru...	[ "Live-attenuated strains of simian immunodeficiency virus ( SIV ) routinely confer apparent sterilizing immunity against pathogenic SIV challenge in rhesus macaques .", "Understanding the mechanisms of protection by live-attenuated SIV may provide important insights into the immune responses needed for protection...	[ "Live-attenuated vaccines can prevent simian immunodeficiency virus ( SIV ) infection upon experimental challenge of rhesus macaques .", "Although safety considerations preclude vaccinating humans with live-attenuated HIV-1 , it may be possible to replicate the types of immunity induced by live-attenuated SIV thr...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	The Lysine Acetyltransferase Activator Brpf1 Governs Dentate Gyrus Development through Neural Stem Cells and Progenitors	journal.pgen.1005034	null	[ [ "Lysine acetylation involves covalent addition of an acetyl moiety to the ε-amino group of a lysine residue and is important for modification of both prokaryotic and eukaryotic proteins [1–3] .", "Proteomic analyses have detected this modification in thousands of mammalian proteins with important roles no...	[ "Lysine acetylation has recently emerged as an important post-translational modification in diverse organisms , but relatively little is known about its roles in mammalian development and stem cells .", "Bromodomain- and PHD finger-containing protein 1 ( BRPF1 ) is a multidomain histone binder and a master activa...	[ "Lysine acetylation refers to addition of the acetyl group to lysine residues after protein synthesis .", "Little is known about how this modification plays a role in the brain and neural stem cells .", "It is catalyzed by a group of enzymes known as lysine acetyltransferases .", "A novel epigenetic regulator...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/genomics", "genetics and genomics/gene discovery", "genetics and genomics/gene expression", "molecular biology/mrna stability", "molecular biology/bioinformatics", "genetics and genomics/bioinformatics" ]	Novel Low Abundance and Transient RNAs in Yeast Revealed by Tiling Microarrays and Ultra High–Throughput Sequencing Are Not Conserved Across Closely Related Yeast Species	journal.pgen.1000299	null	[ [ "Twelve years ago , in a landmark study resulting from the collaborative work of hundreds of scientists around the world , the budding yeast Saccharomyces cerevisiae became the first eukaryote to have its genome fully sequenced [1] .", "The initial analysis of the genome utilized the following ( necessari...	[ "A complete description of the transcriptome of an organism is crucial for a comprehensive understanding of how it functions and how its transcriptional networks are controlled , and may provide insights into the organism's evolution .", "Despite the status of Saccharomyces cerevisiae as arguably the most well-st...	[ "The budding yeast Saccharomyces cerevisiae , because of the relative ease of its genetic manipulation and its ease of handling in the laboratory , has long served as a model on which studies in higher organisms have been based .", "To more fully understand how eukaryotic cells express their genomes , we sought t...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "parastic protozoans", "genetics of disease", "biochemistry", "protein metabolism", "parasite evolution", "genetics", "protozoology", "biology", "microbiology", "plasmodium falciparum", "metabolism", "parasitology" ]	Metabolic QTL Analysis Links Chloroquine Resistance in Plasmodium falciparum to Impaired Hemoglobin Catabolism	journal.pgen.1004085	null	[ [ "Drug resistance is a critical issue facing worldwide malaria control .", "The spread and persistence of chloroquine-resistant ( CQR ) Plasmodium falciparum has rendered chloroquine , an inexpensive and potent drug , ineffective throughout most of the world [1] .", "In sub-Saharan Africa [2] and the i...	[ "Drug resistant strains of the malaria parasite , Plasmodium falciparum , have rendered chloroquine ineffective throughout much of the world .", "In parts of Africa and Asia , the coordinated shift from chloroquine to other drugs has resulted in the near disappearance of chloroquine-resistant ( CQR ) parasites fr...	[ "Chloroquine was formerly a front line drug in the treatment of malaria .", "However , drug resistant strains of the malaria parasite have made this drug ineffective in many malaria endemic regions .", "Surprisingly , the discontinuation of chloroquine therapy has led to the reappearance of drug-sensitive paras...	2014
