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headings list	keywords list	title stringlengths 20 281	id stringlengths 20 20	toc stringlengths 57 522 ⌀	sections list	abstract list	summary list	year stringclasses 13 values
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Systematic Profiling of Poly(A)+ Transcripts Modulated by Core 3’ End Processing and Splicing Factors Reveals Regulatory Rules of Alternative Cleavage and Polyadenylation	journal.pgen.1005166	null	[ [ "Pre-mRNA cleavage and polyadenylation ( C/P ) is a 3’ end processing mechanism employed in eukaryotes for expression of almost all protein-coding transcripts and long non-coding RNAs by RNA polymerase II ( RNAPII ) [1 , 2] .", "The site for C/P , commonly known as the polyA site or pA , is defined by bot...	[ "Alternative cleavage and polyadenylation ( APA ) results in mRNA isoforms containing different 3’ untranslated regions ( 3’UTRs ) and/or coding sequences .", "How core cleavage/polyadenylation ( C/P ) factors regulate APA is not well understood .", "Using siRNA knockdown coupled with deep sequencing , we found...	[ "A gene can express multiple isoforms varying in the 3’ end , a phenomenon called alternative cleavage and polyadenylation , or APA .", "Previous studies have indicated that most eukaryotic genes display APA and the APA profile changes under different physiological and pathological conditions .", "However , how...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "population genetics", "geographical locations", "india", "ethnicities", "molecular biology techniques", "population biology", "genetic footprinting", "research and analysis methods", "europe", "sex chromosomes", "chromosome biology", "x chromosomes", "autosomes", "molecular biology", "r...	European Roma groups show complex West Eurasian admixture footprints and a common South Asian genetic origin	journal.pgen.1008417	null	[ [ "The diaspora of the Roma people , also known with the misnomer of Gypsies , is a not-well documented human movement , which is characterized by recent dispersals and multiple founder events .", "The Roma population is recognized as the largest transnational ethnic minority in Europe , with an estimated p...	[ "The Roma population is the largest transnational ethnic minority in Europe , characterized by a linguistic , cultural and historical heterogeneity .", "Comparative linguistics and genetic studies have placed the origin of European Roma in the Northwest of India .", "After their migration across Persia , they e...	[ "Human demographic processes and admixture events leave traceable footprints in the genomes of the populations and they can modulate the genetic architecture of complex diseases .", "Here , we aim to study the Roma people , an admixed population with a particular demographic history recognized as the largest ethn...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell death", "cellular stress responses", "functional genomics", "rna interference", "signaling networks", "cell growth", "sequence analysis", "gene expression", "biology", "molecular biology", "microarrays", "rna", "cell biology", "nucleic acids", "genomics", "molecular cell biology"...	A Latent Pro-Survival Function for the Mir-290-295 Cluster in Mouse Embryonic Stem Cells	journal.pgen.1002054	null	[ [ "MicroRNAs ( miRNAs ) are endogenous ∼22 nt RNAs that regulate gene expression post-transcriptionally .", "In animals , the ability of miRNAs to accomplish this regulation depends on complementarity between mature miRNA sequences and their mRNA targets .", "Most commonly , partial binding of miRNAs le...	[ "MicroRNAs ( miRNAs ) post-transcriptionally regulate the expression of thousands of distinct mRNAs .", "While some regulatory interactions help to maintain basal cellular functions , others are likely relevant in more specific settings , such as response to stress .", "Here we describe such a role for the mir-...	[ "In this study , we were interested in learning more about the roles of microRNAs—small segments of RNA that help turn off genes—during early development .", "By studying mouse embryonic stem cells , a unique cell type that can give rise to all adult tissues , we found that a number of genes related to cell survi...	2011
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "fish", "medicine and health sciences", "engineering and technology", "signal processing", "vertebrates", "animals", "noise reduction", "simulation and modeling", "animal models", "organisms", "osteichthyes", "developmental biology", "model organisms", "experimental organism systems", "m...	Modeling craniofacial development reveals spatiotemporal constraints on robust patterning of the mandibular arch	journal.pcbi.1006569	null	[ [ "A fundamental question in developmental biology is pattern formation , i . e . the acquisition of positional identity in cells resulting in spatially organized domains of gene expression .", "Computational analyses have long sought to address how patterning occurs in growing tissues that change their siz...	[ "How does pattern formation occur accurately when confronted with tissue growth and stochastic fluctuations ( noise ) in gene expression ?", "Dorso-ventral ( D-V ) patterning of the mandibular arch specifies upper versus lower jaw skeletal elements through a combination of Bone morphogenetic protein ( Bmp ) , End...	[ "Proper development of the body requires boundaries to form between regions in which cells will form different structures , and these boundaries need to be properly organized in space .", "This must occur accurately even in moving , dividing cells and in the presence of the noise that is inherent in all biochemic...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "acanthamoeba", "mycobacterium leprae", "infectious diseases", "bacterial diseases", "medicine and health sciences", "protozoans", "amoebas", "leprosy", "biology and life sciences", "tropical diseases", "actinobacteria", "neglected tropical diseases", "bacteria", "parasitic protozoans", ...	Long-term Survival and Virulence of Mycobacterium leprae in Amoebal Cysts	journal.pntd.0003405	null	[ [ "Human beings have been afflicted by leprosy for over a millennium .", "Leprosy is a chronic granulomatous infection of skin and peripheral nerves caused by the bacillus Mycobacterium leprae .", "The bacilli are slow growing obligate intracellular organisms trophic for macrophages , dendritic cells ( ...	[ "Leprosy is a curable neglected disease of humans caused by Mycobacterium leprae that affects the skin and peripheral nerves and manifests clinically in various forms ranging from self-resolving , tuberculoid leprosy to lepromatous leprosy having significant pathology with ensuing disfiguration disability and socia...	[ "Leprosy is a progressive disease of the skin and nervous system caused by the bacillus , Mycobacterium leprae .", "Implementation of multiple drug therapy ( MDT ) for leprosy has significantly reduced the global cases of leprosy .", "Currently , only a few endemic countries remain where relatively high number ...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing techniques", "genome-wide association studies", "medicine and health sciences", "neuroscience", "cardiovascular medicine", "next-generation sequencing", "mathematics", "statistics (mathematics)", "test statistics", "computational neuroscience", "genome analysis", "molecular biology...	Rare Variants Association Analysis in Large-Scale Sequencing Studies at the Single Locus Level	journal.pcbi.1004993	null	[ [ "Recent advances in next-generation sequencing ( NGS ) technologies have extended the focus of genetic studies of complex traits from that of common to rare variants .", "Having low minor allele frequencies ( MAFs ) , usually defined to be less than 1% to 5% , rare variants are often evolved from recent m...	[ "Genetic association analyses of rare variants in next-generation sequencing ( NGS ) studies are fundamentally challenging due to the presence of a very large number of candidate variants at extremely low minor allele frequencies .", "Recent developments often focus on pooling multiple variants to provide associa...	[ "Next-generation sequencing technologies have allowed genetic association studies of complex traits at the single base-pair resolution , where most genetic variants have extremely low mutation frequencies .", "These rare variants have been the focus of modern statistical-computational genomics due to their potent...	2016
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "biomacromolecule-ligand interactions", "biochemistry", "proteins", "electron transport chain", "biology and life sciences", "bioenergetics", "biophysics", "biophysical simulations" ]	Exploring O2 Diffusion in A-Type Cytochrome c Oxidases: Molecular Dynamics Simulations Uncover Two Alternative Channels towards the Binuclear Site	journal.pcbi.1004010	null	[ [ "Cytochrome c oxidases ( Ccoxs ) are the terminal enzymes of the respiratory chain in eukaryotes and in aerobic prokaryotes ( reviewed in [1] ) .", "These integral membrane proteins belong to the heme-copper oxidases superfamily and couple dioxygen ( O2 ) reduction to the translocation of protons across t...	[ "Cytochrome c oxidases ( Ccoxs ) are the terminal enzymes of the respiratory chain in mitochondria and most bacteria .", "These enzymes couple dioxygen ( O2 ) reduction to the generation of a transmembrane electrochemical proton gradient .", "Despite decades of research and the availability of a large amount of...	[ "Cytochrome c oxidases ( Ccoxs ) , the terminal enzymes of the respiratory electron transport chain in eukaryotes and many prokaryotes , are key enzymes in aerobic respiration .", "These proteins couple the reduction of molecular dioxygen to water with the creation of a transmembrane electrochemical proton gradie...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "gene regulation", "pathogens", "cell cycle and cell division", "cell processes", "microbiology", "fungi", "model organisms", "experimental organism systems", "sequence motif analysis", "fungal pathogens", "schizosaccharomy...	Gene duplication and co-evolution of G1/S transcription factor specificity in fungi are essential for optimizing cell fitness	journal.pgen.1006778	null	[ [ "Eukaryotic cells have evolved complex transcriptional regulatory networks to ensure faithful cell division .", "One example is the G1/S cell cycle network that includes a large set of co-regulated genes whose expression peaks at the G1-to-S transition .", "Activation of G1/S transcription promotes en...	[ "Transcriptional regulatory networks play a central role in optimizing cell survival .", "How DNA binding domains and cis-regulatory DNA binding sequences have co-evolved to allow the expansion of transcriptional networks and how this contributes to cellular fitness remains unclear .", "Here we experimentally e...	[ "Cell cycle progression is essential for the division of living cells .", "The G1/S transition through the cell cycle is promoted by the periodic expression of a large set of genes regulated by a G1/S transcriptional gene network .", "Despite extensive comparative studies in different eukaryotic organisms , lit...	2017
[ "Introduction", "Methods", "Results" ]	[ "infectious diseases/infectious diseases of the nervous system", "public health and epidemiology/infectious diseases", "infectious diseases/epidemiology and control of infectious diseases", "infectious diseases/neglected tropical diseases" ]	Rabies Exposures, Post-Exposure Prophylaxis and Deaths in a Region of Endemic Canine Rabies	journal.pntd.0000339	null	[ [ "Rabies is an acute viral infection which causes horrifying neurological symptoms that inevitably result in death .", "Although human rabies encephalitis remains untreatable [1] , the infection is entirely preventable , both by post-exposure prophylaxis ( PEP ) of bite victims , and by population-level va...	[ "Thousands of human deaths from rabies occur annually despite the availability of effective vaccines following exposure , and for disease control in the animal reservoir .", "Our aim was to assess risk factors associated with exposure and to determine why human deaths from endemic canine rabies still occur .", ...	[ "Thousands of human deaths from rabies occur annually despite availability of effective vaccines for humans following exposure , and for disease control in domestic dog populations .", "We established a 5-year contact-tracing study in northwest Tanzania to investigate risk factors associated with rabies exposure ...	2008
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[]	Vaccination with a chikungunya virus-like particle vaccine exacerbates disease in aged mice	journal.pntd.0007316	null	[ [ "Chikungunya virus ( CHIKV ) is a re-emerging pathogen responsible for causing outbreaks of febrile disease accompanied with debilitating joint pain .", "CHIKV was first discovered in Tanzania in 1952 , but outbreaks became more widespread , encompassing countries in Africa , Asia , Europe , and islands o...	[ "Chikungunya virus ( CHIKV ) is a re-emerging pathogen responsible for causing outbreaks of febrile disease accompanied with debilitating joint pain .", "Symptoms typically persist for two weeks , but more severe and chronic chikungunya illnesses have been reported , especially in the elderly .", "Currently , t...	[ "Chikungunya virus is responsible for outbreaks of febrile illnesses accompanied with debilitating join pain in subtropical and tropical regions of the world .", "The disease caused by chikungunya virus typically resolves itself within weeks , but may be persistent and more severe in elderly individuals .", "Cu...	2019
[ "Introduction", "Results", "Discussion", "Material and Methods" ]	[ "medicine", "infectious diseases", "immunology", "biology" ]	Critical Roles for LIGHT and Its Receptors in Generating T Cell-Mediated Immunity during Leishmania donovani Infection	journal.ppat.1002279	null	[ [ "Tumour necrosis factor ( TNF ) superfamily members are involved in many biological functions , including cell growth and differentiation , apoptosis and organogenesis [1] .", "This broad range of activities is achieved by TNF family members interacting with functional receptors associated with distinct c...	[ "LIGHT ( TNFSF14 ) is a member of the TNF superfamily involved in inflammation and defence against infection .", "LIGHT signals via two cell-bound receptors; herpes virus entry mediator ( HVEM ) and lymphotoxin-beta receptor ( LTβR ) .", "We found that LIGHT is critical for control of hepatic parasite growth in...	[ "Visceral leishmaniasis ( VL ) is a potentially fatal human disease caused by the intracellular protozoan parasites Leishmania donovani and L . infantum ( chagasi ) .", "Parasites infect macrophages throughout the viscera , though the spleen and liver are the major sites of disease .", "VL is responsible for si...	2011
[ "Introduction", "Model", "Results", "Discussion" ]	[ "mathematics", "neuroscience/neurodevelopment", "developmental biology/pattern formation" ]	A Reaction-Diffusion Model of Human Brain Development	journal.pcbi.1000749	null	[ [ "The development of the human brain from the early gestational weeks to the buckling of the first folds at around 20 weeks follows a narrow pathway between determinism and pure randomness .", "On the one hand normal adult individuals offer quite similar - from a pure qualitative and descriptive point of v...	[ "Cortical folding exhibits both reproducibility and variability in the geometry and topology of its patterns .", "These two properties are obviously the result of the brain development that goes through local cellular and molecular interactions which have important consequences on the global shape of the cortex ....	[ "The anatomical variability of the human brain folds remains an unclear and challenging issue .", "However it is clear that this variability is the product of the brain development .", "Several hypotheses coexist for explaining the rapid development of cortical sulci and it is of the highest interest that under...	2010
