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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", "Discussion" ]	[ "physics", "biophysic al simulations", "biophysics theory", "biology", "computational biology", "biophysics simulations", "biophysics" ]	How Molecular Motors Are Arranged on a Cargo Is Important for Vesicular Transport	journal.pcbi.1002032	null	[ [ "Cells are highly organized , and much of this organization results from motors that move cargos along microtubules .", "The single-molecule properties of molecular motors are relatively well understood both experimentally and theoretically .", "With this as a starting point , we investigated how the ...	[ "The spatial organization of the cell depends upon intracellular trafficking of cargos hauled along microtubules and actin filaments by the molecular motor proteins kinesin , dynein , and myosin .", "Although much is known about how single motors function , there is significant evidence that cargos in vivo are ca...	[ "The spatial organization of living cells depends upon a transportation system consisting of molecular motor proteins that act like porters carrying cargos along filaments that are analogous to roads .", "The breakdown of this transportation system has been associated with neurodegenerative diseases such as Alzhe...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "viral immune evasion", "virology", "biology", "microbiology" ]	Enterovirus 71 Protease 2Apro Targets MAVS to Inhibit Anti-Viral Type I Interferon Responses	journal.ppat.1003231	null	[ [ "When viruses infect host cells , the innate immune response is activated as the first line of defense against viral invasion .", "Pathogen associated molecular patterns ( PAMPs ) are sensed by host pattern recognition receptors ( PRRs ) , resulting the expression of type I interferon and proinflammatory ...	[ "Enterovirus 71 ( EV71 ) is the major causative pathogen of hand , foot , and mouth disease ( HFMD ) .", "Its pathogenicity is not fully understood , but innate immune evasion is likely a key factor .", "Strategies to circumvent the initiation and effector phases of anti-viral innate immunity are well known; le...	[ "Enterovirus 71 ( EV71 ) is the causative pathogen of hand , foot , and mouth disease ( HFMD ) .", "Since the 2008 outbreak of HFMD in Fuyang , Anhui province , China , HFMD has been a severe public health concern affecting children .", "The major obstacle hindering HFMD prevention and control efforts is the la...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "rna interference", "microtubules", "anaphase", "metaphase", "enzymes", "cell cycle and cell division", "cell processes", "enzymology", "germ cells", "oocytes", "sumoylation", "epigenetics", "tubulins", "cellular structures and organelles", "cytoskeleton", "genetic interference", "pr...	Dynamic SUMO remodeling drives a series of critical events during the meiotic divisions in Caenorhabditis elegans	journal.pgen.1007626	null	[ [ "Meiosis is a specialized form of cell division where chromosomes are duplicated once and segregated twice , in order to reduce the chromosome number by half to generate haploid gametes .", "In contrast to mitosis , oocyte meiosis in many species occurs in the absence of centrosomes , the microtubule orga...	[ "Chromosome congression and segregation in C . elegans oocytes depend on a complex of conserved proteins that forms a ring around the center of each bivalent during prometaphase; these complexes are then removed from chromosomes at anaphase onset and disassemble as anaphase proceeds .", "Here , we uncover mechani...	[ "Most cells have two sets of chromosomes , one from each parent .", "Meiosis is a specialized form of cell division where chromosomes are duplicated once and segregated twice , in order to generate eggs ( oocytes ) or sperm with only one copy of every chromosome .", "This is necessary so that fertilization will...	2018
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "antimicrobials", "medicine and health sciences", "body fluids", "drugs", "tropical diseases", "microbiology", "parasitic diseases", "wolbachia", "antimalarials", "nematode infections", "developmental biology", "filariasis", "pharmaceutics", "antibiotics", "neglected tropical diseases", ...	In vivo kinetics of Wolbachia depletion by ABBV-4083 in L. sigmodontis adult worms and microfilariae	journal.pntd.0007636	null	[ [ "Onchocerciasis and lymphatic filariasis are neglected tropical diseases that are caused by the filarial nematodes Onchocerca volvulus and Wuchereria bancrofti , Brugia malayi and Brugia timori , respectively [1] .", "During onchocerciasis vision loss and severe dermatitis can occur , whereas one third of...	[ "Depletion of Wolbachia endosymbionts of human pathogenic filariae using 4–6 weeks of doxycycline treatment can lead to permanent sterilization and adult filarial death .", "We investigated the anti-Wolbachia drug candidate ABBV-4083 in the Litomosoides sigmodontis rodent model to determine Wolbachia depletion ki...	[ "Onchocerciasis and lymphatic filariasis represent debilitating neglected tropical diseases that are caused by parasitic filarial nematodes .", "Current efforts to eliminate onchocerciasis are hampered by the lack of drugs that lead to permanent sterilization of the adult worms or provide a macrofilaricidal effec...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Assessment of Efficacy and Quality of Two Albendazole Brands Commonly Used against Soil-Transmitted Helminth Infections in School Children in Jimma Town, Ethiopia	journal.pntd.0004057	null	[ [ "Currently , there is a worldwide upscale in the implementation of programs to control and to eliminate a selection of 10 neglected tropical diseases [1 , 2] .", "Among these , soil-transmitted helminthiasis causes the highest burden on public health .", "It is estimated that more than 1 . 4 billion p...	[ "There is a worldwide upscale in mass drug administration ( MDA ) programs to control the morbidity caused by soil-transmitted helminths ( STHs ) : Ascaris lumbricoides , Trichuris trichiura and hookworm .", "Although anthelminthic drugs which are used for MDA are supplied by two pharmaceutical companies through ...	[ "Soil-transmitted helminths ( STHs ) infect millions of children worldwide .", "To fight STH , large-scale de-worming programs are implemented in which anthelmintic drugs ( either albendazole ( ABZ ) or mebendazole ( MEB ) ) are administered .", "However , there is a wide range of other brands , which are even ...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "computer science", "medicinal chemistry", "computer modeling", "drugs and devices", "chemistry", "biology", "computational biology", "chemical biology" ]	A Cell-based Computational Modeling Approach for Developing Site-Directed Molecular Probes	journal.pcbi.1002378	null	[ [ "Local administration of therapeutic agents or bioimaging probes is commonly used to maximize concentrations at a desired site of action and to minimize side effects or background signals associated with distribution in off-target sites .", "However , in the specific case of inhaled , small molecule thera...	[ "Modeling the local absorption and retention patterns of membrane-permeant small molecules in a cellular context could facilitate development of site-directed chemical agents for bioimaging or therapeutic applications .", "Here , we present an integrative approach to this problem , combining in silico computation...	[ "We have developed an integrative , cell-based modeling approach to facilitate the design and discovery of chemical agents directed to specific sites of action within a living organism .", "Here , a computational , multiscale transport model of the lung was adapted to enable virtual screening of small molecules t...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	IL-10- and TGFβ-mediated Th9 Responses in a Human Helminth Infection	journal.pntd.0004317	null	[ [ "Upon antigen-specific stimulation , CD4+ T cells have the potential to differentiate into various T-helper ( Th ) cell subsets based on the pattern of transcription factors induced and cytokines produced [1] .", "Traditionally associated with the Th2 response , IL-9 is a member of the common γ chain cyto...	[ "Th9 cells are a subset of CD4+ T cells that express the protoypical cytokine , IL-9 .", "Th9 cells are known to effect protective immunity in animal models of intestinal helminth infections .", "However , the role of Th9 cells in human intestinal helminth infections has never been examined .", "To examine th...	[ "Strongyloides stercoralis is a common intestinal parasite affecting about 50–100 million people worldwide .", "It is characterized by a complex lifecycle involving both free- living and parasitic stages and the clinical manifestations range from asymptomatic infection to multi-organ failure .", "It has the pro...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma mansoni", "glycosylamines", "crystal structure", "chemical compounds", "phosphates", "helminths", "enzymes", "condensed matter physics", "enzymology", "nucleotides", "animals", "organic compounds", "purines", "crystallography", "adenosine"...	Crystal Structure of Schistosoma mansoni Adenosine Phosphorylase/5’-Methylthioadenosine Phosphorylase and Its Importance on Adenosine Salvage Pathway	journal.pntd.0005178	null	[ [ "The purine metabolism in the human parasite Schistosoma mansoni was extensively studied in the 1970s and 1980s by Senft and collaborators [1–8] and Dovey [9] .", "These studies demonstrated that adults and schistosomules of S . mansoni do not have the capacity to synthesize purine nucleotides de novo , i...	[ "Schistosoma mansoni do not have de novo purine pathways and rely on purine salvage for their purine supply .", "It has been demonstrated that , unlike humans , the S . mansoni is able to produce adenine directly from adenosine , although the enzyme responsible for this activity was unknown .", "In the present ...	[ "The huge challenge in parasitic chemotherapy development is finding a specific compound to attack the parasite organisms without damaging their host .", "Schistosoma mansoni , which is the causative agent of schistosomiasis , is one of the major health concerns in the developing world .", "Purine bases are ess...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell physiology", "medicine and health sciences", "microbial mutation", "poxviruses", "pathology and laboratory medicine", "crystal structure", "viral transmission and infection", "pathogens", "condensed matter physics", "microbiology", "membrane proteins", "viruses", "membrane fusion", "...	Vaccinia viral A26 protein is a fusion suppressor of mature virus and triggers membrane fusion through conformational change at low pH	journal.ppat.1007826	null	[ [ "Virus entry represents the initial stage of infection and is a target for developing new antiviral therapeutics .", "Poxvirus is a family of enveloped DNA viruses with genomes of ~200 kilobases [1] .", "Vaccinia virus , an orthopoxvirus , is a model system for investigating poxvirus entry into host c...	[ "Vaccinia mature virus requires A26 envelope protein to mediate acid-dependent endocytosis into HeLa cells in which we hypothesized that A26 protein functions as an acid-sensitive membrane fusion suppressor .", "Here , we provide evidence showing that N-terminal domain ( aa1-75 ) of A26 protein is an acid-sensiti...	[ "Vaccinia virus is a complex large DNA virus with a large number of viral membrane proteins to facilitate cell entry .", "Although it is well established that vaccinia mature virus uses endocytosis to enter cells , it remains unclear how it triggers membrane fusion in the acidic environment of endosomes .", "Re...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	The Hos2 Histone Deacetylase Controls Ustilago maydis Virulence through Direct Regulation of Mating-Type Genes	journal.ppat.1005134	null	[ [ "The switch between yeast and hypha stages , or dimorphism , is a key morphological conversion required for the virulence of several animal and plant pathogenic fungi [1–4] .", "This process occurs at specific stages of fungal infection and is tightly controlled .", "The two best studied signalling pa...	[ "Morphological changes are critical for host colonisation in plant pathogenic fungi .", "These changes occur at specific stages of their pathogenic cycle in response to environmental signals and are mediated by transcription factors , which act as master regulators .", "Histone deacetylases ( HDACs ) play cruci...	[ "Many pathogenic fungi need to undergo morphological changes in order to infect their hosts .", "Typically , pathogenic fungi switch from a non-pathogenic yeast-like form to a polarised pathogenic filament .", "This morphological switch is regulated genetically and is triggered by specific environmental conditi...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "gene expression", "genetics", "plant genetics", "biology and life sciences", "genomics", "evolutionary biology", "evolutionary genetics" ]	The Role of cis Regulatory Evolution in Maize Domestication	journal.pgen.1004745	null	[ [ "Changes in the cis regulatory elements ( CREs ) of genes with functionally conserved proteins have been considered a key mechanism , if not the primary mechanism , by which the diverse forms of multicellular eukaryotic organisms evolved [1]–[3] .", "Variation in CREs allows for the deployment of tissue s...	[ "Gene expression differences between divergent lineages caused by modification of cis regulatory elements are thought to be important in evolution .", "We assayed genome-wide cis and trans regulatory differences between maize and its wild progenitor , teosinte , using deep RNA sequencing in F1 hybrid and parent i...	[ "Modification of cis regulatory elements to produce differences in gene expression level , localization , and timing is an important mechanism by which organisms evolve divergent adaptations .", "To examine gene regulatory change during the domestication of maize from its wild progenitor , teosinte , we assessed ...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "immunology", "parasitic diseases", "fibroblasts", "connective tissue cells", "white blood cells", "parasitic intestinal diseases", "animal cells", "connective tissue", "biological tissue", ...	A Trematode Parasite Derived Growth Factor Binds and Exerts Influences on Host Immune Functions via Host Cytokine Receptor Complexes	journal.ppat.1005991	null	[ [ "The trematode Fasciola hepatica is capable of establishing chronic infection in multiple hosts that can last for many years .", "In terms of animal infections F . hepatica is highly prevalent within sheep , cattle and goats throughout temperate regions of the globe with varying levels of infection report...	[ "The trematode Fasciola hepatica is responsible for chronic zoonotic infection globally .", "Despite causing a potent T-helper 2 response , it is believed that potent immunomodulation is responsible for rendering this host reactive non-protective host response thereby allowing the parasite to remain long-lived ."...	[ "Parasitic worms , helminths , can cause long-lived chronic infection in many hosts that they infection .", "The liver fluke , Fasciola hepatica , is one such parasite causing global infection of both humans and animals .", "F . hepatica exerts an influence over the immune system such that it avoids effector me...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "gene regulatory networks", "gene expression", "genetics", "biology and life sciences", "computational biology" ]	Mediation Analysis Demonstrates That Trans-eQTLs Are Often Explained by Cis-Mediation: A Genome-Wide Analysis among 1,800 South Asians	journal.pgen.1004818	null	[ [ "The development of technologies that enable high-throughput , genome-wide measurement of single nucleotide polymorphisms ( SNPs ) and mRNA transcripts have enabled researchers to comprehensively examine the effects of human genetic variation on gene expression .", "Genome-wide studies of expression quant...	[ "A large fraction of human genes are regulated by genetic variation near the transcribed sequence ( cis-eQTL , expression quantitative trait locus ) , and many cis-eQTLs have implications for human disease .", "Less is known regarding the effects of genetic variation on expression of distant genes ( trans-eQTLs )...	