[ "Introduction", "Materials and Methods", "Results and Discussion" ]	[]	Comparative Genomics of Field Isolates of Mycobacterium bovis and M. caprae Provides Evidence for Possible Correlates with Bacterial Viability and Virulence	journal.pntd.0004232	null	[ [ "Mycobacterium tuberculosis has infected more than 2 . 5 billion people worldwide with approximately 9 million new tuberculosis ( TB ) cases reported every year [1] .", "Animal TB is caused by infection with Mycobacterium bovis and closely related members of the M . tuberculosis complex ( MTBC ) such as M...	[ "Mycobacteria of the Mycobacterium tuberculosis complex ( MTBC ) greatly affect humans and animals worldwide .", "The life cycle of mycobacteria is complex and the mechanisms resulting in pathogen infection and survival in host cells are not fully understood .", "Recently , comparative genomics analyses have pr...	[ "Mycobacteria belonging to the Mycobacterium tuberculosis complex infect humans and animals since pre-history and are a serious health problem worldwide .", "Whole-genome sequencing and comparative genomics generate information on the evolution and molecular basis of pathogenicity and transmissibility .", "Howe...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Parasitological Confirmation and Analysis of Leishmania Diversity in Asymptomatic and Subclinical Infection following Resolution of Cutaneous Leishmaniasis	journal.pntd.0004273	null	[ [ "Asymptomatic dermal or visceral leishmaniasis ( VL ) constitute a variable and sometimes high proportion of the naturally exposed population in endemic foci of Leishmania transmission , ranging from 17 to 91% of incident infections [1–3] .", "Although xenodiagnosis has shown that sand flies can acquire i...	[ "The contribution of individuals with subclinical infection to the transmission and endemicity of cutaneous leishmaniasis ( CL ) is unknown .", "Immunological evidence of exposure to Leishmania in residents of endemic areas has been the basis for defining the human population with asymptomatic infection .", "Ho...	[ "A variable and often high proportion of individuals residing in areas where cutaneous leishmaniasis is endemic are exposed to Leishmania parasites , yet do not develop symptoms of disease .", "The role of this asymptomatic population in the transmission of disease is unknown and could interfere with the effectiv...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Transmission Properties of Human PrP 102L Prions Challenge the Relevance of Mouse Models of GSS	journal.ppat.1004953	null	[ [ "Prion diseases are a closely related group of neurodegenerative conditions which affect both humans and animals [1 , 2] .", "They are both experimentally and , in some cases , naturally transmissible within and between mammalian species .", "Cross-species transmission is generally much less efficient...	[ "Inherited prion disease ( IPD ) is caused by autosomal-dominant pathogenic mutations in the human prion protein ( PrP ) gene ( PRNP ) .", "A proline to leucine substitution at PrP residue 102 ( P102L ) is classically associated with Gerstmann-Sträussler-Scheinker ( GSS ) disease but shows marked clinical and neu...	[ "Inherited prion disease ( IPD ) is caused by pathogenic mutations in the human prion protein ( PrP ) gene leading to the formation of lethal prions in the brain .", "To-date the properties of prions causing IPD and their similarities to prions causing other forms of human prion disease remain ill-defined .", "...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "chemical compounds", "parasitic cell cycles", "parasitic diseases", "parasitic protozoans", "cell differentiation", "parasitology", "trypanosoma brucei", "developmental biology", "trypanosoma brucei gambiense", "protozoans", "mitochondria", "bioenergetics", ...	Mitochondrial DNA is critical for longevity and metabolism of transmission stage Trypanosoma brucei	journal.ppat.1007195	null	[ [ "The parasitic protist Trypanosoma brucei undergoes a complex life cycle involving stages within the mammalian bloodstream and its tsetse fly vector .", "In the bloodstream of the mammalian host , the cell population exhibits two major morphotypes: the proliferative long slender bloodstream form ( BSF ) a...	[ "The sleeping sickness parasite Trypanosoma brucei has a complex life cycle , alternating between a mammalian host and the tsetse fly vector .", "A tightly controlled developmental programme ensures parasite transmission between hosts as well as survival within them and involves strict regulation of mitochondrial...	[ "African trypanosomes are single cellular eukaryotes transmitted by tsetse flies that cause important diseases in humans and their livestock .", "For survival these parasites depend on their mitochondrion , an organelle that has its own genome ( ‘mtDNA’ ) and that is traditionally viewed as the ‘power plant’ of c...