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Sources of Variability in a Synthetic Gene Oscillator	journal.pcbi.1004674	null	[ [ "Random fluctuations in gene networks have a variety of origins: e . g . small molecule numbers within cells [1–6] , fluctuations in the environment [7 , 8] , spatial heterogeneity [9] , or the cell cycle [10] .", "A number of experimental and theoretical studies have examined the impact of noise on gene ...	[ "Synthetic gene oscillators are small , engineered genetic circuits that produce periodic variations in target protein expression .", "Like other gene circuits , synthetic gene oscillators are noisy and exhibit fluctuations in amplitude and period .", "Understanding the origins of such variability is key to bui...	[ "A goal of synthetic biology is to design genetic circuits using mathematical models that predict circuit function .", "However , various sources of noise impact gene regulation in different ways .", "This hinders the development of accurate mathematical models , especially when single-cell accuracy is required...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "coronary artery disease", "genome-wide association studies", "genome expression analysis", "medicine", "gene networks", "genetic networks", "cardiovascular", "genome analysis tools", "atherosclerosis", "gene expression", "biology", "transcriptomes", "genetics", "genomics", "genetics of ...	Integrating Genome-Wide Genetic Variations and Monocyte Expression Data Reveals Trans-Regulated Gene Modules in Humans	journal.pgen.1002367	null	[ [ "Owing to the development of genome-wide association studies ( GWAS ) , the last two years have witnessed spectacular successes in the identification of new loci involved in the susceptibility to complex diseases [1] .", "However , most of these associations have yet to be translated into a full understan...	[ "One major expectation from the transcriptome in humans is to characterize the biological basis of associations identified by genome-wide association studies .", "So far , few cis expression quantitative trait loci ( eQTLs ) have been reliably related to disease susceptibility .", "Trans-regulating mechanisms m...	[ "One major expectation from the transcriptome in humans is to help characterize the biological basis of associations identified by genome-wide association studies .", "Here , we take advantage of recent technical and methodological advances to examine the influence of natural genetic variability on >12 , 000 gene...	2011
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "signal transduction", "infectious diseases", "schistosomiasis", "neglected tropical diseases", "biology", "molecular cell biology", "zoology", "parasitic diseases", "helminthology" ]	Functional Mapping of Protein Kinase A Reveals Its Importance in Adult Schistosoma mansoni Motor Activity	journal.pntd.0001988	null	[ [ "Schistosoma mansoni is an important parasitic blood fluke that causes human schistosomiasis , a neglected tropical disease that ranks second only to malaria when considering the number of people infected ( ∼200 million ) and at risk ( ∼779 million ) [1] .", "The life cycle of this parasite is complex inv...	[ "Cyclic AMP ( cAMP ) -dependent protein kinase/protein kinase A ( PKA ) is the major transducer of cAMP signalling in eukaryotic cells .", "Here , using laser scanning confocal microscopy and ‘smart’ anti-phospho PKA antibodies that exclusively detect activated PKA , we provide a detailed in situ analysis of PKA ...	[ "Schistosome blood flukes are formidable parasites .", "They can survive for many years as male-female pairs in the blood vessels of their vertebrate hosts where they copulate and produce large numbers of eggs that become lodged in tissues causing schistosomiasis .", "Over 200 million people are infected with s...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases/viral infections", "infectious diseases/epidemiology and control of infectious diseases", "virology" ]	Rift Valley Fever Virus Seroprevalence in Human Rural Populations of Gabon	journal.pntd.0000763	null	[ [ "Rift Valley fever virus ( RVFV ) is a mosquito-borne RNA virus belonging to the Phlebovirus genus of the Bunyaviridae family .", "RVFV infects both humans and livestock [1] .", "Although severe clinical cases can be observed , infection with RVF virus ( RVFV ) in humans is , in most cases , asymptoma...	[ "Rift Valley fever ( RVF ) is a mosquito-borne viral zoonosis caused by a phlebovirus and transmitted by Aedes mosquitoes .", "Humans can also be infected through direct contact with blood ( aerosols ) or tissues ( placenta , stillborn ) of infected animals .", "Although severe clinical cases can be observed , ...	[ "Rift Valley fever ( RVF ) is a disease transmitted by a mosquito bite ( Aedes ) .", "Humans can also be infected through direct contact with blood ( aerosols ) or tissues ( placenta , stillborn ) of infected animals .", "Although severe clinical cases can be observed , infection with RVF virus ( RVFV ) in huma...	2010
[ "Introduction", "Results", "Discussion", "Material and methods" ]	[ "sequencing techniques", "medicine and health sciences", "microbial mutation", "pathology and laboratory medicine", "293t cells", "pathogens", "biological cultures", "rna extraction", "microbiology", "retroviruses", "viruses", "immunodeficiency viruses", "rna viruses", "molecular biology t...	Global synonymous mutagenesis identifies cis-acting RNA elements that regulate HIV-1 splicing and replication	journal.ppat.1006824	null	[ [ "The HIV-1 genome contains a variety of RNA elements that have important cis-acting functions [1 , 2] .", "Some of these RNA sequences are multi-functional in that they lie in open reading frames and therefore encode proteins as well as performing functions as RNA that are critical during viral replicatio...	[ "The ~9 . 5 kilobase HIV-1 genome contains RNA sequences and structures that control many aspects of viral replication , including transcription , splicing , nuclear export , translation , packaging and reverse transcription .", "Nonetheless , chemical probing and other approaches suggest that the HIV-1 genome ma...	[ "In addition to encoding viral proteins , the HIV-1 genome contains sequence elements that act at the level of RNA to enable replication .", "We undertook an experiment to discover new RNA elements that act in this way by altering nearly the entire coding sequence of the viral genome so as to change the RNA seque...	2018
[ "Introduction", "Results and Discussion", "Materials and Methods" ]	[ "genomics", "genetics", "biology", "computational biology", "evolutionary biology", "genetics and genomics" ]	Alternative Splicing of RNA Triplets Is Often Regulated and Accelerates Proteome Evolution	journal.pbio.1001229	Inclusion or exclusion of single codons at the splice acceptor site of mammalian genes is regulated in a tissue-specific manner, is strongly conserved, and is associated with local accelerated protein evolution.	[ [ "The split structure of eukaryotic genes impacts gene expression and evolution in diverse ways .", "Most directly , the presence of introns enables multiple distinct mRNA and protein products to be produced from the same gene locus through alternative splicing , which is often regulated between tissues or...	[ "Thousands of human genes contain introns ending in NAGNAG ( N any nucleotide ) , where both NAGs can function as 3′ splice sites , yielding isoforms that differ by inclusion/exclusion of three bases .", "However , few models exist for how such splicing might be regulated , and some studies have concluded that NA...	[ "In order to translate a gene into protein , all of the non-coding regions ( introns ) need to be removed from the transcript and the coding regions ( exons ) stitched back together to make an mRNA .", "Most human genes are alternatively spliced , allowing the selection of different combinations of exons to produ...	2012
[ "Introduction", "Results", "Discussion", "Materials & methods" ]	[ "invertebrates", "medicine and health sciences", "rna interference", "body fluids", "neuroscience", "animals", "hormones", "animal models", "physiological processes", "drosophila melanogaster", "model organisms", "homeostasis", "experimental organism systems", "epigenetics", "drosophila"...	The thirsty fly: Ion transport peptide (ITP) is a novel endocrine regulator of water homeostasis in Drosophila	journal.pgen.1007618	null	[ [ "Maintenance of homeostasis is based on ingestion and metabolism of water and nutrients in a manner that reflects the internal needs of the animal , but the precise regulatory mechanisms are incompletely understood [1] .", "Despite the strong evolutionary conservation of the main pathways underlying energ...	[ "Animals need to continuously adjust their water metabolism to the internal and external conditions .", "Homeostasis of body fluids thus requires tight regulation of water intake and excretion , and a balance between ingestion of water and solid food .", "Here , we investigated how these processes are coordinat...	[ "Maintenance of energy and water balance is necessary for survival of all organisms .", "Even a mild dehydration triggers thirst , reduces appetite , and decreases diuresis ( water excretion ) , thereby promoting conservation of water resources and survival under arid conditions .", "Homeostasis is regulated pr...	2018
[ "Introduction", "Results/Discussion", "Materials And Methods" ]	[ "genetics and genomics/chromosome biology" ]	Condensin II Resolves Chromosomal Associations to Enable Anaphase I Segregation in Drosophila Male Meiosis	journal.pgen.1000228	null	[ [ "There are several critical steps that chromosomes must undergo as they transition from their diffuse interphase state to mobile units that can be faithfully transmitted to daughter cells .", "In the germline , faulty segregation leading to the creation of aneuploid gametes is likely a leading cause of ge...	[ "Several meiotic processes ensure faithful chromosome segregation to create haploid gametes .", "Errors to any one of these processes can lead to zygotic aneuploidy with the potential for developmental abnormalities .", "During prophase I of Drosophila male meiosis , each bivalent condenses and becomes sequeste...	[ "Some of the processes that ensure proper chromosome segregation take place upon the chromosomes themselves .", "The chromosomes of Drosophila males undergo an interesting and relatively enigmatic step before entering meiosis , where each paired homologous chromosome becomes clustered into a discrete region of th...	2008
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "fish", "in situ hybridization", "molecular probe techniques", "vertebrates", "animals", "xenopus", "animal models", "osteichthyes", "developmental biology", "model organisms", "amphibians", "experimental organism systems", "molecular biology techniques", "embryos", "genotyping", "rese...	Mutational analysis of dishevelled genes in zebrafish reveals distinct functions in embryonic patterning and gastrulation cell movements	journal.pgen.1007551	null	[ [ "The specification of the dorsoventral ( DV ) axis is tightly linked to , and ultimately determines , the processes that establish the anteroposterior ( AP ) pattern in vertebrate embryos .", "A large body of work has elucidated the induction and patterning processes underlying DV and AP polarities [1 , 2...	[ "Wnt signaling plays critical roles in dorsoventral fate specification and anteroposterior patterning , as well as in morphogenetic cell movements .", "Dishevelled proteins , or Dvls , mediate the activation of Wnt/ß-catenin and Wnt/planar cell polarity pathways .", "There are at least three highly conserved Dv...	[ "The embryogenesis of most animals is first supported by maternal gene products accumulated in the oocyte , and then by the expression of genes from the zygote .", "In all vertebrates , there are at least three Dishevelled ( Dvl ) proteins , which play critical roles in normal development and human diseases .", ...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "bacteriology", "medicine and health sciences", "pathology and laboratory medicine", "gene regulation", "cell cycle and cell division", "pathogens", "cell processes", "bacillus", "microbiology", "messenger rna", "dna transcription", "bacterial sporulation", "prokaryotic models", "experimen...	Transcription and translation of the sigG gene is tuned for proper execution of the switch from early to late gene expression in the developing Bacillus subtilis spore	journal.pgen.1007350	null	[ [ "Cells across all domains of life alter their phenotypes through global changes in gene expression .", "In bacteria , global changes in gene expression drive phenotypic changes critical for growth , development , and pathogenesis .", "For example , the ability of the human pathogen Chlamydia trachomat...	[ "A cascade of alternative sigma factors directs developmental gene expression during spore formation by the bacterium Bacillus subtilis .", "As the spore develops , a tightly regulated switch occurs in which the early-acting sigma factor σF is replaced by the late-acting sigma factor σG .", "The gene encoding σ...	[ "Global changes in gene expression occur during normal cellular growth and development , as well as during cancer cell transformation and bacterial pathogenesis .", "In this study we have investigated the molecular mechanisms that drive the switch from early to late developmental gene expression during spore form...	2018
[ "Introduction", "Materials and Methods", "Results and Discussion" ]	[ "cell motility", "medicine and health sciences", "actin filaments", "classical mechanics", "engineering and technology", "signal processing", "mechanical stress", "osteoblasts", "materials science", "connective tissue cells", "cellular structures and organelles", "cytoskeleton", "materials b...	A Robust Actin Filaments Image Analysis Framework	journal.pcbi.1005063	null	[ [ "Computer vision and image-analytical tools are essential in order to study the biology of cells [29] .", "Several approaches exist for the analysis of filamentous structures [19–21 , 30–36] , consisting in one or several sequential processing steps: pre-processing , filaments network segmentation , and i...	[ "The cytoskeleton is a highly dynamical protein network that plays a central role in numerous cellular physiological processes , and is traditionally divided into three components according to its chemical composition , i . e . actin , tubulin and intermediate filament cytoskeletons .", "Understanding the cytoske...	[ "We propose a novel actin filaments cytoskeleton analysis framework that allows extracting quasi-straight individual fibers in a robust manner , and provides their respective position , orientation , and length as output .", "The proposed framework is defined as a three-steps processing sequence , that can explic...	2016