[ "Expression quantitative trait locus ( eQTL ) studies have demonstrated that human genes can be regulated by genetic variation residing close to the gene ( cis-eQTLs ) or in a distant region or on a different chromosome ( trans-eQTLs ) .", "While cis-eQTL variants are likely to affect transcription factor binding...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "algorithms", "genome-wide association studies", "computer and information sciences", "mathematics", "statistics (mathematics)", "gene regulatory networks", "genome analysis", "genetics", "applied mathematics", "biology and life sciences", "physical sciences", "computational biology", "biost...	AprioriGWAS, a New Pattern Mining Strategy for Detecting Genetic Variants Associated with Disease through Interaction Effects	journal.pcbi.1003627	null	[ [ "Gene-gene interactions have been proposed as one potential explanation of the well-known problem of missing heritability [1] , and a recent report [2] has quantitatively demonstrated that possibility .", "Researchers have long attempted to identify interactions , with methods ranging from evolutionary ge...	[ "Identifying gene-gene interaction is a hot topic in genome wide association studies .", "Two fundamental challenges are: ( 1 ) how to smartly identify combinations of variants that may be associated with the trait from astronomical number of all possible combinations; and ( 2 ) how to test epistatic interaction ...	[ "Genes do not operate in vacuum .", "They interact with each other in many ways .", "Therefore , to figure out genetic causes of disease by case-control association studies , it is important to take interactions into account .", "There are two fundamental challenges in interaction-focused analysis .", "The ...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "cognitive neuroscience", "psychology", "neuroanatomy", "mental health", "signal processing", "biology", "neuroscience", "neuroimaging", "engineering" ]	Developmental Maturation of Dynamic Causal Control Signals in Higher-Order Cognition: A Neurocognitive Network Model	journal.pcbi.1002374	null	[ [ "The development of increasingly sophisticated cognitive skills relies on the maturation of control processes for orienting attention and allocating resources for task relevant information [1] , [2] .", "Such control processes are important for virtually every complex cognitive task , and there is growing...	[ "Cognitive skills undergo protracted developmental changes resulting in proficiencies that are a hallmark of human cognition .", "One skill that develops over time is the ability to problem solve , which in turn relies on cognitive control and attention abilities .", "Here we use a novel multimodal neurocogniti...	[ "The human brain undergoes significant maturational changes between childhood and adulthood that are thought to enable increasingly sophisticated thoughts and behaviors .", "One of the skills that we develop over time is the ability to problem solve , which relies in turn on the ability to control our attention a...	2012
[ "Introduction", "Methods", "Results and Discussion" ]	[ "anatomy", "cell biology", "entomology", "renal physiology", "physiology", "gene expression", "genetics", "gene regulation", "biology and life sciences", "molecular genetics", "renal system", "molecular cell biology", "zoology" ]	Transcriptomic Evidence for a Dramatic Functional Transition of the Malpighian Tubules after a Blood Meal in the Asian Tiger Mosquito Aedes albopictus	journal.pntd.0002929	null	[ [ "The Asian tiger mosquito Aedes albopictus is considered one of the most invasive mosquito species in the world; since 1979 it has spread to over 28 countries outside of its native range in Asia and Southeast Asia , aided by the international trade of used automobile tires [1] , [2] .", "Within the United...	[ "The consumption of a vertebrate blood meal by adult female mosquitoes is necessary for their reproduction , but it also presents significant physiological challenges to mosquito osmoregulation and metabolism .", "The renal ( Malpighian ) tubules of mosquitoes play critical roles in the initial processing of the ...	[ "The Asian tiger mosquito Aedes albopictus is a vector of several medically-important arboviruses and one of the most invasive mosquito species in the world .", "Existing control measures for mosquitoes are presently being challenged by the emergence of resistance to insecticides that target the nervous system ."...	2014
[ "Introduction", "Material and methods", "Results", "Discussion" ]	[ "blood cells", "flow cytometry", "medicine and health sciences", "luciferase", "immune cells", "vesicles", "pathology and laboratory medicine", "enzymes", "pathogens", "antigen-presenting cells", "immunology", "microbiology", "enzymology", "retroviruses", "viruses", "immunodeficiency v...	Dendritic cell maturation, but not type I interferon exposure, restricts infection by HTLV-1, and viral transmission to T-cells	journal.ppat.1006353	null	[ [ "Human T-Lymphotropic Virus type 1 ( HTLV-1 ) infects 5–10 million people [1] .", "HTLV-1 is mainly present in Japan , inter-tropical Africa , the Caribbean and South America [2 , 3] .", "After a long period of clinical latency , HTLV-1 infection leads , in a fraction of infected individuals , either ...	[ "Human T lymphotropic Virus type 1 ( HTLV-1 ) is the etiological agent of Adult T cell Leukemia/Lymphoma ( ATLL ) and HTLV-1-Associated Myelopathy/Tropical Spastic Paraparesis ( HAM/TSP ) .", "Both CD4+ T-cells and dendritic cells ( DCs ) infected with HTLV-1 are found in peripheral blood from HTLV-1 carriers .",...	[ "Human T-Lymphotropic Virus type 1 ( HTLV-1 ) is the etiological agent of Adult T-cell Leukemia/Lymphoma ( ATLL ) and HTLV-1-Associated Myelopathy/Tropical Spastic Paraparesis ( HAM/TSP ) .", "In chronically infected patients , the provirus is mainly detected in the CD4+ T-cell population .", "However , beside ...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "deletion mutation", "mutation", "fungi", "model organisms", "fungal evolution", "research and analysis methods", "saccharomyces", "mycology", "evolutionary genetics", "yeast", "point mutation", "genetic screens", "gene identification and analysis", "genetics", "mutation detection", "b...	High-Throughput Identification of Adaptive Mutations in Experimentally Evolved Yeast Populations	journal.pgen.1006339	null	[ [ "There is a great need for rapid , high-throughput methods to identify adaptive mutations among the growing list of mutations identified in experimentally evolved populations .", "Several recent ‘Evolve and Resequence’ studies [1] , in which populations or clones were sequenced after adaptation to a speci...	[ "High-throughput sequencing has enabled genetic screens that can rapidly identify mutations that occur during experimental evolution .", "The presence of a mutation in an evolved lineage does not , however , constitute proof that the mutation is adaptive , given the well-known and widespread phenomenon of genetic...	[ "Experimental evolution allows us to observe evolution in real time .", "New advances in genome sequencing make it trivial to discover the mutations that have arisen in evolved cultures; however , linking those mutations to particular adaptive traits remains difficult .", "We evaluated the fitness impacts of th...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics", "epigenetics", "biology", "genetics and genomics" ]	Spreading of Heterochromatin Is Limited to Specific Families of Maize Retrotransposons	journal.pgen.1003127	null	[ [ "A substantial fraction of most eukaryotic genomes is composed of transposable elements ( TEs ) [1]–[4] .", "While these TEs are sometimes referred to as “junk” DNA , there is evidence for potential functional roles in some instances [5] .", "Indeed , Barbara McClintock used the term “controlling elem...	[ "Transposable elements ( TEs ) have the potential to act as controlling elements to influence the expression of genes and are often subject to heterochromatic silencing .", "The current paradigm suggests that heterochromatic silencing can spread beyond the borders of TEs and influence the chromatin state of neigh...	[ "Transposable elements comprise a substantial portion of many eukaryotic genomes .", "These mobile fragments of DNA can directly mutate genes through insertions into coding regions but may also affect the gene regulation through nearby insertions .", "There is evidence that the majority of transposable elements...	2012
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "genetics and genomics/comparative genomics", "computational biology/sequence motif analysis", "computational biology/transcriptional regulation", "developmental biology/developmental evolution", "developmental biology/pattern formation", "developmental biology/neurodevelopment", "computational biology/...	A cis-Regulatory Signature for Chordate Anterior Neuroectodermal Genes	journal.pgen.1000912	null	[ [ "The concept of “selector genes” was introduced 30 years ago by Garcia-Bellido to define genes that interpret a transient regulatory state and specify the identity of a given developmental field [1] .", "The question of how embryos execute distinct and unique differentiation programs using these selector ...	[ "One of the striking findings of comparative developmental genetics was that expression patterns of core transcription factors are extraordinarily conserved in bilaterians .", "However , it remains unclear whether cis-regulatory elements of their target genes also exhibit common signatures associated with conserv...	[ "Regional identity in embryos is defined by a few specific transcription factors that activate a large number of target genes through binding to common tags in regulatory sequences .", "In chordates it is unclear if such tags can be identified in the cis-regulatory regions of regionally expressed genes .", "To ...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Disruption of Specific RNA-RNA Interactions in a Double-Stranded RNA Virus Inhibits Genome Packaging and Virus Infectivity	journal.ppat.1005321	null	[ [ "Bluetongue is a vector-borne hemorrhagic disease of livestock and is responsible for considerable economic losses to international livestock industries [1 , 2] .", "The disease is caused by Bluetongue virus ( BTV ) a non-enveloped virus ( a member of Reoviridae family ) with a double-capsid icosahedral p...	[ "Bluetongue virus ( BTV ) causes hemorrhagic disease in economically important livestock .", "The BTV genome is organized into ten discrete double-stranded RNA molecules ( S1-S10 ) which have been suggested to follow a sequential packaging pathway from smallest to largest segment during virus capsid assembly .", ...	[ "Bluetongue virus ( BTV ) is an economically important pathogen of ruminants that belongs to a group of viruses whose genome consists of multiple segments of double-stranded RNA .", "In order for the virus to synthesize viable and infectious progeny , a precise set of the 10 newly replicated BTV segments must be ...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "protein transport", "medicine and health sciences", "biopsy", "hela cells", "biological cultures", "cell processes", "surgical and invasive medical procedures", "epithelial cells", "mutation", "cell cultures", "molecular biology techniques", "digestive system", "research and analysis method...	Attaching and effacing (A/E) lesion formation by enteropathogenic E. coli on human intestinal mucosa is dependent on non-LEE effectors	journal.ppat.1006706	null	[ [ "The gastrointestinal epithelium is an important defense barrier against infections [1] .", "Enteric pathogens have acquired virulence traits that enable them to colonize and break this barrier , by adhering to the epithelium , delivering toxins and invading intestinal epithelial cells .", "To this en...	[ "Enteropathogenic E . coli ( EPEC ) is a human pathogen that causes acute and chronic pediatric diarrhea .", "The hallmark of EPEC infection is the formation of attaching and effacing ( A/E ) lesions in the intestinal epithelium .", "Formation of A/E lesions is mediated by genes located on the pathogenicity isl...	[ "Enteropathogenic E . coli ( EPEC ) causes diarrhea and generates the attaching and effacing ( A/E ) lesion in human gut epithelium .", "A/E lesion formation requires the locus of enterocyte effacement ( LEE ) in the bacterial genome , which encodes a protein injection system delivering the translocated intimin r...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "inflammatory diseases", "body weight", "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "immunology", "diet", "physiological parameters", "signs and symptoms", "nutrition", "obesity", "white blood cells", "inflammation", "animal cells",...	Anti-inflammatory microRNA-146a protects mice from diet-induced metabolic disease	journal.pgen.1007970	null	[ [ "Obesity incidence has reached epidemic rates in recent years , now affecting over one-third of the adult population in the United States and rising in incidence around the world [1] .", "Obesity and its comorbidities , including diabetes , heart disease , stroke , cancer , and infections , account for th...	[ "Identifying regulatory mechanisms that influence inflammation in metabolic tissues is critical for developing novel metabolic disease treatments .", "Here , we investigated the role of microRNA-146a ( miR-146a ) during diet-induced obesity in mice .", "miR-146a is reduced in obese and type 2 diabetic patients ...	[ "Obesity and metabolic disease are on the rise throughout the world , creating a need for research into the interaction between diet and genetics .", "It is known that chronic inflammation contributes to obesity , but it is not well understood how inflammation and inflammatory genes are controlled to prevent obes...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "salaries", "engineering and technology", "sewage", "tropical diseases", "geographical locations", "social sciences", "social geography", "health care", "ethnicities", "bacterial diseases", "neglected tropical diseases", "regional geography", "human geograph...	Geographic and socioeconomic factors associated with leprosy treatment default: An analysis from the 100 Million Brazilian Cohort	journal.pntd.0007714	null	[ [ "Leprosy , also known as Hansen’s disease , is a chronic and potentially disabling infectious disease caused by Mycobacterium leprae that primarily affects peripheral nerves and skin [1 , 2] .", "Since the introduction of multidrug therapy ( MDT ) in 1982 , the global burden of leprosy has been significan...	[ "Although leprosy is largely curable with multidrug therapy , incomplete treatment limits therapeutic effectiveness and is an important obstacle to disease control .", "To inform efforts to improve treatment completion rates , we aimed to identify the geographic and socioeconomic factors associated with leprosy t...	[ "While the leprosy new case detection has been decreasing worldwide since the introduction of multidrug therapy ( MDT ) in the 1980s , treatment default remains an important risk factor for leprosy-associated disability and an obstacle to disease control and elimination .", "Treatment default occurs when an indiv...	2019
