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headings list	keywords list	title stringlengths 20 281	id stringlengths 20 20	toc stringlengths 57 522 ⌀	sections list	abstract list	summary list	year stringclasses 13 values
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Determinants of Health Service Responsiveness in Community-Based Vector Surveillance for Chagas Disease in Guatemala, El Salvador, and Honduras	journal.pntd.0003974	null	[ [ "The prevalence of Chagas disease in Central America decreased from 1 . 7 million in the 1990s to 0 . 4 million in 2010 as a result of successful vector control [1 , 2] .", "Of the two main vectors , Rhodnius prolixus is almost eliminated , but Triatoma dimidiata remains widespread in the region despite g...	[ "Central American countries face a major challenge in the control of Triatoma dimidiata , a widespread vector of Chagas disease that cannot be eliminated .", "The key to maintaining the risk of transmission of Trypanosoma cruzi at lowest levels is to sustain surveillance throughout endemic areas .", "Guatemala ...	[ "Elimination of domiciliated vectors led to a decreased prevalence of Chagas disease in parts of Latin America .", "In Central America , where the domiciliated vector Rhodnius prolixus has been almost eliminated , Triatoma dimidiata , which cannot be eliminated , continues to threaten the population in vast areas...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Plasmodium vivax Transmission in Africa	journal.pntd.0004222	null	[ [ "Malaria in sub-Saharan Africa has historically been almost exclusively attributed to Plasmodium falciparum ( Pf ) .", "The identification of the Duffy antigen as the obligate trans-membrane receptor for P . vivax ( Pv ) infection of red blood cells by Miller et al . during the 1970s [1 , 2] stalled resea...	[ "Malaria in sub-Saharan Africa has historically been almost exclusively attributed to Plasmodium falciparum ( Pf ) .", "Current diagnostic and surveillance systems in much of sub-Saharan Africa are not designed to identify or report non-Pf human malaria infections accurately , resulting in a dearth of routine epi...	[ "Plasmodium vivax ( Pv ) is the most widely distributed malaria parasite globally , but conspicuously “absent” from Africa .", "The majority of African populations do not express the Duffy blood group antigen , which is the only known receptor for Pv infection .", "Since this discovery in the 1970s , the low cl...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "protein metabolism", "gene regulation", "metabolic processes", "regulatory proteins", "metabolic networks", "enzymology", "dna-binding proteins", "network analysis", "enzyme metabolism", "transcription factors", "enzyme chemistry", "computer and information sciences", "transcriptional contr...	A system-wide network reconstruction of gene regulation and metabolism in Escherichia coli	journal.pcbi.1006962	null	[ [ "So far , metabolic processes and gene regulatory events are typically considered individually in system-level investigations .", "However , ample evidence exists that the majority of cellular processes involves both , metabolism and gene regulation , and thus requires their joint examination [1] .", ...	[ "Genome-scale metabolic models have become a fundamental tool for examining metabolic principles .", "However , metabolism is not solely characterized by the underlying biochemical reactions and catalyzing enzymes , but also affected by regulatory events .", "Since the pioneering work of Covert and co-workers a...	[ "Networks—the compact representation of systems in terms of nodes and links—are an efficient data structure for biological information .", "They also allow us to establish relationships between network structure and dynamical function and thus hold the potential of implementing a systems-level view on biological ...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "neuroscience/theoretical neuroscience", "computational biology/computational neuroscience" ]	Towards Reproducible Descriptions of Neuronal Network Models	journal.pcbi.1000456	null	[ [ "Philosophers of science have yet to develop a robust definition and interpretation of models and simulations [39]–[42] .", "Most of that debate focuses on models in physics , but Peck [31] gives an interesting review of models and simulations in ecology , while Aumann [32] thoroughly discusses requiremen...	[ "Progress in science depends on the effective exchange of ideas among scientists .", "New ideas can be assessed and criticized in a meaningful manner only if they are formulated precisely .", "This applies to simulation studies as well as to experiments and theories .", "But after more than 50 years of neuron...	[ "Scientists make precise , testable statements about their observations and models of nature .", "Other scientists can then evaluate these statements and attempt to reproduce or extend them .", "Results that cannot be reproduced will be duly criticized to arrive at better interpretations of experimental results...	2009
[ "Introduction", "Methods and materials", "Results", "Discussion" ]	[ "antimicrobials", "medicine and health sciences", "c-reactive proteins", "chemical compounds", "fibrinogen", "aliphatic amino acids", "pathology and laboratory medicine", "drugs", "tropical diseases", "microbiology", "creatine", "vertebrates", "organic compounds", "animals", "signs and s...	Poor efficacy of preemptive amoxicillin clavulanate for preventing secondary infection from Bothrops snakebites in the Brazilian Amazon: A randomized controlled clinical trial	journal.pntd.0005745	null	[ [ "Bothrops snakebites result in a subcutaneous and muscular lesion at the site of bite , which many times evolve to local complications [1–5] .", "In 2015 , the Brazilian Ministry of Health recorded 18 , 741 snakebites across the country [6] .", "In this country , a higher incidence is observed in the ...	[ "Secondary bacterial infections from snakebites contribute to the high complication rates that can lead to permanent function loss and disabilities .", "Although common in endemic areas , routine empirical prophylactic use of antibiotics aiming to prevent secondary infection lacks a clearly defined policy .", "...	[ "Bothrops genus is responsible by 80–90% of the snakebites in the Brazilian Amazon , resulting in a subcutaneous and muscular lesion at the site of bite , which many times evolve to local complications , mostly secondary bacterial infections .", "In this region , late medical assistance is common and probably con...	2017
[ "Introduction", "Methods", "Discussion" ]	[ "sequencing techniques", "demography", "social sciences", "anthropology", "ancient dna", "contaminants", "neanderthals", "genome sequencing", "materials science", "genome analysis", "paleontology", "dna", "paleogenetics", "molecular biology techniques", "paleoanthropology", "research a...	Joint Estimation of Contamination, Error and Demography for Nuclear DNA from Ancient Humans	journal.pgen.1005972	null	[ [ "When sequencing a human genome using ancient DNA ( aDNA ) recovered from fossils , a common practice is to assess the amount of present-day human contamination in a sequencing library [1 , 2 , 3 , 4 , 5 , 6] .", "Several methods exist to obtain a contamination estimate .", "First , one can look at ‘d...	[ "When sequencing an ancient DNA sample from a hominin fossil , DNA from present-day humans involved in excavation and extraction will be sequenced along with the endogenous material .", "This type of contamination is problematic for downstream analyses as it will introduce a bias towards the population of the con...	[ "When extracting and sequencing ancient DNA from human remains , a recurrent problem is the presence of DNA from the paleontologists , archaeologists or geneticists that may have handled the fossil .", "If a DNA library is highly contaminated , this will introduce biases in downstream analyses , so it is importan...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "computational biology/evolutionary modeling", "evolutionary biology/microbial evolution and genomics" ]	Complex Adaptations Can Drive the Evolution of the Capacitor [PSI+], Even with Realistic Rates of Yeast Sex	journal.pgen.1000517	null	[ [ "[PSI+] is the aggregated prion form of the protein Sup35 [1] .", "[PSI+] aggregates appear spontaneously at a low rate [2] .", "Once established , [PSI+] causes normal Sup35 proteins to misfold to form more [PSI+] [3] .", "This self-catalytic conversion allows for transgenerational inheritance [4...	[ "The [PSI+] prion may enhance evolvability by revealing previously cryptic genetic variation , but it is unclear whether such evolvability properties could be favored by natural selection .", "Sex inhibits the evolution of other putative evolvability mechanisms , such as mutator alleles .", "This paper explores...	[ "Can evolvability evolve ?", "One obvious way to evolve faster is via mutator alleles that increase the mutation rate .", "Unfortunately , recombination will rapidly separate a mutator allele from the advantageous alleles that it creates .", "Mutators , therefore , gain very little benefit from promoting adap...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "bacterial diseases", "infectious diseases", "anthrax", "geography", "veterinary diseases", "social and behavioral sciences", "environmental epidemiology", "epidemiology", "infectious disease epidemiology", "zoonotic diseases", "spatial analysis", "spatial epidemiology", "popul...	Evidence of Local Persistence of Human Anthrax in the Country of Georgia Associated with Environmental and Anthropogenic Factors	journal.pntd.0002388	null	[ [ "Recently it has been suggested that the burden of anthrax has not been fully realized [1] .", "Interest in anthrax as a biological weapon has grown since the 2001 bioterrorist attacks [2] yet the disease is often undervalued as a public health threat .", "Anthrax is considered a neglected zoonosis , ...	[ "Anthrax is a soil-borne disease caused by the bacterium Bacillus anthracis and is considered a neglected zoonosis .", "In the country of Georgia , recent reports have indicated an increase in the incidence of human anthrax .", "Identifying sub-national areas of increased risk may help direct appropriate public...	[ "Anthrax is a zoonotic bacterial disease that occurs nearly worldwide .", "Despite a large number of countries reporting endemic anthrax , persistence of the disease appears to be associated with specific ecological factors related to soil composition and climatic conditions .", "Human cases are most often asso...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genome evolution", "evolutionary biology", "genome sequencing", "dna recombination", "molecular genetics", "dna", "sequence analysis", "transposons", "comparative genomics", "biology", "molecular biology", "nucleic acids", "dna transposons", "dna repair", "genomics", "molecular cell b...	The Paramecium Germline Genome Provides a Niche for Intragenic Parasitic DNA: Evolutionary Dynamics of Internal Eliminated Sequences	journal.pgen.1002984	null	[ [ "Paramecium belongs to the ciliate phylum , a deep radiation of highly diverse unicellular eukaryotes .", "The hallmark of ciliates is nuclear dimorphism: each unicellular organism harbors two kinds of nuclei with distinct organization and function .", "A diploid “germline” micronucleus ( MIC ) underg...	[ "Insertions of parasitic DNA within coding sequences are usually deleterious and are generally counter-selected during evolution .", "Thanks to nuclear dimorphism , ciliates provide unique models to study the fate of such insertions .", "Their germline genome undergoes extensive rearrangements during developmen...	[ "Ciliates are unicellular eukaryotes that rearrange their genomes at every sexual generation when a new somatic macronucleus , responsible for gene expression , develops from a copy of the germline micronucleus .", "In Paramecium , assembly of a functional somatic genome requires precise excision of interstitial ...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "homo (human)", "mammals", "computational biology", "molecular biology", "genetics and genomics" ]	CpG Island Mapping by Epigenome Prediction	journal.pcbi.0030110	null	[ [ "CpG islands are genomic regions characterized by an exceptionally high CpG dinucleotide frequency [1–3] .", "In humans , they are among the most important regulatory regions , with functional roles in both normal and disease-related gene expression [4 , 5] .", "Originally , CpG islands were discovere...	[ "CpG islands were originally identified by epigenetic and functional properties , namely , absence of DNA methylation and frequent promoter association .", "However , this concept was quickly replaced by simple DNA sequence criteria , which allowed for genome-wide annotation of CpG islands in the absence of large...	[ "A key challenge for bioinformatic research is the identification of regulatory regions in the human genome .", "Regulatory regions are DNA elements that control gene expression and thereby contribute to the organism's phenotype .", "An important class of regulatory regions consists of so-called CpG islands , w...	2007
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "geomorphology", "medicine and health sciences", "landforms", "topography", "geographical locations", "social sciences", "biological locomotion", "health care", "infectious disease control", "islands", "infectious diseases", "health economics", "epidemiology", "economics", "walking", "...	Economic analysis of dengue prevention and case management in the Maldives	journal.pntd.0006796	null	[ [ "With approximately half of the world’s population at risk , dengue remains the most important mosquito-borne infection world-wide , [1 , 2] costing almost $9 billion globally per year for prevention and control . [3]", "The ecology of Small Island Developing States and territories ( SIDS ) , particularly...	[ "As tourism is the mainstay of the Maldives’ economy , this country recognizes the importance of controlling mosquito-borne diseases in an environmentally responsible manner .", "This study sought to estimate the economic costs of dengue in this Small Island Developing State of 417 , 492 residents .", "The auth...	[ "As tourism is the mainstay of the Maldives’ economy , this country recognizes the importance of controlling mosquito-borne diseases in an environmentally responsible manner .", "This study sought to estimate the economic costs of dengue in this Small Island Developing State of 417 , 492 residents with an annual ...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Replication and Active Partition of Integrative and Conjugative Elements (ICEs) of the SXT/R391 Family: The Line between ICEs and Conjugative Plasmids Is Getting Thinner	journal.pgen.1005298	null	[ [ "Integrative and conjugative elements ( ICEs ) are highly prevalent and widely distributed in bacterial genomes [1–3] .", "Their ability to self-transfer by conjugation between genetically unrelated bacteria contributes to the emergence of multidrug resistant pathogens in diverse taxonomic groups [4–6] ."...	[ "Integrative and Conjugative Elements ( ICEs ) of the SXT/R391 family disseminate multidrug resistance among pathogenic Gammaproteobacteria such as Vibrio cholerae .", "SXT/R391 ICEs are mobile genetic elements that reside in the chromosome of their host and eventually self-transfer to other bacteria by conjugati...	[ "Integrative and conjugative elements ( ICEs ) constitute a class of mobile genetic elements defined by their ability to integrate into the chromosome of their host cell and to transfer by conjugation .", "Some of the most studied ICEs belong to the SXT/R391 family , which are major drivers of multidrug resistanc...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "vaccines", "oncology", "medicine", "vaccination", "dermatology", "viral vaccines", "skin neoplasms", "clinical immunology", "immunity", "virology", "benign skin neoplasms", "biology", "microbiology", "cancer prevention", "cancer vaccines", "malignant skin neoplasms" ]	Protective Vaccination against Papillomavirus-Induced Skin Tumors under Immunocompetent and Immunosuppressive Conditions: A Preclinical Study Using a Natural Outbred Animal Model	journal.ppat.1003924	null	[ [ "Papillomaviruses ( PVs ) infect mucosal and cutaneous squamous epithelia , where they can cause hyperproliferative lesions .", "In the case of high-risk genital human papillomavirus ( HPV ) types , a causative link has been established between HPV infection and the development of malignant diseases , esp...	