[ "Introduction", "Results/Discussion", "Methods" ]	[ "rheumatology/connective tissue disease", "genetics and genomics/genetics of the immune system", "genetics and genomics/complex traits", "rheumatology/systemic lupus erythematosos", "rheumatology/autoimmunity, autoimmune, and inflammatory diseases", "immunology/genetics of the immune system", "immunolog...	High-Density SNP Screening of the Major Histocompatibility Complex in Systemic Lupus Erythematosus Demonstrates Strong Evidence for Independent Susceptibility Regions	journal.pgen.1000696	null	[ [ "Systemic lupus erythematosus ( SLE ) is the prototypic systemic autoimmune disease characterized by autoantibody production and involvement of multiple organ systems .", "Although the etiology of SLE remains unknown , several lines of evidence underscore the importance of genetic factors , including a hi...	[ "A substantial genetic contribution to systemic lupus erythematosus ( SLE ) risk is conferred by major histocompatibility complex ( MHC ) gene ( s ) on chromosome 6p21 .", "Previous studies in SLE have lacked statistical power and genetic resolution to fully define MHC influences .", "We characterized 1 , 610 C...	[ "Systemic lupus erythematosus ( SLE ) is an autoimmune disease characterized by autoantibody production and involvement of multiple organ systems .", "Although the cause of SLE remains unknown , several lines of evidence underscore the importance of genetic factors .", "As is true for most autoimmune diseases ,...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "diagnostic medicine", "clinical immunology", "immunology" ]	New Approaches with Different Types of Circulating Cathodic Antigen for the Diagnosis of Patients with Low Schistosoma mansoni Load	journal.pntd.0002054	null	[ [ "Schistosomiasis is a disease caused by one of six Schistosoma species , namely Schistosoma haematobium , S . guineensis , S . intercalatum , S . mansoni , S . japonicum , and S . mekongi [1] .", "Schistosomiasis occurs in the tropics and subtropics and is among the most important parasitic diseases world...	[ "Schistosomiasis mansoni is a debilitating and sometimes fatal disease .", "Accurate diagnosis plays a key role in patient management and infection control .", "However , currently available parasitological methods are laborious and lack sensitivity .", "The selection of target antigen candidates has turned o...	[ "Schistosomiasis mansoni is a debilitating and sometimes fatal disease that affects many individuals in Africa and Brazil .", "Currently available diagnostic methods are not sensitive for patients with low parasite load which leads to underreported cases .", "The selection of target diagnostic antigen candidate...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "primates", "biochemistry", "infectious diseases", "in vitro", "immunology", "homo (human)" ]	Role of ABO Secretor Status in Mucosal Innate Immunity and H. pylori Infection	journal.ppat.0040002	null	[ [ "In turbulent systems such as the oro-gastro-intestinal tract , adaptation to local niches requires microbial adherence properties to match host receptors and thereby stabilize microbial colonization or infection .", "H . pylori achieved this goal by developing the BabA and SabA adhesins , which bind to t...	[ "The fucosylated ABH antigens , which constitute the molecular basis for the ABO blood group system , are also expressed in salivary secretions and gastrointestinal epithelia in individuals of positive secretor status; however , the biological function of the ABO blood group system is unknown .", "Gastric mucosa ...	[ "The common ABO blood group antigen system was described in the early 20th century .", "In addition , it has been known for 60 years that the majority of individuals also express the corresponding ABO antigens ( carbohydrate identity tags ) in their saliva , tears , milk , and mucus secretions in the digestive tr...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunomodulation", "immunopathology", "animal models of infection", "pathogenesis", "immunity", "virology", "immunology", "biology", "microbiology", "host-pathogen interaction", "autoimmunity", "immune response", "immunoglobulins" ]	Passively Administered Pooled Human Immunoglobulins Exert IL-10 Dependent Anti-Inflammatory Effects that Protect against Fatal HSV Encephalitis	journal.ppat.1002071	null	[ [ "Herpes simplex virus ( HSV ) is the leading cause of sporadic encephalitis , which , although rare , can be fatal or result in severe neurological deficits in survivors [1] .", "We reported previously that dysregulated CNS inflammatory responses cause fatal HSE in 129S6 ( 129 ) mice .", "Most importa...	[ "HSV-1 is the leading cause of sporadic encephalitis in humans .", "HSV infection of susceptible 129S6 mice results in fatal encephalitis ( HSE ) caused by massive inflammatory brainstem lesions comprising monocytes and neutrophils .", "During infection with pathogenic microorganisms or autoimmune disease , IgG...	[ "We show that fatal HSV encephalitis ( HSE ) is caused by excessive brainstem inflammation .", "Once brainstem inflammation is initiated , antiviral drugs that inhibit only viral replication are ineffective in protecting against fatal HSE .", "Infusion of high doses of pooled human IgG ( IVIG ) is an effective ...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "immunology", "microbiology", "host-pathogen interaction", "bacterial diseases", "immunomodulation", "bacterial pathogens", "infectious diseases", "biology", "infectious disease modeling", "immune response", "computer science", "immunity", "innate immunity", "tularemia" ]	A Mathematical Model of CR3/TLR2 Crosstalk in the Context of Francisella tularensis Infection	journal.pcbi.1002757	null	[ [ "Receptor-mediated engagement followed by phagocytosis by professional phagocytes is the first critical step in microbial clearance or , in the case of intracellular pathogens , entry to a safe niche .", "The molecular mechanisms underlying phagocytosis are complex , usually involving more than one recept...	[ "Complement Receptor 3 ( CR3 ) and Toll-like Receptor 2 ( TLR2 ) are pattern recognition receptors expressed on the surface of human macrophages .", "Although these receptors are essential components for recognition by the innate immune system , pathogen coordinated crosstalk between them can suppress the product...	[ "In the current work we construct a highly contextual model of membrane-proximal crosstalk between the ERK and PI3K cascades that is initiated through contact with F . tularensis .", "The model is used to test the hypothesis that phagocytic signaling downstream from CR3 is responsible for an early inhibition of E...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "viral hemorrhagic fevers", "infectious diseases", "crimean-congo hemorrhagic fever", "neglected tropical diseases", "biology", "genomics", "viral diseases", "genetics and genomics" ]	Multiple Crimean-Congo Hemorrhagic Fever Virus Strains Are Associated with Disease Outbreaks in Sudan, 2008–2009	journal.pntd.0001159	null	[ [ "Crimean-Congo hemorrhagic fever ( CCHF ) , caused by Crimean-Congo hemorrhagic fever virus ( CCHFV ) , is a tick-borne virus with a tripartite RNA genome ( segments designated S , M , and L ) .", "CCHFV can be transmitted to humans by the bite of an Ixodid tick and by contact with blood or tissue from in...	[ "Crimean-Congo hemorrhagic fever ( CCHF ) activity has recently been detected in the Kordufan region of Sudan .", "Since 2008 , several sporadic cases and nosocomial outbreaks associated with high case-fatality have been reported in villages and rural hospitals in the region .", "In the present study , we descr...	[ "The tick-borne virus which causes the disease Crimean-Congo hemorrhagic fever ( CCHF ) is known to be widely distributed throughout much of Africa , Southern Europe , the Middle East , Central Asia , and Southern Russia .", "Humans contract the virus from contact with infected people , infected animals ( which d...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "homo (human)", "in vitro", "computational biology", "mus (mouse)", "neuroscience", "drosophila", "genetics and genomics", "saccharomyces" ]	Huntingtin Interacting Proteins Are Genetic Modifiers of Neurodegeneration	journal.pgen.0030082	null	[ [ "Huntington's Disease ( HD ) is a member of a family of dominantly inherited neurodegenerative diseases caused by expansion in a glutamine-encoding CAG tract .", "HD occurs when the polyglutamine ( polyQ ) tract in huntingtin ( Htt ) expands beyond ~35 glutamine ( Q ) repeats and manifests with movement d...	[ "Huntington's disease ( HD ) is a fatal neurodegenerative condition caused by expansion of the polyglutamine tract in the huntingtin ( Htt ) protein .", "Neuronal toxicity in HD is thought to be , at least in part , a consequence of protein interactions involving mutant Htt .", "We therefore hypothesized that g...	[ "Huntington's Disease ( HD ) is a fatal inherited neurodegenerative disease , which typically begins in middle age and progresses with symptoms of severe uncontrolled movements and cognitive dysfunction .", "HD is uniformly fatal with death occurring ten to 15 years after onset of symptoms .", "There is current...	2007
[ "Introduction", "Material and Methods", "Results", "Discussion" ]	[ "public health and epidemiology/epidemiology", "infectious diseases/helminth infections" ]	Prevalence and Risk Factors of Porcine Cysticercosis in Angónia District, Mozambique	journal.pntd.0000594	null	[ [ "Porcine cysticercosis is an infection caused by the larval stage of Taenia solium , a zoonotic tapeworm that is transmitted among humans and between humans and pigs .", "The life cycle of this parasite includes pigs as the normal intermediate hosts , harbouring the larval cysticerci , and humans as defin...	[ "Taenia solium is an important zoonosis in many developing countries .", "Cysticercosis poses a serious public health risk and incurs sizeable economic losses to pig production .", "Because data on the epidemiology of porcine cysticercosis in Mozambique are scarce , the present study was conducted to determine ...	[ "Porcine cysticercosis is an infection of pigs caused by the larval stage of Taenia solium , a tapeworm that causes taeniosis in humans .", "The disease is very common in pigs from many developing countries around the world and poses a serious public health risk and causes significant economic losses in pig produ...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Meta-Analysis of Genome-Wide Association Studies Identifies Six New Loci for Serum Calcium Concentrations	journal.pgen.1003796	null	[ [ "Normal calcium homeostasis is regulated by three major hormones acting on their corresponding receptors in gut , kidney , and bone: parathyroid hormone ( PTH ) release governed by the calcium-sensing receptor ( CASR ) , calcitonin , and the active metabolite of vitamin D , 1 , 25 ( OH ) 2-D .", "Despite ...	[ "Calcium is vital to the normal functioning of multiple organ systems and its serum concentration is tightly regulated .", "Apart from CASR , the genes associated with serum calcium are largely unknown .", "We conducted a genome-wide association meta-analysis of 39 , 400 individuals from 17 population-based coh...	[ "Calcium is vital to many biological processes and its serum concentration is tightly regulated .", "Family studies have shown that serum calcium is under strong genetic control .", "Apart from CASR , the genes associated with serum calcium are largely unknown .", "We conducted a genome-wide association meta-...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases/bacterial infections", "infectious diseases/neglected tropical diseases" ]	Phase Change Material for Thermotherapy of Buruli Ulcer: A Prospective Observational Single Centre Proof-of-Principle Trial	journal.pntd.0000380	null	[ [ "Buruli ulcer ( BU ) is a chronic necrotizing disease of skin and soft tissue caused by Mycobacterium ulcerans [1] .", "The disease starts as a subcutaneous nodule , papule or plaque that eventually ulcerates and progresses over months to years .", "In BU lesions , clumps of extra-cellular acid-fast o...	[ "Buruli ulcer ( BU ) is an infection of the subcutaneous tissue leading to chronic necrotizing skin ulcers .", "The causative pathogen , Mycobacterium ulcerans , grows best at 30°C–33°C and not above 37°C .", "We explored the safety , tolerability and efficacy of phase change material ( PCM ) , a novel heat app...	[ "Buruli ulcer is an infection of the subcutaneous tissue leading to chronic necrotizing skin ulcers .", "The causative pathogen , Mycobacterium ulcerans , grows best at 30°C–33°C and not above 37°C , and this property makes the application of heat a treatment option .", "We achieved a breakthrough in heat treat...	2009
[ "Introduction", "Methods", "Results", "Discussion", "Conclusions" ]	[ "invertebrates", "medicine and health sciences", "ecology and environmental sciences", "water resources", "pathology and laboratory medicine", "education", "sociology", "social sciences", "animals", "health care", "diarrhea", "signs and symptoms", "gastroenterology and hepatology", "infect...	A Cluster-Randomized Controlled Trial to Reduce Diarrheal Disease and Dengue Entomological Risk Factors in Rural Primary Schools in Colombia	journal.pntd.0005106	null	[ [ "Integrating the control of diseases can reduce their burden while relieving resource-strained public health budgets [1–3] .", "Many tropical diseases are co-endemic and have overlapping risk factors and strategies for control and prevention .", "Recent assessments of co-occurrence and co-infection of...	[ "As many neglected tropical diseases are co-endemic and have common risk factors , integrated control can efficiently reduce disease burden and relieve resource-strained public health budgets .", "Diarrheal diseases and dengue fever are major global health problems sharing common risk factors in water storage con...	[ "Many tropical diseases co-occur in the same areas and have overlapping risk factors and strategies for control and prevention .", "Therefore , integrating several diseases in control activities can be both effective and cost-efficient .", "We evaluated sets of diarrhea and dengue interventions in rural primary...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cellular stress responses", "genetic mutation", "genetics", "molecular genetics", "biology", "molecular cell biology", "gene function" ]	The Yeast Environmental Stress Response Regulates Mutagenesis Induced by Proteotoxic Stress	journal.pgen.1003680	null	[ [ "Sensing and responding to environmental cues are ubiquitous cellular functions essential for survival .", "Budding yeast cells respond to a variety of stresses by inducing or repressing specific sets of genes in a stereotypical fashion that , to a certain degree , does not depend on the identity of the s...	[ "Conditions of chronic stress are associated with genetic instability in many organisms , but the roles of stress responses in mutagenesis have so far been elucidated only in bacteria .", "Here , we present data demonstrating that the environmental stress response ( ESR ) in yeast functions in mutagenesis induced...	[ "Cellular capability to mutate its DNA plays an important role in evolution and impinges on medical issues , including acquisition of mutator phenotypes by cancer cells and emergence of drug-resistant pathogens .", "Whether and how the environment affects rates of mutation has been studied predominantly in the co...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell physiology", "cell fusion", "chromosome structure and function", "dna-binding proteins", "organisms", "telomeres", "fungi", "dna", "epigenetics", "molecular biology techniques", "chromatin", "research and analysis methods", "telomere length", "artificial gene amplification and extens...	Histone depletion prevents telomere fusions in pre-senescent cells	journal.pgen.1007407	null	[ [ "Telomeres are highly specialized nucleoprotein structures that hide the ends of chromosomes from double-strand break ( DSB ) repair and DNA damage checkpoint activities .", "In this way , telomeres protect the chromosome ends from fusions and degradations and from eliciting an erroneous DNA damage respon...	[ "Upon telomerase inactivation , telomeres gradually shorten with each cell division until cells enter replicative senescence .", "In Saccharomyces cerevisiae , the kinases Mec1/ATR and Tel1/ATM protect the genome during pre-senescence by preventing telomere-telomere fusions ( T-TFs ) and the subsequent genetic in...	[ "Telomere shortening upon telomerase inactivation leads to an irreversible cell division arrest known as replicative senescence , which is considered as a tumor suppressor mechanism .", "Since pre-senescence is critical for tissue homeostasis , cells are endowed with recombination mechanisms that facilitate the r...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "organismal evolution", "genome evolution", "insertion mutation", "microbiology", "mutation", "microbial evolution", "population biology", "genome complexity", "molecular evolution", "evolutionary genetics", "population metrics", "population size", "phenotypes", "genetics", "biology and ...	Different Evolutionary Paths to Complexity for Small and Large Populations of Digital Organisms	journal.pcbi.1005066	null	[ [ "The relative importance of adaptive ( i . e . , selection ) versus non-adaptive ( i . e . , drift ) mechanisms in shaping the evolution of complexity is still a matter of contention among evolutionary biologists [1–6] .", "In molecular evolution , the role of non-adaptive evolutionary processes such as g...	[ "A major aim of evolutionary biology is to explain the respective roles of adaptive versus non-adaptive changes in the evolution of complexity .", "While selection is certainly responsible for the spread and maintenance of complex phenotypes , this does not automatically imply that strong selection enhances the c...	