[ "Introduction", "Results", "Discussion", "Models" ]	[]	Analysis of Initial Cell Spreading Using Mechanistic Contact Formulations for a Deformable Cell Model	journal.pcbi.1003267	null	[ [ "The dynamics of initial cell spreading – that is during the first few minutes – are governed by energy release through binding events of cell surface molecules , rather than by active cellular processes such as e . g . tension generated by stress fibers .", "These molecular binding events dominate the to...	[ "Adhesion governs to a large extent the mechanical interaction between a cell and its microenvironment .", "As initial cell spreading is purely adhesion driven , understanding this phenomenon leads to profound insight in both cell adhesion and cell-substrate interaction .", "It has been found that across a wide...	[ "How cells spread on a newly encountered surface is an important issue , since it hints at how cells interact physically with the specific material in general .", "It has been shown before that many cell types have very similar early spreading behavior .", "This observation has been linked to the mechanical nat...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "chemical characterization", "parasitic diseases", "parasitic protozoans", "electromagnetic radiation", "bioluminescence imaging", "optical analysis", "respiratory system", "lymph nodes", "protozoans", "lymphatic system", "stomach", "digestive system", "rese...	Unraveling Chagas disease transmission through the oral route: Gateways to Trypanosoma cruzi infection and target tissues	journal.pntd.0005507	null	[ [ "Human Chagas disease ( American trypanosomiasis ) is a neglected tropical illness caused by the protozoan Trypanosoma cruzi .", "Infection affects 6–8 million people worldwide and is considered a global health problem .", "Chagas disease is endemic in Mexico , Central America and South America and is...	[ "Oral transmission of Trypanosoma cruzi , the causative agent of Chagas disease , is the most important route of infection in Brazilian Amazon and Venezuela .", "Other South American countries have also reported outbreaks associated with food consumption .", "A recent study showed the importance of parasite con...	[ "Oral transmission of Trypanosoma cruzi associated with food/beverage consumption is presently an important route of infection in Brazil and Venezuela .", "Colombia , Bolivia , Argentina and Ecuador have also reported to have acute cases of Chagas disease transmission through the oral route .", "Significant stu...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	IL-33/ST2 Correlates with Severity of Haemorrhagic Fever with Renal Syndrome and Regulates the Inflammatory Response in Hantaan Virus-Infected Endothelial Cells	journal.pntd.0003514	null	[ [ "Hantaan virus ( HTNV ) is a member of the Bunyaviridae family [1] .", "HTNV can cause severe lethal haemorrhagic fever with renal syndrome ( HFRS ) in humans , which is characterised by increased capillary permeability and thrombocytopenia .", "At present , the pathogenesis of HFRS remains unclear ."...	[ "Hantaan virus ( HTNV ) causes a severe lethal haemorrhagic fever with renal syndrome ( HFRS ) in humans .", "Despite a limited understanding of the pathogenesis of HFRS , the importance of the abundant production of pro-inflammatory cytokines has been widely recognized .", "Interleukin 33 ( IL-33 ) has been de...	[ "Hantaan virus ( HTNV ) causes human hemorrhagic fever with renal syndrome ( HFRS ) with a mortality rate of approximately 15% in Asia .", "At present , the primary treatment for HFRS is limited to critical care management and the use of anti-viral drugs , such as Ribavirin .", "However , the cytokine storm at ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunology" ]	Humans Lack iGb3 Due to the Absence of Functional iGb3-Synthase: Implications for NKT Cell Development and Transplantation	journal.pbio.0060172	Controversy surrounds the glycolipid iGb3. Our data show that humans do not express this lipid. This has important implications in natural killer T cell development, self-recognition, and transplantation.	[ [ "Identification of endogenous antigens that regulate NKT cell development and self-recognition represents a major goal in immunology .", "This unique population of T cells is characterised by expression of an invariant Vα14Jα18 TCR—Vα24Jα18 in humans—and the recognition of glycolipid antigens presented by...	[ "The glycosphingolipid isoglobotrihexosylceramide , or isogloboside 3 ( iGb3 ) , is believed to be critical for natural killer T ( NKT ) cell development and self-recognition in mice and humans .", "Furthermore , iGb3 may represent an important obstacle in xenotransplantation , in which this lipid represents the ...	[ "Identification of endogenous antigens that regulate natural killer T ( NKT ) cell development and function is a major goal in immunology .", "Originally the glycosphingolipid , iGb3 , was suggested to be the main endogenous ligand in both mice and humans .", "However , recent studies have challenged this hypot...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology and life sciences", "plant science" ]	Heat-Induced Release of Epigenetic Silencing Reveals the Concealed Role of an Imprinted Plant Gene	journal.pgen.1004806	null	[ [ "It has been long recognized that transcriptional gene silencing ( TGS ) in plants is associated mainly with increased levels of DNA methylation [1] , [2] .", "DNA methylation is found in cytosines ( C ) residing in CG , CHG and CHH sequence contexts ( where H stands for A , T or C ) .", "Methyltransf...	[ "Epigenetic mechanisms suppress the transcription of transposons and DNA repeats; however , this suppression can be transiently released under prolonged heat stress .", "Here we show that the Arabidopsis thaliana imprinted gene SDC , which is silent during vegetative growth due to DNA methylation , is activated b...	[ "In plants , expression of certain imprinted genes is restricted to embryo nourishing tissue , the endosperm .", "Since these genes are silenced by epigenetic mechanisms during vegetative growth , it has been assumed that they have no role in this phase of the plant life cycle .", "Here , we report on heat-medi...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Efficient Characterization of Parametric Uncertainty of Complex (Bio)chemical Networks	journal.pcbi.1004457	null	[ [ "Chemical reaction networks ( CRNs ) form the basis for analyzing , for instance , cell signaling processes because they capture how molecular species such as proteins interact through reactions , for example , to form larger macromolecular complexes .", "In the limit of ( sufficiently ) high copy numbers...	[ "Parametric uncertainty is a particularly challenging and relevant aspect of systems analysis in domains such as systems biology where , both for inference and for assessing prediction uncertainties , it is essential to characterize the system behavior globally in the parameter space .", "However , current method...	[ "In various scientific domains , in particular in systems biology , dynamic mathematical models of increasing complexity are being developed and analyzed to study biochemical reaction networks .", "A major challenge in dealing with such models is the uncertainty in parameters such as kinetic constants; how to eff...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology" ]	Induction of GADD34 Is Necessary for dsRNA-Dependent Interferon-β Production and Participates in the Control of Chikungunya Virus Infection	journal.ppat.1002708	null	[ [ "During their replication in host cells , RNA and DNA viruses generate RNA intermediates , which elicit antiviral responses mostly through type-I interferon ( IFN ) production [1] , [2] .", "Several families of proteins are known to sense double-stranded RNA ( dsRNA ) , including endocytic Toll-like recep...	[ "Nucleic acid sensing by cells is a key feature of antiviral responses , which generally result in type-I Interferon production and tissue protection .", "However , detection of double-stranded RNAs in virus-infected cells promotes two concomitant and apparently conflicting events .", "The dsRNA-dependent prote...	[ "Nucleic acids detection by multiple molecular sensors results in type-I interferon production , which protects cells and tissues from viral infections .", "At the intracellular level , the detection of double-stranded RNA by one of these sensors , the dsRNA-dependent protein kinase also leads to the profound inh...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "immunology/immunomodulation", "immunology/immunity to infections", "immunology/immune response", "infectious diseases/protozoal infections" ]	IL-17 Produced during Trypanosoma cruzi Infection Plays a Central Role in Regulating Parasite-Induced Myocarditis	journal.pntd.0000604	null	[ [ "Trypanosoma cruzi is an intracellular protozoan parasite that causes Chagas' disease , the major cause of infectious heart disease in Latin America .", "It is estimated that 13 million people are infected with T . cruzi in the Central and South America , and 75 million are at potential risk of infection ...	[ "Chagas disease is a neglected disease caused by the intracellular parasite Trypanosoma cruzi .", "Around 30% of the infected patients develop chronic cardiomyopathy or megasyndromes , which are high-cost morbid conditions .", "Immune response against myocardial self-antigens and exacerbated Th1 cytokine produc...	[ "Chagas disease is caused by the intracellular parasite Trypanosoma cruzi .", "This infection has been considered one of the most neglected diseases and affects several million people in the Central and South America .", "Around 30% of the infected patients develop digestive and cardiac forms of the disease .",...	2010
[ "Introduction", "Methods", "Results", "Discussion and review of the literature" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "mycetoma", "pathogens", "tropical diseases", "microbiology", "geographical locations", "surgical and invasive medical procedures", "acremonium", "nocardia", "signs and symptoms", "pharmaceutics", "neglected tropical diseas...	Review of 21 cases of mycetoma from 1991 to 2014 in Rio de Janeiro, Brazil	journal.pntd.0005301	null	[ [ "Mycetoma is a chronic subcutaneous infections caused by the inoculation of filamentous fungi ( eumycetoma ) or aerobic filamentous bacteria ( actinomycetoma ) that form grains in the affected tissues [1] .", "It´s considered a neglected disease by the World Health Organization ( WHO ) since 2016 and rema...	[ "Mycetoma is caused by the subcutaneous inoculation of filamentous fungi or aerobic filamentous bacteria that form grains in the tissue .", "The purpose of this study is to describe the epidemiologic , clinic , laboratory , and therapeutic characteristics of patients with mycetoma at the Oswaldo Cruz Foundation i...	[ "Mycetoma is a major health problem in tropical areas and is prevalent among people of low socio-economic status .", "As in many other regions of the world , the incidence and prevalence of mycetoma in Brazil is unknown .", "This study describes some aspects of mycetoma patients in 24 years of experience at the...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "behavioral and social aspects of health", "sociology", "tropical diseases", "social sciences", "anthropology", "parasitic diseases", "filariasis", "pharmaceutics", "global health", "neglected tropical diseases", "cultural anthropology", "lymphatic filariasis"...	The division of labour between community medicine distributors influences the reach of mass drug administration: A cross-sectional study in rural Uganda	journal.pntd.0007685	null	[ [ "For public interventions , the first-informed individuals influence the spread of information and uptake within the target population [1] .", "Understanding who should be the first-informed individuals or the deliverers of an intervention is a widespread challenge for any area of public policy , but in p...	[ "Despite decades of community-based mass drug administration ( MDA ) for neglected tropical diseases , it remains an open question as to what constitutes the best combination of community medicine distributors ( CMDs ) for achieving high ( >65%/75% ) treatment rates within a village .", "Routine community-based M...	[ "Community-based mass drug administration ( MDA ) uses volunteers within at-risk communities to distribute preventive chemotherapies en masse for neglected tropical diseases .", "Treatment rates achieved by community medicine distributors ( CMDs ) vary widely and can undermine morbidity control .", "We studied ...	2019
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Predicting the Risk of Rheumatoid Arthritis and Its Age of Onset through Modelling Genetic Risk Variants with Smoking	journal.pgen.1003808	null	[ [ "Rheumatoid arthritis ( RA ) is a common chronic inflammatory disorder .", "It results in substantial morbidity and disability alongside high medical and societal costs [1] , [2] .", "There is therefore growing interest in preventing its development .", "Such prevention requires an ability to reli...	[ "The improved characterisation of risk factors for rheumatoid arthritis ( RA ) suggests they could be combined to identify individuals at increased disease risks in whom preventive strategies may be evaluated .", "We aimed to develop an RA prediction model capable of generating clinically relevant predictive data...	[ "Rheumatoid arthritis ( RA ) is a common , incurable disease with major individual and health service costs .", "Preventing its development is therefore an important goal .", "Being able to predict who will develop RA would allow researchers to look at ways to prevent it .", "Many factors have been found that...	2013
[ "Introduction", "Methods", "Results", "Discussion", "Conclusion" ]	[]	Costs of Testing for Ocular Chlamydia trachomatis Infection Compared to Mass Drug Administration for Trachoma in The Gambia: Application of Results from the PRET Study	journal.pntd.0003670	null	[ [ "Trachoma , caused by ocular infection with Chlamydia trachomatis ( Ct ) , is the leading infectious cause of blindness worldwide and is estimated to cause 3 . 6% of the world’s blindness [1] .", "The presence of follicles and inflammation in the upper tarsal conjunctiva , known as active trachoma , is ch...	[ "Mass drug administration ( MDA ) treatment of active trachoma with antibiotic is recommended to be initiated in any district where the prevalence of trachoma inflammation , follicular ( TF ) is ≥10% in children aged 1–9 years , and then to continue for at least three annual rounds before resurvey .", "In The Gam...	[ "Trachoma , caused by infection with a bacterium ( chlamydia ) is controlled by mass drug administration ( MDA ) , which is recommended yearly for districts in which a trachoma problem has been found to exist .", "The decision , after several rounds , that MDA is no longer needed is currently based on clinical si...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genome-wide association studies", "genome sequencing", "genomics", "heredity", "genetics", "biology", "quantitative traits", "genetics and genomics", "complex traits" ]	Fine Mapping of Five Loci Associated with Low-Density Lipoprotein Cholesterol Detects Variants That Double the Explained Heritability	journal.pgen.1002198	null	[ [ "In the past few years , genome-wide association studies ( GWAS ) have identified hundreds of genetic variants associated with quantitative traits and diseases , providing valuable information about their underlying mechanisms ( for a recent example , see [1] ) .", "More than 2 , 000 common variants appea...	[ "Complex trait genome-wide association studies ( GWAS ) provide an efficient strategy for evaluating large numbers of common variants in large numbers of individuals and for identifying trait-associated variants .", "Nevertheless , GWAS often leave much of the trait heritability unexplained .", "We hypothesized...	[ "Despite the striking success of genome-wide association studies in identifying genetic loci associated with common complex traits and diseases , much of the heritable risk for these traits and diseases remains unexplained .", "A higher resolution investigation of the genome through sequencing studies is expected...	2011