[ "Certain cutaneous human papillomaviruses ( HPVs ) , which are ubiquitous and acquired early during childhood , can cause a variety of skin tumors and are likely involved in the development of non-melanoma skin cancer , especially in immunosuppressed patients .", "Hence , the burden of these clinical manifestatio...	[ "Organ transplant recipients ( OTR ) frequently suffer from fulminant warts that are induced by cutaneous human papillomaviruses ( HPV ) .", "Moreover , some skin HPV types may also be involved in the development of non-melanoma skin cancer .", "Mimicking the situation of immunosuppressed OTR who acquire cutane...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology and life sciences", "microbiology", "medicine and health sciences" ]	A Critical Role for IL-17RB Signaling in HTLV-1 Tax-Induced NF-κB Activation and T-Cell Transformation	journal.ppat.1004418	null	[ [ "The retrovirus human T-cell leukemia virus type 1 ( HTLV-1 ) infects between 10–20 million people worldwide [1] .", "HTLV-1 is the etiological agent of the neuroinflammatory disease HTLV-1-associated myelopathy ( HAM/TSP ) and adult T-cell leukemia ( ATL ) , a CD4+CD25+ T-cell malignancy [2] , [3] .", ...	[ "Human T-cell leukemia virus type 1 ( HTLV-1 ) infection is linked to the development of adult T-cell leukemia ( ATL ) and the neuroinflammatory disease HTLV-1 associated myelopathy/tropical spastic paraparesis ( HAM/TSP ) .", "The HTLV-1 Tax protein functions as a potent viral oncogene that constitutively activa...	[ "The retrovirus HTLV-1 is the causative agent of an aggressive lymphoproliferative disorder known as adult T-cell leukemia ( ATL ) .", "The HTLV-1 Tax regulatory protein constitutively activates the host NF-κB transcription factor to promote T-cell proliferation , survival and cell transformation .", "However ,...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry", "enzyme structure", "protein chemistry", "cofactors", "biochemistry simulations", "proteins", "biophysic al simulations", "enzymes", "protein structure", "biology", "computational biology", "biophysics simulations", "biophysics" ]	Substrate-Specific Reorganization of the Conformational Ensemble of CSK Implicates Novel Modes of Kinase Function	journal.pcbi.1002695	null	[ [ "The Src family of tyrosine kinases ( SFKs ) is comprised of modular signaling enzymes involved in the control of cellular growth and differentiation .", "The members of this family contain three important structural domains: a C-terminal tyrosine kinase domain ( comprised of a small and large lobe ) , wh...	[ "Protein kinases use ATP as a phosphoryl donor for the posttranslational modification of signaling targets .", "It is generally thought that the binding of this nucleotide induces conformational changes leading to closed , more compact forms of the kinase domain that ideally orient active-site residues for effici...	[ "The Src protein kinases are integral members of numerous signaling pathways involved in cellular growth and differentiation .", "The master regulator of the Src family is the protein kinase Csk , which adds a phosphate to the C-terminal tail , inhibiting Src Kinase function .", "Proper regulation of these sign...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "mathematics/statistics", "public health and epidemiology/infectious diseases", "immunology/immune response", "computational biology" ]	Quantitative Analysis of Immune Response and Erythropoiesis during Rodent Malarial Infection	journal.pcbi.1000946	null	[ [ "Malarial infection of humans is a major cause of morbidity and mortality , continuing to cause around 250 million cases and close to a million deaths annually [1] .", "The vast majority of severe cases and deaths are due to Plasmodium falciparum , which is endemic in most of sub-Saharan Africa and other ...	[ "Malarial infection is associated with complex immune and erythropoietic responses in the host .", "A quantitative understanding of these processes is essential to help inform malaria therapy and for the design of effective vaccines .", "In this study , we use a statistical model-fitting approach to investigate...	[ "Malaria is a disease caused by a protozoan parasite of the genus Plasmodium .", "Every year there are around 250 million human cases of malaria , resulting in around a million deaths .", "Most of the severe cases and deaths are due to Plasmodium falciparum , which is endemic in much of sub-Saharan Africa and o...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "stem cells", "biology", "adult stem cells" ]	The RNA–Methyltransferase Misu (NSun2) Poises Epidermal Stem Cells to Differentiate	journal.pgen.1002403	null	[ [ "Stem cells are defined by their ability to continuously maintain their population ( self-renewal ) while generating progeny ( differentiation ) .", "During self-renewal , stem cells have to avoid cell cycle exit and differentiation; however , when differentiating they have to evade uncontrolled prolifera...	[ "Homeostasis of most adult tissues is maintained by balancing stem cell self-renewal and differentiation , but whether post-transcriptional mechanisms can regulate this process is unknown .", "Here , we identify that an RNA methyltransferase ( Misu/Nsun2 ) is required to balance stem cell self-renewal and differe...	[ "We demonstrate that the RNA methyltransferase activity of Misu/NSun2 is required for the proper maintenance of the epidermal differentiation program , and thus post-transcriptional mechanisms are involved in controlling the balance between stem cell self-renewal and differentiation ." ]	2011
[ "Introduction", "Results/Discussion", "Methods" ]	[ "computer and information sciences", "systems science", "mathematics", "stem cells", "animal cells", "cell biology", "embryonic stem cells", "single cell primary cell culture", "cell culturing techniques", "biology and life sciences", "cellular types", "physical sciences", "biological cultur...	Construction and Validation of a Regulatory Network for Pluripotency and Self-Renewal of Mouse Embryonic Stem Cells	journal.pcbi.1003777	null	[ [ "mESCs are derived from the inner cell mass of a developing blastocyst and can be propagated indefinitely in culture .", "Cultured mESCs can contribute to all adult cell populations , including the germ-line .", "Human ESCs have similar in-vitro differentiation potential .", "It is now established...	[ "A 30-node signed and directed network responsible for self-renewal and pluripotency of mouse embryonic stem cells ( mESCs ) was extracted from several ChIP-Seq and knockdown followed by expression prior studies .", "The underlying regulatory logic among network components was then learned using the initial netwo...	[ "For this study we first constructed a directed and signed network consisting of 15 pluripotency regulators and 15 lineage commitment markers that extensively interact to regulate mouse embryonic stem cells fate decisions from data available in the public domain .", "Given the connectivity structure of this netwo...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "genome-wide association studies", "rheumatology", "medicine and health sciences", "immunology", "clinical medicine", "genome analysis", "molecular genetics", "epigenetics", "chromatin", "systemic lupus erythematosus", "genome complexity", "chromosome biology", "lupus erythematosus", "gene...	Profiling RNA-Seq at multiple resolutions markedly increases the number of causal eQTLs in autoimmune disease	journal.pgen.1007071	null	[ [ "The autoimmune diseases are a family of heritable , often debilitating , complex disorders in which immune dysfunction leads to loss of tolerance to self-antigens and chronic inflammation [1] .", "Genome-wide association studies ( GWAS ) have now detected hundreds of susceptibility loci contributing to r...	[ "Genome-wide association studies have identified hundreds of risk loci for autoimmune disease , yet only a minority ( ~25% ) share genetic effects with changes to gene expression ( eQTLs ) in immune cells .", "RNA-Seq based quantification at whole-gene resolution , where abundance is estimated by culminating expr...	[ "It is well acknowledged that non-coding genetic variants contribute to disease susceptibility through alteration of gene expression levels ( known as eQTLs ) .", "Identifying the variants that are causal to both disease risk and changes to expression levels has not been easy and we believe this is in part due to...	2017
[ "Introduction", "Results and Discussion", "Materials and Methods" ]	[ "biochemistry", "meiosis", "telomeres", "cell division", "transmembrane proteins", "chromosome biology", "proteins", "biology", "molecular cell biology" ]	Analysis of Meiosis in SUN1 Deficient Mice Reveals a Distinct Role of SUN2 in Mammalian Meiotic LINC Complex Formation and Function	journal.pgen.1004099	null	[ [ "Nuclear anchorage and movement , including the directed repositioning of components within the nucleus , are essential for coordinated cell division , proliferation and development [1] .", "As these processes are largely dependent on cytoskeletal components , the cytoskeleton needs to interact with both ...	[ "LINC complexes are evolutionarily conserved nuclear envelope bridges , composed of SUN ( Sad-1/UNC-84 ) and KASH ( Klarsicht/ANC-1/Syne/homology ) domain proteins .", "They are crucial for nuclear positioning and nuclear shape determination , and also mediate nuclear envelope ( NE ) attachment of meiotic telomer...	[ "Correct genome haploidization during meiosis requires tightly regulated chromosome movements that follow a highly conserved choreography during prophase I . Errors in these movements cause subsequent meiotic defects , which typically lead to infertility .", "At the beginning of meiotic prophase , chromosome ends...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "medicine and health sciences", "nucleic acid synthesis", "rna extraction", "microbiology", "animals", "wolbachia", "animal models", "viruses", "virus effects on host gene expression", "drosophila melanogaster", "model organisms", "rna viruses", "experimental organism syst...	Wolbachia elevates host methyltransferase expression to block an RNA virus early during infection	journal.ppat.1006427	null	[ [ "Heritable symbioses are pervasive in nature and exceedingly common in the insect world , where many endosymbiotic associations have been described [1] .", "Wolbachia pipientis is an alpha-proteobacterial , maternally transmitted endosymbiont that invades insect host populations by manipulating host repro...	[ "Wolbachia pipientis is an intracellular endosymbiont known to confer host resistance against RNA viruses in insects .", "However , the causal mechanism underlying this antiviral defense remains poorly understood .", "To this end , we have established a robust arthropod model system to study the tripartite inte...	[ "Effective vector control is critically important to reduce the incidence of diseases caused by arthropod transmitted viruses .", "One proposed strategy involves the use of endosymbiotic bacteria Wolbachia pipientis as a novel biocontrol agent to prevent RNA virus transmission in mosquitoes .", "Previous work i...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "developmental biology", "genetics and genomics" ]	Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm	journal.pbio.0060027	ChIP/chip analysis indicates that sequence-specific transcription factors bind to overlapping sets of thousands of genomic regions in Drosophila embryos, but most regions are bound at low levels and many may not be functional targets of these factors.	[ [ "Deciphering the transcriptional information contained in the extensive cis-acting sequences that direct intricate patterns of gene expression in animals is a major challenge in biology .", "Animal genomes encode several hundred ( e . g . , Drosophila ) to several thousand ( e . g . , human ) transcriptio...	[ "Identifying the genomic regions bound by sequence-specific regulatory factors is central both to deciphering the complex DNA cis-regulatory code that controls transcription in metazoans and to determining the range of genes that shape animal morphogenesis .", "We used whole-genome tiling arrays to map sequences ...	[ "One of the largest classes of regulatory proteins in animals , sequence-specific DNA binding transcription factors determine in which cells genes will be expressed and so control the development of an animal from a single cell to a morphologically complex adult .", "Understanding how this process is coordinated ...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/bacterial infections", "microbiology/medical microbiology" ]	BosR (BB0647) Controls the RpoN-RpoS Regulatory Pathway and Virulence Expression in Borrelia burgdorferi by a Novel DNA-Binding Mechanism	journal.ppat.1001272	null	[ [ "Bacterial gene expression is primarily controlled at the transcriptional level , which requires a central DNA-dependent RNA polymerase ( RNAP ) consisting of catalytic core ( α2ββ'ω; E ) and a dissociable σ factor [1] .", "Gene transcription occurs when the Eσ-promoter closed complex ( CC ) is converted ...	[ "In Borrelia burgdorferi ( Bb ) , the Lyme disease spirochete , the alternative σ factor σ54 ( RpoN ) directly activates transcription of another alternative σ factor , σS ( RpoS ) which , in turn , controls the expression of virulence-associated membrane lipoproteins .", "As is customary in σ54-dependent gene co...	[ "Lyme disease , caused by the bacterium Borrelia burgdorferi ( Bb ) , remains the most common arthropod-borne illness in the United States .", "A critical strategy for Bb to maintain its presence in nature is adaptation to its diverse tick and mammalian ( mouse ) hosts .", "To accomplish this , Bb encodes a pot...	2011