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "signal transduction", "molecular cell biology", "protein interactions", "biology", "microbiology", "proteomics", "molecular biology", "parasitology", "pathogenesis" ]	Quantitative in vivo Analyses Reveal Calcium-dependent Phosphorylation Sites and Identifies a Novel Component of the Toxoplasma Invasion Motor Complex	journal.ppat.1002222	null	[ [ "The phylum Apicomplexa is a large group of obligate intracellular parasites of wide medical and agricultural significance .", "Alone , Toxoplasma gondii infects between 30- 80% of people worldwide and is one the most common infectious agents of humans .", "Toxoplasma transmission occurs by exposure t...	[ "Apicomplexan parasites depend on the invasion of host cells for survival and proliferation .", "Calcium-dependent signaling pathways appear to be essential for micronemal release and gliding motility , yet the target of activated kinases remains largely unknown .", "We have characterized calcium-dependent phos...	[ "Apicomplexan parasites are a group of obligate intracellular pathogens of wide medical and agricultural significance .", "Included within this phylum is Plasmodium spp , the causative agents to malaria and the ubiquitous parasite Toxoplasma , which inflicts disease burden on AIDS patients , transplant recipients...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "diagnostic radiology", "lens disorders", "enzymology", "fibroblasts", "magnetic resonance imaging", "connective tissue cells", "enzyme metabolism", "cellular structures and organelles", "enzyme chemistry", "research and analysis methods", "imaging techniques", ...	Mutations in PIK3C2A cause syndromic short stature, skeletal abnormalities, and cataracts associated with ciliary dysfunction	journal.pgen.1008088	null	[ [ "Identifying the genetic basis of diseases with Mendelian inheritance provides insight into gene function , susceptibility to disease , and can guide the development of new therapeutics .", "To date , ~50% of the genes underlying Mendelian phenotypes have yet to be discovered [1] .", "The disease gene...	[ "PIK3C2A is a class II member of the phosphoinositide 3-kinase ( PI3K ) family that catalyzes the phosphorylation of phosphatidylinositol ( PI ) into PI ( 3 ) P and the phosphorylation of PI ( 4 ) P into PI ( 3 , 4 ) P2 .", "At the cellular level , PIK3C2A is critical for the formation of cilia and for receptor m...	[ "Identifying the genetic basis of rare disorders can provide insight into gene function , susceptibility to disease , guide the development of new therapeutics , improve opportunities for genetic counseling , and help clinicians evaluate and potentially treat complicated clinical presentations .", "However , it i...	2019
[ "Introduction", "Results and Discussion", "Materials and Methods" ]	[ "genomics", "immune cells", "immunity", "gene expression", "genetics", "t cells", "epigenetics", "molecular genetics", "biology", "dna modification", "immunology", "allergy and hypersensitivity", "genetics of disease", "immune response", "human genetics" ]	DNA Methylation Changes Separate Allergic Patients from Healthy Controls and May Reflect Altered CD4+ T-Cell Population Structure	journal.pgen.1004059	null	[ [ "The modest effects of genetic variants in inflammatory diseases indicate the importance of epigenetic mechanisms like DNA methylation to disease pathology .", "However , studies of inflammatory diseases have shown conflicting results .", "In monozygotic twins discordant for multiple sclerosis ( MS ) ...	[ "Altered DNA methylation patterns in CD4+ T-cells indicate the importance of epigenetic mechanisms in inflammatory diseases .", "However , the identification of these alterations is complicated by the heterogeneity of most inflammatory diseases .", "Seasonal allergic rhinitis ( SAR ) is an optimal disease model...	[ "T-cells , a type of white blood cell , are an important part of the immune-system in humans .", "T-cells allow us to adapt our immune-response to the various infectious agents we encounter during life .", "However , T-cells can also cause disease when they target the body's own cells , e . g . Psoriasis , or w...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Cortical Overexpression of Neuronal Calcium Sensor-1 Induces Functional Plasticity in Spinal Cord Following Unilateral Pyramidal Tract Injury in Rat	journal.pbio.1000399	Overexpression of neuronal calcium sensor 1 in cortical neurons can help restore axonal plasticity and regeneration following axonal injury in adult rats, and can also improve behavioral function.	[ [ "Spinal cord injury is a significant clinical problem that produces life long disability , although in a minority of patients some degree of recovery can occur spontaneously without any therapeutic intervention [1] , [2] .", "There are several possible mechanisms that could be responsible for this , one b...	[ "Following trauma of the adult brain or spinal cord the injured axons of central neurons fail to regenerate or if intact display only limited anatomical plasticity through sprouting .", "Adult cortical neurons forming the corticospinal tract ( CST ) normally have low levels of the neuronal calcium sensor-1 ( NCS1...	[ "Following trauma to the central nervous system ( brain or spinal cord ) , neurons show very little capacity to re-grow their axons , which can lead to a permanent loss of function in those regions .", "In this study , we show that this failure of axon re-growth is associated with low intracellular levels of a sm...	2010