[ "Introduction", "Results and discussion", "Methods" ]	[ "carbohydrate metabolism", "metabolic networks", "brassica", "glucose metabolism", "optimization", "model organisms", "mathematics", "network analysis", "experimental organism systems", "plants", "thermodynamics", "research and analysis methods", "arabidopsis thaliana", "computer and infor...	On the effects of alternative optima in context-specific metabolic model predictions	journal.pcbi.1005568	null	[ [ "Genome-scale metabolic models ( GEMs ) have proven instrumental in characterizing the activity of metabolic pathways in different biological scenarios .", "The activity of all metabolic reactions is specified by the flux distribution , which can be readily inferred from GEMs through the usage of constrai...	[ "The integration of experimental data into genome-scale metabolic models can greatly improve flux predictions .", "This is achieved by restricting predictions to a more realistic context-specific domain , like a particular cell or tissue type .", "Several computational approaches to integrate data have been pro...	[ "Recent methodological developments have facilitated the integration of high-throughput data into genome-scale models to obtain context-specific metabolic reconstructions .", "A unique solution to this data integration problem often may not be guaranteed , leading to a multitude of context-specific predictions eq...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "gene networks", "rna interference", "gene regulation", "immunology", "gene function", "bacterial diseases", "neglected tropical diseases", "epigenetics", "molecular genetics", "signaling pathways", "infectious diseases", "inflammation", "extracellular matrix", "gene expressi...	Conjunctival MicroRNA Expression in Inflammatory Trachomatous Scarring	journal.pntd.0002117	null	[ [ "Chlamydia trachomatis ( Ct ) is the causative agent of trachoma , the leading cause of blindness that results from infection .", "Forty million people have active trachoma and eight million people suffer with unoperated trichiasis [1] .", "Repeated infection of the conjunctiva by this intracellular b...	[ "Trachoma is a fibrotic disease of the conjunctiva initiated by Chlamydia trachomatis infection .", "This blinding disease affects over 40 million people worldwide yet the mechanisms underlying its pathogenesis remain poorly understood .", "We have investigated host microRNA ( miR ) expression in health ( N ) a...	[ "Trachoma is a debilitating disease that affects 40 million people worldwide .", "It can cause progressive fibrosis of the upper eyelid and blindness , yet the mechanism is poorly understood .", "We have investigated the expression of short sequences of genetic material ( microRNA ) that regulate gene expressio...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular probe techniques", "dna-binding proteins", "microbiology", "viruses", "dna replication", "dna viruses", "dna", "molecular biology techniques", "microbial genetics", "gel electrophoresis", "research and analysis methods", "electrophoretic techniques", "electrophoretic blotting", ...	Live-Cell Imaging of Vaccinia Virus Recombination	journal.ppat.1005824	null	[ [ "Genetic recombination serves an essential role as a mechanism for repairing DNA damage , especially the double-stranded breaks that are produced when the replication machinery encounters single-stranded nicks in template DNA .", "In the field of virology , recombination was first used to define and map b...	[ "Recombination between co-infecting poxviruses provides an important mechanism for generating the genetic diversity that underpins evolution .", "However , poxviruses replicate in membrane-bound cytoplasmic structures known as factories or virosomes .", "These are enclosed structures that could impede DNA mixin...	[ "Recombination plays a critical role in DNA repair and also creates the genetic diversity that underpins evolution .", "This has important implications for viruses , since recombination may create new pathogens with new infectious properties .", "It has long been known that hybrids can be recovered from cells c...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology", "microbiology", "host-pathogen interaction", "bacterial pathogens" ]	Opposing Roles for Interferon Regulatory Factor-3 (IRF-3) and Type I Interferon Signaling during Plague	journal.ppat.1002817	null	[ [ "Type I interferons ( IFN-I ) are expressed by macrophages and epithelial cells as part of the first line of defense against infection , and the IFN-I receptor ( IFNAR ) is expressed by most cells [1] .", "IFN-I signaling following bacterial infection leads to the production of pro-inflammatory cytokines ...	[ "Type I interferons ( IFN-I ) broadly control innate immunity and are typically transcriptionally induced by Interferon Regulatory Factors ( IRFs ) following stimulation of pattern recognition receptors within the cytosol of host cells .", "For bacterial infection , IFN-I signaling can result in widely variant re...	[ "Type I interferons ( IFN-I ) broadly stimulate innate immunity against viral , bacterial and parasitic pathogens .", "Many bacterial pathogens induce IFN-I through phosphorylation of Interferon Regulatory Factor 3 ( IRF-3 ) allowing it to bind promoters containing Interferon Stimulated Response Elements ( ISRE )...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "cell biology/cellular death and stress responses", "cell biology/cell signaling", "mathematics", "biophysics/biomacromolecule-ligand interactions", "computational biology/systems biology" ]	Bistability in Apoptosis by Receptor Clustering	journal.pcbi.1000956	null	[ [ "Apoptosis is a coordinated cell death program employed by multicellular organisms that plays a central role in many physiological processes .", "Normal function of apoptosis is critical for development , tissue homeostasis , cell termination , and immune response , and its disruption is associated with p...	[ "Apoptosis is a highly regulated cell death mechanism involved in many physiological processes .", "A key component of extrinsically activated apoptosis is the death receptor Fas which , on binding to its cognate ligand FasL , oligomerize to form the death-inducing signaling complex .", "Motivated by recent exp...	[ "Many prominent diseases , most notably cancer , arise from an imbalance between the rates of cell growth and death in the body .", "This is often due to mutations that disrupt a cell death program called apoptosis .", "Here , we focus on the extrinsic pathway of apoptotic activation which is initiated upon det...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "bacteriology", "evolutionary biology", "microbiology", "gtpase signaling", "microbial evolution", "signaling in cellular processes", "comparative genomics", "biology", "evolutionary genetics", "signal transduction", "genomics", "molecular cell biology", "genomic evolution", "evolutionary ...	A Response Regulator Interfaces between the Frz Chemosensory System and the MglA/MglB GTPase/GAP Module to Regulate Polarity in Myxococcus xanthus	journal.pgen.1002951	null	[ [ "The ability of cells to generate polarized distributions of signaling proteins facilitates many biological processes including cell growth , division , differentiation and motility [1] .", "The spatial confinement of the activity of signaling proteins lays the foundation for processes that require locali...	[ "How cells establish and dynamically change polarity are general questions in cell biology .", "Cells of the rod-shaped bacterium Myxococcus xanthus move on surfaces with defined leading and lagging cell poles .", "Occasionally , cells undergo reversals , which correspond to an inversion of the leading-lagging ...	[ "Most cells are spatially organized with proteins localizing to specific regions .", "The ability of cells to polarize facilitates many processes including motility .", "Myxococcus xanthus cells move in the direction of their long axis and occasionally change direction of movement by undergoing reversals .", ...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "bacteriology", "infectious diseases", "medicine and health sciences", "diagnostic medicine", "medical microbiology", "virology", "molecular probe techniques", "biology and life sciences", "molecular biology techniques", "microbiology", "tropical diseases", "parasitic diseases", "molecular b...	An Integrated Lab-on-Chip for Rapid Identification and Simultaneous Differentiation of Tropical Pathogens	journal.pntd.0003043	null	[ [ "Many infectious diseases are more prevalent in the tropical and subtropical regions where ecological , geographical and socioeconomic factors facilitate their propagation .", "The high diversity of such tropical pathogens include bacteria , fungi , helminths , parasites , and viruses that mirrors the ric...	[ "Tropical pathogens often cause febrile illnesses in humans and are responsible for considerable morbidity and mortality .", "The similarities in clinical symptoms provoked by these pathogens make diagnosis difficult .", "Thus , early , rapid and accurate diagnosis will be crucial in patient management and in t...	[ "Tropical diseases consist of a group of debilitating and fatal infections that occur primarily in rural and urban settings of tropical and subtropical countries .", "While the primary indices of an infection are mostly the presentation of clinical signs and symptoms , outcomes due to an infection with tropical p...	2014
[ "Introduction", "Methods", "Results", "Observations of the distribution of yaws in Bankim", "Discussion" ]	[ "children", "medicine and health sciences", "pathology and laboratory medicine", "education", "sociology", "tropical diseases", "geographical locations", "social sciences", "health care", "treponematoses", "bacterial diseases", "age groups", "signs and symptoms", "pharmaceutics", "neglec...	Yaws resurgence in Bankim, Cameroon: The relative effectiveness of different means of detection in rural communities	journal.pntd.0005557	null	[ [ "Yaws is an infectious , debilitating , and disfiguring disease of poverty that mainly affects children and adolescents living in rural communities in tropical areas of Africa , the Pacific Islands , and Southeast Asia with high levels of rainfall .", "Caused by the spirochete bacteria Treponema pallidum ...	[ "Yaws is an infectious , debilitating and disfiguring disease of poverty that mainly affects children in rural communities in tropical areas .", "In Cameroon , mass-treatment campaigns carried out in the 1950s reduced yaws to such low levels that it was presumed the disease was eradicated .", "In 2010 , an epid...	[ "Yaws is an infectious and disfiguring disease of poverty primarily affecting children in rural communities in tropical areas .", "Yaws is easily treated by a single dose of antibiotics and is on the World Health Organization’s eradication list .", "Yaws was thought eradicated in the Cameroon in the 1950s follo...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "mus (mouse)", "molecular biology", "developmental biology" ]	Cis- and Trans-Acting Elements Regulate the Mouse Psmb9 Meiotic Recombination Hotspot	journal.pgen.0030100	null	[ [ "In most eukaryotes , the formation of at least one reciprocal exchange , or crossover ( CO ) , per chromosome pair between nonsister chromatids provides the physical connection that is required for the segregation of homologous chromosomes at the first meiotic division .", "The molecular mechanism of mei...	[ "In most eukaryotes , the prophase of the first meiotic division is characterized by a high level of homologous recombination between homologous chromosomes .", "Recombination events are not distributed evenly within the genome , but vary both locally and at large scale .", "Locally , most recombination events ...	[ "In most sexually reproducing species , during meiosis a high level of recombination between homologous chromosomes is induced .", "These events are not evenly distributed in the genome but clustered in small regions called hotspots .", "The genetic factors controlling their activity in mammals are still poorly...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "paleozoology", "paleobiology", "vertebrate paleontology", "earth sciences", "paleontology", "biology and life sciences", "evolutionary theory", "evolutionary biology", "evolutionary processes" ]	Rates of Dinosaur Body Mass Evolution Indicate 170 Million Years of Sustained Ecological Innovation on the Avian Stem Lineage	journal.pbio.1001853	Early dinosaurs showed rapid evolutionary rates, which were sustained on the line leading to birds. Maintenance of evolvability in key lineages might explain the uneven distribution of trait diversity among groups of animal species.	[ [ "Much of extant biodiversity may have arisen from a small number of adaptive radiations occurring on large spatiotemporal scales [1]–[3] .", "Under the niche-filling model of adaptive radiation , ecological opportunities arise from key innovations , the extinction of competitors , or geographic dispersal ...	[ "Large-scale adaptive radiations might explain the runaway success of a minority of extant vertebrate clades .", "This hypothesis predicts , among other things , rapid rates of morphological evolution during the early history of major groups , as lineages invade disparate ecological niches .", "However , few st...	[ "Animals display huge morphological and ecological diversity .", "One possible explanation of how this diversity evolved is the \"niche filling\" model of adaptive radiation—under which evolutionary rates are highest early in the evolution of a group , as lineages diversify to fill disparate ecological niches .",...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology/germ cells", "genetics and genomics/chromosome biology", "cell biology/nuclear structure and function" ]	A Yeast Two-Hybrid Screen for SYP-3 Interactors Identifies SYP-4, a Component Required for Synaptonemal Complex Assembly and Chiasma Formation in Caenorhabditis elegans Meiosis	journal.pgen.1000669	null	[ [ "The synaptonemal complex ( SC ) is a proteinaceous structure formed between each pair of homologous chromosomes during meiotic prophase I . Meiotic recombination unfolds , and crossover events are completed , in the context of this structure .", "The formation of these crossover events is a prerequisite ...	[ "The proper assembly of the synaptonemal complex ( SC ) between homologs is critical to ensure accurate meiotic chromosome segregation .", "The SC is a meiotic tripartite structure present from yeast to humans , comprised of proteins assembled along the axes of the chromosomes and central region ( CR ) proteins t...	[ "Meiosis is a two-part cell division program that ensures the formation of haploid gametes ( e . g . eggs and sperm ) , which can then reconstitute a species' ploidy through fertilization .", "A critical step towards accomplishing this task is the accurate segregation of homologous chromosomes away from each othe...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases", "immunology", "medicine and health sciences" ]	Toll-Like Receptor 8 Agonist and Bacteria Trigger Potent Activation of Innate Immune Cells in Human Liver	journal.ppat.1004210	null	[ [ "The liver is an essential organ at the center of carbohydrate , lipid and protein metabolisms .", "It is crucial for clearing toxins and pathogens that reach the circulatory compartment from the gut .", "The liver is also home to abundant populations of innate immune cells ( monocytes , NK and NKT ce...	[ "The ability of innate immune cells to sense and respond to impending danger varies by anatomical location .", "The liver is considered tolerogenic but is still capable of mounting a successful immune response to clear various infections .", "To understand whether hepatic immune cells tune their response to dif...	[ "The ability of human pathogens , like HBV , HCV or Plasmodium spp .", "to infect the liver might be influenced by its tolerogenic features .", "However , hepatic tolerance is not absolute since protective immunity can be triggered .", "Our goal was to define how to deliberately elicit an intrahepatic protect...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "sequencing techniques", "invertebrates", "medicine and health sciences", "luciferase", "rna interference", "gene regulation", "enzymes", "microbiology", "enzymology", "animals", "viruses", "epigenetics", "molecular biology techniques", "rna sequencing", "insect vectors", "research and...	The Antiviral RNAi Response in Vector and Non-vector Cells against Orthobunyaviruses	journal.pntd.0005272	null	[ [ "Orthobunyaviruses are endemic in tropical and subtropical regions worldwide and are transmitted by mosquitoes , midges , ticks or other arthropods .", "The Orthobunyavirus genus within the Bunyaviridae family comprises at least 30 viruses that can cause disease in humans , including Oropouche virus ( ORO...	[ "Vector arthropods control arbovirus replication and spread through antiviral innate immune responses including RNA interference ( RNAi ) pathways .", "Arbovirus infections have been shown to induce the exogenous small interfering RNA ( siRNA ) and Piwi-interacting RNA ( piRNA ) pathways , but direct antiviral ac...	[ "A number of orthobunyaviruses such as Oropouche virus , La Crosse virus and Schmallenberg virus are important global human or animal pathogens transmitted by arthropod vectors .", "Further understanding of the antiviral control mechanisms in arthropod vectors is key to developing novel prevention strategies base...	2017