[ "Since the early days of theoretical population genetics .", "scientists have debated the role of population size in shaping evolutionary dynamics .", "Do large populations possess an evolutionary advantage towards complexity due to the strength of natural selection in these populations ?", "Or do small popul...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "computational biology/systems biology", "computational biology/genomics" ]	Is My Network Module Preserved and Reproducible?	journal.pcbi.1001057	null	[ [ "Network methods are frequently used in genomic and systems biologic studies , but also in general data mining applications , to describe the pairwise relationships of a large number of variables [1] , [2] .", "For example , gene co-expression networks can be constructed on the basis of gene expression da...	[ "In many applications , one is interested in determining which of the properties of a network module change across conditions .", "For example , to validate the existence of a module , it is desirable to show that it is reproducible ( or preserved ) in an independent test network .", "Here we study several type...	[ "In network applications , one is often interested in studying whether modules are preserved across multiple networks .", "For example , to determine whether a pathway of genes is perturbed in a certain condition , one can study whether its connectivity pattern is no longer preserved .", "Non-preserved modules ...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/bacterial infections", "genetics and genomics/gene function", "microbiology/cellular microbiology and pathogenesis", "microbiology" ]	The Bicarbonate Transporter Is Essential for Bacillus anthracis Lethality	journal.ppat.1000210	null	[ [ "Bacillus anthracis is a Gram-positive , endospore-forming bacterium that is the etiological agent of anthrax .", "Anthrax is primarily a disease of grazing herbivores with human infections as the result of either direct contact with infected animal products or intentional dispersion of anthrax spores as ...	[ "In the pathogenic bacterium Bacillus anthracis , virulence requires induced expression of the anthrax toxin and capsule genes .", "Elevated CO2/bicarbonate levels , an indicator of the host environment , provide a signal ex vivo to increase expression of virulence factors , but the mechanism underlying induction...	[ "Hospital-acquired bacterial infections are a growing public health concern .", "The bacteria responsible for these infections are often resistant to multiple antibiotics , making the problem of nosocomial infections even more dramatic and the need for new antibacterial treatment more urgent .", "Bacteria rely ...	2008
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Ex Vivo Host and Parasite Response to Antileishmanial Drugs and Immunomodulators	journal.pntd.0003820	null	[ [ "The outcome of treatment of leishmaniasis and other infectious diseases is multi-factorial involving host as well as microbial determinants; yet evaluation of antimicrobial drug susceptibility is limited to assessment of drug effects on microbial pathogens and toxicity .", "However , the efficacy of anti...	[ "Therapeutic response in infectious disease involves host as well as microbial determinants .", "Because the immune and inflammatory response to Leishmania ( Viannia ) species defines the outcome of infection and efficacy of treatment , immunomodulation is considered a promising therapeutic strategy .", "Howeve...	[ "Host determinants of the response to infection have increasingly been recognized as therapeutically relevant targets .", "Despite the pathogenesis of dermal leishmaniasis being mediated by the immune and inflammatory response , in vitro anti-leishmanial drug screening has been based on antimicrobial effect witho...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The Complex Contributions of Genetics and Nutrition to Immunity in Drosophila melanogaster	journal.pgen.1005030	null	[ [ "There is strong intuition that dietary nutrition affects the quality of immune defense , and this intuition is well supported scientifically .", "Starvation increases susceptibility to infection in insects as well as humans [1 , 2] , and specific dietary components such as vitamins , carbohydrates , and ...	[ "Both malnutrition and undernutrition can lead to compromised immune defense in a diversity of animals , and “nutritional immunology” has been suggested as a means of understanding immunity and determining strategies for fighting infection .", "The genetic basis for the effects of diet on immunity , however , has...	[ "Previous studies have indicated that dietary nutrition influences immune defense in a variety of animals , but the mechanistic and genetic basis for that influence is largely unknown .", "We use the model insect Drosophila melanogaster to conduct an unbiased genome-wide mapping study to identify genes responsibl...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "spectrometric identification of proteins", "lysosomes", "medicine and health sciences", "vesicles", "hela cells", "biological cultures", "light microscopy", "stable isotope labeling by amino acids in cell culture", "fibroblasts", "cargo proteins", "immunoprecipitation", "microscopy", "conne...	Role of the AP-5 adaptor protein complex in late endosome-to-Golgi retrieval	journal.pbio.2004411	null	[ [ "Adaptor protein ( AP ) complexes are a family of 5 evolutionarily ancient heterotetramers [1] , which facilitate the transport of cargo from one membrane compartment of the cell to another .", "The most recently discovered AP complex , AP-5 [2] , had escaped detection for over 10 years , because its subu...	[ "The AP-5 adaptor protein complex is presumed to function in membrane traffic , but so far nothing is known about its pathway or its cargo .", "We have used CRISPR-Cas9 to knock out the AP-5 ζ subunit gene , AP5Z1 , in HeLa cells , and then analysed the phenotype by subcellular fractionation profiling and quantit...	[ "Eukaryotic cells contain multiple membrane-bound compartments , each with a distinct function and molecular composition .", "Proteins are transported from one compartment to another by vesicular carriers .", "Formation of these carriers requires coat proteins , which both shape the membrane into a vesicle and ...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Molecular Characterisation of Chikungunya Virus Infections in Trinidad and Comparison of Clinical and Laboratory Features with Dengue and Other Acute Febrile Cases	journal.pntd.0004199	null	[ [ "Chikungunya virus ( CHIKV; Family Togaviridae , genus Alphavirus ) is the aetiological agent of chikungunya fever ( CHIKF ) , which presents as an acute onset high fever with headache , back pain , muscle and joint pain .", "The joint pain can vary in intensity but is often very intense , predominates at...	[ "Local transmission of Chikungunya virus ( CHIKV ) was first documented in Trinidad and Tobago ( T&T ) in July 2014 preceding a large epidemic .", "At initial presentation , it is difficult to distinguish chikungunya fever ( CHIKF ) from other acute undifferentiated febrile illnesses ( AUFIs ) , including life-th...	[ "Chikungunya virus ( CHIKV ) recently emerged in the Americas and caused a major epidemic of chikungunya fever ( CHIKF ) .", "While not usually life threatening , CHIKF is a debilitating and often chronic illness resulting in major morbidity and economic losses .", "It is difficult to distinguish CHIKF from oth...	2015
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "ruminants", "helminths", "vertebrates", "animals", "mammals", "trematodes", "veterinary diagnostics", "materials science", "materials physics", "sedimentation", "molecular biology techniques", "veterinary science", "veterinary medicine", ...	Scrambled eggs: A highly sensitive molecular diagnostic workflow for Fasciola species specific detection from faecal samples	journal.pntd.0005931	null	[ [ "Fasciolosis , due to Fasciola hepatica and Fasciola gigantica , is an important zoonotic production-limiting disease of ruminants [1] .", "In 2005 , an estimated 91 million people across 8 countries were considered at risk of contracting this neglected tropical disease , with children the most likely to ...	[ "Fasciolosis , due to Fasciola hepatica and Fasciola gigantica , is a re-emerging zoonotic parasitic disease of worldwide importance .", "Human and animal infections are commonly diagnosed by the traditional sedimentation and faecal egg-counting technique .", "However , this technique is time-consuming and pron...	[ "Fasciolosis caused by infection with F . hepatica , F . gigantica and their hybrid strains is an important health issue in medical and veterinary sciences .", "The economic impacts of infection and disease on production animals is of particular concern in low-income rural areas of developing countries , includin...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology/animal models of infection", "virology" ]	Transmission of Influenza Virus in a Mammalian Host Is Increased by PB2 Amino Acids 627K or 627E/701N	journal.ppat.1000252	null	[ [ "Repeated introductions of avian H5N1 influenza viruses into the human population have resulted in more than 380 reported cases of severe disease since 2003 .", "Greater than half of these cases have been fatal , highlighting the extreme pathogenicity of H5N1 influenza in humans .", "Furthermore , hig...	[ "Since 2003 , more than 380 cases of H5N1 influenza virus infection of humans have been reported .", "Although the resultant disease in these cases was often severe or fatal , transmission of avian influenza viruses between humans is rare .", "The precise nature of the barrier blocking human-to-human spread is ...	[ "To cause a pandemic , an influenza virus must transmit efficiently from human to human .", "The viral factors that enable person-to-person spread of influenza viruses remain elusive .", "Using the guinea pig , an animal which we have previously shown to model the human transmission of influenza , we have ident...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "neurological disorders", "genetics and genomics/gene function", "molecular biology/dna repair", "genetics and genomics/functional genomics" ]	A Genome-Scale DNA Repair RNAi Screen Identifies SPG48 as a Novel Gene Associated with Hereditary Spastic Paraplegia	journal.pbio.1000408	We have identified a novel gene in a genome-wide, double-strand break DNA repair RNAi screen and show that is involved in the neurological disease hereditary spastic paraplegia.	[ [ "Mutations in DNA repair genes are associated with different diseases and disorders including cancer [1] , accelerated aging [2] , and neuronal degeneration [3] .", "Neurons appear to be particularly vulnerable to mutations in DNA repair genes , possibly due to the lack of proliferation and high oxidative...	[ "DNA repair is essential to maintain genome integrity , and genes with roles in DNA repair are frequently mutated in a variety of human diseases .", "Repair via homologous recombination typically restores the original DNA sequence without introducing mutations , and a number of genes that are required for homolog...	[ "All cells in our bodies have to cope with numerous lesions to their DNA .", "Cells use a battery of genes to repair DNA and maintain genome integrity .", "Given the importance of an intact genome , it is not surprising that genes with roles in DNA repair are mutated in many human diseases .", "Here , we pres...	2010
[ "Introduction", "Results/Discussion", "Methods" ]	[ "computer and information sciences", "psychology", "biology and life sciences", "social sciences", "computerized simulations" ]	Optimal Behavioral Hierarchy	journal.pcbi.1003779	null	[ [ "Since the earliest days of psychology and neuroscience , a core objective within both fields has been to understand the formal structure of behavior [1]–[4] .", "In pursuing this question , both in humans and in other animals , a crucial and recurring observation has been that behavior displays a hierarc...	[ "Human behavior has long been recognized to display hierarchical structure: actions fit together into subtasks , which cohere into extended goal-directed activities .", "Arranging actions hierarchically has well established benefits , allowing behaviors to be represented efficiently by the brain , and allowing so...	[ "In order to accomplish everyday tasks , we often divide them up into subtasks: to make spaghetti , we ( 1 ) get out a pot , ( 2 ) fill it with water , ( 3 ) bring the water to a boil , and so forth .", "But how do we learn to subdivide our goals in this way ?", "Work from computer science suggests that the way...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "blood cells", "children", "medicine and health sciences", "body fluids", "pathology and laboratory medicine", "vomiting", "blood counts", "pediatrics", "physiological processes", "age groups", "mathematics", "forecasting", "statistics (mathematics)", "signs and symptoms", "platelets", ...	The value of daily platelet counts for predicting dengue shock syndrome: Results from a prospective observational study of 2301 Vietnamese children with dengue	journal.pntd.0005498	null	[ [ "Dengue is the most important mosquito-borne viral infection affecting humans .", "Incidence has increased dramatically over the last 50 years , with approximately 100 million symptomatic dengue infections now estimated to occur annually across more than 100 countries [1 , 2] .", "Although the majorit...	[ "Dengue is the most important mosquito-borne viral infection to affect humans .", "Although it usually manifests as a self-limited febrile illness , complications may occur as the fever subsides .", "A systemic vascular leak syndrome that sometimes progresses to life-threatening hypovolaemic shock is the most s...	[ "Dengue is a very common , potentially serious , mosquito-borne viral infection .", "The spectrum of clinical disease is broad .", "Dengue shock syndrome ( DSS ) , seen primarily in children , is the most serious life-threatening manifestation .", "Early identification of children presenting with dengue who a...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics", "biology", "evolutionary biology", "zoology", "marine biology" ]	Rod Monochromacy and the Coevolution of Cetacean Retinal Opsins	journal.pgen.1003432	null	[ [ "Cetacea [dolphins , porpoises , and whales] represents a remarkable example of aquatic specialization within Mammalia [1] .", "With their return to river and marine environments , the ancestors of modern toothed cetaceans ( Odontoceti ) and baleen whales ( Mysticeti ) underwent extensive modifications th...	[ "Cetaceans have a long history of commitment to a fully aquatic lifestyle that extends back to the Eocene .", "Extant species have evolved a spectacular array of adaptations in conjunction with their deployment into a diverse array of aquatic habitats .", "Sensory systems are among those that have experienced r...	[ "The emergence of Cetacea ( whales , dolphins , porpoises ) represents a profound transition in the history of life .", "Living cetaceans have evolved a spectacular array of adaptations in association with their return to aquatic habitats .", "Aquatic environments impose challenging constraints on sensory syste...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "invertebrates", "helminths", "hookworms", "animals", "plasmid construction", "necator americanus", "organisms", "developmental biology", "dna construction", "molecular biology techniques", "genotyping", "extraction techniques", "research and analysis methods", "artificial gene amplificati...	Isothermal Diagnostic Assays for Monitoring Single Nucleotide Polymorphisms in Necator americanus Associated with Benzimidazole Drug Resistance	journal.pntd.0005113	null	[ [ "Intestinal helminths cause a major burden on human health in developing countries , infecting more than 2 billion people worldwide [1] .", "Hookworms are one of the major STHs and the second most prevalent intestinal helminth of humans [2] , infecting an estimated 438 . 9 million people in resource-const...	[ "Soil-transmitted helminths ( STHs ) are the most prevalent intestinal helminths of humans , and a major cause of morbidity in tropical and subtropical countries .", "The benzimidazole ( BZ ) drugs albendazole ( ABZ ) and mebendazole ( MBZ ) are used for treatment of human STH infections and this use is increasin...	