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "innate immune system", "medicine and health sciences", "immune physiology", "cytokines", "immunology", "parasitic diseases", "vaccines", "preventive medicine", "developmental biology", "immunologic adjuvants", "molecular development", "infectious disease control", "vaccination and immunizat...	Yeast-expressed recombinant As16 protects mice against Ascaris suum infection through induction of a Th2-skewed immune response	journal.pntd.0005769	null	[ [ "Ascaris lumbricoides , Trichuris trichiura and the hookworm Necator americanus are the three major soil-transmitted helminths ( STH ) that infect more than one billion poor people in the world and are the leading neglected tropical diseases ( NTDs ) in terms of disability-adjusted life years ( DALYs ) [1] ."...	[ "Ascariasis remains the most common helminth infection in humans .", "As an alternative or complementary approach to global deworming , a pan-anthelminthic vaccine is under development targeting Ascaris , hookworm , and Trichuris infections .", "As16 and As14 have previously been described as two genetically re...	[ "Roundworms ( Ascaris ) infect more than 700 million people living in poverty worldwide and cause malnutrition and physical and mental developmental delays in children .", "As an alternative or complementary approach to global deworming , a pan-anthelminthic vaccine is under development that targets ascariasis in...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma mansoni", "medicine and health sciences", "surface water", "helminths", "tropical diseases", "geographical locations", "uganda", "parasitic diseases", "animals", "health care", "age groups", "pharmaceutics", "drug administration", "neglected...	The prevalence of schistosomiasis in Uganda: A nationally representative population estimate to inform control programs and water and sanitation interventions	journal.pntd.0007617	null	[ [ "Schistosomiasis is a neglected water-based , vector-borne disease transmitted indirectly through freshwater snails , estimated to affect more than 240 million individuals worldwide with 700–800 million people living at risk of infection [1–3] .", "In sub-Saharan Africa , approximately 280 , 000 deaths pe...	[ "To improve schistosomiasis control programs in Uganda , where intestinal schistosomiasis is a widespread public health problem , a country-wide assessment of the disease prevalence among all age ranges is needed .", "Few studies have aimed to quantify the relationships between disease prevalence and water and sa...	[ "Schistosomiasis is a neglected tropical disease in sub-Saharan Africa that has remained intractable despite efforts to eliminate it through mass drug administration .", "The transmission cycle is perpetuated when sanitation infrastructure does not adequately capture infected urine or feces and local water bodies...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "soil-transmitted helminths", "parasitic intestinal diseases", "trichuriasis", "infectious disease epidemiology", "epidemiology", "neglected tropical diseases", "infectious disease control", "ascariasis", "parasitic diseases", "helminth infection" ]	Risk Factors for Soil-Transmitted Helminth Infections during the First 3 Years of Life in the Tropics; Findings from a Birth Cohort	journal.pntd.0002718	null	[ [ "Soil-transmitted helminths ( STH ) , including A . lumbricoides lumbricoides , T . trichiura trichiura , and hookworm , are estimated to infect more than 2 billion humans worldwide [1] of which 51 million children are considered to be at risk of morbidity [2] .", "An estimated 35 million or more disabili...	[ "Soil-transmitted helminths ( STH ) infect more than 2 billion humans worldwide , causing significant morbidity in children .", "There are few data on the epidemiology and risk factors for infection in pre-school children .", "To investigate risk factors for infection in early childhood , we analysed data prosp...	[ "Soil-transmitted helminths ( STH ) are intestinal worms that cause significant morbidity in school age and pre-school children in developing countries .", "Infections are associated with poverty , particularly through lack of access to sanitation and clean drinking water .", "Current control strategies rely on...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	A FRET-Based DNA Biosensor Tracks OmpR-Dependent Acidification of Salmonella during Macrophage Infection	journal.pbio.1002116	Rather than using the cadaverine operon to combat the acid conditions of the macrophage vacuole, Salmonella allows its cytoplasm to become acidified, which in turn drives secretion of effectors into the host cell.	[ [ "Gram-negative pathogens use type III secretion systems ( T3SS ) to secrete effectors into the host , which promote virulence and alter host signaling functions .", "Salmonella enterica serovar Typhimurium encodes two T3SS on Salmonella pathogenicity islands 1 and 2 ( SPI-1 and SPI-2 ) .", "Their uniq...	[ "In bacteria , one paradigm for signal transduction is the two-component regulatory system , consisting of a sensor kinase ( usually a membrane protein ) and a response regulator ( usually a DNA binding protein ) .", "The EnvZ/OmpR two-component system responds to osmotic stress and regulates expression of outer ...	[ "The human pathogenic bacteria Salmonella encounters extreme and diverse conditions during the course of host infection .", "Survival and adaptation inside the host requires highly regulated virulence factors .", "When Salmonella is engulfed by a macrophage , it forms a vacuole-type structure that is actively a...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/genomics", "molecular biology/histone modification", "genetics and genomics/plant genetics and gene expression", "developmental biology/plant growth and development", "molecular biology/dna methylation", "genetics and genomics/epigenetics", "molecular biology/chromatin structure" ...	H3K27me3 Profiling of the Endosperm Implies Exclusion of Polycomb Group Protein Targeting by DNA Methylation	journal.pgen.1001152	null	[ [ "Polycomb group ( PcG ) proteins are evolutionary conserved master regulators of cell identity and balance the decision between cell proliferation and cell differentiation [1] .", "PcG proteins act in multimeric complexes that repress transcription of target genes; the best characterized complexes are the...	[ "Polycomb group ( PcG ) proteins act as evolutionary conserved epigenetic mediators of cell identity because they repress transcriptional programs that are not required at particular developmental stages .", "Each tissue is likely to have a specific epigenetic profile , which acts as a blueprint for its developme...	[ "Cell identity is established by the evolutionary conserved Polycomb group ( PcG ) proteins that repress transcriptional programs which are not required at particular developmental stages .", "The plant FERTILIZATION INDEPENDENT SEED ( FIS ) PcG complex is specifically expressed in the endosperm where it is essen...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/gene function", "developmental biology/developmental molecular mechanisms", "genetics and genomics/gene expression" ]	A Pax3/Dmrt2/Myf5 Regulatory Cascade Functions at the Onset of Myogenesis	journal.pgen.1000897	null	[ [ "The Pax family of transcriptional regulators play key roles in the onset of organogenesis and cell lineage specification during development [1] .", "Pax3 and Pax7 regulate skeletal muscle formation .", "Skeletal muscle progenitors in the trunk and limbs of vertebrates derive from somites , from the d...	[ "All skeletal muscle progenitor cells in the body derive from the dermomyotome , the dorsal epithelial domain of developing somites .", "These multipotent stem cells express Pax3 , and this expression is maintained in the myogenic lineage where Pax3 plays an important role .", "Identification of Pax3 targets is...	[ "It is well established that skeletal muscle derives from segmented structures called somites that form on either side of the axis of the embryo .", "The part of the somite that contains muscle stem cells is called the dermomyotome .", "These cells express the transcription factor Pax3 , which regulates muscle ...	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "body fluids", "pathology and laboratory medicine", "pathogens", "tropical diseases", "microbiology", "parasitic diseases", "salmonellosis", "retroviruses", "viruses", "diarrhea", "bacterial diseases", "immunodeficiency viruses", "signs and symptoms", "rna...	Multi-drug resistant non-typhoidal Salmonella associated with invasive disease in western Kenya	journal.pntd.0006156	null	[ [ "Non-typhoidal Salmonella ( NTS ) is a leading cause of bacteremia in Africa [1] .", "Whereas NTS commonly manifests as self-limiting diarrhea in immune-competent individuals , NTS bacteremia occurs at high rates in young children ( 175–388 cases per 100 , 000 ) [2 , 3] and HIV-infected adults ( 2000–7500...	[ "Non-typhoidal Salmonella ( NTS ) is a leading cause of bloodstream infections in Africa , but the various contributions of host susceptibility versus unique pathogen virulence factors are unclear .", "We used data from a population-based surveillance platform ( population ~25 , 000 ) between 2007–2014 and NTS ge...	[ "Though NTS is normally associated with self-limiting gastroenteritis in humans , it is a leading cause of bloodstream infection in Africa .", "The biological mechanisms that contribute to invasiveness in NTS in Africa are unclear .", "In this paper we address which specific host and pathogen risk factors are a...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "public health and epidemiology", "parasitic intestinal diseases", "clinical epidemiology", "epidemiology", "gastroenterology and hepatology", "parasitic diseases", "helminth infection" ]	Synergism between Prior Anisakis simplex Infections and Intake of NSAIDs, on the Risk of Upper Digestive Bleeding: A Case-Control Study	journal.pntd.0001214	null	[ [ "Upper gastrointestinal bleeding ( UGIB ) is a relatively frequent and potentially lethal multicausal medical emergency [1] .", "Gastric and duodenal ulcers are a major cause of UGIB , and bleeding from these lesions is frequently related to intake of non-steroidal anti-inflammatory drugs ( NSAIDs ) [2] ....	[ "The aim of this study was to investigate the relationship between prior Anisakis infections and upper gastrointestinal bleeding ( UGIB ) , and its interaction with non-steroidal anti-inflammatory drug ( NSAID ) intake .", "We conducted a hospital-based case-control study covering 215 UGIB cases and 650 controls ...	[ "Anisakiasis is a worldwide re-emerging disease produced by the consumption of raw , lightly cooked , smoked or marinated fish containing live Anisakis larvae .", "In acute anisakiasis , mucosal lesions generated by the larvae may provoke upper gastrointestinal bleeding ( UGIB ) .", "However , the effect of pas...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "animal models of infection", "infectious diseases", "mycobacteria", "medicine and health sciences", "medical microbiology", "microbial pathogens", "biology and life sciences", "immunology", "microbiology", "bacterial pathogens", "pediatrics" ]	Bacillus Calmette-Guerin Infection in NADPH Oxidase Deficiency: Defective Mycobacterial Sequestration and Granuloma Formation	journal.ppat.1004325	null	[ [ "M . bovis BCG ( Bacillus Calmette Guérin ) is an attenuated strain of M . bovis , used as a vaccine against tuberculosis .", "BCG vaccination has a proven efficacy only early in life ( <1 year of age ) , in particular against tuberculous meningitis and miliary tuberculosis .", "Thus , the WHO recomme...	[ "Patients with chronic granulomatous disease ( CGD ) lack generation of reactive oxygen species ( ROS ) through the phagocyte NADPH oxidase NOX2 .", "CGD is an immune deficiency that leads to frequent infections with certain pathogens; this is well documented for S . aureus and A . fumigatus , but less clear for ...	[ "The vaccine Mycobacterium bovis BCG is administrated to prevent early age tuberculosis in endemic areas .", "BCG is a live vaccine with a low incidence of complications .", "However , local or disseminated BCG infection may occur , in particular in immunodeficient individuals .", "Chronic granulomatous disea...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	HupA, the main undecaprenyl pyrophosphate and phosphatidylglycerol phosphate phosphatase in Helicobacter pylori is essential for colonization of the stomach	journal.ppat.1007972	null	[ [ "The biogenesis of many bacterial cell-envelope polysaccharides ( i . e . , peptidoglycan ( PGN ) , lipopolysaccharides ( LPS ) , teichoic acids , enterobacterial common antigen ) requires the translocation , across the cytoplasmic membrane , of glycan units that are produced inside the cytoplasm [1] .", ...	[ "The biogenesis of bacterial cell-envelope polysaccharides requires the translocation , across the plasma membrane , of sugar sub-units that are produced inside the cytoplasm .", "To this end , the hydrophilic sugars are anchored to a lipid phosphate carrier ( undecaprenyl phosphate ( C55-P ) ) , yielding membran...	[ "Helicobacter pylori colonizes the human’s gastric mucosa and infects around 50% of the world’s population .", "This pathogen is responsible for chronic gastritis , peptic ulcers and in worst cases leads to gastric cancer .", "It has been classified as a class I carcinogen by the World Health Organization in 19...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology", "computational biology", "biophysics simulations", "biophysics" ]	Assessing the Relative Stability of Dimer Interfaces in G Protein-Coupled Receptors	journal.pcbi.1002649	null	[ [ "G Protein-Coupled Receptors ( GPCRs ) have been reported to associate in the cell membrane to form dimers/oligomers .", "While incontrovertible evidence exists for the constitutive dimerization of disulfide-linked family C GPCRs [1] , the interpretation of oligomerization studies of members of the larges...	[ "Considerable evidence has accumulated in recent years suggesting that G protein-coupled receptors ( GPCRs ) associate in the plasma membrane to form homo- and/or heteromers .", "Nevertheless , the stoichiometry , fraction and lifetime of such receptor complexes in living cells remain topics of intense debate .",...	[ "G Protein-Coupled Receptors ( GPCRs ) are the largest family of membrane proteins targeted by drugs in clinical practice .", "Despite being at the forefront of biomedical research for many years , there is still considerable uncertainty about how GPCRs function at a molecular level .", "Although substantial ev...	2012
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "medicine and health sciences", "rna interference", "gene regulation", "regulatory proteins", "immunology", "dna-binding proteins", "animals", "animal models", "bacterial diseases", "drosophila melanogaster", "model organisms", "experimental organism systems", "transcripti...	Comparative transcriptomics reveals CrebA as a novel regulator of infection tolerance in D. melanogaster	journal.ppat.1006847	null	[ [ "To combat infection , a host activates a combination of immune and physiological responses .", "While detection of microbial presence is sufficient to stimulate the innate immune response , physiological responses to infection occur as a consequence of microbial growth and virulence , and can therefore b...	[ "Host responses to infection encompass many processes in addition to activation of the immune system , including metabolic adaptations , stress responses , tissue repair , and other reactions .", "The response to bacterial infection in Drosophila melanogaster has been classically described in studies that focused...	[ "How does an organism survive infection ?", "How generic or specific is the host response to diverse pathogens ?", "To address these questions , we infected fruit flies with 10 different bacteria that vary in their ability to kill flies and measured changes in global gene expression .", "In general , we found...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell physiology", "bacterial diseases", "infectious diseases", "infectious diseases of the nervous system", "medicine and health sciences", "cell biology", "pathology and laboratory medicine", "host-pathogen interactions", "medical microbiology", "meningitis", "bacterial meningitis", "microbi...	Differential Activation of Acid Sphingomyelinase and Ceramide Release Determines Invasiveness of Neisseria meningitidis into Brain Endothelial Cells	journal.ppat.1004160	null	[ [ "Neisseria meningitidis ( Nm , the meningococcus ) is a frequently found asymptomatic colonizer of the upper respiratory tract , which under certain circumstances may penetrate the mucosal membrane , reach the bloodstream and cause septicemia and/or meningitis .", "During the course of infection N . menin...	[ "The interaction with brain endothelial cells is central to the pathogenicity of Neisseria meningitidis infections .", "Here , we show that N . meningitidis causes transient activation of acid sphingomyelinase ( ASM ) followed by ceramide release in brain endothelial cells .", "In response to N . meningitidis i...	[ "Neisseria meningitidis , an obligate human pathogen , is a causative agent of septicemia and meningitis worldwide .", "Meningococcal infection manifests in a variety of forms , including meningitis , meningococcemia with meningitis or meningococcemia without obvious meningitis .", "The interaction of N . menin...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Synaptotagmin-1 and -7 Are Redundantly Essential for Maintaining the Capacity of the Readily-Releasable Pool of Synaptic Vesicles	journal.pbio.1002267	Synaptotagmins function not only as calcium sensors in triggering synaptic vesicle fusion but also contribute to the preparation of synaptic vesicles for fusion, being required for full priming of vesicles ready for subsequent triggering of exocytosis.	[ [ "Synaptic vesicles are released within a few hundred microseconds of Ca2+ influx into a presynaptic terminal [1 , 2] .", "Exocytosis of synaptic vesicles is carried out by neuronal soluble NSF-attachment protein receptor ( SNARE ) and Sec1/Munc18-like ( SM ) proteins and triggered by Ca2+ binding to synap...	[ "In forebrain neurons , Ca2+ triggers exocytosis of readily releasable vesicles by binding to synaptotagmin-1 and -7 , thereby inducing fast and slow vesicle exocytosis , respectively .", "Loss-of-function of synaptotagmin-1 or -7 selectively impairs the fast and slow phase of release , respectively , but does no...	[ "Neurons communicate with each other at specialized contact points called synapses .", "Presynaptic neurons store chemical neurotransmitters within presynaptic vesicles at the nerve terminal .", "During synaptic transmission , the presynaptic vesicles fuse with the plasma membrane , releasing their neurotransmi...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases/neglected tropical diseases", "public health and epidemiology/epidemiology", "infectious diseases/helminth infections", "public health and epidemiology/infectious diseases", "public health and epidemiology/social and behavioral determinants of health" ]	Seroprevalence to the Antigens of Taenia solium Cysticercosis among Residents of Three Villages in Burkina Faso: A Cross-Sectional Study	journal.pntd.0000555	null	[ [ "Taenia solium is a tapeworm transmitted among humans and between humans and pigs .", "Taeniasis is acquired by humans when eating raw or undercooked pork contaminated with cysticerci , the larval stage of T . solium .", "When ingested , the cysticerci migrate to the intestine of humans where they est...	[ "There is limited published information on the prevalence of human cysticercosis in West Africa .", "The aim of this pilot study was to estimate the prevalence of Taenia solium cysticercosis antigens in residents of three villages in Burkina Faso .", "Three villages were selected: The village of Batondo , selec...	[ "Taenia solium cysticercosis is a neglected tropical zoonosis transmitted between humans and pigs .", "This infection is particularly prevalent in areas where sanitation , hygiene and pig management practices are poor .", "There is very little information about the importance of this infection in West Africa , ...	2009