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Toxocariasis Diagnosed in International Travelers at the Institute of Tropical Medicine, Antwerp, Belgium, from 2000 to 2013	journal.pntd.0003559	null	[ [ "Toxocariasis , caused by intestinal roundworm of dogs ( Toxocara canis ) or cats ( Toxocara catis ) , is a zoonotic infection with a worldwide distribution [1 , 2] .", "Humans can get infected by ingestion of embryonated eggs present on the soil , plants or soil-dwelling invertebrates contaminated by dog...	[ "Although infection with Toxocara canis or T . catis ( commonly referred as toxocariasis ) appears to be highly prevalent in ( sub ) tropical countries , information on its frequency and presentation in returning travelers and migrants is scarce .", "In this study , we reviewed all cases of asymptomatic and sympt...	[ "Toxocariasis is a zoonosis of worldwide distribution caused by dog ( Toxocara canis ) or cat ( T . catis ) roundworm that can be fully asymptomatic or may cause significant disease such as a the systemic syndrome called visceral larva migrans as well as neurological or eye manifestations .", "Toxocariasis prevai...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology", "neuroscience", "molecular biology" ]	A Role for the PERIOD:PERIOD Homodimer in the Drosophila Circadian Clock	journal.pbio.1000003	The circadian molecular clock model needs to be extended by adding the PERIOD:PERIOD homodimer as a functional unit in rhythm generation in Drosophila. Blocking this dimerization leads to faulty nuclear localization, reduced repressor activity, and impaired behavioral rhythms.	[ [ "Circadian clocks likely evolved because they provide organisms with the advantage to anticipate changes of environmental conditions .", "Thanks to such clocks , metabolism , physiology , and behavior can be tuned to occur at advantageous times during the 24-h day [1] .", "Molecularly , circadian cloc...	[ "Circadian clocks in eukaryotes rely on transcriptional feedback loops , in which clock genes repress their own transcription resulting in molecular oscillations with a period of ∼24 h .", "In Drosophila , the clock proteins Period ( PER ) and Timeless ( TIM ) operate in such a feedback loop , whereby they first ...	[ "The current models of circadian clocks in flies and mammals involve the formation of complexes between clock proteins in the cytoplasm .", "These complexes are usually heterodimers ( that is , made up of two different clock proteins ) and appear to enter the nucleus at certain times of the circadian day in order...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Impaired Mitochondrial Energy Production Causes Light-Induced Photoreceptor Degeneration Independent of Oxidative Stress	journal.pbio.1002197	Some mitochondrial disorders cause blindness through increased oxidative stress. This study shows that in other such disorders, light-activated photoreceptors degenerate because the shortfall in mitochondrial energy production impairs rhodopsin trafficking and induces toxicity.	[ [ "The causes of progressive dysfunction or death of photoreceptors ( PRs ) is genetically heterogeneous in humans [1] .", "PR degeneration is a complex process influenced by numerous genes and environmental factors .", "Although prolonged exposure to sunlight is one of the major causes of retinal degen...	[ "Two insults often underlie a variety of eye diseases including glaucoma , optic atrophy , and retinal degeneration—defects in mitochondrial function and aberrant Rhodopsin trafficking .", "Although mitochondrial defects are often associated with oxidative stress , they have not been linked to Rhodopsin trafficki...	[ "Mitochondrial dysfunction is associated with a number of metabolic and neurological diseases such as Leigh syndrome and progressive blindness .", "Increased oxidative stress , which is often associated with mitochondrial dysfunction , is thought to be a common cause of disease progression .", "Here , we identi...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "proteins", "protein structure", "biology", "dna-binding proteins" ]	The Velvet Family of Fungal Regulators Contains a DNA-Binding Domain Structurally Similar to NF-κB	journal.pbio.1001750	This study reveals an important family of fungal regulatory proteins to be transcription factors that contain a DNA-binding “velvet” domain structurally related to that of mammalian NFkB.	