[ "Hookworms are amongst the major STHs and the second most prevalent intestinal helminth of humans .", "Large-scale treatment with the benzimidazoles ( BZs ) albendazole or mebendazole is the major control strategy against STHs in mass drug administration ( MDA ) programs .", "Prolonged and repeated treatment wi...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genomics", "functional genomics", "genome evolution", "chromosome biology", "genomic evolution", "biology", "evolutionary biology", "comparative genomics", "chromatin", "genetics and genomics" ]	Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection	journal.pgen.1002789	null	[ [ "Understanding the molecular basis of phenotypic differences between humans and other primates has been a priority in medicine , behavior , and evolution research [1]–[3] .", "The genetic basis for these differences can now be explored genome-wide due in part to the rising number of completely sequenced p...	[ "Understanding the molecular basis for phenotypic differences between humans and other primates remains an outstanding challenge .", "Mutations in non-coding regulatory DNA that alter gene expression have been hypothesized as a key driver of these phenotypic differences .", "This has been supported by different...	[ "The human genome shares a remarkable amount of genomic sequence with our closest living primate relatives .", "Researchers have long sought to understand what regions of the genome are responsible for unique species-specific traits .", "Previous studies have shown that many genes are differentially expressed b...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "schistosomiasis", "neglected tropical diseases" ]	Dynamics of Th17 Cells and Their Role in Schistosoma japonicum Infection in C57BL/6 Mice	journal.pntd.0001399	null	[ [ "CD4+ T cells play an important role in the initiation of immune responses against an infection by providing help to other cells and by taking on a variety of effector functions during immune reactions .", "Upon antigenic stimulation , naive CD4+ T cells activate , expand and differentiate into different ...	[ "The current knowledge of immunological responses to schistosomiasis , a major tropical helminthic disease , is insufficient , and a better understanding of these responses would support vaccine development or therapies to control granuloma-associated immunopathology .", "CD4+ T cells play critical roles in both ...	[ "Th17 immune cells secrete the IL-17 cytokine and contribute to host defenses against certain infections .", "Recent studies linked IL-17 with the severity of liver inflammation and suggested that Th17 cells contribute to the pathology in schistosomiasis , a serious disease caused by parasitic worms such as Schis...	2011
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Ebola Virus RNA Editing Depends on the Primary Editing Site Sequence and an Upstream Secondary Structure	journal.ppat.1003677	null	[ [ "Filoviruses ( ebolaviruses ( EBOV ) and marburgviruses ( MARV ) ) cause severe hemorrhagic fever in humans and nonhuman primates [1] .", "They contain a non-segmented negative-sense single-stranded RNA genome accommodating seven genes ( NP , VP35 , VP40 , GP , VP30 , VP24 , and L ) to produce seven struc...	[ "Ebolavirus ( EBOV ) , the causative agent of a severe hemorrhagic fever and a biosafety level 4 pathogen , increases its genome coding capacity by producing multiple transcripts encoding for structural and nonstructural glycoproteins from a single gene .", "This is achieved through RNA editing , during which non...	[ "Ebola virus ( EBOV ) causes severe hemorrhagic fever with case fatality rates of up to 90% and no therapy or vaccine currently available .", "A better understanding of the EBOV life cycle is important to develop new countermeasures against this virus; however , research with live EBOV is restricted to high conta...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "viral transmission and infection", "microbiology", "parasitic diseases", "protozoan life cycles", "parasitic protozoans", "developmental biology", "protozoans", "lipid analysis", "lipids", "life cycles", "protozoan infections", "molecular biology", "amastig...	Host triacylglycerols shape the lipidome of intracellular trypanosomes and modulate their growth	journal.ppat.1006800	null	[ [ "Infection with the protozoan parasite Trypanosoma cruzi underlies the development of human Chagas disease , a progressive and debilitating condition characterized by cardiac and gastrointestinal disturbances [1] .", "With an estimated 8 million people infected [2] and limited treatment options [3] , this...	[ "Intracellular infection and multi-organ colonization by the protozoan parasite , Trypanosoma cruzi , underlie the complex etiology of human Chagas disease .", "While T . cruzi can establish cytosolic residence in a broad range of mammalian cell types , the molecular mechanisms governing this process remain poorl...	[ "The development of human Chagas disease is associated with persistent intracellular infection with the protozoan parasite , Trypanosoma cruzi , which displays tropism for tissues with characteristically high fatty acid flux , such as heart and adipose tissues .", "Previous studies have highlighted fatty acid met...	2017
[ "Introduction", "Model", "Results", "Discussion" ]	[ "forms of evolution", "theoretical biology", "biology", "computational biology", "evolutionary biology", "evolutionary processes" ]	Implications of Behavioral Architecture for the Evolution of Self-Organized Division of Labor	journal.pcbi.1002430	null	[ [ "Division of labor is ubiquitous in nature .", "The major evolutionary transitions , such as the separation of germ and soma and the transition from prokaryotes to eukaryotes , were accompanied by an increase in division of labor [1] .", "The transition from solitary to eusocial in insects encompasses...	[ "Division of labor has been studied separately from a proximate self-organization and an ultimate evolutionary perspective .", "We aim to bring together these two perspectives .", "So far this has been done by choosing a behavioral mechanism a priori and considering the evolution of the properties of this mecha...	[ "In insect colonies , different individuals specialize in different tasks related to colony maintenance and growth .", "Unveiling why this division of labor evolved and how individuals decide which task to take on is crucial for our understanding of complex group behavior .", "Here we model the evolution of gen...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases/neglected tropical diseases" ]	Prospects for the Development of Odour Baits to Control the Tsetse Flies Glossina tachinoides and G. palpalis s.l.	journal.pntd.0000632	null	[ [ "Tsetse flies ( Diptera: Glossinidae ) infest ∼10 million km2 of sub-Saharan Africa where they transmit trypanosomes which cause Human African Trypanosomiasis ( HAT; also known as sleeping sickness ) and African Animal Trypanosomiasis ( AAT; also known as Nagana ) .", "This complex of diseases has an impo...	[ "Field studies were done of the responses of Glossina palpalis palpalis in Côte d'Ivoire , and G . p .", "gambiensis and G . tachinoides in Burkina Faso , to odours from humans , cattle and pigs .", "Responses were measured either by baiting ( 1 . ) biconical traps or ( 2 . ) electrocuting black targets with na...	[ "Sleeping sickness , otherwise known as Human African Trypanosomiasis , continues to be a serious threat to human health .", "This disease , which is transmitted by tsetse flies , normally afflicts poor and isolated communities .", "No vaccines or prophylactic drugs are available to prevent the disease , which ...	2010
[ "Introduction", "Results and discussion", "Materials and methods" ]	[ "plant anatomy", "stem anatomy", "guard cells", "plant cell biology", "stomata", "pollen", "plant science", "plants", "flowering plants", "flower anatomy", "anthers", "leaves", "stamens", "flowers", "plant cells", "eukaryota", "cell biology", "biology and life sciences", "cellula...	INDUCER OF CBF EXPRESSION 1 is a male fertility regulator impacting anther dehydration in Arabidopsis	journal.pgen.1007695	null	[ [ "The stamen is the male reproductive organ of flowering plants and at a gross level comprises the filament and the anther [1 , 2] .", "The late phase of stamen development including filament elongation , anther dehiscence , and pollen maturation , is an essential process in which mature pollen grains are ...	[ "INDUCER OF CBF EXPRESSION 1 ( ICE1 ) encodes a MYC-like basic helix-loop-helix ( bHLH ) transcription factor playing a critical role in plant responses to chilling and freezing stresses and leaf stomata development .", "However , no information connecting ICE1 and reproductive development has been reported .", ...	[ "INDUCER OF CBF EXPRESSION 1 ( ICE1 ) is a basic helix-loop-helix transcription factor playing multiple roles in Arabidopsis .", "It was initially identified as the activator of C-Repeat Binding Factor 3 ( CBF3 ) , a core modulator triggering cold acclimation .", "ICE1 also activates Flowering Locus C ( FLC ) ,...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "sequence analysis", "genome complexity", "functional genomics", "genome evolution", "gene regulation", "genetics", "molecular genetics", "comparative genomics", "biology", "genomics", "evolutionary biology", "genomic evolution", "computational biology", "evolutionary genetics" ]	Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs	journal.pgen.1003470	null	[ [ "There is a growing appreciation that the functional repertoire of metazoan genomes includes much more than protein-coding sequences [1]–[3] .", "Recent functional genomic studies have revealed , in particular , the widespread occurrence , bewildering diversity , and functional significance of noncoding R...	[ "Advances in vertebrate genomics have uncovered thousands of loci encoding long noncoding RNAs ( lncRNAs ) .", "While progress has been made in elucidating the regulatory functions of lncRNAs , little is known about their origins and evolution .", "Here we explore the contribution of transposable elements ( TEs...	[ "An unexpected layer of complexity in the genomes of humans and other vertebrates lies in the abundance of genes that do not appear to encode proteins but produce a variety of non-coding RNAs .", "In particular , the human genome is currently predicted to contain 5 , 000–10 , 000 independent gene units generating...	2013
[ "Introduction", "Methods", "Results and discussion", "Conclusions" ]	[ "livestock", "medicine and health sciences", "pathology and laboratory medicine", "ruminants", "pathogens", "tropical diseases", "microbiology", "vertebrates", "animals", "mammals", "brucellosis", "bacterial diseases", "neglected tropical diseases", "bacteria", "bacterial pathogens", "...	Brucellosis Seropositivity in Animals and Humans in Ethiopia: A Meta-analysis	journal.pntd.0005006	null	[ [ "Brucellosis is one of the neglected zoonotic diseases , and there have been several reports that addressed its global importance [1–3] .", "The transmission of Brucella spp .", "of zoonotic importance—Brucella melitensis , Brucella abortus , Brucella suis and Brucella canis—is either horizontal or ve...	[ "The objectives of this study were to assess the heterogeneities of estimates and to estimate the seroprevalence of brucellosis in animals and humans in Ethiopia .", "Data from 70 studies covering 75879 animals and 2223 humans were extracted .", "Rose Bengal Plate Test ( RBPT ) and Complement Fixation Test ( CF...	[ "Brucellosis is one of the neglected zoonotic diseases with major outcomes of reproductive wastage in livestock and debilitating illnesses in humans .", "Ethiopia is one of the sub-Saharan African countries with the largest animal and second largest human population .", "The aim of this study was to estimate th...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "invertebrates", "gene regulation", "regulatory proteins", "dna-binding proteins", "animals", "notch signaling", "cell differentiation", "animal models", "developmental biology", "crystals", "drosophila melanogaster", "model organisms", "materials science", "experimental o...	Control of RUNX-induced repression of Notch signaling by MLF and its partner DnaJ-1 during Drosophila hematopoiesis	journal.pgen.1006932	null	[ [ "Proper blood cell development requires the finely tuned regulation of transcription factors and signaling pathways activity .", "Consequently mutations affecting key regulators of hematopoiesis such as members of the RUNX transcription factor family or components of the Notch signaling pathway are associ...	[ "A tight regulation of transcription factor activity is critical for proper development .", "For instance , modifications of RUNX transcription factors dosage are associated with several diseases , including hematopoietic malignancies .", "In Drosophila , Myeloid Leukemia Factor ( MLF ) has been shown to contro...	[ "Tight regulation of proteins level is required for proper development .", "Notably , the aberrant expression of key transcription factors or signaling pathway components controlling blood cell development contributes to hematological diseases such as leukemia .", "In this report , we use Drosophila as a model ...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/disease models", "genetics and genomics/animal genetics" ]	Fragile X Mental Retardation Protein Regulates Proliferation and Differentiation of Adult Neural Stem/Progenitor Cells	journal.pgen.1000898	null	[ [ "Fragile X syndrome , one of the most common forms of inherited mental retardation , is caused by the functional loss of fragile X mental retardation protein ( FMRP/Fmrp ) [1] .", "Patients with fragile X syndrome show an array of deficits in motor control , cognition , learning , and memory , although th...	[ "Fragile X syndrome ( FXS ) , the most common form of inherited mental retardation , is caused by the loss of functional fragile X mental retardation protein ( FMRP ) .", "FMRP is an RNA–binding protein that can regulate the translation of specific mRNAs .", "Adult neurogenesis , a process considered important ...	[ "Fragile X syndrome , the most common cause of inherited mental retardation , results from the loss of functional Fragile X mental retardation protein ( FMRP ) .", "FMRP is an RNA–binding protein and is known to bind to specific mRNAs and to regulate their translation both in vitro and in vivo .", "Adult neurog...	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "genetics and genomics/genomics", "computer science/applications", "genetics and genomics/complex traits", "computer science/numerical analysis and theoretical computing", "genetics and genomics/bioinformatics", "genetics and genomics/population genetics" ]	Tracing Sub-Structure in the European American Population with PCA-Informative Markers	journal.pgen.1000114	null	[ [ "The first Europeans from the Old World to land in what is now US territory were Columbus' men in 1493 .", "The initial colonization of the region by the Spanish , English , Scots and Irish , French , Dutch , Swedes , Germans , Italians and Portuguese during the 16th and 17th centuries was followed in the...	[ "Genetic structure in the European American population reflects waves of migration and recent gene flow among different populations .", "This complex structure can introduce bias in genetic association studies .", "Using Principal Components Analysis ( PCA ) , we analyze the structure of two independent Europea...	[ "Genetic association studies search to identify disease susceptibility genes through the analysis of genetic markers such as single nucleotide polymorphisms ( SNPs ) in large numbers of cases and controls .", "In such settings , the existence of sub-structure in the population under study ( i . e . differences in...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases" ]	Single Cell Analysis of Lymph Node Tissue from HIV-1 Infected Patients Reveals that the Majority of CD4+ T-cells Contain One HIV-1 DNA Molecule	journal.ppat.1003432	null	[ [ "The genetic diversity of human immunodeficiency virus ( HIV-1 ) allows the virus to develop resistance to antiviral therapy and escape immune pressure .", "Several different mechanisms contribute to genetic diversity including rapid , high-level virus turnover ( ca . 108–109 cells are infected and die ev...	