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "epidemiology", "arthropod vectors", "parasitic diseases", "disease vectors", "nematode infections" ]	Identification of Human Semiochemicals Attractive to the Major Vectors of Onchocerciasis	journal.pntd.0003450	null	[ [ "Onchocerca volvulus , the etiological agent of “river blindness” , remains a major public health threat in much of Africa and in a cross-border focus between Venezuela and Brazil [1] .", "Recent studies suggest that mass distribution of Mectizan ( ivermectin ) may be effective in achieving local eliminat...	[ "Entomological indicators are considered key metrics to document the interruption of transmission of Onchocerca volvulus , the etiological agent of human onchocerciasis .", "Human landing collection is the standard employed for collection of the vectors for this parasite .", "Recent studies reported the develop...	[ "Human landing collections , which are the current standard for collecting the black fly vectors of Onchocerca volvulus , the causative agent of river blindness , are inefficient and pose certain ethical issues .", "As entomological methods are among the primary techniques recommended by the international communi...	2015
[ "Introduction", "Design and implementation", "Results and discussion", "Availability and future directions" ]	[]	Recentrifuge: Robust comparative analysis and contamination removal for metagenomics	journal.pcbi.1006967	null	[ [ "In the case of low microbial biomass samples , there is very little native DNA from microbes; the library preparation and sequencing methods will return sequences whose principal source is contamination [5 , 6] .", "Sequencing of RNA requiring additional steps introduces still further biases and artifact...	[ "Metagenomic sequencing is becoming widespread in biomedical and environmental research , and the pace is increasing even more thanks to nanopore sequencing .", "With a rising number of samples and data per sample , the challenge of efficiently comparing results within a specimen and between specimens arises .", ...	[ "Whether in a clinical or environmental sample , metagenomics can reveal what microorganisms exist and what they do .", "It is indeed a powerful tool for the study of microbial communities which requires equally powerful methods of analysis .", "Current challenges in the analysis of metagenomic data include the...	2019
[ "Introduction", "Materials and Methods", "Results", "Discussion", "Supporting Information" ]	[ "chicken", "eubacteria", "computational biology" ]	Prediction of Functional Sites Based on the Fuzzy Oil Drop Model	journal.pcbi.0030094	null	[ [ "Because of the growing number of structural genomics projects oriented toward obtaining a large number of protein structures in rapid and automated processes [1–4] , there is a need to predict protein function ( or its functionally important residues ) by examining its structure .", "There have been a va...	[ "A description of many biological processes requires knowledge of the 3-D structure of proteins and , in particular , the defined active site responsible for biological function .", "Many proteins , the genes of which have been identified as the result of human genome sequencing , and which were synthesized exper...	[ "We present here a method of defining functional site recognition in proteins .", "The active site ( enzymatic cavity or ligand-binding site ) is localized on the basis of hydrophobicity deficiency , which is understood as the difference between empirical ( dependent on amino acid positions ) and idealized ( 3-D ...	2007
[ "Introduction", "Materials and Methods", "Results/Discussion" ]	[]	Shaking the Tree: Multi-locus Sequence Typing Usurps Current Onchocercid (Filarial Nematode) Phylogeny	journal.pntd.0004233	null	[ [ "The Onchocercidae ( Spirurida ) , commonly referred to as filariae , are a family of parasitic nematodes characterised by a wide host-range in squamates , crocodilians , amphibians , mammals and birds [1] .", "As several filarial species are agents of human and veterinary diseases [2–4] , the Onchocercid...	[ "During the past twenty years , a number of molecular analyses have been performed to determine the evolutionary relationships of Onchocercidae , a family of filarial nematodes encompassing several species of medical or veterinary importance .", "However , opportunities for broad taxonomic sampling have been scar...	[ "Filariae are predominantly tissue-dwelling nematodes of the Onchocercidae ( Spirurida ) .", "They are parasites of terrestrial vertebrates and some of them are particularly well known as agents of human diseases in tropical environments ( e . g . onchocercosis , lymphatic filariosis , loaosis ) .", "Because of...	2015
[ "Introduction", "Results/Discussion", "Methods" ]	[ "genetics and genomics/comparative genomics", "computational biology/sequence motif analysis", "computational biology/transcriptional regulation", "genetics and genomics/gene expression", "physiology/genomics", "computational biology/comparative sequence analysis", "genetics and genomics/bioinformatics"...	Promoter Complexity and Tissue-Specific Expression of Stress Response Components in Mytilus galloprovincialis, a Sessile Marine Invertebrate Species	journal.pcbi.1000847	null	[ [ "The majority of molluscan species go through two principal developmental phases , a larval embryo ( motile phase ) followed by a clumping structure ( sessile phase ) , when they are permanently attached to an underwater substrate .", "This lifecycle , common amongst marine invertebrates , poses challenge...	[ "The mechanisms of stress tolerance in sessile animals , such as molluscs , can offer fundamental insights into the adaptation of organisms for a wide range of environmental challenges .", "One of the best studied processes at the molecular level relevant to stress tolerance is the heat shock response in the genu...	[ "Adaptation of sessile animals , such as molluscs , to stress is achieved by a number of molecular mechanisms , few of which are clearly understood .", "Insights from this research can provide clues about stress tolerance both for sessile and mobile organisms .", "The Mediterranean mussel , of the genus Mytilus...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	hnRNP K Coordinates Transcriptional Silencing by SETDB1 in Embryonic Stem Cells	journal.pgen.1004933	null	[ [ "Long terminal repeat ( LTR ) retrotransposons , also called endogenous retroviruses ( ERVs ) , are the relics of ancient and more recent germline retroviral integrations , comprising ~8–10% of the mouse and human genomes , respectively [1] .", "De novo retrotransposition of these parasitic elements is re...	[ "Retrotransposition of endogenous retroviruses ( ERVs ) poses a substantial threat to genome stability .", "Transcriptional silencing of a subset of these parasitic elements in early mouse embryonic and germ cell development is dependent upon the lysine methyltransferase SETDB1 , which deposits H3K9 trimethylatio...	[ "Retroelements , including endogenous retroviruses ( ERVs ) , pose a significant threat to genome stability .", "In mouse embryonic stem ( ES ) cells , the enzyme SETDB1 safeguards the genome against transcription of specific ERVs by depositing a repressive mark H3K9 trimethylation ( H3K9me3 ) .", "Although SET...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "computational biology/population genetics", "genetics and genomics/microbial evolution and genomics", "evolutionary biology/microbial evolution and genomics", "microbiology/immunity to infections", "computational biology/molecular genetics", "microbiology/microbial evolution and genomics", "computation...	The Effect of Immune Selection on the Structure of the Meningococcal Opa Protein Repertoire	journal.ppat.1000020	null	[ [ "The Opacity ( Opa ) proteins of the bacterial pathogen Neisseria meningitidis mediate adhesion to and invasion of the human nasopharyngeal epithelium [1] via interaction with cell surface saccharides [2] and members of the carcinoembryonic antigen cell adhesion molecule ( CEACAM ) family of proteins [3] , [4...	[ "The opa genes of the Gram negative bacterium Neisseria meningitidis encode Opacity-associated outer membrane proteins whose role is to promote adhesion to the human host tissue during colonisation and invasion .", "Each meningococcus contains 3–4 opa loci , each of which may be occupied by one of a large number ...	[ "Neisseria meningitidis is a globally important pathogen that causes 2 , 000–3 , 000 cases of invasive meningococcal disease annually in the United Kingdom .", "The meningococcal Opa proteins are important in mediating adhesion to and invasion of human tissues , and are important for evasion of the host immune re...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biophysics/macromolecular assemblies and machines", "molecular biology/transcription initiation and activation", "biochemistry/macromolecular assemblies and machines", "biochemistry/transcription and translation", "biophysics/transcription and translation" ]	Molecular Architecture of the Human Mediator–RNA Polymerase II–TFIIF Assembly	journal.pbio.1000603	The authors perform a cryo-EM study of the 1.9 MDa human Mediator-RNA polymerase II-TFIIF assembly, which reveals the structural organization of the human transcription initiation apparatus.	[ [ "In humans , the transcription initiation machinery consists of Mediator , pol II , TFIIA , TFIIB , TFIID , TFIIE , TFIIF , and TFIIH and approximates 3 . 5 MDa in size .", "This large assembly can exist in various structural and functional states [1] .", "When not in an activated state that supports ...	[ "The macromolecular assembly required to initiate transcription of protein-coding genes , known as the Pre-Initiation Complex ( PIC ) , consists of multiple protein complexes and is approximately 3 . 5 MDa in size .", "At the heart of this assembly is the Mediator complex , which helps regulate PIC activity and i...	[ "Transcription initiation in humans is regulated by a macromolecular complex formed by the RNA polymerase II enzyme ( pol II ) , Mediator , and the general transcription factors TFIIA , TFIIB , TFIID , TFIIE , TFIIF , and TFIIH .", "Collectively , these factors are known as the Pre-Initiation Complex ( PIC ) .", ...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "inflammation", "clinical immunology", "immunity", "immunology", "biology", "fungal diseases" ]	Type I Interferons Promote Fatal Immunopathology by Regulating Inflammatory Monocytes and Neutrophils during Candida Infections	journal.ppat.1002811	null	[ [ "Fungal sepsis is a frequent cause of death in the intensive care unit , with Candida spp .", "being among the most common microbial pathogens isolated from septic patients .", "Worldwide , C . albicans ( Ca ) represents the most prevalent isolate recovered from human candidemic patients .", "The ...	[ "Invasive fungal infections by Candida albicans ( Ca ) are a frequent cause of lethal sepsis in intensive care unit patients .", "While a contribution of type I interferons ( IFNs-I ) in fungal sepsis remains unknown , these immunostimulatory cytokines mediate the lethal effects of endotoxemia and bacterial sepsi...	[ "Inflammation constitutes a major host response in many microbial infections .", "Innate immune cells orchestrate the inflammatory response to kill pathogens and clear infections .", "However , invasive infections by pathogenic microbes including the fungus Candida albicans , can result in an uncontrolled hyper...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/chromosome biology", "molecular biology/dna repair" ]	Dual Roles for DNA Polymerase Theta in Alternative End-Joining Repair of Double-Strand Breaks in Drosophila	journal.pgen.1001005	null	[ [ "DNA double-strand breaks ( DSBs ) and interstrand crosslinks pose serious threats to cell survival and genome stability .", "Because these lesions compromise both strands of the double helix , they impede DNA replication and transcription and therefore must be removed in a timely and coordinated manner ....	[ "DNA double-strand breaks are repaired by multiple mechanisms that are roughly grouped into the categories of homology-directed repair and non-homologous end joining .", "End-joining repair can be further classified as either classical non-homologous end joining , which requires DNA ligase 4 , or “alternative” en...	[ "DNA double-strand breaks , in which both strands of the DNA double helix are cut , must be recognized and accurately repaired in order to promote cell survival and prevent the accumulation of mutations .", "However , error-prone repair occasionally occurs , even when accurate repair is possible .", "We have in...	2010