[ [ "The fungal and the animal kingdom are related as they both belong to the ophistokonts with a common ancestor existing about 1 billion years ago [1] , [2] .", "Animals have evolved with an elaborate inflammation and immune system for self-defence .", "Inflammation , the immune system , and animal deve...	[ "Morphological development of fungi and their combined production of secondary metabolites are both acting in defence and protection .", "These processes are mainly coordinated by velvet regulators , which contain a yet functionally and structurally uncharacterized velvet domain .", "Here we demonstrate that th...	[ "In many fungi , developmental processes and the synthesis of nonessential chemicals ( secondary metabolites ) are regulated by various external stimuli , such as light .", "Although fungi employ them for defensive purposes , secondary metabolites range from useful antibiotics to powerful toxins , so understandin...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "public health and epidemiology", "epidemiology", "neurology", "neurological disorders" ]	Comprehensive Research Synopsis and Systematic Meta-Analyses in Parkinson's Disease Genetics: The PDGene Database	journal.pgen.1002548	null	[ [ "Parkinson's disease ( PD ) is the second most common neurodegenerative disease with a prevalence of ∼1% over 60 years of age [1] .", "Approximately 5–10% of the patients show an autosomal dominant or recessive mode of inheritance , and several causative genes have been identified , e . g . SNCA , LRRK2 ,...	[ "More than 800 published genetic association studies have implicated dozens of potential risk loci in Parkinson's disease ( PD ) .", "To facilitate the interpretation of these findings , we have created a dedicated online resource , PDGene , that comprehensively collects and meta-analyzes all published studies in...	[ "The genetic basis of Parkinson's disease is complex , i . e . it is determined by a number of different disease-causing and disease-predisposing genes .", "Especially the latter have proven difficult to find , evidenced by more than 800 published genetic association studies , typically showing discrepant results...	2012
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "taxonomy", "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "evolutionary biology", "pathogens", "immunology", "microbiology", "genetic mapping", "plasmid construction", "retroviruses", "viruses", "immunodeficiency viruses", "animal mod...	HIV-1 competition experiments in humanized mice show that APOBEC3H imposes selective pressure and promotes virus adaptation	journal.ppat.1006348	null	[ [ "Apolipoprotein B mRNA editing enzyme catalytic polypeptide-like 3 ( APOBEC3; A3 ) enzymes are cellular single-stranded DNA cytosine deaminases that are specifically encoded in mammals [1 , 2] .", "Rodents including mice ( Mus musculus ) have a single A3 gene , while primates including humans ( Homo sapie...	[ "APOBEC3 ( A3 ) family proteins are DNA cytosine deaminases recognized for contributing to HIV-1 restriction and mutation .", "Prior studies have demonstrated that A3D , A3F , and A3G enzymes elicit a robust anti-HIV-1 effect in cell cultures and in humanized mouse models .", "Human A3H is polymorphic and can b...	[ "Human APOBEC3 family proteins are known as intrinsic defenses against HIV-1 , whereas HIV-1 Vif counteracts APOBEC3-mediated anti-viral action .", "Using a hematopoietic stem cell-transplanted humanized mouse model , we demonstrated that endogenous APOBEC3D , APOBEC3F and APOBEC3G play pivotal roles in restricti...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma mansoni", "helminths", "metabolic processes", "dna-binding proteins", "light microscopy", "animals", "dna replication", "microscopy", "genome analysis", "dna", "research and analysis methods", "genomics", "proteins", "fluorescence microscopy...	Inhibition of histone methyltransferase EZH2 in Schistosoma mansoni in vitro by GSK343 reduces egg laying and decreases the expression of genes implicated in DNA replication and noncoding RNA metabolism	journal.pntd.0006873	null	[ [ "Schistosomiasis is a chronic and debilitating disease caused by trematodes of the genus Schistosoma and is one of the most prevalent and neglected diseases of tropical and subtropical regions , affecting more than 250 million people in 78 countries [1 , 2] .", "Despite efforts to control schistosomiasis ...	[ "The possibility of emergence of praziquantel-resistant Schistosoma parasites and the lack of other effective drugs demand the discovery of new schistosomicidal agents .", "In this context the study of compounds that target histone-modifying enzymes is extremely promising .", "Our aim was to investigate the eff...	