[ "Genetic recombination contributes to the diversity of human immunodeficiency virus ( HIV-1 ) .", "Productive HIV-1 recombination is , however , dependent on both the number of HIV-1 genomes per infected cell and the genetic relationship between these viral genomes .", "A detailed analysis of the number of prov...	[ "One of the greatest challenges facing treatment and vaccine development for human immunodeficiency virus ( HIV-1 ) is the genetic diversity of the virus .", "One of the main factors contributing to HIV-1 diversity is recombination between two genetically different viral RNA genomes that enter a cell in the same ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Prodomain Removal Enables Neto to Stabilize Glutamate Receptors at the Drosophila Neuromuscular Junction	journal.pgen.1004988	null	[ [ "Synapse development is a highly orchestrated process that enables proper establishment of neural circuits and development of the nervous system .", "Crucial to synapse assembly is the recruitment and stabilization of neurotransmitter receptor complexes at synaptic sites [1] .", "Receptor complexes ca...	[ "Stabilization of neurotransmitter receptors at postsynaptic specializations is a key step in the assembly of functional synapses .", "Drosophila Neto ( Neuropillin and Tolloid-like protein ) is an essential auxiliary subunit of ionotropic glutamate receptor ( iGluR ) complexes required for the iGluRs clustering ...	[ "Synapse development is initiated by genetic programs , but is coordinated by neuronal activity , by communication between the pre- and postsynaptic compartments , and by cellular signals that integrate the status of the whole organisms and its developmental progression .", "The molecular mechanisms underlining t...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases/epidemiology and control of infectious diseases" ]	Feasibility of Onchocerciasis Elimination with Ivermectin Treatment in Endemic Foci in Africa: First Evidence from Studies in Mali and Senegal	journal.pntd.0000497	null	[ [ "Onchocerciasis control strategies have evolved significantly over the last three decades .", "The Onchocerciasis Control Programme in West Africa ( OCP ) [1] , launched in 1975 , used aerial larviciding of vector breeding sites in river rapids .", "This strategy was very successful in interrupting on...	[ "Mass treatment with ivermectin is a proven strategy for controlling onchocerciasis as a public health problem , but it is not known if it can also interrupt transmission and eliminate the parasite in endemic foci in Africa where vectors are highly efficient .", "A longitudinal study was undertaken in three hyper...	[ "The control of onchocerciasis , or river blindness , is based on annual or six-monthly ivermectin treatment of populations at risk .", "This has been effective in controlling the disease as a public health problem , but it is not known whether it can also eliminate infection and transmission to the extent that t...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular neuroscience", "animal genetics", "genetic screens", "genetics", "biology", "neuroscience", "genetics and genomics" ]	dyschronic, a Drosophila Homolog of a Deaf-Blindness Gene, Regulates Circadian Output and Slowpoke Channels	journal.pgen.1002671	null	[ [ "In diverse phyla , circadian systems act to synchronize changes in arousal and internal physiology to optimal time periods for feeding , courtship , and other ethologically relevant behaviors .", "In Drosophila , the molecular basis of the internal clock that drives such rhythmic alterations in behavior ...	[ "Many aspects of behavior and physiology are under circadian control .", "In Drosophila , the molecular clock that regulates rhythmic patterns of behavior has been extensively characterized .", "In contrast , genetic loci involved in linking the clock to alterations in motor activity have remained elusive .", ...	[ "In most organisms , endogenous circadian clocks help to restrict adaptive activities such as foraging and mating to ecologically appropriate periods of the day–night cycle .", "The fruit fly Drosophila melanogaster has been a crucial genetic model system for understanding the molecular underpinnings of the clock...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "helminths", "tropical diseases", "mathematical models", "parasitic diseases", "animals", "pharmaceutics", "sexually transmitted diseases", "drug administration", "neglected tropical diseases", "population biology", "onchocerciasis", "popula...	The effect of assortative mixing on stability of low helminth transmission levels and on the impact of mass drug administration: Model explorations for onchocerciasis	journal.pntd.0006624	null	[ [ "Onchocerciasis prevalence varies widely between geographical locations , with nodule and microfiladermia ( mf ) prevalence levels in adults ranging from just above 0% to over 80% [1 , 2] .", "Onchocerciasis control programmes historically aimed for morbidity control and focussed interventions on so-calle...	[ "Stable low pre-control prevalences of helminth infection are not uncommon in field settings , yet it is poorly understood how such low levels can be sustained , thereby challenging efforts to model them .", "Disentangling possible facilitating mechanisms is important , since these may differently affect interven...	[ "Most mathematical models for parasitic worm infections predict that at low prevalences transmission will fade out spontaneously because of the low mating probability of male and female worms .", "However , sustained low prevalence situations do exist in reality .", "Low prevalence areas have become of particul...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "cell processes", "microbiology", "parasitic diseases", "parasitic protozoans", "animal models", "model organisms", "protozoans", "glycosylation", "pharmacology", "glycoproteins", "research and analysis methods", "antimicrobial resistance", "proteins", "mo...	Carbohydrate-Binding Non-Peptidic Pradimicins for the Treatment of Acute Sleeping Sickness in Murine Models	journal.ppat.1005851	null	[ [ "Human African trypanosomiasis or sleeping sickness is a neglected disease caused by the protozoan parasite Trypanosoma brucei .", "Treatments are largely insufficient and unsatisfactory and new approaches for drug design are highly necessary .", "T . brucei parasites living in the mammalian host rely...	[ "Current treatments available for African sleeping sickness or human African trypanosomiasis ( HAT ) are limited , with poor efficacy and unacceptable safety profiles .", "Here , we report a new approach to address treatment of this disease based on the use of compounds that bind to parasite surface glycans leadi...	[ "Trypanosoma brucei , the causative agent of African trypanosomiasis , is coated with a dense layer of the variant surface glycoprotein ( VSG ) , which plays an essential role in antigenic variation and the ability of the parasite to evade the immune system .", "VSGs are N-glycosylated with complex and/or mannose...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "immune cells", "protein interactions", "immunology", "microbiology", "protein abundance", "parasitic diseases", "parasitology", "parastic protozoans", "leishmania", "neglected tropical diseases", "immunomodulation", "infectious diseases", "membranes and sorting", "biology", ...	Immunomodulatory Impact of Leishmania-Induced Macrophage Exosomes: A Comparative Proteomic and Functional Analysis	journal.pntd.0002185	null	[ [ "Exosomes are 40–100 nm vesicles that are released by many eukaryotic cells .", "These vesicles are formed through invagination of the membrane into the multivesicular endosome ( MVE ) and can be released from the cell upon fusion of the MVE with the plasma membrane [1] .", "Although exosomes were onc...	[ "Released by many eukaryotic cells , the exosomes are 40–100 nm vesicles shown to operate over the complex processes of cell-cell communication .", "Among the metazoan cell lineages known to generate exosomes is the mononuclear phagocyte lineage , a lineage that parasites such as Leishmania are known to subvert a...	[ "Secreted vesicles , such as exosomes , are now considered as an important route of communication among eukaryotic cells .", "Depending on the donor cell source and protein content , these vesicles are expected to distinctly impact the recipient cell properties .", "Here , three groups of exosomes released by t...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Efficient "Shotgun" Inference of Neural Connectivity from Highly Sub-sampled Activity Data	journal.pcbi.1004464	null	[ [ "It is now possible to image hundreds of neurons simultaneously at high spatiotemporal resolution [1] or tens of thousands of neurons at low spatiotemporal resolution [2] .", "The number of recorded neurons is expected to continue to grow exponentially [3] .", "This , in principle , provides the oppor...	[ "Inferring connectivity in neuronal networks remains a key challenge in statistical neuroscience .", "The “common input” problem presents a major roadblock: it is difficult to reliably distinguish causal connections between pairs of observed neurons versus correlations induced by common input from unobserved neur...	[ "Optical imaging of the activity in a neuronal network is limited by the scanning speed of the imaging device .", "Therefore , typically , only a small fixed part of the network is observed during the entire experiment .", "However , in such an experiment , it can be hard to infer from the observed activity pat...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "animal types", "medicine and health sciences", "pathology and laboratory medicine", "vertebrates", "pets and companion animals", "dogs", "parasitic protozoans", "animals", "mammals", "parasitic diseases", "protozoans", "veterinary diagnostics", "molecular biology techniques", "zoology", ...	Widespread Trypanosoma cruzi infection in government working dogs along the Texas-Mexico border: Discordant serology, parasite genotyping and associated vectors	journal.pntd.0005819	null	[ [ "Chagas disease , a potentially deadly cardiac disease of humans and dogs , is caused by the flagellated protozoan parasite Trypanosoma cruzi .", "The parasite is transmitted by infected hematophagous triatomine insects , commonly known as ‘kissing bugs’ .", "Chagas disease is estimated to infect near...	[ "Chagas disease , caused by the vector-borne protozoan Trypanosoma cruzi , is increasingly recognized in the southern U . S . Government-owned working dogs along the Texas-Mexico border could be at heightened risk due to prolonged exposure outdoors in habitats with high densities of vectors .", "We quantified wor...	[ "Chagas disease , a potentially deadly cardiac disease of humans , canines and other mammals is caused by the parasite Trypanosoma cruzi .", "The parasite is primarily transmitted to dogs by ingestion of infected triatomine ‘kissing bug’ vectors or through contact with the insect’s feces .", "Previous studies c...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "nuclear staining", "cardiovascular anatomy", "developmental biology", "mutation", "epicardium", "embryos", "immunologic techniques", "research and analysis methods", "specimen preparation and treatment", "embryology", "myocardium", "staining", "immunoassays...	Non-muscle myosin IIB (Myh10) is required for epicardial function and coronary vessel formation during mammalian development	journal.pgen.1007068	null	[ [ "A functional coronary vasculature is essential to supply the heart with oxygenated blood .", "Cessation of the coronary circulation deprives the working myocardium of oxygen and nutrients , leading to irreversible damage to cardiac muscle and myocardial infarction .", "Coronary artery disease is the ...	[ "The coronary vasculature is an essential vessel network providing the blood supply to the heart .", "Disruptions in coronary blood flow contribute to cardiac disease , a major cause of premature death worldwide .", "The generation of treatments for cardiovascular disease will be aided by a deeper understanding...	[ "In order for the heart to function properly it must have its own blood supply .", "Blood is delivered to the heart through a system of vessels called the coronary vasculature .", "During development , some of the cells that form the coronary vessels originate from the epicardium , the outer layer of the heart ...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Genetic Architecture Promotes the Evolution and Maintenance of Cooperation	journal.pcbi.1003339	null	[ [ "The evolution of cooperation in microbial populations is a fascinating , rich and controversial evolutionary problem [1]–[6] .", "The theoretical understanding of cooperation has been gradually advancing for decades , and recently those insights have also been applied to practical , medical problems , su...	[ "When cooperation has a direct cost and an indirect benefit , a selfish behavior is more likely to be selected for than an altruistic one .", "Kin and group selection do provide evolutionary explanations for the stability of cooperation in nature , but we still lack the full understanding of the genomic mechanism...	[ "Cooperation is a much studied and debated phenomena in the microbial world marked by a key question: Given the survival of the fittest evolutionary paradigm , why do individuals act in seemingly altruistic ways , paying a cost to help others ?", "Kin selection and group selection , together with mathematical too...	2013
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "invertebrates", "innate immune system", "medicine and health sciences", "immune physiology", "cytokines", "pathology and laboratory medicine", "cestodes", "helminths", "pathogens", "immunology", "tropical diseases", "microbiology", "parasitic diseases", "animals", "animal models", "pr...	The ectodomains of the lymphocyte scavenger receptors CD5 and CD6 interact with tegumental antigens from Echinococcus granulosus sensu lato and protect mice against secondary cystic echinococcosis	journal.pntd.0006891	null	[ [ "The mammalian innate immune system relies on a limited number of germline-encoded and non-clonally distributed receptors for pathogen recognition , which have evolved to identify the so called pathogen associated molecular patterns ( PAMPs ) : conserved microbial structures , essential for their survival and...	[ "Scavenger Receptors ( SRs ) from the host’s innate immune system are known to bind multiple ligands to promote the removal of non-self or altered-self targets .", "CD5 and CD6 are two highly homologous class I SRs mainly expressed on all T cells and the B1a cell subset , and involved in the fine tuning of activa...	[ "Scavenger Receptors ( SRs ) are constituents of host’s innate immune system able to sense and remove altered-self and/or pathogen components .", "Data on their interaction with helminth parasites is scarce .", "In this work , we describe that CD5 and CD6 -two lymphoid SRs previously reported to interact with c...	2018
[ "Introduction", "Results and discussion", "Materials and methods" ]	[ "homologous chromosomes", "chromosome structure and function", "invertebrate genomics", "chromosome mapping", "genome analysis", "molecular biology techniques", "chromosome walking", "structural genomics", "research and analysis methods", "genomic libraries", "imaging techniques", "gene mappin...	Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling	journal.pgen.1007872	null	[ [ "In terms of organization , chromosomal DNA is among the most challenging of biological molecules to study .", "It is massive , differs in sequence and structure from one region to the next , and often comes in pairs of homologs that defy easy distinction .", "Nevertheless , much progress has been mad...	[ "Chromosome organization is crucial for genome function .", "Here , we present a method for visualizing chromosomal DNA at super-resolution and then integrating Hi-C data to produce three-dimensional models of chromosome organization .", "Using the super-resolution microscopy methods of OligoSTORM and OligoDNA-...	[ "Questions regarding the impact of chromosome structure on genome function are focusing increasingly on the manner in which chromosomes are organized within the nucleus .", "In fact , studies of processes as diverse as gene activation and repression as well as genome repair and stability are all querying how the ...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "biology" ]	Imaginal Discs – A New Source of Chromosomes for Genome Mapping of the Yellow Fever Mosquito Aedes aegypti	journal.pntd.0001335	null	[ [ "Ae .", "aegypti is a principal vector for yellow fever , dengue and chikungunya viruses [1] , [2] .", "These diseases have a significant worldwide impact on human health .", "Yellow fever affects up to 600 million lives and is responsible for about 30 , 000 deaths annually [3] .", "Dengue fev...	[ "The mosquito Aedes aegypti is the primary global vector for dengue and yellow fever viruses .", "Sequencing of the Ae .", "aegypti genome has stimulated research in vector biology and insect genomics .", "However , the current genome assembly is highly fragmented with only ∼31% of the genome being assigned t...	[ "Dengue fever is an emerging health threat to as much as half of the human population around the world .", "No vaccines or drug treatments are currently available .", "Thus , disease prevention is largely based on efforts to control its major mosquito vector Ae .", "aegypti .", "Novel vector control strateg...	2011