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "glycosylamines", "computational biology", "animals", "invertebrate genomics", "animal models", "drosophila melanogaster", "model organisms", "experimental organism systems", "genome analysis", "drosophila", "adenosine", "research and analysis methods", "genomic libraries"...	Adaptation of A-to-I RNA editing in Drosophila	journal.pgen.1006648	null	[ [ "Genomic mutations are the major sources for phenotypic changes and adaptation [1–4] .", "In diploid multicellular organisms , a nonsynonymous DNA mutation ( a mutation that alters the amino acid sequence of a protein ) will permanently affect the protein products in all the cells ( soma or germline ) tha...	[ "Adenosine-to-inosine ( A-to-I ) editing is hypothesized to facilitate adaptive evolution by expanding proteomic diversity through an epigenetic approach .", "However , it is challenging to provide evidences to support this hypothesis at the whole editome level .", "In this study , we systematically characteriz...	[ "Adenosine-to-inosine ( A-to-I ) RNA editing is an evolutionarily conserved mechanism that alters RNA sequences at the co-transcriptional or post-transcriptional level .", "RNA editing is hypothesized to facilitate adaptation in that it expands the transcriptomic and proteomic diversity .", "However , evidence ...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "rift valley fever virus", "pathology and laboratory medicine", "pathogens", "tropical diseases", "microbiology", "geographical locations", "viruses", "rift valley fever", "south africa", "rna viruses", "neglected tropical diseases", "bunyaviruses", "veterin...	A comparative genome analysis of Rift Valley Fever virus isolates from foci of the disease outbreak in South Africa in 2008-2010	journal.pntd.0006576	null	[ [ "Rift Valley fever ( RVF ) , a mosquito-borne viral disease , affects humans and some species of ruminants including sheep , cattle , goats and buffalos .", "The causative agent , Rift Valley Fever virus ( RVFV ) , belongs to the genus Phlebovirus in the family Phenuiviridae [1] .", "The disease in li...	[ "Rift Valley fever ( RVF ) is a re-emerging zoonotic disease responsible for major losses in livestock production , with negative impact on the livelihoods of both commercial and resource-poor farmers in sub-Sahara African countries .", "The disease remains a threat in countries where its mosquito vector thrives ...	[ "A single RVF virus serotype exists , yet differences in virulence and pathogenicity of the virus have been observed .", "This necessitates the need for detailed genetic characterization of various isolates of the virus .", "Some of the RVF virus isolates that caused the 2008–2010 disease outbreaks in South Afr...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "invertebrates", "symbiosis", "animals", "wolbachia", "animal models", "drosophila melanogaster", "model organisms", "stem cells", "bacteria", "drosophila", "research and analysis methods", "animal cells", "stem cell niche", "insects", "arthropoda", "cell biology", "biology and life ...	Extreme Divergence of Wolbachia Tropism for the Stem-Cell-Niche in the Drosophila Testis	journal.ppat.1004577	null	[ [ "The evolutionary interests of males and females are frequently divergent .", "Sexual conflict arises when phenotypes that enhance the reproductive success of one sex reduces the fitness of the other sex [1] .", "A well-characterized example in Drosophila is sperm competition between males .", "Sp...	[ "Microbial tropism , the infection of specific cells and tissues by a microorganism , is a fundamental aspect of host-microbe interactions .", "The intracellular bacteria Wolbachia have a peculiar tropism for the stem cell niches in the Drosophila ovary , the microenvironments that support the cells producing the...	[ "Microbes evolve to infect structures favoring their transmission in host populations .", "A large fraction of insects are infected with Wolbachia bacteria .", "Usually Wolbachia are transmitted the same way we inherit our mitochondria , via the eggs from the mother .", "In fruit flies , to favor maternal tra...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genome-wide association studies", "organismal evolution", "evolutionary ecology", "population genetics", "microbiology", "escherichia coli", "mutation", "prokaryotic models", "model organisms", "coevolution", "microbial evolution", "forms of evolution", "biology", "evolutionary genetics",...	Ongoing Phenotypic and Genomic Changes in Experimental Coevolution of RNA Bacteriophage Qβ and Escherichia coli	journal.pgen.1002188	null	[ [ "Host–parasite coevolution has been a topic of intense research interest in various fields from basic science of molecular evolution to agricultural and medical applications [1]–[5] .", "According to the Red Queen hypothesis or arms race dynamics , coevolution leads to complex but continuous change , adap...	[ "According to the Red Queen hypothesis or arms race dynamics , coevolution drives continuous adaptation and counter-adaptation .", "Experimental models under simplified environments consisting of bacteria and bacteriophages have been used to analyze the ongoing process of coevolution , but the analysis of both pa...	[ "To examine the ongoing changes driven by host–parasite interactions , we have constructed a coevolution model consisting of Escherichia coli and the lytic RNA bacteriophage Qβ ( Qβ ) in a spatially unstructured environment .", "In coevolution through 54 daily copropagations of the parasite and its host , E . col...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "systems biology", "biology", "genetics and genomics" ]	Integration of the Transcriptome and Glycome for Identification of Glycan Cell Signatures	journal.pcbi.1002813	null	[ [ "Glycosylation , a broad term covering the addition of oligosaccharides ( glycans ) to proteins and lipids followed by their subsequent modification during transit through the secretory apparatus , is an intricate intracellular process whose complexity hinders ready interpretation from mass spectral and other...	[ "Abnormalities in glycan biosynthesis have been conclusively linked to many diseases but the complexity of glycosylation has hindered the analysis of glycan data in order to identify glycoforms contributing to disease .", "To overcome this limitation , we developed a quantitative N-glycosylation model that interp...	[ "Glycans are the sugar attachments that are found on proteins and lipids .", "These highly variable and structurally diverse sugar chains confer distinctive characteristics to the cell surface .", "Recent research has revealed that these glycan profiles can represent important signatures of disease states and t...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Use of Pentamidine As Secondary Prophylaxis to Prevent Visceral Leishmaniasis Relapse in HIV Infected Patients, the First Twelve Months of a Prospective Cohort Study	journal.pntd.0004087	null	[ [ "Visceral leishmaniasis ( VL ) is a fatal-but treatable- disease caused by a protozoan belonging to the Leishmania donovani complex .", "While the Indian-subcontinent , East-Africa and Brazil share the major disease burden , it was long known as a rare pediatric disease in the Mediterranean basin .", ...	[ "Visceral leishmaniasis ( VL ) has become an important opportunistic infection in persons with HIV-infection in VL-endemic areas .", "The co-infection leads to profound immunosuppression and high rate of annual VL recurrence .", "This study assessed the effectiveness , safety and feasibility of monthly pentamid...	[ "Relapse of visceral leishmaniasis ( VL ) among HIV co-infected patients occurs universally .", "Evidence on the use of secondary prophylaxis especially in anthroponotic transmission regions was lacking .", "It was found out now that secondary prophylaxis in addition to antiretroviral therapy for VL in people w...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases/neglected tropical diseases", "infectious diseases/epidemiology and control of infectious diseases" ]	The Development of an Age-Structured Model for Trachoma Transmission Dynamics, Pathogenesis and Control	journal.pntd.0000462	null	[ [ "Trachoma is the leading infectious cause of blindness in the world; 8 million people are blind or severely visually impaired due to trachoma and 63 million have active disease [1] .", "It is due to repeated conjunctival infection with the bacterium Chlamydia trachomatis , and the “SAFE” control strategy ...	[ "Trachoma , the worldwide leading infectious cause of blindness , is due to repeated conjunctival infection with Chlamydia trachomatis .", "The effects of control interventions on population levels of infection and active disease can be promptly measured , but the effects on severe ocular sequelae require long-te...	[ "Trachoma is the worldwide leading infectious cause of blindness and is due to repeated conjunctival infection with Chlamydia trachomatis bacteria .", "The effects of control interventions on population levels of infection and active disease can be promptly measured , but the effects on severe ocular disease outc...	2009
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "computational biology/population genetics", "evolutionary biology/evolutionary and comparative genetics", "microbiology/microbial evolution and genomics", "genetics and genomics/chromosome biology", "computational biology/evolutionary modeling", "genetics and genomics/population genetics" ]	Evolution of Mutational Robustness in the Yeast Genome: A Link to Essential Genes and Meiotic Recombination Hotspots	journal.pgen.1000533	null	[ [ "Mating and meiosis are the masterpieces of an evolutionary invention thought to meet the challenges of changing environmental conditions that need to be solved by mutational inventions .", "Among the many hypotheses that govern the various benefits of mating and meiosis [1] , two main hypotheses stand ou...	[ "Deleterious mutations inevitably emerge in any evolutionary process and are speculated to decisively influence the structure of the genome .", "Meiosis , which is thought to play a major role in handling mutations on the population level , recombines chromosomes via non-randomly distributed hot spots for meiotic...	[ "Sexual life cycles constitute a costly alternative to vegetative modes of reproduction .", "Two categories of hypotheses seek to explain why sexual life cycles exist: those investigating the selective advantages that have driven the evolution of individual parts of this life cycle and those rationalizing the adv...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "dengue virus", "invertebrates", "medicine and health sciences", "pathology and laboratory medicine", "japan", "pathogens", "geographical locations", "microbiology", "mathematical models", "animals", "viruses", "probability distribution", "mathematics", "rna viruses", "convolution", "i...	Assessing dengue control in Tokyo, 2014	journal.pntd.0007468	null	[ [ "Dengue fever is a vector-borne viral disease , caused by dengue virus ( DENV ) and transmitted by Aedes aegypti and Aedes albopictus [1–4] .", "There are four antigenically related serotypes ( DENV1 to 4 ) , and first infection with one serotype is often self-limiting [5] , eliciting specific acquired im...	[ "In summer 2014 , an autochthonous outbreak of dengue occurred in Tokyo , Japan , in which Yoyogi Park acted as the focal area of transmission .", "Recognizing the outbreak , concerted efforts were made to control viral spread , which included mosquito control , public announcement of the outbreak , and a total b...	[ "Evaluating the interventions implemented during an outbreak of mosquito-borne disease is of utmost importance , offering lessons for future control strategies .", "By retrospectively analyzing data of the first autochthonous dengue epidemic of the 21st century in Tokyo , Japan , we assessed the effectiveness of ...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "chemistry", "biology" ]	Structural and Functional Insights into the HIV-1 Maturation Inhibitor Binding Pocket	journal.ppat.1002997	null	[ [ "Over 20 antiretroviral inhibitors have been approved for clinical use in HIV-1-infected patients .", "These drugs fall into several classes , mostly targeting the viral enzymes reverse transcriptase ( RT ) , protease ( PR ) , and integrase ( IN ) .", "A fusion inhibitor specific for the viral transme...	[ "Processing of the Gag precursor protein by the viral protease during particle release triggers virion maturation , an essential step in the virus replication cycle .", "The first-in-class HIV-1 maturation inhibitor dimethylsuccinyl betulinic acid [PA-457 or bevirimat ( BVM ) ] blocks HIV-1 maturation by inhibiti...	[ "Maturation of HIV-1 particles , which occurs as they bud off from the infected cell , is triggered by the step-wise cleavage of the major viral structural polyprotein , Pr55Gag , to individual , mature Gag proteins .", "The viral protease is the enzyme responsible for Gag polyprotein cleavage .", "Maturation i...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases/neglected tropical diseases", "genetics and genomics/gene function", "cell biology/cell signaling" ]	Gene Conversion Transfers the GAF-A Domain of Phosphodiesterase TbrPDEB1 to One Allele of TbrPDEB2 of Trypanosoma brucei	journal.pntd.0000455	null	[ [ "Cyclic nucleotide-specific phosphodiesterases ( PDEs ) are crucial players in cyclic nucleotide signalling of eukaryotic cells .", "Several of the human PDEs have become important drug targets , and all eleven human PDE families are under intense study for the development of new therapeutic PDE-inhibitor...	[ "Chromosome 9 of Trypanosoma brucei contains two closely spaced , very similar open reading frames for cyclic nucleotide specific phosphodiesterases TbrPDEB1 and TbrPDEB2 .", "They are separated by 2379 bp , and both code for phosphodiesterases with two GAF domains in their N-terminal moieties and a catalytic dom...	[ "Cyclic nucleotide specific phosphodiesterases are important regulators of cyclic nucleotide signalling in eukaryotes .", "In many organisms , including humans and trypanosomes , some of these enzymes contain specific domains ( GAF domains ) that bind cyclic nucleotides , and that are involved in the regulation o...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biophysics", "homo (human)" ]	Image-Based Modeling Reveals Dynamic Redistribution of DNA Damage into Nuclear Sub-Domains	journal.pcbi.0030155	null	[ [ "DNA damage induced by ionizing radiation ( IR ) elicits microscopically visible nuclear domains ( i . e . , foci ) marked by recruitment of certain proteins ( e . g . , 53BP1 ) or by particular modifications such as histone phosphorylation ( e . g . , γH2AX ) or as a result of both ( e . g . , phosphorylated...	[ "Several proteins involved in the response to DNA double strand breaks ( DSB ) form microscopically visible nuclear domains , or foci , after exposure to ionizing radiation .", "Radiation-induced foci ( RIF ) are believed to be located where DNA damage occurs .", "To test this assumption , we analyzed the spati...	[ "DNA damages are daily cellular events .", "If such events are left unchecked in an organism , they can lead to DNA mutations and possibly cancer over a long period of time .", "Consequently , cells have very efficient DNA repair machinery .", "Many studies have focused on the different molecular factors invo...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "behavioral neuroscience", "animal genetics", "physiology", "genetics", "integrative physiology", "biology", "anatomy and physiology", "neuroscience", "learning and memory", "genetics and genomics" ]	Three Dopamine Pathways Induce Aversive Odor Memories with Different Stability	journal.pgen.1002768	null	[ [ "Mechanisms underlying memory can be as simple as a modulation of monosynaptic connection in the gill withdraw reflex of Aplysia [1] .", "Alternatively memory formation and storage may require dynamic interaction of distinct neuropiles in a brain [2] .", "In Drosophila melanogaster , a neuronal circui...	[ "Animals acquire predictive values of sensory stimuli through reinforcement .", "In the brain of Drosophila melanogaster , activation of two types of dopamine neurons in the PAM and PPL1 clusters has been shown to induce aversive odor memory .", "Here , we identified the third cell type and characterized aversi...	[ "Punishment not only repels animals but also drives the formation of aversive memory of contiguous stimuli .", "Guided by the memory , animals can later avoid the cues that predict negative outcome .", "How is a punishing event represented in the brain ?", "We have found that at least three types of dopamine ...	2012