[ "Schistosomiasis is a chronic and debilitating disease caused by a trematode of the genus Schistosoma .", "The current strategy for the control of the disease involves treatment with praziquantel , the only available drug .", "The development of new drugs is therefore a top priority .", "Drugs that inhibit hi...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "genome-wide association studies", "medicine and health sciences", "breast tumors", "gene regulation", "cancer risk factors", "variant genotypes", "cancers and neoplasms", "genetic mapping", "oncology", "genome analysis", "molecular genetics", "small interfering rnas", "transcriptional contr...	SNPs near the cysteine proteinase cathepsin O gene (CTSO) determine tamoxifen sensitivity in ERα-positive breast cancer through regulation of BRCA1	journal.pgen.1007031	null	[ [ "Approximately 80% of breast tumors express estrogen receptor α ( ER ) [1–3] , a receptor that binds and mediates many of the effects of estrogens .", "Estrogen signaling is known to modulate several processes relevant to breast cancer cell proliferation , predominately as a result of the activity of ER a...	[ "Tamoxifen is one of the most commonly employed endocrine therapies for patients with estrogen receptor α ( ERα ) -positive breast cancer .", "Unfortunately the clinical benefit is limited due to intrinsic and acquired drug resistance .", "We previously reported a genome-wide association study that identified c...	[ "Many studies have demonstrated that germline genetic variation can contribute to both breast cancer disease risk and treatment response .", "However , the underlying mechanisms associated with these biomarkers often remains understudied .", "As part of functional genomic studies following up a case-control gen...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "evolutionary biology/developmental molecular mechanisms", "developmental biology/developmental evolution", "evolutionary biology/nuclear structure and function" ]	Species-Specific Heterochromatin Prevents Mitotic Chromosome Segregation to Cause Hybrid Lethality in Drosophila	journal.pbio.1000234	Early embryonic lethality of interspecies hybrids in Drosophila can be caused by defects in mitotic segregation of paternal X chromatids carrying a critical domain of heterochromatic DNA.	[ [ "A critical stage of speciation is the development of reproductive isolating mechanisms that prevent gene exchange between diverging populations .", "Hybrid sterility and lethality are major components of reproductive isolation .", "A key to understanding how these hybrid incompatibilities ( HIs ) evo...	[ "Postzygotic reproductive barriers such as sterility and lethality of hybrids are important for establishing and maintaining reproductive isolation between species .", "Identifying the causal loci and discerning how they interfere with the development of hybrids is essential for understanding how hybrid incompati...	[ "Speciation is most commonly understood to occur when two species can no longer reproduce with each other , and sterility and lethality of hybrids formed between different species are widely observed causes of such reproductive isolation .", "Several protein-coding genes have been previously discovered to cause h...	2009
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "physics", "statistical mechanics", "theoretical biology", "evolutionary biology", "population modeling", "evolutionary modeling", "population genetics", "biology", "computational biology", "population biology", "genetics and genomics" ]	Noise Driven Evolutionary Waves	journal.pcbi.1002005	null	[ [ "Our computer model , illustrated in figure 1 , provides the setting for the competition of two types , mutants and wild type , in a spatially extended population .", "It consists of a linear array of sub-populations , called demes .", "Individuals have a chance per generation to jump to one of the ne...	[ "Adaptation in spatially extended populations entails the propagation of evolutionary novelties across habitat ranges .", "Driven by natural selection , beneficial mutations sweep through the population in a “wave of advance” .", "The standard model for these traveling waves , due to R . Fisher and A . Kolmogor...	[ "Mutations that increase an organism's fitness are the fuel for biological evolution .", "When such beneficial mutations enter a spatially extended population , they spread through the population in a “wave of advance” , first described by R . Fisher and A . Kolmogorov .", "The force driving these traveling wav...	2011