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "vector biology", "virology", "biology", "microbiology", "host-pathogen interaction" ]	Mosquito Cellular Factors and Functions in Mediating the Infectious entry of Chikungunya Virus	journal.pntd.0002050	null	[ [ "Chikungunya virus ( CHIKV ) is an arthropod-borne virus of the genus Alphaviruses , belonging to the family Togaviridae .", "It is an enveloped , single-stranded , positive-sense RNA virus with a genome size of approximately 12 , 000 nucleotides .", "CHIKV virions measure 60–70 nm in diameter and it ...	[ "Chikungunya virus ( CHIKV ) is an arthropod-borne virus responsible for recent epidemics in the Asia Pacific regions .", "A customized gene expression microarray of 18 , 760 transcripts known to target Aedes mosquito genome was used to identify host genes that are differentially regulated during the infectious e...	[ "Deciphering the much neglected aspects of cellular factors in contributing to the infectious entry of CHIKV into mosquito cells may enhance our understanding of the conservation or diversity of these host factors amongst mammalian and arthropod for successful CHIKV replication .", "The study revealed that the in...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry", "enzyme structure", "biochemical simulations", "enzymes", "protein structure", "biology", "computational biology", "macromolecular structure analysis" ]	Identification of a Novel Class of Farnesylation Targets by Structure-Based Modeling of Binding Specificity	journal.pcbi.1002170	null	[ [ "Protein prenylation is a post-translational modification in which a prenyl group ( farnesyl or geranylgeranyl ) is attached to the protein via a thioether bond to a cysteine at or near the carboxy terminus of the protein ( reviewed in [1] , [2] ) .", "Protein farnesyltransferase ( FTase ) and geranylgera...	[ "Farnesylation is an important post-translational modification catalyzed by farnesyltransferase ( FTase ) .", "Until recently it was believed that a C-terminal CaaX motif is required for farnesylation , but recent experiments have revealed larger substrate diversity .", "In this study , we propose a general str...	[ "Linear sequence motifs serve as recognition sites for protein-protein interactions as well as for post-translational modifications .", "One such motif is the CaaX box located at protein C-termini that serves as prenylation site .", "This prenylation is critical for many signal transduction related proteins and...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "fluorescence imaging", "medicine and health sciences", "pathology and laboratory medicine", "engineering and technology", "signal processing", "pathogens", "animals", "wolbachia", "molecular biology techniques", "insect vectors", "bacteria", "research and analysis methods",...	Direct nucleic acid analysis of mosquitoes for high fidelity species identification and detection of Wolbachia using a cellphone	journal.pntd.0006671	null	[ [ "Mosquitoes are vectors that can transmit an array of pathogens that often cause devastating human diseases [1] .", "Traditionally considered a problem for tropical regions , mosquitoes are increasingly becoming a global public health challenge [2 , 3] due to a changing global environment , urbanization ,...	[ "Manipulation of natural mosquito populations using the endosymbiotic bacteria Wolbachia is being investigated as a novel strategy to reduce the burden of mosquito-borne viruses .", "To evaluate the efficacy of these interventions , it will be critical to determine Wolbachia infection frequencies in Aedes aegypti...	[ "Mosquitoes spread many human pathogens and novel approaches are required to reduce the burden of mosquito-borne disease .", "One promising approach is transferring Wolbachia into Aedes aegypti mosquitoes where it blocks transmission of arboviruses like dengue , Zika and Yellow fever viruses and spreads through m...	2018
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[]	Oxytocin blocks enhanced motivation for alcohol in alcohol dependence and blocks alcohol effects on GABAergic transmission in the central amygdala	journal.pbio.2006421	null	[ [ "Alcohol use disorder is a global public health issue; 6% of the world’s population is subject to morbidity and mortality from alcohol [1] .", "Alcohol dependence ( reflecting dysfunction equivalent to moderate to severe alcohol use disorder ) is a chronic , relapsing disorder that develops as a result of...	[ "Oxytocin administration has been reported to decrease consumption , withdrawal , and drug-seeking associated with several drugs of abuse and thus represents a promising pharmacological approach to treat drug addiction .", "We used an established rat model of alcohol dependence to investigate oxytocin’s effects o...	[ "Alcohol use disorder is characterized by a reduction in reward function and gain in stress function .", "The neuropeptide oxytocin is involved in the regulation of both reward and stress systems .", "We tested the hypothesis that oxytocin administration could normalize the dysregulations that occur in alcohol ...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology/cell signaling", "immunology/innate immunity", "infectious diseases/viral infections", "biochemistry/bioinformatics", "biotechnology/protein chemistry and proteomics", "immunology/immunity to infections" ]	Quantitative Subcellular Proteome and Secretome Profiling of Influenza A Virus-Infected Human Primary Macrophages	journal.ppat.1001340	null	[ [ "Influenza A viruses are negative-stranded RNA viruses that are capable of infecting a variety of avian and mammalian species .", "These viruses are responsible for the annual epidemics that cause severe illnesses in millions of people worldwide .", "Influenza A virus and secondary bacterial infection...	[ "Influenza A viruses are important pathogens that cause acute respiratory diseases and annual epidemics in humans .", "Macrophages recognize influenza A virus infection with their pattern recognition receptors , and are involved in the activation of proper innate immune response .", "Here , we have used high-th...	[ "Influenza A viruses are negative-stranded RNA viruses that are capable of infecting a variety of avian and mammalian species .", "These viruses are responsible for the annual epidemics that cause severe illnesses in millions of people worldwide .", "The initial innate immune responses to influenza A viruses ha...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[]	Floral regulators FLC and SOC1 directly regulate expression of the B3-type transcription factor TARGET OF FLC AND SVP 1 at the Arabidopsis shoot apex via antagonistic chromatin modifications	journal.pgen.1008065	null	[ [ "The transition from vegetative to reproductive development in plants is controlled by a complex transcriptional network that responds both to environmental cues and endogenous hormonal signals [1 , 2] .", "In Arabidopsis thaliana , the MADS-box transcription factor FLOWERING LOCUS C ( FLC ) plays a major...	[ "Integration of environmental and endogenous cues at plant shoot meristems determines the timing of flowering and reproductive development .", "The MADS box transcription factor FLOWERING LOCUS C ( FLC ) of Arabidopsis thaliana is an important repressor of floral transition , which blocks flowering until plants a...	[ "The initiation of flowering in plants is exquisitely sensitive to environmental signals , ensuring that reproduction occurs at the appropriate time of year .", "The sensitivity of these responses depends upon strong repression of flowering under inappropriate conditions .", "FLOWERING LOCUS C ( FLC ) and SHORT...	2019
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "gene regulation", "regulatory proteins", "dna-binding proteins", "fibroblasts", "cell differentiation", "developmental biology", "stem cells", "connective tissue cells", "transcription factors", "sequence motif analysis", "epigenetics", "chromatin", "resear...	coTRaCTE predicts co-occurring transcription factors within cell-type specific enhancers	journal.pcbi.1006372	null	[ [ "In multicellular organisms , all cells carry the same genetic information , yet they differentiate during development into a variety of cell types with different morphology and function .", "This cell type differentiation is brought about by the execution of distinct gene expression programs .", "The...	[ "Cell-type specific gene expression is regulated by the combinatorial action of transcription factors ( TFs ) .", "In this study , we predict transcription factor ( TF ) combinations that cooperatively bind in a cell-type specific manner .", "We first divide DNase hypersensitive sites into cell-type specificall...	[ "Differentiation of multicellular organisms into a variety of cell types with different morphology and function is the result of cell-type specific gene expression .", "The most important regulators of gene expression are transcription factors ( TFs ) binding to cis-regulatory sequences , such as enhancers or pro...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell death", "cell cycle and cell division", "cell processes", "animal models", "model organisms", "cytokinesis", "microtubule polymerization", "molecular genetics", "cell nucleus", "cellular structures and organelles", "research and analysis methods", "cell proliferation", "gene disruption...	Genetic Deletion of SEPT7 Reveals a Cell Type-Specific Role of Septins in Microtubule Destabilization for the Completion of Cytokinesis	journal.pgen.1004558	null	[ [ "Cytokinesis as final step of cell division is essential for cell proliferation , but there is a considerable degree of diversity in its underlying mechanisms among eukaryotes .", "Even within one organism , such as the amoeba Dictyostelium discoideum , cytokinesis may proceed by different mechanisms for ...	[ "Cytokinesis terminates mitosis , resulting in separation of the two sister cells .", "Septins , a conserved family of GTP-binding cytoskeletal proteins , are an absolute requirement for cytokinesis in budding yeast .", "We demonstrate that septin-dependence of mammalian cytokinesis differs greatly between cell...	[ "Cytokinesis is the finalizing step of the complex scenario of mitosis , leading to separation of two sister cells .", "The cellular mechanism of cytokinesis in eukaryotes differs at least between yeasts , plants and animals .", "So far , it is also not clear whether all mammalian cells follow the same mechanis...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "t. cruzi", "infectious diseases", "immunology", "eukaryotes" ]	Bradykinin B2 Receptors of Dendritic Cells, Acting as Sensors of Kinins Proteolytically Released by Trypanosoma cruzi, Are Critical for the Development of Protective Type-1 Responses	journal.ppat.0030185	null	[ [ "Chagas disease , the chronic cardiomyopathy caused by infection with the intracellular parasitic protozoan Trypanosoma cruzi , remains a major health problem in Central and South America [1] .", "Although acute Chagas disease may have a fatal outcome , the blood parasitemia , tissue parasite burden ( liv...	[ "Although the concept that dendritic cells ( DCs ) recognize pathogens through the engagement of Toll-like receptors is widely accepted , we recently suggested that immature DCs might sense kinin-releasing strains of Trypanosoma cruzi through the triggering of G-protein-coupled bradykinin B2 receptors ( B2R ) .", ...	[ "Antibodies and IFN-γ-producing effector T cells are essential for the immune control of infection by Trypanosoma cruzi , the intracellular protozoa that causes human Chagas disease .", "Despite the potency of anti-parasite immunity , the parasites are not cleared from their intracellular niches .", "Instead , ...	2007
[ "Introduction", "Methods", "Results and Discussion" ]	[ "applied microbiology", "medicine", "diagnostic medicine", "pathology", "veterinary microbiology", "clinical pathology", "biology", "microbiology", "veterinary science", "clinical microbiology" ]	Whole Genome Analysis of Leptospira licerasiae Provides Insight into Leptospiral Evolution and Pathogenicity	journal.pntd.0001853	null	[ [ "Leptospirosis is a globally important tropical infectious disease that takes a disproportionate toll in tropical regions [1] .", "Caused by more than 250 serovars of spirochetes distributed among nine species of pathogenic Leptospira and at least five known species of intermediate Leptospira [2] , the bu...	[ "The whole genome analysis of two strains of the first intermediately pathogenic leptospiral species to be sequenced ( Leptospira licerasiae strains VAR010 and MMD0835 ) provides insight into their pathogenic potential and deepens our understanding of leptospiral evolution .", "Comparative analysis of eight lepto...	[ "Leptospirosis is one of the most common diseases transmitted by animals worldwide and is important because it is a major cause of febrile illness in tropical areas and also occurs in epidemic form associated with natural disasters and flooding .", "The mechanisms through which Leptospira cause disease are not we...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The Fitness Consequences of Aneuploidy Are Driven by Condition-Dependent Gene Effects	journal.pbio.1002155	A novel method to create thousands of aneuploid strains in Saccharomyces cerevisiae allows the authors to dissect the complex role of aneuploidy in adaptation and evolution.	[ [ "Aneuploidy , a class of mutation infamous for its disruption of development [1] and oncogenic connections [2 , 3] , is a genetic alteration that changes the copy number of many genes with a single mutational event ( reviewed in [4] ) .", "Despite its close connection to cancer , a phenomenon characterize...	[ "Aneuploidy is a hallmark of tumor cells , and yet the precise relationship between aneuploidy and a cell’s proliferative ability , or cellular fitness , has remained elusive .", "In this study , we have combined a detailed analysis of aneuploid clones isolated from laboratory-evolved populations of Saccharomyces...	[ "Aneuploidy ( altered copy number of genomic regions ) is observed in the majority of tumors , but it remains unclear whether aneuploidy is a cause or consequence of cancer .", "Evidence from the yeast Saccharomyces cerevisiae and mammalian cells has shown that aneuploid cells tend to grow more slowly than normal...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "organisms", "signal transduction", "developmental biology", "organism development", "molecular complexes", "cell biology", "gene regulatory networks", "gene expression", "genetics", "biology and life sciences", "molecular genetics", "molecular biology techniques", "computational biology", ...	GLD-4-Mediated Translational Activation Regulates the Size of the Proliferative Germ Cell Pool in the Adult C. elegans Germ Line	journal.pgen.1004647	null	[ [ "During development , tissues grow to form functional organs .", "In adulthood , animal tissues remain constant in size , in part , as a result of the dynamic balance between self-renewal/proliferation and differentiation .", "Perturbation of this balance affects tissue homeostasis and , consequently ...	