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma mansoni", "medicine and health sciences", "body fluids", "enzyme-linked immunoassays", "pathology and laboratory medicine", "helminths", "tropical diseases", "parasitic diseases", "animals", "urine", "neglected tropical diseases", "immunologic t...	Accuracy of parasitological and immunological tests for the screening of human schistosomiasis in immigrants and refugees from African countries: An approach with Latent Class Analysis	journal.pntd.0005593	null	[ [ "Schistosomiasis is a fluke worm infection affecting at least 78 countries and more than 200 million people worldwide , and causing an estimated burden of 3 . 3 million disability-adjusted life-years ( DALYs ) [1 , 2] .", "Ninety-three percent of the global cases occur in sub-Saharan Africa , mostly cause...	[ "Schistosomiasis is a neglected infection affecting millions of people , mostly living in sub-Saharan Africa .", "Morbidity and mortality due to chronic infection are relevant , although schistosomiasis is often clinically silent .", "Different diagnostic tests have been implemented in order to improve screenin...	[ "Schistosomiasis is probably the most important of the neglected tropical diseases ( NTD ) caused by helminthes ( worms ) .", "It is acquired bathing in freshwater in endemic areas .", "The life cycle is complex and involves freshwater snails .", "Schistosomiasis , caused by Schistosoma mansoni , S . haematob...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public health and epidemiology", "social and behavioral sciences", "cost-effectiveness analysis", "non-clinical medicine", "neglected tropical diseases", "cost effectiveness", "immunizations", "infectious diseases", "cholera", "health economics", "public health", "economics", ...	Costs of Illness Due to Cholera, Costs of Immunization and Cost-Effectiveness of an Oral Cholera Mass Vaccination Campaign in Zanzibar	journal.pntd.0001844	null	[ [ "Despite efforts to improve water supply and sanitation , cholera still represents a serious public health burden in low- and middle-income countries .", "In 2009 , more than 220 , 000 cases and almost 5 , 000 deaths were reported to the World Health Organization ( WHO ) [1] .", "Due to underreporting...	[ "The World Health Organization ( WHO ) recommends oral cholera vaccines ( OCVs ) as a supplementary tool to conventional prevention of cholera .", "Dukoral , a killed whole-cell two-dose OCV , was used in a mass vaccination campaign in 2009 in Zanzibar .", "Public and private costs of illness ( COI ) due to end...	[ "Despite efforts to improve water supply and sanitation , cholera still represents a serious burden in developing countries .", "Use of oral cholera vaccines ( OCVs ) in endemic and epidemic situations has recently shown a promising potential to mitigate this burden .", "To provide local decision-makers with sp...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "sequencing techniques", "messenger rna", "parasitic protozoans", "parasitology", "developmental biology", "trypanosoma brucei gambiense", "protozoans", "genome analysis", "energy-producing organelles", "mitochondria", "bioenergetics", "molecular biology techniques", "rna sequencing", "cel...	Analysis of the Trypanosoma brucei EATRO 164 Bloodstream Guide RNA Transcriptome	journal.pntd.0004793	null	[ [ "The life cycle of Trypanosoma brucei involves two distinct environments , the animal host and the insect vector .", "These environments are distinct in temperature and nutrient composition , providing a unique challenge to T . brucei as it cycles between hosts .", "In the bloodstream , trypanosomes e...	[ "The mitochondrial genome of Trypanosoma brucei contains many cryptogenes that must be extensively edited following transcription .", "The RNA editing process is directed by guide RNAs ( gRNAs ) that encode the information for the specific insertion and deletion of uridylates required to generate translatable mRN...	[ "Trypanosoma brucei is the causative agent of African sleeping sickness , a disease that threatens millions of people in sub-Saharan Africa .", "During its life cycle , Trypanosoma brucei lives in either its mammalian host or its insect vector .", "These environments are very different , and the transition betw...	2016
[ "Introduction", "Material and Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "ecology and environmental sciences", "viral transmission and infection", "population genetics", "conservation genetics", "microbiology", "animals", "viral vectors", "population biology", "insect vectors", "microbial genetics", "conservation b...	Genetic Drift, Purifying Selection and Vector Genotype Shape Dengue Virus Intra-host Genetic Diversity in Mosquitoes	journal.pgen.1006111	null	[ [ "Due to the low fidelity of their RNA-dependent RNA polymerase , rapid replication kinetics and large population size , RNA viruses consist of a heterogeneous intra-host population of related mutants , sometimes referred to as a quasispecies [1] .", "This mutant swarm as a whole defines the properties of ...	[ "Due to their error-prone replication , RNA viruses typically exist as a diverse population of closely related genomes , which is considered critical for their fitness and adaptive potential .", "Intra-host demographic fluctuations that stochastically reduce the effective size of viral populations are a challenge...	[ "During infection of their arthropod vectors , arthropod-borne viruses ( arboviruses ) such as dengue viruses traverse several anatomical barriers that are believed to cause dramatic reductions in population size .", "Such population bottlenecks challenge the maintenance of viral genetic diversity , which is cons...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology and life sciences" ]	daf-31 Encodes the Catalytic Subunit of N Alpha-Acetyltransferase that Regulates Caenorhabditis elegans Development, Metabolism and Adult Lifespan	journal.pgen.1004699	null	[ [ "Animal development is a complex process that involves hierarchical gene regulatory networks and is influenced by environmental conditions .", "When food is abundant , the post-embryonic development of C . elegans consists of four larval stages ( L1–L4 ) and the adult .", "During the L1 stage , enviro...	[ "The Caenorhabditis elegans dauer larva is a facultative state of diapause .", "Mutations affecting dauer signal transduction and morphogenesis have been reported .", "Of these , most that result in constitutive formation of dauer larvae are temperature-sensitive ( ts ) .", "The daf-31 mutant was isolated in ...	[ "The development of a living organism is influenced by the environmental conditions such as nutrient availability .", "Under starvation conditions , the C . elegans larvae will enter a special developmental stage called dauer larva .", "An insulin-like signaling pathway controls dauer formation as well as adult...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Serology for Trachoma Surveillance after Cessation of Mass Drug Administration	journal.pntd.0003555	null	[ [ "Trachoma , caused by the bacterium Chlamydia trachomatis ( Ct ) , is the leading infectious cause of blindness worldwide [1] .", "Infection can manifest clinically in a number of ways , including follicular conjunctivitis , classified as “trachomatous inflammation-follicular” ( TF ) in the WHO simplified...	[ "Trachoma , caused by Chlamydia trachomatis ( Ct ) , is the leading infectious cause of blindness worldwide .", "Yearly azithromycin mass drug administration ( MDA ) plays a central role in efforts to eliminate blinding trachoma as a public health problem .", "Programmatic decision-making is currently based on ...	[ "Trachoma is the leading infectious cause of blindness .", "The infectious agent , Chlamydia trachomatis , can be treated with a single oral dose of azithromycin .", "Donated drug is a cornerstone of programs dedicated to the elimination of trachoma as a public health problem .", "Azithromycin is given to the...	2015
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "genetics and genomics/gene discovery", "microbiology/immunity to infections", "genetics and genomics/complex traits", "genetics and genomics/genetics of disease", "microbiology/parasitology", "infectious diseases/protozoal infections", "immunology/immunity to infections" ]	Genetic Mapping Identifies Novel Highly Protective Antigens for an Apicomplexan Parasite	journal.ppat.1001279	null	[ [ "The protozoan phylum Apicomplexa contains pathogens of substantial medical and veterinary importance including Plasmodium , Toxoplasma , Cryptosporidium , Eimeria , Neospora and Theileria species .", "Despite several decades of effort vaccines protective against these and other related parasites are scar...	[ "Apicomplexan parasites are responsible for a myriad of diseases in humans and livestock; yet despite intensive effort , development of effective sub-unit vaccines remains a long-term goal .", "Antigenic complexity and our inability to identify protective antigens from the pool that induce response are serious ch...	[ "Protozoan parasites are responsible for serious diseases in humans and livestock species .", "Vaccination is a declared intervention of choice with these infections , but even after many years of effort few effective vaccines are available .", "Identification of the right antigens for inclusion in sub-unit vac...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry", "cell biology", "proteins", "prions", "fungal genetics", "chaperone proteins", "genetics", "genetic elements", "biology and life sciences", "epigenetics", "molecular genetics" ]	Functional Diversification of Hsp40: Distinct J-Protein Functional Requirements for Two Prions Allow for Chaperone-Dependent Prion Selection	journal.pgen.1004510	null	[ [ "Yeast prions are amyloid aggregates of functional yeast proteins that are both self-templating and heritable to daughter cells [1] , [2] , [3] , [4] .", "The best studied yeast prion , called [PSI+] , is the aggregated form of the yeast translation termination factor Sup35 [5] , [6] .", "[PSI+] cells...	[ "Yeast prions are heritable amyloid aggregates of functional yeast proteins; their propagation to subsequent cell generations is dependent upon fragmentation of prion protein aggregates by molecular chaperone proteins .", "Mounting evidence indicates the J-protein Sis1 may act as an amyloid specificity factor , r...	[ "Multiple neurodegenerative disorders such as Alzheimer's , Parkinson's and Creutzfeldt-Jakob disease are associated with the accumulation of fibrous protein aggregates collectively termed ‘amyloid . ’ In the baker's yeast Saccharomyces cerevisiae , multiple proteins form intracellular amyloid aggregates known as y...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "veterinary microbiology", "biochemistry", "biology and life sciences", "veterinary science" ]	Both α2,3- and α2,6-Linked Sialic Acids on O-Linked Glycoproteins Act as Functional Receptors for Porcine Sapovirus	journal.ppat.1004172	null	[ [ "Caliciviruses ( family Caliciviridae ) are small ( 27–40 nm ) , non-enveloped , icosahedral viruses that possess a single-strand , plus-sense genomic RNA of 7–8 kb [1] .", "Caliciviruses are important veterinary and human pathogens which are associated with a broad spectrum of diseases in their respectiv...	[ "Sapovirus , a member of the Caliciviridae family , is an important cause of acute gastroenteritis in humans and pigs .", "Currently , the porcine sapovirus ( PSaV ) Cowden strain remains the only cultivable member of the Sapovirus genus .", "While some caliciviruses are known to utilize carbohydrate receptors ...	[ "Although enteropathogenic sapoviruses and noroviruses are leading causes of acute gastroenteritis in both humans and animals , the study of viral pathogenesis and immunity of these ubiquitous pathogens has been hampered due to the lack of a fully permissive cell culture system .", "Porcine sapovirus Cowden strai...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "sequencing techniques", "united states", "medicine and health sciences", "immune physiology", "pathology and laboratory medicine", "evolutionary biology", "pathogens", "split-decomposition method", "immunology", "geographical locations", "microbiology", "retroviruses", "viruses", "immunod...	Accurate predictions of population-level changes in sequence and structural properties of HIV-1 Env using a volatility-controlled diffusion model	journal.pbio.2001549	null	[ [ "HIV-1 is the primary etiologic agent of the global AIDS pandemic .", "Soon after identification of HIV-1 in the early 1980s , the tremendous sequence diversity of circulating strains was appreciated [1 , 2] .", "The genetic diversity of HIV-1 has posed a major obstacle to development of an efficaciou...	[ "The envelope glycoproteins ( Envs ) of HIV-1 continuously evolve in the host by random mutations and recombination events .", "The resulting diversity of Env variants circulating in the population and their continuing diversification process limit the efficacy of AIDS vaccines .", "We examined the historic cha...	[ "HIV-1 is the causative agent of the global AIDS pandemic .", "The envelope glycoproteins ( Envs ) of HIV-1 constitute a primary target for antibody-based vaccines .", "However , the diversity of Envs in the population limits the potential efficacy of this approach .", "Accurate estimates of the range of vari...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "biochemistry", "medicine and health sciences", "peptides", "proteins", "biology and life sciences", "pharmacology", "proteomics", "tropical diseases", "parasitic diseases" ]	Crovirin, a Snake Venom Cysteine-Rich Secretory Protein (CRISP) with Promising Activity against Trypanosomes and Leishmania	journal.pntd.0003252	null	[ [ "The pathogenic trypanosomatids from the genera Leishmania and Trypanosoma infect over 20 million people worldwide , with an annual incidence of ∼3 million new infections in at least 88 countries .", "An additional 400 million people are at risk of infection by exposure to insect vectors harboring parasit...	[ "The neglected human diseases caused by trypanosomatids are currently treated with toxic therapy with limited efficacy .", "In search for novel anti-trypanosomatid agents , we showed previously that the Crotalus viridis viridis ( Cvv ) snake venom was active against infective forms of Trypanosoma cruzi .", "Her...	[ "The pathogenic trypanosomatid parasites of the genera Leishmania and Trypanosoma infect over 20 million people worldwide , with an annual incidence of ∼3 million new infections .", "An additional 400 million people are at risk of infection by exposure to parasite-infected insects which act as disease vectors .",...	2014
[ "Introduction", "Results", "Discussion" ]	[ "medicine and health sciences", "post-exposure prophylaxis", "immunology", "tropical diseases", "geographical locations", "vertebrates", "dogs", "animals", "mammals", "vaccines", "preventive medicine", "rabies", "neglected tropical diseases", "infectious disease control", "vaccination an...	An evaluation of Brazil’s surveillance and prophylaxis of canine rabies between 2008 and 2017	journal.pntd.0007564	null	[ [ "Dog-mediated rabies in humans has been reduced by over 99% in Latin America , but 106 cases in dogs were still reported in 2014 [1] .", "Dog vaccination and prompt administration of post-exposure prophylaxis ( PEP ) for bite victims are essential to the successful reduction of human cases of rabies acros...	[ "An effective surveillance system is critical for the elimination of canine rabies in Latin America .", "Brazil has made substantial progress towards canine rabies elimination , but outbreaks still occurred in the last decade in two states .", "Brazil uses a health information system ( SINAN ) to record patient...	[ "Dog-mediated rabies has declined to only a few cases in Latin America over the last decade .", "Brazil has the largest human and dog population of Latin America .", "Despite the decline of canine rabies , the country’s public health system still spends millions of dollars annually on half a million patients se...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The Convallis Rule for Unsupervised Learning in Cortical Networks	journal.pcbi.1003272	null	[ [ "Animal learning is believed to occur primarily through changes in synaptic strengths .", "Experimental work has revealed an increasingly detailed picture of synaptic plasticity [1] , [2] , at the level of both phenomenology and cellular mechanisms .", "However an understanding of synaptic plasticity'...	[ "The phenomenology and cellular mechanisms of cortical synaptic plasticity are becoming known in increasing detail , but the computational principles by which cortical plasticity enables the development of sensory representations are unclear .", "Here we describe a framework for cortical synaptic plasticity terme...	[ "The circuits of the sensory cortex are able to extract useful information from sensory inputs because of their exquisitely organized synaptic connections .", "These connections are wired largely through experience-dependent synaptic plasticity .", "Although many details of both the phenomena and cellular mecha...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "diabetes and endocrinology", "neuroscience" ]	Postmitotic Specification of Drosophila Insulinergic Neurons from Pioneer Neurons	journal.pbio.0060058	A genetic analysis in the fruit fly reveals similarities between the transcriptional programmes regulating insulin production in mammalian pancreatic β-cells and insect neurons.	[ [ "Insulin , a key regulator of carbohydrate and lipid metabolism , is secreted by the ß-cells of the pancreas [1] .", "Deficiencies in insulin signalling underlie type I diabetes and also the more widespread type II diabetes often associated with obesity [2 , 3] .", "Considerable effort , therefore , h...	[ "Insulin and related peptides play important and conserved functions in growth and metabolism .", "Although Drosophila has proved useful for the genetic analysis of insulin functions , little is known about the transcription factors and cell lineages involved in insulin production .", "Within the embryonic cent...	[ "Genetic studies using invertebrate model organisms such as Drosophila have provided many new insights into the functions of insulin and related peptides .", "It has , however , been more difficult to use Drosophila to study the regulation of insulin , at least in part because the relevant insulinergic cell linea...	2008