[ "Introduction", "Results", "Discussion", "Materials & Methods" ]	[]	Convergent Evolution During Local Adaptation to Patchy Landscapes	journal.pgen.1005630	null	[ [ "The convergent evolution of similar phenotypes in response to similar selection pressures is a testament to the power that selection has to sculpt phenotypic variation .", "In some cases this convergence extends to the molecular level , with disparate taxa converging to the same phenotype through paralle...	[ "Species often encounter , and adapt to , many patches of similar environmental conditions across their range .", "Such adaptation can occur through convergent evolution if different alleles arise in different patches , or through the spread of shared alleles by migration acting to synchronize adaptation across t...	[ "Often , a large species range will include patches where the species differs because it has adapted to locally differing conditions .", "For instance , rock pocket mice are often found with a coat color that matches the rocks they live in , these color differences are controlled genetically , and mice that don’t...	2015
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "biotechnology", "systems biology", "biochemistry", "theoretical biology", "biology", "computational biology", "marine biology" ]	Flux Balance Analysis of Cyanobacterial Metabolism: The Metabolic Network of Synechocystis sp. PCC 6803	journal.pcbi.1003081	null	[ [ "Almost all life on Earth ultimately depends on oxygenic photosynthesis to capture solar energy and convert atmospheric carbon into organic compounds that serve as nutrients for heterotrophic organisms .", "Photosynthesis and the assimilation of inorganic carbon are evolutionarily old processes , with sig...	[ "Cyanobacteria are versatile unicellular phototrophic microorganisms that are highly abundant in many environments .", "Owing to their capability to utilize solar energy and atmospheric carbon dioxide for growth , cyanobacteria are increasingly recognized as a prolific resource for the synthesis of valuable chemi...	[ "Phototrophic microorganisms hold great promises as a resource to generate high-value products and biofuels using only atmospheric carbon dioxide , light , and some minerals .", "In particular cyanobacteria , the only known prokaryotes capable of oxygen-evolving photosynthesis , have attracted recent attention as...	2013
[ "Introduction", "Results", "Discussion", "Models" ]	[ "physics", "systems biology", "developmental biology", "plant science", "condensed-matter physics", "organism development", "mathematics", "theoretical biology", "plant biology", "biology", "computational biology", "biophysics", "nonlinear dynamics", "genetics and genomics" ]	Noise and Robustness in Phyllotaxis	journal.pcbi.1002389	null	[ [ "The shoot apex is a major organizer of the aerial architecture of vascular plants .", "Lateral organs ( leaves and flowers ) are successively initiated as primordia at the shoot apex yielding a regular arrangement on the stem known as phyllotaxis .", "Two main categories of phyllotactic patterns are ...	[ "A striking feature of vascular plants is the regular arrangement of lateral organs on the stem , known as phyllotaxis .", "The most common phyllotactic patterns can be described using spirals , numbers from the Fibonacci sequence and the golden angle .", "This rich mathematical structure , along with the exper...	[ "How living organisms affected by natural , stochastic variability achieve regular developmental patterns is a challenging question in biology .", "A fitting field of investigation is provided by phyllotaxis , the regular arrangements of lateral organs such as leaves or flowers on the stem of vascular plants , as...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "test evaluation", "diagnostic medicine", "leishmaniasis", "protozoan infections", "parasitic diseases" ]	Leishmaniasis Direct Agglutination Test: Using Pictorials as Training Materials to Reduce Inter-Reader Variability and Improve Accuracy	journal.pntd.0001946	null	[ [ "Up until the 1990's accurate visceral leishmaniasis ( VL ) diagnosis necessitated parasitological confirmation by microscopy or culture of the blood , bone-marrow , lymph nodes or spleen [1] .", "Microscopic detection of parasites in clinical material from the spleen is still considered the reference sta...	[ "The Direct Agglutination Test ( DAT ) has a high diagnostic accuracy and remains , in some geographical areas , part of the diagnostic algorithm for Visceral Leishmaniasis ( VL ) .", "However , subjective interpretation of results introduces potential for inter-reader variation .", "We report an assessment of ...	[ "Until the 1990's accurate Visceral Leishmaniasis ( VL ) diagnosis necessitated parasitological confirmation by microscopy or culture of the blood , bone-marrow , lymph nodes or spleen .", "These techniques are invasive and splenic aspirates are associated with a risk of serious bleeding .", "This has led to th...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "parasite evolution", "population genetics", "immunology", "microbiology", "host-pathogen interaction", "parasitic diseases", "plasmodium falciparum", "parasitology", "genome sequencing", "adaptive immunity", "infectious diseases", "genetic polymorphism", "biology", "protozoa...	Population Genomic Scan for Candidate Signatures of Balancing Selection to Guide Antigen Characterization in Malaria Parasites	journal.pgen.1002992	null	[ [ "Evolutionary and population genetic analyses of pathogens should help discover mechanisms of pathogenesis , immune evasion and drug resistance .", "Application of these approaches to malaria parasites is a high priority , as there is an ongoing need to identify targets of immunity as potential vaccine ca...	[ "Acquired immunity in vertebrates maintains polymorphisms in endemic pathogens , leading to identifiable signatures of balancing selection .", "To comprehensively survey for genes under such selection in the human malaria parasite Plasmodium falciparum , we generated paired-end short-read sequences of parasites i...	[ "The memory component of acquired immune responses selects for distinctive patterns of polymorphism in genes encoding important target antigens of pathogens .", "These are detectable by surveying for evidence of balancing selection , as previously illustrated in analyses of genes encoding malaria parasite antigen...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology/microbial physiology and metabolism", "cell biology", "microbiology/microbial evolution and genomics", "cell biology/microbial growth and development", "microbiology", "evolutionary biology", "evolutionary biology/morphogenesis and cell biology" ]	A Tether for Woronin Body Inheritance Is Associated with Evolutionary Variation in Organelle Positioning	journal.pgen.1000521	null	[ [ "Membrane bound organelles are fundamental constituents of eukaryotic cells that execute wide-ranging functions associated with growth and development .", "Some organelle functions are ubiquitous while others are only found in evolutionarily related organisms and perform lifestyle supporting adaptive func...	[ "Eukaryotic organelles evolve to support the lifestyle of evolutionarily related organisms .", "In the fungi , filamentous Ascomycetes possess dense-core organelles called Woronin bodies ( WBs ) .", "These organelles originate from peroxisomes and perform an adaptive function to seal septal pores in response to...	[ "In the kingdom Fungi , tubular cells called hyphae grow by tip extension and lateral branching to produce an interconnected multicellular syncytium and this unique cellular architecture is especially suited to foraging , long distance transport , and invasive growth .", "Major groups of fungi have independently ...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "health services research", "engineering and technology", "transportation", "pathogens", "tropical diseases", "geographical locations", "microbiology", "ebola hemorrhagic fever", "health care", "organisms", "viruses", "fi...	Fears and Misperceptions of the Ebola Response System during the 2014-2015 Outbreak in Sierra Leone	journal.pntd.0005077	null	[ [ "Countries without the capacity to conduct surveillance , monitor , or control outbreaks are particularly at risk for negative consequences of infectious disease epidemics [1] .", "These countries’ inability to swiftly contain infectious diseases can result in global vulnerability to epidemic spread [2] ....	[ "Future infectious disease epidemics are likely to disproportionately affect countries with weak health systems , exacerbating global vulnerability .", "To decrease the severity of epidemics in these settings , lessons can be drawn from the Ebola outbreak in West Africa .", "There is a dearth of literature on p...	[ "To decrease the severity of epidemics in countries with under-developed health system capacity to control outbreaks , lessons can be drawn from the Ebola outbreak in West Africa .", "This is the first study , to our knowledge , to use qualitative research methods to understand community members’ perceptions of u...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Genome-Wide Scan and Test of Candidate Genes in the Snail Biomphalaria glabrata Reveal New Locus Influencing Resistance to Schistosoma mansoni	journal.pntd.0004077	null	[ [ "Approximately one-sixth of the global burden of infectious disease in humans is due to parasites transmitted by invertebrate hosts [1] .", "A major avenue to combat these diseases lies in understanding the genetic and biochemical basis for natural variation in host resistance [2] , [3] .", "The ident...	[ "New strategies to combat the global scourge of schistosomiasis may be revealed by increased understanding of the mechanisms by which the obligate snail host can resist the schistosome parasite .", "However , few molecular markers linked to resistance have been identified and characterized in snails .", "Here w...	[ "Aquatic snails transmit schistosome blood flukes , causing a parasitic disease second only to malaria in its global health impact .", "The mechanisms by which some snails naturally resist infection are poorly understood , but if characterized could enable protocols to interfere with transmission of the disease ....	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "microbiology/immunity to infections", "infectious diseases/fungal infections", "microbiology/innate immunity", "immunology/innate immunity", "cell biology/cytoskeleton" ]	A Novel Pseudopodial Component of the Dendritic Cell Anti-Fungal Response: The Fungipod	journal.ppat.1000760	null	[ [ "The innate immune response against fungal pathogens is effected by macrophages , neutrophils and dendritic cells ( DC ) .", "DC may encounter opportunistic fungi , such as Candida species , in cutaneous and mucosal tissue as well as in disseminated infections associated with serious disease .", "The ...	[ "Fungal pathologies are seen in immunocompromised and healthy humans .", "C-type lectins expressed on immature dendritic cells ( DC ) recognize fungi .", "We report a novel dorsal pseudopodial protrusion , the “fungipod” , formed by DC after contact with yeast cell walls .", "These structures have a convolute...	[ "Yeasts are normal microbial commensals of humans and a significant source of opportunistic infections , especially in immunocompromised individuals .", "We report a novel cellular protrusive structure , the fungipod , which participates in the host-microbe interaction between human immature dendritic cells ( DC ...	2010
[ "Introduction", "Results", "Discussion", "Methods", "Supporting Information" ]	[ "yeast and fungi", "computational biology", "biophysics", "genetics and genomics", "saccharomyces" ]	Molecular Basis for Evolving Modularity in the Yeast Protein Interaction Network	journal.pcbi.0030226	null	[ [ "Scale-free networks have been proposed as universal models to describe diverse complex systems such as the Internet , social interactions , and metabolic and proteomic networks [1 , 2] .", "The scale-free “topology” is defined by a power-law distribution: A ( n ) ∝ n−γ , where A ( n ) is the abundance of...	[ "Scale-free networks are generically defined by a power-law distribution of node connectivities .", "Vastly different graph topologies fit this law , ranging from the assortative , with frequent similar-degree node connections , to a modular structure .", "Using a metric to determine the extent of modularity , ...	[ "The protein interaction network or interactome emerged as a powerful descriptor in the large-scale phenotypic studies of the post-genomic era .", "A major concern in such analysis is the integration of interactomic information with other phenotypic descriptors such as expression profile , co-localization , devel...	2007
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases/sexually transmitted diseases", "infectious diseases/infectious diseases of the nervous system", "infectious diseases/viral infections", "infectious diseases/epidemiology and control of infectious diseases" ]	Genetic Characterization of Human T-Cell Lymphotropic Virus Type 1 in Mozambique: Transcontinental Lineages Drive the HTLV-1 Endemic	journal.pntd.0001038	null	[ [ "Human T-cell lymphotropic virus type 1 was the first oncogenic human retrovirus to be identified in 1980 [1] In 1982 , the second type , HTLV-2 , was discovered [2] .", "These two human viruses originated independently through zoonotic infections from lineages of simian T-lymphotropic virus ( STLV-1 and ...	[ "Human T-Cell Lymphotropic Virus Type 1 ( HTLV-1 ) is the etiological agent of adult T-cell leukemia ( ATL ) and HTLV-1-associated myelopathy/tropical spastic paraparesis ( HAM/TSP ) .", "It has been estimated that 10–20 million people are infected worldwide , but no successful treatment is available .", "Recen...	[ "Human T-cell lymphotropic virus type 1 ( HTLV-1 ) is the causative agent of Adult T-Cell Leukemia/Lymphoma ( ATL ) , the Tropical Spastic Paraparesis/HTLV-1-associated Myelopathy ( TSP/HAM ) and other inflammatory diseases , including dermatitis , uveitis , and myositis .", "It is estimated that 2–8% of the infe...	2011
[ "Introduction", "Methods", "Results/Discussion" ]	[ "computational biology", "biophysics/rna structure" ]	Efficient Algorithms for Probing the RNA Mutation Landscape	journal.pcbi.1000124	null	[ [ "RNA's ubiquitous role in regulation and development is now understood to be much more important than previously believed .", "Apart from messenger RNA ( mRNA ) , transfer RNA ( tRNA ) and ribosomal RNA ( rRNA ) , there are many important enzymatic and regulatory functions of RNA , and it seems clear that...	[ "The diversity and importance of the role played by RNAs in the regulation and development of the cell are now well-known and well-documented .", "This broad range of functions is achieved through specific structures that have been ( presumably ) optimized through evolution .", "State-of-the-art methods , such ...	[ "Evolution is a central concept in biology .", "This phenomenon can be observed at all levels of the organization of life—from single molecules to multicellular organisms .", "Here , we focus our attention on the implication of evolution at the level of nucleic acid sequences .", "In this context , RNA sequen...	2008
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "antigen-presenting cells", "immunology", "microbiology", "developmental biology", "clinical medicine", "cytotoxic t cells", "microbial growth and development", "bacteria", "white blood cells", "major histocompatibility complex",...	Mycobacterium tuberculosis-specific CD4+ and CD8+ T cells differ in their capacity to recognize infected macrophages	journal.ppat.1007060	null	[ [ "Unlike most disease-causing pathogens , Mycobacterium tuberculosis ( Mtb ) , the cause of tuberculosis ( TB ) , persists in humans because of its highly evolved ability to evade and subvert the host immunity [1] .", "Mtb subverts vesicular trafficking , prevents phagolysosome fusion , and replicates in a...	[ "Containment of Mycobacterium tuberculosis ( Mtb ) infection requires T cell recognition of infected macrophages .", "Mtb has evolved to tolerate , evade , and subvert host immunity .", "Despite a vigorous and sustained CD8+ T cell response during Mtb infection , CD8+ T cells make limited contribution to protec...	[ "Immunodominant antigens elicit a large majority of T cells during an infection , and it is presumed that these T cells go on to recognize infected cells .", "Immunodominant antigens produced by Mycobacterium tuberculosis ( Mtb ) have been incorporated into vaccines , but whether T cells specific for these antige...	2018