[ "To avoid organ dysfunction as a consequence of tissue diminution or tumorous growth , a tight balance between cell proliferation and differentiation is maintained in metazoans .", "However , cell-intrinsic gene expression mechanisms controlling adult tissue homeostasis remain poorly understood .", "By focusing...	[ "Throughout adulthood , animal tissue homeostasis requires adult stem cell activities .", "A tight balance between self-renewal and differentiation protects against tissue overgrowth or loss .", "This balance is strongly influenced by niche-mediated signaling pathways that primarily trigger a transcriptional re...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Linking Transcriptional Changes over Time in Stimulated Dendritic Cells to Identify Gene Networks Activated during the Innate Immune Response	journal.pcbi.1003323	null	[ [ "The innate immune system is the primary host response to invading pathogens .", "The innate immune response is characterized by germline-encoded pattern-recognition receptors ( PRRs ) that detect and bind to specific microbial components , also known as pathogen-associated molecular patterns ( PAMPs ) ."...	[ "The innate immune response is primarily mediated by the Toll-like receptors functioning through the MyD88-dependent and TRIF-dependent pathways .", "Despite being widely studied , it is not yet completely understood and systems-level analyses have been lacking .", "In this study , we identified a high-probabil...	[ "The innate immune response is the first level of protection in organisms against invading pathogens .", "It consists of a large number of proteins functioning in signaling cascades triggered by the binding of fragments from microbes to specific cellular receptors .", "Disruptions in these pathways can lead to ...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "mathematics", "statistics", "biostatistics", "statistical methods" ]	Bayesian Estimation of Mixture Models with Prespecified Elements to Compare Drug Resistance in Treatment-Naïve and Experienced Tuberculosis Cases	journal.pcbi.1002973	null	[ [ "Tuberculosis ( TB ) is an infectious disease caused by Mycobacterium tuberculosis and is transmitted between hosts through the respiratory route .", "The appearance of TB resistant to multiple antibiotics threatens global control strategies that depend on the efficacy of standard combinations of these dr...	[ "We propose a Bayesian approach for estimating branching tree mixture models to compare drug-resistance pathways ( i . e . patterns of sequential acquisition of resistance to individual antibiotics ) that are observed among Mycobacterium tuberculosis isolates collected from treatment-naïve and treatment-experienced...	[ "Drug-resistant tuberculosis ( TB ) initially arises as a result of the sporadic appearance and subsequent selection of drug-resistant M . tuberculosis mutants .", "Such strains may or may not be associated with fitness costs affecting their ability to transmit and cause disease .", "Resistant pathogens collect...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell death", "cell processes", "dna-binding proteins", "germ cells", "dna damage", "age groups", "dna", "homologous recombination", "animal cells", "proteins", "histones", "people and places", "biochemistry", "young adults", "cell biology", "nucleic acids", "apoptosis", "genetics"...	JMJD-5/KDM8 regulates H3K36me2 and is required for late steps of homologous recombination and genome integrity	journal.pgen.1006632	null	[ [ "Cells have developed several pathways to promptly remove DNA lesions of different types in order to prevent dangerous outcomes such as cell death , DNA deletions and chromosomal rearrangements that can contribute to human diseases [1–3] .", "Double strand breaks ( DSBs ) , involving both DNA strands , ca...	[ "The eukaryotic genome is organized in a three-dimensional structure called chromatin , constituted by DNA and associated proteins , the majority of which are histones .", "Post-translational modifications of histone proteins greatly influence chromatin structure and regulate many DNA-based biological processes ....	[ "DNA damage repair occurs in the context of chromatin and it is influenced by post-translational modifications of histone proteins .", "The level of methylation at lysine 36 of histone 3 ( H3K36 ) plays an important role in early phases of DNA damage repair by recruiting early repair factors at the site breaks an...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "plant science", "plant biology", "biology", "microbiology" ]	Synergistic Roles of Eukaryotic Translation Elongation Factors 1Bγ and 1A in Stimulation of Tombusvirus Minus-Strand Synthesis	journal.ppat.1002438	null	[ [ "Plus-stranded ( + ) RNA viruses recruit numerous host proteins to facilitate their replication and spread [1] , [2] .", "Among the identified host proteins are RNA-binding proteins ( RBPs ) , such as ribosomal proteins , translation factors and RNA-modifying enzymes [1]–[5] .", "The subverted host pr...	[ "Host factors are recruited into viral replicase complexes to aid replication of plus-strand RNA viruses .", "In this paper , we show that deletion of eukaryotic translation elongation factor 1Bgamma ( eEF1Bγ ) reduces Tomato bushy stunt virus ( TBSV ) replication in yeast host .", "Also , knock down of eEF1Bγ ...	[ "RNA viruses recruit numerous host proteins to facilitate their replication and spread .", "Among the identified host proteins are RNA-binding proteins ( RBPs ) , such as ribosomal proteins , translation factors and RNA-modifying enzymes .", "In this paper , the authors show that deletion of eukaryotic translat...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "sequencing techniques", "taxonomy", "medicine and health sciences", "pathology and laboratory medicine", "evolutionary biology", "viral transmission and infection", "pathogens", "population genetics", "microbiology", "retroviruses", "viruses", "immunodeficiency viruses", "genome sequencing"...	Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus	journal.ppat.1005619	null	[ [ "The global spread of HIV-1 has been fueled predominantly by HSX transmission , with MSM representing a second major risk group [1] .", "As was first established over two decades ago , HIV-1 undergoes a severe population bottleneck upon transmission with only a limited number of variants from the diverse ...	[ "Due to the stringent population bottleneck that occurs during sexual HIV-1 transmission , systemic infection is typically established by a limited number of founder viruses .", "Elucidation of the precise forces influencing the selection of founder viruses may reveal key vulnerabilities that could aid in the dev...	[ "While the global spread of HIV-1 has been fueled by sexual transmission the genetic determinants underlying the transmission bottleneck remains poorly understood .", "Here we characterized founder virus population diversity from next generation sequencing data in a cohort of 74 acute and early HIV-1 infected ind...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunology", "biology", "neuroscience" ]	CLEC5A Regulates Japanese Encephalitis Virus-Induced Neuroinflammation and Lethality	journal.ppat.1002655	null	[ [ "The Flavivirus genus includes the mosquito-borne dengue , Japanese encephalitis and yellow fever viruses [1] , infections of which can result in clinical syndromes such as hemorrhagic fever and encephalitis .", "There are four serotypes of dengue virus ( DV ) , which can give rise to severe hemorrhagic s...	[ "CLEC5A/MDL-1 , a member of the myeloid C-type lectin family expressed on macrophages and neutrophils , is critical for dengue virus ( DV ) -induced hemorrhagic fever and shock syndrome in Stat1−/− mice and ConA-treated wild type mice .", "However , whether CLEC5A is involved in the pathogenesis of viral encephal...	[ "Japanese encephalitis ( JE ) is one of the most common forms of viral encephalitis worldwide , and the common complication post viral encephalitis is permanent neuropsychiatric sequelae resulting from severe neuroinflammation .", "However , specific treatment to inhibit JEV-induced neuroinflammation is not avail...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "tropical diseases", "geographical locations", "sudan", "south sudan", "health care", "bacterial diseases", "eye diseases", "sexually transmitted diseases", "neglected tropical diseases", "sanitation", "eyes", "africa", "public and occupational health", "i...	Prevalence of trachoma within refugee camps serving South Sudanese refugees in White Nile State, Sudan: Results from population-based surveys	journal.pntd.0007491	null	[ [ "Trachoma , the leading infectious cause of blindness , is caused by infection with the bacterium Chlamydia trachomatis [1] .", "Infection occurs through personal contact via hands , clothes , and flies that have been in contact with the infected discharge from the eyes or nose of an infected person .", ...	[ "The world is witnessing mass displacement of populations which could impact global efforts to eliminate neglected tropical diseases such as trachoma .", "On the African continent , South Sudan has experienced high levels of population displacement .", "Population based baseline trachoma surveys were conducted ...	[ "Ministries of health in multiple countries have made progress in reducing the prevalence of trachoma , the leading cause of infectious blindness .", "With the increase in displaced populations throughout the world , the work of these national programs could be put at risk as formerly endemic or non-endemic distr...	2019
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "public health and epidemiology", "epidemiology", "infectious disease epidemiology", "neglected tropical diseases", "leptospirosis" ]	Risk Factors and Predictors of Severe Leptospirosis in New Caledonia	journal.pntd.0001991	null	[ [ "Leptospirosis is a major threat to public health but little is known about the actual disease burden , and consequently , the disease has been neglected .", "Nevertheless , it is recognized as the most widespread zoonosis worldwide and an important and possibly emerging infectious disease .", "It occ...	[ "Leptospirosis is a major public health concern in New Caledonia ( NC ) and in other tropical countries .", "Severe manifestations of the disease are estimated to occur in 5–15% of all human infections worldwide and factors associated with these forms are poorly understood .", "Our objectives were to identify r...	[ "Leptospirosis is a neglected tropical disease and a public health concern worldwide .", "Factors responsible for the progression towards severe forms have not been clearly established .", "However , pathogen- as well as host-related factors are both believed to play a role in the development of severe leptospi...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "biotechnology", "invertebrates", "medicine and health sciences", "rna interference", "neuroscience", "animals", "biological locomotion", "animal models", "analysis of variance", "drosophila melanogaster", "model organisms", "mathematics", "statistics (mathematics)", "experimental organism...	Calcium and cAMP directly modulate the speed of the Drosophila circadian clock	journal.pgen.1007433	null	[ [ "Circadian clocks impose a daily rhythmicity to the behavior and physiology of multicellular organisms .", "In animals , the circadian system consists of a principal circadian pacemaker located in the central nervous system ( CNS ) as well as of autonomous circadian pacemakers located in most peripheral t...	[ "Circadian clocks impose daily periodicities to animal behavior and physiology .", "At their core , circadian rhythms are produced by intracellular transcriptional/translational feedback loops ( TTFL ) .", "TTFLs may be altered by extracellular signals whose actions are mediated intracellularly by calcium and c...	[ "Circadian clocks impose daily periodicities to animal behavior and physiology .", "At their core , circadian rhythms are produced by intracellular transcriptional/translational feedback loops ( TTFL ) .", "TTFLs may be altered by extracellular signals whose actions are mediated intracellularly by calcium and c...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "biotechnology", "antimicrobials", "medicine and health sciences", "urea", "pathology and laboratory medicine", "chemical compounds", "ureases", "small molecules", "enzymes", "pathogens", "drugs", "enzymology", "microbiology", "organic compounds", "helicobacter", "pharmacology", "bac...	Metallochaperone UreG serves as a new target for design of urease inhibitor: A novel strategy for development of antimicrobials	journal.pbio.2003887	null	[ [ "Enzymes have been proven to serve as important drug targets , and enzyme inhibitors are among the most successful drugs [1] .", "One dominant strategy for enzyme-targeted drug design lies in the discovery or synthesis of structure analogues of substrates that resemble the enzyme’s reactivity [2] .", ...	[ "Urease as a potential target of antimicrobial drugs has received considerable attention given its versatile roles in microbial infection .", "Development of effective urease inhibitors , however , is a significant challenge due to the deeply buried active site and highly specific substrate of a bacterial urease ...	[ "Urease , a metalloenzyme that catalyzes the hydrolysis of urea , plays important roles in the survival and virulence of many microbial pathogens , and has long been considered an important drug target for the development of novel antimicrobials .", "However , its deeply buried active site and highly specific sub...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "bacterial diseases", "infectious diseases", "gram negative", "immunity", "innate immunity", "pseudomonas infections", "staphylococci", "microbial pathogens", "host-pathogen interaction", "biology", "microbiology", "staphylococcal infection", "bacterial pathogens", "gram posi...	Clonal Expansion during Staphylococcus aureus Infection Dynamics Reveals the Effect of Antibiotic Intervention	journal.ppat.1003959	null	[ [ "Staphylococcus aureus is an opportunistic human pathogen that causes skin and tissue abscesses , occasionally leading to severe systemic illness and death [1] .", "Whilst the process of lesion formation itself is becoming better defined [2] , the dynamics of a bacterial population within the host during ...	[ "To slow the inexorable rise of antibiotic resistance we must understand how drugs impact on pathogenesis and influence the selection of resistant clones .", "Staphylococcus aureus is an important human pathogen with populations of antibiotic-resistant bacteria in hospitals and the community .", "Host phagocyte...	[ "Staphylococcus aureus is a major cause of human disease , made even more notable due to the spread of antibiotic resistance .", "We used a combination of animal models to study the spread of bacteria between organs during an infection and the resulting effect of antibiotic intervention .", "We found that S . a...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "environmental epidemiology", "infectious disease epidemiology", "epidemiology", "spatial epidemiology" ]	Spatial Distribution of the Risk of Dengue and the Entomological Indicators in Sumaré, State of São Paulo, Brazil	journal.pntd.0002873	null	[ [ "Dengue is a disease caused by any of four virus ( DENV-1 , DENV-2 , DENV-3 and DENV-4; Flaviviridae: Flavivirus ) and has become a major global health issue .", "An epidemic similar to dengue was registered in 1699 in Central America .", "In Philadelphia , USA , a major epidemic occurred in 1780 and ...	[ "Dengue fever is a major public health problem worldwide , caused by any of four virus ( DENV-1 , DENV-2 , DENV-3 and DENV-4; Flaviviridae: Flavivirus ) , transmitted by Aedes aegypti mosquito .", "Reducing the levels of infestation by A . aegypti is one of the few current strategies to control dengue fever .", ...	[ "Dengue is a disease caused by a virus which has four serotypes DENV-1 , DENV-2 , DENV-3 and DENV-4 .", "In Americas , A . aegypti is acknowledged as the only dengue vector in America .", "Currently the only strategy to prevent dengue is controlling A . aegypti mosquitoes .", "The generalized additive model w...	2014

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