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	The Risk of Dengue Virus Transmission in Dar es Salaam, Tanzania during an Epidemic Period of 2014	journal.pntd.0004313	null	[ [ "Dengue is one of the most important mosquito-borne viral diseases in the tropics and subtropics .", "Although the exact global burden of dengue cases is unknown , recent estimates indicate that 390 million dengue infections occur annually .", "Of these , 96 million cases manifests clinically [1] with...	[ "In 2010 , 2012 , 2013 and 2014 dengue outbreaks have been reported in Dar es Salaam , Tanzania .", "However , there is no comprehensive data on the risk of transmission of dengue in the country .", "The objective of this study was to assess the risk of transmission of dengue in Dar es Salaam during the 2014 ep...	[ "Until 2010 , little was known about Dengue in Tanzania .", "Since then , four outbreaks have been reported in Dar es Salaam City .", "This study was therefore carried out to assess the risk of transmission of dengue in Dar es Salaam during an outbreak in 2014 .", "In this study adult mosquitoes were collecte...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The Arabidopsis SWI2/SNF2 Chromatin Remodeler BRAHMA Regulates Polycomb Function during Vegetative Development and Directly Activates the Flowering Repressor Gene SVP	journal.pgen.1004944	null	[ [ "Plant development takes place in distinct phases , each of which is characterized by the activation of a particular set of genes and the repression of others .", "Precise control of gene expression in each phase is crucial for proper growth and development .", "The transition from the vegetative to t...	[ "The chromatin remodeler BRAHMA ( BRM ) is a Trithorax Group ( TrxG ) protein that antagonizes the functions of Polycomb Group ( PcG ) proteins in fly and mammals .", "Recent studies also implicate such a role for Arabidopsis ( Arabidopsis thaliana ) BRM but the molecular mechanisms underlying the antagonism are ...	[ "In flowering plants , the proper transition from vegetative growth to flowering is critical for their reproductive success and must be controlled precisely .", "Multiple genes have been shown to regulate the floral transition in response to environmental and endogenous cues .", "Among them is SHORT VEGETATIVE ...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "immunopathology", "immunology", "biology", "microbiology", "immune response", "pathogenesis" ]	Foxp3 and IL-10 Expression Correlates with Parasite Burden in Lesional Tissues of Post Kala Azar Dermal Leishmaniasis (PKDL) Patients	journal.pntd.0001171	null	[ [ "Leishmaniasis constitutes various forms of globally widespread group of neglected diseases caused by an obligatory intracellular protozoan parasite of genus Leishmania .", "It is currently endemic in 88 countries and overall prevalence is estimated as 12 million with 350 million at risk .", "Visceral...	[ "Post kala-azar dermal leishmaniasis ( PKDL ) , a sequel to visceral leishamaniasis ( VL ) in 5–15% cases , constitutes a parasite reservoir important in disease transmission .", "The precise immunological cause of PKDL outcome remains obscure .", "However , overlapping counter regulatory responses with elevate...	[ "Post kala azar dermal leishamniasis ( PKDL ) , an unusual dermatosis develops in 5–15% of apparently cured visceral leishmaniasis cases in India and in about 60% of cases in Sudan .", "PKDL cases assume importance since they constitute a major human reservoir for the parasite .", "Inadequate treatment of VL , ...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "systems biology", "developmental biology", "model organisms", "genetics", "synthetic biology", "biology" ]	Subtle Changes in Motif Positioning Cause Tissue-Specific Effects on Robustness of an Enhancer's Activity	journal.pgen.1004060	null	[ [ "Gene expression is initiated by the binding of transcription factors ( TFs ) to cis-regulatory modules ( CRMs ) such as enhancer elements , which give rise to specific patterns of temporal and spatial activity [1] .", "Recent years have seen a dramatic increase in the ability to identify the location of ...	[ "Deciphering the specific contribution of individual motifs within cis-regulatory modules ( CRMs ) is crucial to understanding how gene expression is regulated and how this process is affected by sequence variation .", "But despite vast improvements in the ability to identify where transcription factors ( TFs ) b...	[ "Transcription is initiated through the binding of transcription factors ( TFs ) to specific motifs that are dispersed throughout the genome .", "Genomics methods have helped to discern which motifs for a TF are occupied and which are not , yet it is poorly understood why certain combinations of bound motifs , an...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "diabetic endocrinology", "cancer risk factors", "signaling networks", "computerized simulations", "oncology", "mathematical computing", "mathematics", "hormonal causes of cancer", "insulin", "theoretical biology", "endocrinology", "regulatory networks", "computing methods", ...	Computational Modeling and Analysis of Insulin Induced Eukaryotic Translation Initiation	journal.pcbi.1002263	null	[ [ "Insulin , the primary hormone regulating the level of glucose in the bloodstream , modulates a variety of cellular and enzymatic processes in normal and diseased cells [1]–[7] .", "The regulation of cellular function by insulin and insulin-like growth factors I/II ( IGF-I/II ) is a highly complex process...	[ "Insulin , the primary hormone regulating the level of glucose in the bloodstream , modulates a variety of cellular and enzymatic processes in normal and diseased cells .", "Insulin signals are processed by a complex network of biochemical interactions which ultimately induce gene expression programs or other pro...	[ "Insulin is a hormone produced by the body that regulates uptake of glucose from the bloodstream .", "The cellular response to insulin is governed by a complex network of intracellular interactions that ultimately influence cell growth and metabolism .", "Because of its central role in physiology , insulin sign...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "rheumatology", "gene expression", "genetics", "gene regulation", "molecular genetics", "biology", "human genetics", "genetics of disease", "dna transcription", "gene function" ]	The Identification of Trans-acting Factors That Regulate the Expression of GDF5 via the Osteoarthritis Susceptibility SNP rs143383	journal.pgen.1003557	null	[ [ "Osteoarthritis ( OA ) is a common disease of the synovial joints , affecting millions of people worldwide .", "It is a chronic , highly disabling disease , characterised by the progressive loss of articular cartilage , changes in the subchondral bone , and variable levels of synovial inflammation [1] .",...	[ "rs143383 is a C to T transition SNP located in the 5′untranslated region ( 5′UTR ) of the growth differentiation factor 5 gene GDF5 .", "The T allele of the SNP is associated with increased risk of osteoarthritis ( OA ) in Europeans and in Asians .", "This susceptibility is mediated by the T allele producing l...	[ "GDF5 is an important growth factor that plays a vital role in the development and repair of articulating joints .", "rs143383 is a polymorphism within the regulatory region of the GDF5 gene and has two allelic forms , C and T . Genetic studies have demonstrated that the T allele is associated with an increased r...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "public health and epidemiology", "public health and epidemiology/epidemiology", "public health and epidemiology/preventive medicine", "public health and epidemiology/infectious diseases" ]	Spatiotemporal Trends and Climatic Factors of Hemorrhagic Fever with Renal Syndrome Epidemic in Shandong Province, China	journal.pntd.0000789	null	[ [ "Hemorrhagic fever with renal syndrome ( HFRS ) , a rodent-borne disease caused by Hantaviruses ( HV ) , is characterized by fever , acute renal dysfunction , and hemorrhagic manifestations .", "HFRS , initially described clinically at the turn of the 20th century , is primarily distributed in the Asian a...	[ "Hemorrhagic fever with renal syndrome ( HFRS ) is a rodent-borne disease caused by Hantaviruses .", "It is endemic in all 31 provinces , autonomous regions , and metropolitan areas in mainland China where human cases account for 90% of the total global cases .", "Shandong Province is among the most serious end...	[ "Hemorrhagic fever with renal syndrome ( HFRS ) , a rodent-borne disease caused by Hantaviruses , is characterized by fever , acute renal dysfunction and hemorrhagic manifestations .", "At present , it is endemic in all 31 provinces , autonomous regions , and metropolitan areas in mainland China where human cases...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetic mutation", "microbiology", "nucleotides", "model organisms", "mutation types", "dna replication", "dna", "dna synthesis", "biology", "molecular biology", "mutagenesis", "biochemistry", "nucleic acids", "genetics", "yeast and fungal models", "dna repair", "saccharomyces cerev...	Mismatch Repair Balances Leading and Lagging Strand DNA Replication Fidelity	journal.pgen.1003016	null	[ [ "Three processes operate to ensure faithful replication of the eukaryotic nuclear genome [1] , [2] .", "The first is the ability of DNA polymerases α , δ and ε to selectively insert correct rather than incorrect nucleotides onto correctly aligned rather than misaligned primer-templates .", "The second...	[ "The two DNA strands of the nuclear genome are replicated asymmetrically using three DNA polymerases , α , δ , and ε .", "Current evidence suggests that DNA polymerase ε ( Pol ε ) is the primary leading strand replicase , whereas Pols α and δ primarily perform lagging strand replication .", "The fact that these...	[ "The stability of complex and highly organized nuclear genomes partly depends on the ability of mismatch repair ( MMR ) to correct a variety of different mismatches generated as the leading and lagging strand templates are copied by three polymerases , each with different fidelity .", "Here we provide the first c...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "classical mechanics", "applied mathematics", "social sciences", "neuroscience", "simulation and modeling", "perception", "algorithms", "optimization", "cognitive psychology", "mathematics", "vision", "research and analysis methods", "research assessment", "physics", "psychology", "ine...	Bayesian comparison of explicit and implicit causal inference strategies in multisensory heading perception	journal.pcbi.1006110	null	[ [ "Visuo-vestibular integration in heading perception presents an ideal case to characterize the details of the causal inference strategy in multisensory perception .", "While a wealth of published studies have shown that integration of visual and vestibular self-motion cues increases perceptual precision [...	[ "The precision of multisensory perception improves when cues arising from the same cause are integrated , such as visual and vestibular heading cues for an observer moving through a stationary environment .", "In order to determine how the cues should be processed , the brain must infer the causal relationship un...	[ "As we interact with objects and people in the environment , we are constantly exposed to numerous sensory stimuli .", "For safe navigation and meaningful interaction with entities in the environment , our brain must determine if the sensory inputs arose from a common or different causes in order to determine whe...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "reproductive system", "immune physiology", "microcephaly", "pathology and laboratory medicine", "body fluids", "viral transmission and infection", "spleen", "pathogens", "animal models of disease", "microbiology", "animal models", "viruses", "developmental ...	A Susceptible Mouse Model for Zika Virus Infection	journal.pntd.0004658	null	[ [ "Zika virus ( ZIKV ) is a mosquito-borne flavivirus first isolated from a sentinel rhesus macaque placed in the Zika forest in Uganda in 1947; thereafter , ZIKV was isolated from a pool of Aedes africanus mosquitoes from the same forested area [1] .", "During the 1960s-1980s evidence for ZIKV infection wa...	[ "Zika virus ( ZIKV ) is a mosquito-borne pathogen which has recently spread beyond Africa and into Pacific and South American regions .", "Despite first being detected in 1947 , very little information is known about the virus , and its spread has been associated with increases in Guillain-Barre syndrome and micr...	[ "Since first being recognised in 1947 , Zika virus ( ZIKV ) has mainly been associated with a mild illness with symptoms including a limited fever and rash .", "In 2007 the virus spread from Africa into French Polynesia and then onwards across Pacific regions and into South America .", "In these new regions , Z...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell death", "medicine and health sciences", "gene regulation", "carcinomas", "cell processes", "cancers and neoplasms", "oncology", "micrornas", "mitochondria", "bioenergetics", "cellular structures and organelles", "research and analysis methods", "specimen preparation and treatment", "...	Overexpression of Mitochondria Mediator Gene TRIAP1 by miR-320b Loss Is Associated with Progression in Nasopharyngeal Carcinoma	journal.pgen.1006183	null	[ [ "Nasopharyngeal carcinoma ( NPC ) is the most prevalent head and neck malignancy in Southeast Asia , especially in Southern China [1] .", "A majority of NPC patients are diagnosed at advanced stages , leading to approximately 30% of NPC patients developing treatment failure [2] .", "Although NPC is a ...	[ "The therapeutic strategy for advanced nasopharyngeal carcinoma ( NPC ) is still challenging .", "It is an urgent need to uncover novel treatment targets for NPC .", "Therefore , understanding the mechanisms underlying NPC tumorigenesis and progression is essential for the development of new therapeutic strateg...	[ "The therapeutic strategy for advanced nasopharyngeal carcinoma ( NPC ) is still challenging .", "The most urgent need for NPC is novel treatment targets .", "Therefore , understanding the mechanisms underlying NPC tumorigenesis and progression is essential for the development of new therapeutic strategies .", ...	2016