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "turkey (country)", "medicine and health sciences", "immune physiology", "enzyme-linked immunoassays", "pathology and laboratory medicine", "crimean-congo hemorrhagic fever", "immunology", "tropical diseases", "geographical locations", "peptide libraries", "neglected tropical diseases", "glyco...	Epitope-mapping of the glycoprotein from Crimean-Congo hemorrhagic fever virus using a microarray approach	journal.pntd.0006598	null	[ [ "Crimean-Congo hemorrhagic fever virus ( CCHFV ) is a tick-borne viral zoonosis distributed in Africa , Asia , eastern Europe and the Balkans .", "Ticks belonging to the genus Hyalomma are considered the principal vectors and the broad geographic distribution of the virus correlates with that of the vecto...	[ "Crimean-Congo hemorrhagic fever virus ( CCHFV ) causes severe acute human disease with lethal outcome .", "The knowledge about the immune response for this human health threat is highly limited .", "In this study , we have screened the glycoprotein of CCHFV for novel linear B-cell epitopic regions using a micr...	[ "Crimean-Congo hemorrhagic fever ( CCHF ) is a widespread disease caused by a tick-borne virus belonging to the genus Orthonairovirus of the Nairoviridae family .", "The virus is responsible for outbreaks of severe viral hemorrhagic fever with a case fatality rate of approximately 30% .", "The CCHF virus is tra...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular biology/histone modification", "molecular biology/chromatin structure", "molecular biology/transcription initiation and activation" ]	Chromatin Landscape Dictates HSF Binding to Target DNA Elements	journal.pgen.1001114	null	[ [ "Signal-dependent activation of transcription is a highly regulated process that is dictated by transcriptional activators that selectively identify and function at sequence-specific DNA motifs .", "The most basic function of sequence specific activators is to discriminate between binding sites in the con...	[ "Sequence-specific transcription factors ( TFs ) are critical for specifying patterns and levels of gene expression , but target DNA elements are not sufficient to specify TF binding in vivo .", "In eukaryotes , the binding of a TF is in competition with a constellation of other proteins , including histones , wh...	[ "Many Transcription Factors ( TFs ) have been shown to bind DNA in a sequence-specific manner .", "However , only a sub-set of possible binding sites are occupied in vivo , and it remains unclear how TFs discriminate between sequences of equal predicted binding affinity .", "We set out to determine how a specif...	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "sequencing techniques", "chemical bonding", "molecular dynamics", "dna-binding proteins", "sequence motif analysis", "dna", "dna structure", "molecular biology techniques", "hydrogen bonding", "research and analysis methods", "physical chemistry", "sequence analysis", "bioinformatics", "p...	Predicting the mechanism and rate of H-NS binding to AT-rich DNA	journal.pcbi.1006845	null	[ [ "Bacterial chromosomal DNA is organized within the nucleoid , which is distinctly different from the cytoplasm .", "The organization of the nucleoid in bacteria involves a group of DNA binding proteins known as architectural proteins .", "The Histone-like Nucleoid Structuring protein ( H-NS ) is a arc...	[ "Bacteria contain several nucleoid-associated proteins that organize their genomic DNA into the nucleoid by bending , wrapping or bridging DNA .", "The Histone-like Nucleoid Structuring protein H-NS found in many Gram-negative bacteria is a DNA bridging protein and can structure DNA by binding to two separate DNA...	[ "The Histone-like Nucleoid Structuring protein ( H-NS ) occurs in enterobacteria , such as Salmonella typhimurium and Escherichia coli , and structures DNA by forming filaments along DNA duplexes .", "Several nucleotide sequences have been identified to which H-NS binds with high affinity .", "Yet , obtaining h...	2019
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "body fluids", "tropical diseases", "bile", "microbiology", "parasitic diseases", "parasitic protozoans", "metabolomics", "protozoans", "metabolites", "malarial parasites", "hematology", "biochemistry", "diagnostic medicine", "blood", "anatomy", "virol...	Towards Improving Point-of-Care Diagnosis of Non-malaria Febrile Illness: A Metabolomics Approach	journal.pntd.0004480	null	[ [ "The introduction of malaria rapid diagnostic tests ( RDT ) has revealed that febrile illnesses in the tropics and subtropics are more commonly caused by non-malaria pathogens than by malaria [1–5] .", "Bacterial bloodstream infections ( BSI ) are considered the most severe non-malaria febrile illness , w...	[ "Non-malaria febrile illnesses such as bacterial bloodstream infections ( BSI ) are a leading cause of disease and mortality in the tropics .", "However , there are no reliable , simple diagnostic tests for identifying BSI or other severe non-malaria febrile illnesses .", "We hypothesized that different infecti...	[ "In the tropics , malaria is commonly attributed to be the cause of most childhood fevers , while in fact this condition is more commonly caused by other pathogens that are clinically indistinguishable from malaria .", "These so-called non-malaria febrile illnesses include bacterial bloodstream infections , which...	2016
[ "Introduction", "Models", "Results", "Discussion" ]	[ "bacteriology", "protein interactions", "dna-binding proteins", "microbiology", "database searching", "bacterial genetics", "microbial genetics", "sequence similarity searching", "thermodynamics", "microbial genomics", "research and analysis methods", "bacterial genomics", "sequence analysis...	Mechanisms of fast and stringent search in homologous pairing of double-stranded DNA	journal.pcbi.1005421	null	[ [ "Homologous pairing of DNA molecules is involved in many fundamental biological processes , including homologous recombination in meiosis , interaction between alleles on homologous chromosomes ( transvection ) [1] , and homologous repair of double strand breaks [2] .", "Recent experiments have shown that...	[ "Self-organization in the cell relies on the rapid and specific binding of molecules to their cognate targets .", "Correct bindings must be stable enough to promote the desired function even in the crowded and fluctuating cellular environment .", "In systems with many nearly matched targets , rapid and stringen...	[ "Protein folding and the binding of sequence dependent proteins to DNA are examples of self-assembling systems in which the binding energy varies continuously throughout the interaction .", "Previous theoretical work has highlighted the importance of dividing the interaction into separate stages characterized by ...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "cell death", "protein interactions", "protein interaction networks", "cell processes", "alternative splicing", "mathematics", "forecasting", "statistics (mathematics)", "network analysis", "genome analysis", "research and analysis methods", "computer and information sciences", "protein-prot...	Domain-based prediction of the human isoform interactome provides insights into the functional impact of alternative splicing	journal.pcbi.1005717	null	[ [ "Protein-protein interaction ( PPI ) networks ( also known as interactome networks ) have been extensively studied in systems biology to understand genotype-phenotype relationships and several have been constructed for different model organisms such as human , yeast and bacteria [1–10] .", "The increase i...	[ "Alternative splicing is known to remodel protein-protein interaction networks ( “interactomes” ) , yet large-scale determination of isoform-specific interactions remains challenging .", "We present a domain-based method to predict the isoform interactome from the reference interactome .", "First , we construct...	[ "Protein-protein interaction networks have been extensively used in systems biology to study the role of proteins in cell function and disease .", "However , current network biology studies typically assume that one gene encodes one protein isoform , ignoring the effect of alternative splicing .", "Alternative ...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases", "infectious diseases/neglected tropical diseases", "public health and epidemiology/global health", "infectious diseases/epidemiology and control of infectious\n diseases", "public health and epidemiology/infectious diseases", "microbiology/parasitology" ]	Assessment of the Anthelmintic Efficacy of Albendazole in School Children in Seven Countries Where Soil-Transmitted Helminths Are Endemic	journal.pntd.0000948	null	[ [ "The three major Soil-Transmitted Helminths ( STH ) , Ascaris", "lumbricoides ( roundworm ) , Trichuris trichiura", "( whipworm ) and Necator americanus/Ancylostoma duodenale ( the", "hookworms ) are amongst the most widespread parasites worldwide .", "An estimated 4 . 5", "billion individ...	[ "The three major soil-transmitted helminths ( STH ) Ascaris", "lumbricoides , Trichuris trichiura and", "Necator americanus/Ancylostoma duodenale are among the", "most widespread parasites worldwide .", "Despite the global expansion of", "preventive anthelmintic treatment , standard operating procedures t...	[ "Soil-transmitted helminths ( roundworms , whipworms and hookworms ) infect millions", "of children in ( sub ) tropical countries , resulting in malnutrition , growth", "stunting , intellectual retardation and cognitive deficits .", "Currently , there is a", "need to closely monitor anthelmintic drug effica...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "dengue virus", "medicine and health sciences", "enzyme-linked immunoassays", "immune physiology", "pathology and laboratory medicine", "pathogens", "immunology", "geographical locations", "microbiology", "india", "viruses", "vaccines", "age groups", "rna viruses", "infectious disease co...	Stratified sero-prevalence revealed overall high disease burden of dengue but suboptimal immunity in younger age groups in Pune, India	journal.pntd.0006657	null	[ [ "Dengue disease is an important emerging public health problem in countries of tropical and subtropical regions .", "[1–3] Estimated annual global burden of disease is approximately 390 million infections , 96 million clinical cases , and 20 thousand deaths , with almost 34% of total dengue cases occurrin...	[ "In India , dengue disease is emerging as the most important vector borne public health problem due to rapid and unplanned urbanization , high human density and week management of the disease .", "Clinical cases are grossly underreported and not much information is available on prevalence and incidence of the dis...	[ "Dengue disease , transmitted through the bite of DENV infected mosquitoes , is an increasing health problem in the Asian subcontinent , including India .", "Dengue ranges from mild undifferentiated fever to circulatory shock and potentially death .", "Clinical disease gives an incomplete picture of the magnitu...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biotechnology", "systems biology", "functional genomics", "model organisms", "biology", "genomics", "microbiology", "genetics and genomics", "parasitology", "parasite physiology" ]	Dynamic Epigenetic Regulation of Gene Expression during the Life Cycle of Malaria Parasite Plasmodium falciparum	journal.ppat.1003170	null	[ [ "In spite of worldwide efforts , malaria remains one of the most devastating illnesses with an estimated 216 million episodes leading to 655 , 000 deaths in 2010 [1] .", "The effectiveness of current treatment strategies is attenuated by increasing resistance of malaria parasites to the available chemothe...	[ "Epigenetic mechanisms are emerging as one of the major factors of the dynamics of gene expression in the human malaria parasite , Plasmodium falciparum .", "To elucidate the role of chromatin remodeling in transcriptional regulation associated with the progression of the P . falciparum intraerythrocytic developm...	[ "Malaria is a devastating parasitic disease caused by the protozoan protist Plasmodium falciparum .", "The complex life cycle of P . falciparum comprises various morphological and functionally distinct forms and is completed in two different hosts .", "Various regulatory mechanisms are employed by these parasit...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	FANCI Regulates Recruitment of the FA Core Complex at Sites of DNA Damage Independently of FANCD2	journal.pgen.1005563	null	[ [ "Fanconi anemia ( FA ) is a rare genetic disorder characterized by bone marrow failure , congenital malformations and cancer susceptibility [1] .", "Eighteen FA genes have been identified ( FANC-A , -B , -C , -D1/BRCA2 , -D2 , -E , -F , -G , -I , -J/BRIP1 , -L , -M , -N/PALB2 , -O/RAD51C , -P/SLX4 , -Q/XP...	[ "The Fanconi anemia ( FA ) -BRCA pathway mediates repair of DNA interstrand crosslinks .", "The FA core complex , a multi-subunit ubiquitin ligase , participates in the detection of DNA lesions and monoubiquitinates two downstream FA proteins , FANCD2 and FANCI ( or the ID complex ) .", "However , the regulatio...	[ "Fanconi anemia is a genetic disease characterized by bone marrow failure , congenital malformations and cancer predisposition .", "Cells derived from Fanconi anemia patients have a dysfunctional FA-BRCA pathway and are deficient in the repair of a specific form of DNA damage , DNA interstrand-crosslinks , that a...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "biology", "microbiology", "fungal diseases" ]	Msb2 Shedding Protects Candida albicans against Antimicrobial Peptides	journal.ppat.1002501	null	[ [ "Crosstalk between pathogens and the human host determines the outcome of microbial colonization and disease [1] .", "Pathogen-host communication occurs between cells and secreted proteins of both organisms .", "Surface structures of the important human fungal pathogen Candida albicans bind to dectin ...	[ "Msb2 is a sensor protein in the plasma membrane of fungi .", "In the human fungal pathogen C . albicans Msb2 signals via the Cek1 MAP kinase pathway to maintain cell wall integrity and allow filamentous growth .", "Msb2 doubly epitope-tagged in its large extracellular and small cytoplasmic domain was efficient...	[ "Microbial pathogens are attacked by antimicrobial peptides ( AMPs ) produced by the human host .", "AMPs kill pathogens and recruit immune cells to the site of infection .", "In defense , the human fungal pathogen Candida albicans continuously cleaves and secretes a glycoprotein fragment of the surface protein...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/population genetics", "computational biology/systems biology", "computational biology/transcriptional regulation" ]	Characterizing Dynamic Changes in the Human Blood Transcriptional Network	journal.pcbi.1000671	null	[ [ "Elucidating networks that define biological pathways underlying complex biological processes is an important goal of systems biology .", "Large-scale molecular profiling technologies have enabled measurements of mRNA and protein expression on the scale of whole genomes .", "As a result , understandin...	[ "Gene expression data generated systematically in a given system over multiple time points provides a source of perturbation that can be leveraged to infer causal relationships among genes explaining network changes .", "Previously , we showed that food intake has a large impact on blood gene expression patterns ...	[ "Peripheral blood is the most readily accessible human tissue for clinical studies and experimental research more generally .", "Large-scale molecular profiling technologies have enabled measurements of mRNA expression on the scale of whole genomes .", "Understanding the relationships between human blood gene e...	2010