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Behavioural Contagion Explains Group Cohesion in a Social Crustacean	journal.pcbi.1004290	null	[ [ "Aggregation is one of the most common social phenomena .", "Although it may be a response to the heterogeneities of the environment of individuals sharing the same needs , aggregation is frequently the joint response of individuals to the presence of conspecifics and the environment [1] , [2] .", "Th...	[ "In gregarious species , social interactions maintain group cohesion and the associated adaptive values of group living .", "The understanding of mechanisms leading to group cohesion is essential for understanding the collective dynamics of groups and the spatio-temporal distribution of organisms in environment ....	[ "Terrestrial isopods , commonly named woodlice or pill bugs , are commonly distributed soil-dwelling arthropods , particularly important in soils as macro-decomposers of leaf litter .", "Many species of woodlice are synanthropic and , for this reason , are easily observable in gardens , urban parks or composts ."...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "plant biochemistry", "innate immune system", "plant science", "medicine and health sciences", "plant microbiology", "pathology and laboratory medicine", "immunity", "medical microbiology", "host-pathogen interactions", "microbial pathogens", "plant pathology", "biology and l...	Functionally Redundant RXLR Effectors from Phytophthora infestans Act at Different Steps to Suppress Early flg22-Triggered Immunity	journal.ppat.1004057	null	[ [ "Plants possess innate defense mechanisms to resist microbial infection [1] , [2] .", "Efficient plant disease resistance is based on two evolutionarily linked layers of innate immunity .", "One layer involves cell surface transmembrane receptors that recognize invariant microbial structures termed pa...	[ "Genome sequences of several economically important phytopathogenic oomycetes have revealed the presence of large families of so-called RXLR effectors .", "Functional screens have identified RXLR effector repertoires that either compromise or induce plant defense responses .", "However , limited information is ...	[ "Phytophthora species are among the most devastating crop pathogens worldwide .", "P . infestans is a pathogen of tomato and potato plants .", "The genome of P . infestans has been sequenced , revealing the presence of a large number of host-targeting RXLR effector proteins that are thought to manipulate cellul...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases/epidemiology and control of infectious diseases" ]	Ruminant Brucellosis in the Kafr El Sheikh Governorate of the Nile Delta, Egypt: Prevalence of a Neglected Zoonosis	journal.pntd.0000944	null	[ [ "Brucellosis is one of the most common zoonotic diseases worldwide , and as such poses a major threat to human health and animal production [1]–[2] .", "It is considered a neglected zoonosis by the World Health Organization ( WHO ) , and has been identified as having the highest public health burden acros...	[ "Brucellosis is a neglected tropical zoonosis allegedly reemerging in Middle Eastern countries .", "Infected ruminants are the primary source of human infection; consequently , estimates of the frequency of ruminant brucellosis are useful elements for building effective control strategies .", "Unfortunately , t...	[ "Brucellosis is a zoonosis of mammals caused by bacteria of the genus Brucella .", "It is responsible for a vast global burden imposed on human health through disability and on animal productivity .", "In humans brucellosis causes a range of flu-like symptoms and chronic debilitating illness .", "In livestock...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "oncology", "ecology", "yeast and fungi", "microbiology", "evolutionary biology", "genetics and genomics" ]	Mitotic Recombination Accelerates Adaptation in the Fungus Aspergillus nidulans	journal.pgen.0030068	null	[ [ "Sexual cycles involve an alternation between a haploid and a diploid phase .", "The relative duration of both ploidy phases may differ strikingly among taxa .", "Extremes are , on the one hand , diploid multicellular animals and plants with haploidy restricted to the gamete stage , and on the other h...	[ "Understanding the prevalence of sexual reproduction in eukaryotes is a hard problem .", "At least two aspects still defy a fully satisfactory explanation , the functional significance of genetic recombination and the great variation among taxa in the relative lengths of the haploid and diploid phases in the sexu...	[ "Sexual reproduction involves an alternation of ploidy .", "Haploid gametes , carrying a single set of chromosomes , fuse to form a diploid zygote with a double set of chromosomes .", "The gametes are formed from diploid progenitor cells by meiosis , which involves genetic recombination—the key evolutionary asp...	2007

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