[ "Introduction", "Materials and Methods", "Results and Discussion" ]	[ "biology and life sciences", "veterinary science", "medicine and health sciences" ]	Identification of Parasitic Communities within European Ticks Using Next-Generation Sequencing	journal.pntd.0002753	null	[ [ "Due to the combination of increased human and animal movement , socio-economic and environmental changes , as well as the complex interactions between reservoirs , pathogens , and human populations , more emerging diseases are being identified and the epidemiology of ancient diseases is changing , particular...	[ "Risk assessment of tick-borne and zoonotic disease emergence necessitates sound knowledge of the particular microorganisms circulating within the communities of these major vectors .", "Assessment of pathogens carried by wild ticks must be performed without a priori , to allow for the detection of new or unexpec...	[ "Diseases transmitted by ticks have diverse etiology ( viral , bacterial , parasitic ) and are responsible for high morbidity and mortality rates around the world , both in humans and animals .", "The emergence or re-emergence of tick-borne diseases is increasingly becoming a problem as the geographical distribut...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "theoretical biology", "biology", "computational biology", "biophysics" ]	Conformational Spread in the Flagellar Motor Switch: A Model Study	journal.pcbi.1002523	null	[ [ "Bacterial chemotaxis enables the cell to move towards favorable environments .", "This sensing ability relies closely on collective coordination of several operation modules in the signal transduction pathway ( reviewed in [1][2] ) .", "The first component of this system is responsible for detecting ...	[ "The reliable response to weak biological signals requires that they be amplified with fidelity .", "In E . coli , the flagellar motors that control swimming can switch direction in response to very small changes in the concentration of the signaling protein CheY-P , but how this works is not well understood .", ...	[ "Bacteria swim to find nutrients or to avoid toxins .", "Their swimming is powered by the rotation of flagella ( hair-like structures ) that act as propellers .", "Each flagellum is driven by a rotary molecular engine ( the bacterial flagellar motor ) that can rotate in either a counterclockwise or clockwise di...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Variability of Gene Expression Identifies Transcriptional Regulators of Early Human Embryonic Development	journal.pgen.1005428	null	[ [ "The regulatory program that ensures that a human embryo can develop successfully starting from a single cell zygote is one of the most fascinating examples of systems-level genetic control .", "During development , individual cells must quickly respond to internal and external signals while the number of...	[ "An analysis of gene expression variability can provide an insightful window into how regulatory control is distributed across the transcriptome .", "In a single cell analysis , the inter-cellular variability of gene expression measures the consistency of transcript copy numbers observed between cells in the same...	[ "In order to function properly , cells express specific sets of genes that are regulated via complex transcriptional programs .", "During early stages of development , when an embryo consists of only a handful of cells , it is vital that these cells work together so that the embryo can develop into a healthy baby...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "public health and epidemiology", "evolutionary ecology", "mathematics", "ecology", "evolutionary biology", "epidemiology", "statistics", "theoretical ecology", "biology", "population biology", "statistical methods" ]	Phylodynamic Inference and Model Assessment with Approximate Bayesian Computation: Influenza as a Case Study	journal.pcbi.1002835	null	[ [ "Many infectious pathogens , most notably RNA viruses , evolve on the same time scale as their ecological dynamics [1] .", "One of the perhaps best documented examples are human influenza A viruses , which cause substantial morbidity and mortality as they escape host immunity predominantly through the evo...	[ "A key priority in infectious disease research is to understand the ecological and evolutionary drivers of viral diseases from data on disease incidence as well as viral genetic and antigenic variation .", "We propose using a simulation-based , Bayesian method known as Approximate Bayesian Computation ( ABC ) to ...	[ "The infectious disease dynamics of many viral pathogens like influenza , norovirus and coronavirus are inextricably tied to their evolution .", "This interaction between evolutionary and ecological processes complicates our ability to understand the infectious disease behavior of rapidly evolving pathogens .", ...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	MAPK Signaling Pathway Alters Expression of Midgut ALP and ABCC Genes and Causes Resistance to Bacillus thuringiensis Cry1Ac Toxin in Diamondback Moth	journal.pgen.1005124	null	[ [ "The Gram-positive entomopathogen Bacillus thuringiensis ( Bt ) is the most widely used biopesticide due to its highly specific activity and environmental safety [1] .", "The insecticidal activity of Bt is largely attributed to diverse δ-endotoxins ( Cry toxins ) produced during sporulation [2] .", "T...	[ "Insecticidal crystal toxins derived from the soil bacterium Bacillus thuringiensis ( Bt ) are widely used as biopesticide sprays or expressed in transgenic crops to control insect pests .", "However , large-scale use of Bt has led to field-evolved resistance in several lepidopteran pests .", "Resistance to Bt ...	[ "Biopesticide and transgenic crops based on Bacillus thuringiensis ( Bt ) Cry toxins are widely used worldwide , yet the development of field resistance seriously threatens their sustainability .", "Unraveling these resistance mechanisms are of great importance for delaying insect field resistance evolution .", ...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "helminth infections", "infectious diseases", "medicine and health sciences", "neglected tropical diseases", "tropical diseases", "soil-transmitted helminthiases", "parasitic diseases" ]	Helminth Colonization Is Associated with Increased Diversity of the Gut Microbiota	journal.pntd.0002880	null	[ [ "Today , approximately a quarter of the world's population carries soil-transmitted helminths [1] .", "In an endemic tropical environment , more than 70% of the population may be infected with helminths [2] , which is indicative of our helminth exposure during the course of human evolution .", "Just a...	[ "Soil-transmitted helminths colonize more than 1 . 5 billion people worldwide , yet little is known about how they interact with bacterial communities in the gut microbiota .", "Differences in the gut microbiota between individuals living in developed and developing countries may be partly due to the presence of ...	[ "Soil-transmitted helminths are carried by large numbers of people in developing countries .", "These parasites live in the gut and may interact with bacterial communities in the gut , also called the gut microbiota .", "To determine whether there are alterations to the gut microbiota that are associated with h...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Investigation of the First Case of Dengue Virus Infection Acquired in Western Australia in Seven Decades: Evidence of Importation of Infected Mosquitoes?	journal.pntd.0004114	null	[ [ "Dengue fever is caused by a mosquito-borne flavivirus , dengue virus ( DENV ) , and is responsible for a significant disease burden globally with an estimated 390 million cases of dengue fever per annum , of which 96 million result in symptomatic disease [1] .", "The incubation period is 3 to 14 days [2]...	[ "In October 2013 , a locally-acquired case of dengue virus ( DENV ) infection was reported in Western Australia ( WA ) where local dengue transmission has not occurred for over 70 years .", "Laboratory testing confirmed recent DENV infection and the case demonstrated a clinically compatible illness .", "The inf...	[ "Dengue fever transmission in Western Australia ceased in the 1940s and there are currently no known dengue vector species present .", "Despite this , a locally acquired of dengue fever was reported in 2013 with the most likely location of exposure the township of Point Samson in Pilbara region in the north-west ...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases/neglected tropical diseases", "infectious diseases/helminth infections", "chemical biology/protein chemistry and proteomics" ]	Enzymatic Shaving of the Tegument Surface of Live Schistosomes for Proteomic Analysis: A Rational Approach to Select Vaccine Candidates	journal.pntd.0000993	null	[ [ "The persistence of adult schistosomes in the bloodstream for decades means they must deploy unique and effective immune evasion strategies at their interface with the host .", "The 1 cm-long worms are covered by a naked syncytial layer of cytoplasm , the tegument , connected by cytoplasmic tubules to und...	[ "The membrane-associated and membrane-spanning constituents of the Schistosoma mansoni tegument surface , the parasite's principal interface with the host bloodstream , have recently been characterized using proteomic techniques .", "Biotinylation of live worms using membrane-impermeant probes revealed that only ...	[ "Adult schistosome parasites can reside in the host bloodstream for decades surrounded by components of the immune system .", "It was originally proposed that their survival depended on the secretion of an inert bilayer , the membranocalyx , to protect the underlying plasma membrane from attack .", "We have inv...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "bacteriology", "medicine", "shigellosis infections", "protein interactions", "macromolecular assemblies", "host-pathogen interaction", "microbiology", "globular proteins", "bacterial biochemistry", "protein classes", "bacterial diseases", "protein folding", "protein structure", "bacterial...	A Substrate-Fusion Protein Is Trapped inside the Type III Secretion System Channel in Shigella flexneri	journal.ppat.1003881	null	[ [ "T3SS are found in numerous Gram-negative bacteria and share strong homologies among different invasive pathogens .", "Using the T3SS , bacteria are able to secrete effector proteins that translocate into the host-cell where they target metabolic or signal transduction pathways for example [1][2] .", ...	[ "The Type III Secretion System ( T3SS ) is a macromolecular complex used by Gram-negative bacteria to secrete effector proteins from the cytoplasm across the bacterial envelope in a single step .", "For many pathogens , the T3SS is an essential virulence factor that enables the bacteria to interact with and manip...	[ "Type III Secretion Systems ( T3SS ) secrete bacterial effector proteins from the cytoplasm across the cell wall , but mechanistic details of this process remain mostly elusive .", "We locked the T3SS of Shigella flexneri in an actively secreting state by expression of substrate fusions that consist of a function...	2014
[ "Introduction", "Methods", "Results", "Discussion", "Conclusion" ]	[ "medicine and health sciences", "ecology and environmental sciences", "rivers", "demography", "cancer treatment", "clinical oncology", "tropical diseases", "vertebrates", "parasitic diseases", "animals", "health care", "freshwater fish", "oncology", "foodborne trematodiases", "clinical m...	Uncovering the Pathogenic Landscape of Helminth (Opisthorchis viverrini) Infections: A Cross-Sectional Study on Contributions of Physical and Social Environment and Healthcare Interventions	journal.pntd.0005175	null	[ [ "Helminthiases , which include foodborne trematodiases , lymphatic filariasis , schistosomiasis , and soil-transmitted helminthiases , are the most common neglected tropical diseases ( NTDs ) in southeast Asia [1] .", "They disproportionally affect the poor or marginalized population in developing countri...	[ "Helminth infections have proven recalcitrant to control by chemotherapy in many parts of Southeast Asia and indeed farther afield .", "This study isolates and examines the influence of different aspects of the physical and social environment , and uneven intervention effort contributing to the pathogenic landsca...	[ "Many of the large-scale helminth control programs around the world have primarily relied upon drug treatment .", "Reliance on drug treatment alone does not deal with the ultimate causes of infection , resulting in reduced infection levels only in the short-term .", "Re-emergence of infections and possibly even...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "leptospirosis", "bacterial diseases", "infectious diseases", "veterinary diseases", "zoonoses", "medicine and health sciences", "environmental epidemiology", "epidemiology", "neglected tropical diseases", "biology and life sciences", "population biology", "tropical diseases", "veterinary sc...	Epidemiology of Leptospira Transmitted by Rodents in Southeast Asia	journal.pntd.0002902	null	[ [ "The World Health Organization ( WHO ) estimates the global burden of leptospirosis at over one million severe human cases per year , with a growing number of countries reporting leptospirosis outbreaks [1] , [2] .", "Leptospirosis can represent up to 20–40% of idiopathic febrile illness [3] , [4] .", ...	[ "Leptospirosis is the most common bacterial zoonoses and has been identified as an important emerging global public health problem in Southeast Asia .", "Rodents are important reservoirs for human leptospirosis , but epidemiological data is lacking .", "We sampled rodents living in different habitats from seven...	[ "Leptospirosis is the most prevalent bacterial zoonosis worldwide .", "Rodents are believed to be the main reservoirs of Leptospira , yet little epidemiological research has been conducted on rodents from Southeast Asia .", "Previous studies suggest that activities which place humans in microenvironments shared...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "computational biology/molecular dynamics", "public health and epidemiology/global health", "biophysics/protein folding" ]	Molecular Structures of Quiescently Grown and Brain-Derived Polymorphic Fibrils of the Alzheimer Amyloid Aβ9-40 Peptide: A Comparison to Agitated Fibrils	journal.pcbi.1000693	null	[ [ "A number of human diseases known as amyloidoses [1] , [2] are associated with the presence of amyloid plaques in organs and tissues .", "The main constituents of these plaques are fibrillar aggregates arising from the pathological self-assembly of normally soluble proteins .", "The etiology of amyloi...	[ "The presence of amyloid deposits consisting primarily of Amyloid-β ( Aβ ) fibril in the brain is a hallmark of Alzheimer's disease ( AD ) .", "The morphologies of these fibrils are exquisitely sensitive to environmental conditions .", "Using molecular dynamics simulations combined with data from previously pub...	[ "Amyloid diseases are characterized by the presence of amyloid fibrils on organs and tissue in the body .", "Alzheimer's disease , Parkinson's diseases and Type II Diabetes are all examples of amyloid diseases .", "Determining the structure of amyloid fibrils is critical for understanding the mechanism of fibri...	2010
[ "Introduction", "Methods", "Results and Discussion" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "ecology", "staphylococcus", "medical microbiology", "host-pathogen interactions", "microbial pathogens", "parasitology", "biology and life sciences", "microbiology", "pathogenesis", "bacterial pathogens", "microbial ecolog...	Scabies Mites Alter the Skin Microbiome and Promote Growth of Opportunistic Pathogens in a Porcine Model	journal.pntd.0002897	null	[ [ "Scabies is a skin disease caused by the parasitic mite Sarcoptes scabiei variety hominis in humans .", "It is common worldwide , predominantly affecting overcrowded , socio-economically disadvantaged populations [1] .", "Scabies is ubiquitous and a significant public health burden in the developing w...	[ "The resident skin microbiota plays an important role in restricting pathogenic bacteria , thereby protecting the host .", "Scabies mites ( Sarcoptes scabiei ) are thought to promote bacterial infections by breaching the skin barrier and excreting molecules that inhibit host innate immune responses .", "Epidemi...	[ "Scabies is a neglected , contagious skin disease caused by a parasitic mite Sarcoptes scabiei .", "It is highly prevalent world-wide , and now recognized as a possible underlying factor for secondary bacterial infections with potential serious downstream complications .", "There is currently few experimental d...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology/persistence and latency", "immunology/immunity to infections", "virology/animal models of infection" ]	A Single CD8+ T Cell Epitope Sets the Long-Term Latent Load of a Murid Herpesvirus	journal.ppat.1000177	null	[ [ "Gamma-herpesviruses characteristically persist in lymphocytes .", "Since the pool of latent genomes is constantly drained by viral reactivation , it must be replenished by virus-driven lymphoproliferation; this in turn is limited by host T cells; the steady-state viral load reflects an equilibrium of the...	[ "The pathogenesis of persistent viral infections depends critically on long-term viral loads .", "Yet what determines these loads is largely unknown .", "Here , we show that a single CD8+ T cell epitope sets the long-term latent load of a lymphotropic gamma-herpesvirus , Murid herpesvirus-4 ( MuHV-4 ) .", "Th...	[ "Persistent viruses present a major challenge to the immune response .", "Gamma-herpesviruses are a prime example , and the archetypal family member , Epstein-Barr virus ( EBV ) , has been studied for many years .", "A major unanswered question with EBV is why long-term virus loads—a key pathogenesis outcome—va...	2008

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