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "mosquitoes", "vector biology", "biology", "microbiology", "vectors and hosts" ]	Tracing the Tiger: Population Genetics Provides Valuable Insights into the Aedes (Stegomyia) albopictus Invasion of the Australasian Region	journal.pntd.0002361	null	[ [ "The Asian tiger mosquito Aedes ( Stegomyia ) albopictus , originally described by Skuse from Calcutta , India , in 1894 , is considered native to the Southeast Asian region where the larvae are often found in forest tree holes – a characteristic that assists its current global expansion via rapid adaptation ...	[ "The range of the Asian tiger mosquito Aedes albopictus is expanding globally , raising the threat of emerging and re-emerging arbovirus transmission risks including dengue and chikungunya .", "Its detection in Papua New Guinea's ( PNG ) southern Fly River coastal region in 1988 and 1992 placed it 150 km from mai...	[ "The range of the Asian tiger mosquito Aedes albopictus is expanding globally , raising the threat of emerging and re-emerging arbovirus transmission risks , including chikungunya and dengue .", "Detection of Ae .", "albopictus in southern Papua New Guinea ( PNG ) in 1988 and 1992 placed it 150 km from mainland...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "animal genetics", "cell differentiation", "germ cells", "animal models", "developmental biology", "caenorhabditis elegans", "model organisms", "molecular development", "signaling in cellular processes", "fertilization", "biology", "molecular biology", "signal transduction", "cell biology"...	TRY-5 Is a Sperm-Activating Protease in Caenorhabditis elegans Seminal Fluid	journal.pgen.1002375	null	[ [ "A general feature of sexual reproduction is the generation of motile sperm that can navigate to an egg .", "To assist this process , males transfer their sperm along with seminal fluid , which enhances their reproductive success in a variety of ways ( reviewed in [1] , [2] ) .", "Seminal fluid factor...	[ "Seminal fluid proteins have been shown to play important roles in male reproductive success , but the mechanisms for this regulation remain largely unknown .", "In Caenorhabditis elegans , sperm differentiate from immature spermatids into mature , motile spermatozoa during a process termed sperm activation .", ...	[ "Sexual reproduction requires the generation of highly specialized gametes , eggs and sperm , that must encounter one another and fuse together to form a zygote .", "Males provide not only sperm but also seminal fluid , which contains a variety of factors that promote male fertility through effects on sperm and o...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology", "viral enzymes", "biology", "microbiology" ]	Molecular Basis for Nucleotide Conservation at the Ends of the Dengue Virus Genome	journal.ppat.1002912	null	[ [ "Most RNA viruses maintain the specific sequences present at the ends of their genomes .", "The 5′ genome end may carry a cap structure to ensure both genome stability and efficient translation [1] .", "The 3′-end may carry a poly ( A ) tail or adopt specific 3′-end sequences required for viral replic...	[ "The dengue virus ( DV ) is an important human pathogen from the Flavivirus genus , whose genome- and antigenome RNAs start with the strictly conserved sequence pppAG .", "The RNA-dependent RNA polymerase ( RdRp ) , a product of the NS5 gene , initiates RNA synthesis de novo , i . e . , without the use of a pre-e...	[ "The 5′- and 3′-ends of RNA virus genomes have evolved towards efficient replication , translation , and escape from defense mechanisms of the host cell .", "Little is known about how RNA viruses conserve or restore the correct ends of their genomes .", "The Flavivirus genus of positive-strand RNA viruses conta...	2012
[ "Introduction", "Materials and Methods", "Results and Discussion" ]	[ "medicine", "parasitic diseases", "biological transport", "sequence analysis", "infectious diseases", "proteins", "membranes and sorting", "biology", "biochemistry", "cell biology", "transmembrane transport proteins", "computational biology", "molecular cell biology", "metabolism" ]	The ATP-Binding Cassette Proteins of the Deep-Branching Protozoan Parasite Trichomonas vaginalis	journal.pntd.0001693	null	[ [ "Trichomonas vaginalis is a human-infective parasitic protozoan that is the most prevalent causative agent for non-viral sexually transmitted infections , with an estimated annual incidence of at least 170 million new cases of trichomoniasis worldwide [1] .", "Characteristic of other parabasalids in the o...	[ "The ATP binding cassette ( ABC ) proteins are a family of membrane transporters and regulatory proteins responsible for diverse and critical cellular process in all organisms .", "To date , there has been no attempt to investigate this class of proteins in the infectious parasite Trichomonas vaginalis .", "We ...	[ "The parasite Trichomonas vaginalis infects in excess of 100 million people per year , and is a contributory factor to enhanced transmission rates of HIV , the causative virus in AIDS .", "As such , T . vaginalis infection is an important public health concern .", "Understanding the biology of the organism is i...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "buruli ulcer", "socioeconomic aspects of health", "public health and epidemiology", "drugs and devices", "global health", "drug policy", "neglected tropical diseases", "public health" ]	Towards Rational Use of Antibiotics for Suspected Secondary Infections in Buruli Ulcer Patients	journal.pntd.0002010	null	[ [ "Buruli ulcer ( BU ) is a neglected , emerging disease caused by Mycobacterium ulcerans .", "BU usually starts as a nodule , papule , plaque , or oedema .", "When left alone , the lesion breaks open and a typical painless ulcer with undermined edges appears which can progress to a large necrotic lesio...	[ "The emerging disease Buruli ulcer is treated with streptomycin and rifampicin and surgery if necessary .", "Frequently other antibiotics are used during treatment .", "Information on prescribing behavior of antibiotics for suspected secondary infections and for prophylactic use was collected retrospectively ."...	[ "Buruli ulcer ( BU ) is a neglected , emerging disease caused by Mycobacterium ulcerans .", "BU usually starts as a nodule , papule , plaque , or oedema .", "When left alone , the lesion breaks open and a typical painless ulcer with undermined edges appears which can progress to a large necrotic lesion .", "B...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "adaptive immunity", "immune cells", "mathematics", "clinical immunology", "immunity", "immunologic subspecialties", "statistics", "t cells", "immunoassays", "immunology", "biology", "biostatistics", "immunologic techniques", "tumor immunology", "statistical methods", "im...	Hierarchical Modeling for Rare Event Detection and Cell Subset Alignment across Flow Cytometry Samples	journal.pcbi.1003130	null	[ [ "Flow cytometry is the prototypical assay for multi-parameter single cell analysis , and is essential in vaccine development , monitoring of T cell-based immune therapies and the search for immune biomarkers .", "In many clinical research applications , the cell subsets of interest are antigen specific T ...	[ "Flow cytometry is the prototypical assay for multi-parameter single cell analysis , and is essential in vaccine and biomarker research for the enumeration of antigen-specific lymphocytes that are often found in extremely low frequencies ( 0 . 1% or less ) .", "Standard analysis of flow cytometry data relies on v...	[ "The use of flow cytometry to count antigen-specific T cells is essential for vaccine development , monitoring of immune-based therapies and immune biomarker discovery .", "Analysis of such data is challenging because antigen-specific cells are often present in frequencies of less than 1 in 1 , 000 peripheral blo...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetic mutation", "microbiology", "host-pathogen interaction", "gene function", "fungi", "microbial growth and development", "fungal reproduction", "mycology", "gene expression", "microbial pathogens", "biology", "pathogenesis", "molecular biology", "signal transduction", "genetics", ...	Two Novel Transcriptional Regulators Are Essential for Infection-related Morphogenesis and Pathogenicity of the Rice Blast Fungus Magnaporthe oryzae	journal.ppat.1002385	null	[ [ "Eukaryotic organisms , including fungi , can sense and respond to extracellular cues via various signaling pathways for regulating a variety of developmental and differential cellular processes .", "Among these pathways , the conserved cyclic AMP-dependent protein kinase A ( cAMP/PKA ) signaling pathway ...	[ "The cyclic AMP-dependent protein kinase A signaling pathway plays a major role in regulating plant infection by the rice blast fungus Magnaporthe oryzae .", "Here , we report the identification of two novel genes , MoSOM1 and MoCDTF1 , which were discovered in an insertional mutagenesis screen for non-pathogenic...	[ "Magnaporthe oryzae , the causal agent of rice blast disease , is an important model fungal pathogen for understanding the molecular basis of plant-fungus interactions .", "In M . oryzae , the conserved cAMP/PKA signaling pathway has been demonstrated to be crucial for regulating infection-related morphogenesis a...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "comparative sequence analysis", "chemical characterization", "crystal structure", "electricity", "condensed matter physics", "integrins", "electrostatics", "sequence motif analysis", "crystallography", "cellular structures and organelles", "research and analysis methods", "sequence analysis",...	High Affinity vs. Native Fibronectin in the Modulation of αvβ3 Integrin Conformational Dynamics: Insights from Computational Analyses and Implications for Molecular Design	journal.pcbi.1005334	null	[ [ "Integrins are heterodimeric cell adhesion receptors , composed by the association of α and β subunits .", "They are typically characterized by a bilobular head and two legs that span the plasma membrane .", "Integrin ectodomains have been crystallized in a bent , genuflexed conformation ( correspondi...	[ "Understanding how binding events modulate functional motions of multidomain proteins is a major issue in chemical biology .", "We address several aspects of this problem by analyzing the differential dynamics of αvβ3 integrin bound to wild type ( wtFN10 , agonist ) or high affinity ( hFN10 , antagonist ) mutants...	[ "Interactions between proteins are at the basis of all biological processes in the cell .", "In this context , the study of conformational responses of protein receptors to the binding of endogenous ligands may be a source of inspiration for the design of small molecule modulators that permit to control such biol...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "chronic kidney disease", "tropical diseases", "biomarkers", "bacterial diseases", "crops", "neglected tropical diseases", "medical risk factors", "kidneys", "plants", "veterinary science", "research and analysis methods", "sugarcane", "infectious diseases",...	Leptospirosis as a risk factor for chronic kidney disease: A systematic review of observational studies	journal.pntd.0007458	null	[ [ "Globally , the incidence , mortality and disability due to chronic kidney disease ( CKD ) have increased , mainly driven by established risk factors such as diabetes and hypertension . [1 , 2]", "Despite the growing body of evidence on CKD , those cases that are not related to well-known risk factors , i...	[ "Leptospirosis is a worldwide prevalent zoonosis and chronic kidney disease ( CKD ) is a leading global disease burden .", "Because of pathophysiological changes in the kidney , it has been suggested that these conditions may be associated .", "However , the extent of this interaction has not been synthetized ....	[ "Leptospirosis is an infection that can affect the kidneys acutely , though it seems that even after the acute infection there could be risk of a long-term impaired kidney function .", "The evidence on this matter is sparse and limited , thus the need to comprehensively seek , synthetize and appraise the availabl...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immune evasion", "viral immune evasion", "viral persistence and latency", "viral transmission and infection", "virology", "biology and life sciences", "immunology", "immune suppression", "microbiology", "immune response" ]	Early Virus-Host Interactions Dictate the Course of a Persistent Infection	journal.ppat.1004588	null	[ [ "The innate antiviral immune response is primarily triggered by recognition of virally derived molecules , a . k . a . pathogen associated molecular patterns ( PAMPs ) , by host cell pathogen recognition receptors ( PRR ) , resulting in the induction of type-I interferons ( IFN-I ) , a group of molecules that...	[ "Many persistent viral infections are characterized by a hypofunctional T cell response and the upregulation of negative immune regulators .", "These events occur days after the initiation of infection .", "However , the very early host-virus interactions that determine the establishment of viral persistence re...	[ "Lymphocytic Choriomenengitis Virus ( LCMV ) is an important model for the investigation of the pathogenesis of persistent viral infections .", "As with humans infected with hepatitis C and Human Immunodeficiency Virus-1 , adult mice persistently infected with immunosuppressive strains of LCMV express high levels...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "infectious diseases", "medicine and health sciences", "biology and life sciences", "microbiology", "agriculture" ]	The Expanding Functions of Cellular Helicases: The Tombusvirus RNA Replication Enhancer Co-opts the Plant eIF4AIII-Like AtRH2 and the DDX5-Like AtRH5 DEAD-Box RNA Helicases to Promote Viral Asymmetric RNA Replication	journal.ppat.1004051	null	[ [ "Host factors co-opted for replication of plus-stranded ( + ) RNA viruses are critical in each step of the well-orchestrated infection process .", "After translation of the viral mRNA-sense genomic RNA ( s ) , the viral ( + ) RNA and the viral replication proteins together with host RNA-binding proteins (...	[ "Replication of plus-strand RNA viruses depends on recruited host factors that aid several critical steps during replication .", "Several of the co-opted host factors bind to the viral RNA , which plays multiple roles , including mRNA function , as an assembly platform for the viral replicase ( VRC ) , template f...	[ "Genome-wide screens for host factors affecting tombusvirus replication in yeast indicated that subverted cellular RNA helicases likely play major roles in virus replication .", "Tombusviruses do not code for their own helicases and they might recruit host RNA helicases to aid their replication in infected cells ...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "animal genetics", "genetics", "biology", "microbiology", "host-pathogen interaction", "genetics of disease", "genetics and genomics" ]	Genetic Control of Resistance to Trypanosoma brucei brucei Infection in Mice	journal.pntd.0001173	null	[ [ "Sleeping sickness ( African trypanosomiasis ) continues to pose a major threat to 60 million people in 36 countries in sub-Saharan Africa .", "The estimated number of new cases is currently between 50 000 and 70 000 per year ( WHO 2006 – African trypanosomiasis - http://www . who . int/mediacentre/factsh...	[ "Trypanosoma brucei brucei infects livestock , with severe effects in horses and dogs .", "Mouse strains differ greatly in susceptibility to this parasite .", "However , no genes controlling these differences were mapped .", "We studied the genetic control of survival after T . b .", "brucei infection using...	[ "Trypanosoma brucei are extracellular protozoa transmitted to mammalian host by the tsetse fly .", "They developed several mechanisms that subvert host's immune defenses .", "Therefore analysis of genes affecting host's resistance to infection can reveal critical aspects of host-parasite interactions .", "Try...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Mapping and Modelling the Geographical Distribution and Environmental Limits of Podoconiosis in Ethiopia	journal.pntd.0003946	null	[ [ "Podoconiosis is a form of elephantiasis that predominantly affects barefoot subsistence farmers in areas with red volcanic soil .", "It is characterized by bilateral swelling of the lower legs with mossy and nodular changes to the skin , and causes considerable disability .", "The aetiology is not fu...	[ "Ethiopia is assumed to have the highest burden of podoconiosis globally , but the geographical distribution and environmental limits and correlates are yet to be fully investigated .", "In this paper we use data from a nationwide survey to address these issues .", "Our analyses are based on data arising from t...	[ "Podoconiosis is a neglected tropical disease that results in swelling of the lower legs and feet .", "It is common among barefoot individuals with prolonged contact with irritant soils of volcanic origin .", "The disease causes significant social and economic burden .", "The disease can be prevented by consi...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "ecology and environmental sciences", "metagenomics", "functional genomics", "metabolites", "microbial ecosystems", "ecology", "ecosystems", "metabolic processes", "genetics", "biology and life sciences", "genomics", "ecosystem functioning", "metabolism", "fermentation" ]	Inferring Aggregated Functional Traits from Metagenomic Data Using Constrained Non-negative Matrix Factorization: Application to Fiber Degradation in the Human Gut Microbiota	journal.pcbi.1005252	null	[ [ "Whole Genome Shotgun ( WGS ) metagenomics is increasingly used to study the structure and functions of complex microbial ecosystems .", "Thanks to a huge research effort , these high-throughput approaches are constantly improving and have already provided valuable information .", "Recent achievements...	[ "Whole Genome Shotgun ( WGS ) metagenomics is increasingly used to study the structure and functions of complex microbial ecosystems , both from the taxonomic and functional point of view .", "Gene inventories of otherwise uncultured microbial communities make the direct functional profiling of microbial communit...	[ "Microbial communities are highly complex ecosystems , harboring a high taxonomic diversity , rapidly varying in time .", "Focusing on the functional traits of microorganisms instead of species offers an interesting and complementary insight since quite often , owing to environmental selection pressure , traits a...	2016
[ "Introduction", "Results", "Discussion", "Material and methods" ]	[ "cell cycle and cell division", "cell processes", "mitosis", "fungi", "model organisms", "experimental organism systems", "protein structure", "rna alignment", "saccharomyces", "research and analysis methods", "sequence analysis", "rna structure", "sequence alignment", "animal studies", ...	Amn1 governs post-mitotic cell separation in Saccharomyces cerevisiae	journal.pgen.1007691	null	[ [ "The switch between effective and inhibited separation of mother and daughter cells in eukaryotic mitosis represents a fundamental process for understanding the evolution of organizational and functional complexity of organisms , and also has significant medical and industrial value [1–3] .", "It has been...	[ "Post-mitotic cell separation is one of the most prominent events in the life cycle of eukaryotic cells , but the molecular underpinning of this fundamental biological process is far from being concluded and fully characterized .", "We use budding yeast Saccharomyces cerevisiae as a model and demonstrate AMN1 as ...	[ "Separation of mother and daughter cells after mitosis in eukaryotes enacts various functional and/or developmental needs and has significant medical and industrial implications .", "How this cellular behaviour is regulated is far from being concluded .", "We report here a novel Amn1 mediated post-mitotic cell ...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases/neglected tropical diseases", "cell biology/cell growth and division", "cell biology/microbial growth and development", "biochemistry/macromolecular assemblies and machines", "infectious diseases/protozoal infections" ]	Characterization of a Subunit of the Outer Dynein Arm Docking Complex Necessary for Correct Flagellar Assembly in Leishmania donovani	journal.pntd.0000586	null	[ [ "Protozoan parasites of the genus Leishmania cause a variety of diseases in humans collectively termed as leishmaniasis .", "The pathologies range from self-healing cutaneous lesions ( Leishmania major ) to fatal visceral involvement ( Leishmania donovani ) .", "Two million new infections are estimate...	[ "In order to proceed through their life cycle , Leishmania parasites switch between sandflies and mammals .", "The flagellated promastigote cells transmitted by the insect vector are phagocytized by macrophages within the mammalian host and convert into the amastigote stage , which possesses a rudimentary flagell...	[ "Leishmania parasites are responsible for the disease leishmaniasis .", "They are spread through sandflies .", "The primary hosts are mammals , including humans .", "They occur in two different morphological forms .", "The flagellated promastigotes live in the gut of the sandfly vector .", "After transmis...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "biochemistry", "in vitro", "biophysics", "neuroscience" ]	Structural and Thermodynamic Properties of Selective Ion Binding in a K+ Channel	journal.pbio.0050121	Ion selectivity of the KcSA K+ channel is assessed through a combination of thermodynamic measurements of ion binding and structural analysis of ion-bound and ion-free conformations.	[ [ "Potassium channels conduct K+ ions at nearly diffusion-limited rates , and at the same time , they prevent Na+ ions from conducting [1] .", "The ability to distinguish between K+ ions ( Pauling ionic radius 1 . 33 Å ) and Na+ ions ( Pauling ionic radius 0 . 95 Å ) occurs within a segment of the pore know...	[ "Thermodynamic measurements of ion binding to the Streptomyces lividans K+ channel were carried out using isothermal titration calorimetry , whereas atomic structures of ion-bound and ion-free conformations of the channel were characterized by x-ray crystallography .", "Here we use these assays to show that the i...	[ "The exquisite selectivity of potassium ion ( K+ ) channels in cellular membranes allows them to pass K+ ions while restricting the closely related sodium ( Na+ ) ions , and thereby maintain the electrical potential across cellular membranes .", "In this study , we address the fundamental question: how does the K...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "specimen preparation and treatment", "neurobiology of disease and regeneration", "mechanical treatment of specimens", "medicine and health sciences", "specimen disruption", "anatomy", "neural homeostasis", "electroporation", "nervous system", "neurology", "biology and life sciences", "motor s...	The Vesicle Protein SAM-4 Regulates the Processivity of Synaptic Vesicle Transport	journal.pgen.1004644	null	[ [ "Neurons innervate their targets at synapses distant from the soma .", "Most components of these synaptic specializations , including synaptic vesicles ( SVs ) , active zone proteins and mitochondria , are synthesized in the soma and then transported along axons on the microtubule cytoskeleton [1] .", ...	[ "Axonal transport of synaptic vesicles ( SVs ) is a KIF1A/UNC-104 mediated process critical for synapse development and maintenance yet little is known of how SV transport is regulated .", "Using C . elegans as an in vivo model , we identified SAM-4 as a novel conserved vesicular component regulating SV transport...	[ "Most cellular components of neurons are synthesized in the cell body and must be transported great distances to form synapses at the ends of axons and dendrites .", "Neurons use a specialized axonal transport system consisting of microtubule cytoskeletal tracks and numerous molecular motors to shuttle specific c...	2014
[ "Introduction", "Materials & methods", "Results", "Discussion" ]	[ "cancer genomics", "medicine and health sciences", "basic cancer research", "oncology", "genomic databases", "mutation", "genome analysis", "mutation databases", "research and analysis methods", "sequence analysis", "bioinformatics", "proteins", "biological databases", "gene ontologies", ...	Oncodomains: A protein domain-centric framework for analyzing rare variants in tumor samples	journal.pcbi.1005428	null	[ [ "In recent years , studies analyzing sequenced tumor genomes have seen a drastic increase in their sample sizes , growing from only a handful samples to cohorts of several thousand patients .", "This rise in availability of sequenced tumor samples has enabled the comparative analysis of tumors originating...	[ "The fight against cancer is hindered by its highly heterogeneous nature .", "Genome-wide sequencing studies have shown that individual malignancies contain many mutations that range from those commonly found in tumor genomes to rare somatic variants present only in a small fraction of lesions .", "Such rare so...	[ "The analysis of somatic variants in sequenced tumor samples is important for understanding the molecular disruptions that underlie the vast differences in individual cancer phenotypes or response to treatment .", "In order to understand which somatic mutations are functionally important for the initiation or pro...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "flow cytometry", "medicine and health sciences", "immune cells", "immune physiology", "pathology and laboratory medicine", "spleen", "pathogens", "antiviral therapy", "immunology", "microbiology", "retroviruses", "viruses", "immunodeficiency viruses", "animal models", "...	In vivo activation of latent HIV with a synthetic bryostatin analog effects both latent cell "kick" and "kill" in strategy for virus eradication	journal.ppat.1006575	null	[ [ "HIV/AIDS is a catastrophic pandemic that has claimed an estimated 35 million lives .", "Approximately 37 million individuals are currently HIV-positive .", "In 2015 , 2 . 1 million individuals were newly infected , and 1 . 1 million died of AIDS-related illnesses [1] .", "Antiretroviral therapy (...	[ "The ability of HIV to establish a long-lived latent infection within resting CD4+ T cells leads to persistence and episodic resupply of the virus in patients treated with antiretroviral therapy ( ART ) , thereby preventing eradication of the disease .", "Protein kinase C ( PKC ) modulators such as bryostatin 1 c...	[ "HIV can persist for many years in a latent ( non-expressing ) state in individuals treated with antiretroviral therapy , and these latently-infected cells represent a major barrier to curing HIV infection .", "One potential approach to eliminating the reservoir cells is to induce them to express viral proteins w...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "meiosis", "chromosome biology", "genetics", "epigenetics", "biology", "genomics" ]	Ikbkap/Elp1 Deficiency Causes Male Infertility by Disrupting Meiotic Progression	journal.pgen.1003516	null	[ [ "Meiosis is a fundamental and highly regulated process that takes place during gamete generation .", "Faithful execution of this process is essential for maintaining genome integrity .", "Errors and various types of disruption during meiosis can cause aneuploidy and result in developmental defects , i...	[ "Mouse Ikbkap gene encodes IKAP—one of the core subunits of Elongator—and is thought to be involved in transcription .", "However , the biological function of IKAP , particularly within the context of an animal model , remains poorly characterized .", "We used a loss-of-function approach in mice to demonstrate ...	[ "The process of meiosis is responsible for gamete formation and ensures that offspring will inherit a complete set of chromosomes from each parent .", "Errors arising during this process generally result in spontaneous abortions , birth defects , or infertility .", "Many genes that are essential in regulating m...	2013
[ "Introduction", "Methods", "Results and discussion" ]	[ "deletion mutation", "protein interactions", "crystal structure", "condensed matter physics", "mutation", "substitution mutation", "protein structure", "mutation databases", "crystallography", "research and analysis methods", "sequence analysis", "solid state physics", "bioinformatics", "p...	PremPDI estimates and interprets the effects of missense mutations on protein-DNA interactions	journal.pcbi.1006615	null	[ [ "There has been a rapid development of genome-wide techniques in the last decade along with significant lowering of the cost of gene sequencing , which generated widely available genomic data .", "However , the interpretation of genomic data and prediction of the association of genetic variations with dis...	[ "Protein-DNA interactions play important roles in regulations of many vital cellular processes , including transcription , translation , DNA replication and recombination .", "Sequence variants occurring in these DNA binding proteins that alter protein-DNA interactions may cause significant perturbations or compl...	[ "Developing methods for accurate prediction of effects of amino acid substitutions on protein-DNA interactions is important for a wide range of biomedical applications such as understanding disease-causing mechanism of missense mutations and guiding protein engineering .", "Very few methods have been developed fo...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry/molecular evolution", "genetics and genomics/animal genetics", "genetics and genomics/gene discovery", "genetics and genomics/comparative genomics", "evolutionary biology/evolutionary and comparative genetics", "genetics and genomics/functional genomics", "computational biology/comparative...	Discovery of Candidate Disease Genes in ENU–Induced Mouse Mutants by Large-Scale Sequencing, Including a Splice-Site Mutation in Nucleoredoxin	journal.pgen.1000759	null	[ [ "Genome sequences are essential tools for comparative and mutational analyses [1] , [2] .", "As a part of the Mouse Genome Sequencing Consortium , we sequenced mouse Chromosome 11 in the C57BL/6J mouse strain .", "The 2002 draft mouse genome reported 8681 gaps in mouse Chromosome 11 , and was estimate...	[ "An accurate and precisely annotated genome assembly is a fundamental requirement for functional genomic analysis .", "Here , the complete DNA sequence and gene annotation of mouse Chromosome 11 was used to test the efficacy of large-scale sequencing for mutation identification .", "We re-sequenced the 14 , 000...	[ "Here we show that tiny DNA lesions can be found in huge amounts of DNA sequence data , similar to finding a needle in a haystack .", "These lesions identify many new candidates for disease genes associated with birth defects , infertility , and growth .", "Further , our data suggest that we know very little ab...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "organismal evolution", "microbial mutation", "medicine and health sciences", "pathology and laboratory medicine", "evolutionary biology", "pathogens", "biological cultures", "microbiology", "retroviruses", "viruses", "immunodeficiency viruses", "rna viruses", "microbial evolution", "cell ...	Experimental Estimation of the Effects of All Amino-Acid Mutations to HIV’s Envelope Protein on Viral Replication in Cell Culture	journal.ppat.1006114	null	[ [ "HIV evolves rapidly: the envelope ( Env ) proteins of two viral strains within a single infected host diverge as much in a year as the typical human and chimpanzee ortholog has diverged over ∼5-million years [1–4] .", "This rapid evolution is central to HIV’s biology .", "Most humans infected with HI...	[ "HIV is notorious for its capacity to evade immunity and anti-viral drugs through rapid sequence evolution .", "Knowledge of the functional effects of mutations to HIV is critical for understanding this evolution .", "HIV’s most rapidly evolving protein is its envelope ( Env ) .", "Here we use deep mutational...	[ "HIV is infamous for the rapid evolution of its surface protein , Env .", "The ability to measure the effects of all mutations to Env under defined selection pressures in the lab would open the door to better understanding the factors that shape this evolution .", "However , this is a daunting experimental task...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "biomacromolecule-ligand interactions", "biochemistry", "protein interactions", "proteins", "protein structure", "biology", "chemical biology", "drug discovery" ]	A Structural Biology Approach to Understand Human Lymphatic Filarial Infection	journal.pntd.0002662	null	[ [ "Lymphatic filariasis is a mosquito borne infection caused by Wuchereria bancrofti , Brugia malayi or Brugia timori that affects 120 million people in 73 countries and another 1100 million people are at the risk of contracting this dreadful disease [1] , [2] .", "Infection is initiated when infective mosq...	[ "The presence of aspartic protease inhibitor in filarial parasite Brugia malayi ( Bm-Aspin ) makes it interesting to study because of the fact that the filarial parasite never encounters the host digestive system .", "Here , the aspartic protease inhibition kinetics of Bm-Aspin and its NMR structural characterist...	[ "Filariasis is a parasitic infectious tropical disease caused by thread like filarial nematodes .", "These worms occupy the lymph nodes and in chronic cases they lead to the disease “elephantiasis . ”", "Over 120 million people have already been affected by it , and 40 million are seriously disfigured by this d...	2014

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