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headings list	keywords list	title stringlengths 20 281	id stringlengths 20 20	toc stringlengths 57 522 ⌀	sections list	abstract list	summary list	year stringclasses 13 values
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biofilms", "biotechnology", "medicine and health sciences", "pathology and laboratory medicine", "fibrinogen", "gene regulation", "pathogens", "microbiology", "rabbits", "vertebrates", "staphylococcus aureus", "animals", "mammals", "animal models", "model organisms", "glycoproteins", ...	The Staphylococcus aureus Global Regulator MgrA Modulates Clumping and Virulence by Controlling Surface Protein Expression	journal.ppat.1005604	null	[ [ "Staphylococcus aureus is a human commensal that asymptomatically colonizes the nares , throat , and skin of ~30% of the population [1 , 2] .", "It is also a pervasive opportunistic pathogen that is the most common infectious agent isolated from hospital inpatients in the US [3] .", "S . aureus causes...	[ "Staphylococcus aureus is a human commensal and opportunistic pathogen that causes devastating infections in a wide range of locations within the body .", "One of the defining characteristics of S . aureus is its ability to form clumps in the presence of soluble fibrinogen , which likely has a protective benefit ...	[ "Staphylococcus causes a wide range of diseases , ranging from skin infections to deadly invasive condition like endocarditis , septicemia , osteomyelitis , and pneumonia .", "In this work we examine the ArlRS two-component regulatory system , which controls interactions with the host plasma protein fibrinogen ."...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "hemodynamics", "biophysic al simulations", "vascular biology", "biology", "computational biology", "cardiovascular" ]	Angiogenesis: An Adaptive Dynamic Biological Patterning Problem	journal.pcbi.1002983	null	[ [ "Vascular systems develop , adapt and remodel in response to local and systemic needs [1] .", "Over hours to days , blood vessels form and grow ( vasculogenesis and angiogenesis ) , undergo structural adaptation ( remodeling ) , or regress ( pruning ) [2] .", "These processes of vascular network patte...	[ "Formation of functionally adequate vascular networks by angiogenesis presents a problem in biological patterning .", "Generated without predetermined spatial patterns , networks must develop hierarchical tree-like structures for efficient convective transport over large distances , combined with dense space-fill...	[ "The blood vessels provide an efficient system for transport of substances to all parts of the body .", "They are capable of growing or regressing during development , in response to changing functional needs , and in disease states .", "This is achieved by structural adaptation , i . e . changes in the diamete...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "clinical immunology", "immunity", "heredity", "gastroenterology and hepatology", "genetics", "inflammatory bowel disease", "population genetics", "biology", "immunology", "genetics and genomics" ]	Association of a Functional Variant in the Wnt Co-Receptor LRP6 with Early Onset Ileal Crohn's Disease	journal.pgen.1002523	null	[ [ "Ileal Crohn's disease ( CD ) belongs to the group of inflammatory bowel diseases characterized by chronic intestinal inflammation , ulceration and consequent diarrhoea [1] .", "Both , environmental and inherited factors contribute to the disease risk [2] , [3] and different genetic backgrounds likely exp...	[ "Ileal Crohn's Disease ( CD ) , a chronic small intestinal inflammatory disorder , is characterized by reduced levels of the antimicrobial peptides DEFA5 ( HD-5 ) and DEFA6 ( HD-6 ) .", "Both of these α-defensins are exclusively produced in Paneth cells ( PCs ) at small intestinal crypt bases .", "Different ile...	[ "Crohn's Disease ( CD ) is to date incurable and is characterized by severe , reoccurring inflammations that can affect different intestinal locations .", "The complicated and multifactorial pathogenesis is not completely understood but involves disturbed epithelial barriers and immune reactions against the comme...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "traditional medicine", "medicine and health sciences", "tropical diseases", "geographical locations", "social sciences", "parasitic diseases", "herbs", "health care", "bacterial diseases", "complementary and alternative medicine", "plants", "africa", "public and occupational health", "inf...	Health-Seeking Behaviour towards Poverty-Related Disease (PRDs): A Qualitative Study of People Living in Camps and on Campuses in Cameroon	journal.pntd.0005218	null	[ [ "Even though a large number of diseases in low-income countries like Cameroon are preventable and treatable , they still form a big threat to people’s health and well-being .", "The critical connection between diseases and poverty has caught the attention of national and international health agencies who ...	[ "Poverty-Related Diseases ( PRDs ) emphasize poverty as a ‘breeding-ground’ for a range of diseases .", "The study presented here starts from the premise that poverty is a general condition that can limit people’s capacity to prevent , mitigate or treat diseases .", "Using an interpretation of health seeking be...	[ "People’s living conditions are a crucial factor for health and diseases .", "In developing countries like Cameroon , poverty is a major condition affecting the way people deal with health issues .", "We studied people’s a health-seeking behaviour action in two settings: camps , housing labourers of the Cameroo...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "computational biology/transcriptional regulation", "computational biology" ]	Analysis of Combinatorial Regulation: Scaling of Partnerships between Regulators with the Number of Governed Targets	journal.pcbi.1000755	null	[ [ "Regulating the spatial and temporal activity of genes is essential to the smooth functioning of biological processes in the cell .", "The two primary processes for mediating this regulation are transcription and phosphorylation .", "As a part of the former type of regulation , certain proteins called...	[ "Through combinatorial regulation , regulators partner with each other to control common targets and this allows a small number of regulators to govern many targets .", "One interesting question is that given this combinatorial regulation , how does the number of regulators scale with the number of targets ?", ...	[ "A regulatory network consists of regulators such as transcription factors or kinases that control the expression or activity of their target genes .", "Almost always , there are multiple regulators partnering together to control their targets .", "Compared to more commonplace contexts , these regulators can be...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "animal models", "developmental biology", "embryology", "model organisms", "organism development", "signaling", "molecular development", "cell migration", "biology", "morphogenesis", "mouse", "pattern formation" ]	Nodal Dependent Differential Localisation of Dishevelled-2 Demarcates Regions of Differing Cell Behaviour in the Visceral Endoderm	journal.pbio.1001019	null	[ [ "The anterior visceral endoderm ( AVE ) is a specialised sub-set of the visceral endoderm ( VE ) that is responsible for inducing anterior pattern in the underlying epiblast ( reviewed in [1]–[4] ) .", "It is induced at the distal tip of the egg-cylinder in a Nodal dependent manner [5]–[7] .", "From t...	[ "The anterior visceral endoderm ( AVE ) , a signalling centre within the simple epithelium of the visceral endoderm ( VE ) , is required for anterior-posterior axis specification in the mouse embryo .", "AVE cells migrate directionally within the VE , thereby properly positioning the future anterior of the embryo...	[ "The orientation of the head-tail axis is determined during embryogenesis by the movements of a subset of cells called the AVE ( anterior visceral endoderm ) .", "These cells migrate from their initial position within the simple epithelium of the visceral endoderm ( VE ) to a location from which they eventually i...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Dynamic filopodial forces induce accumulation, damage, and plastic remodeling of 3D extracellular matrices	journal.pcbi.1006684	null	[ [ "The Extracellular Matrix ( ECM ) is a scaffolding medium that helps transmit mechanical signals among cells in cancer [1 , 2] , fibrosis [3 , 4] , vascular networks [5 , 6] , and more generally , morphogenesis [7 , 8] .", "The mechanical and biochemical properties of the ECM impact cell behavior .", ...	[ "The mechanical properties of the extracellular matrix ( ECM ) –a complex , 3D , fibrillar scaffold of cells in physiological environments–modulate cell behavior and can drive tissue morphogenesis , regeneration , and disease progression .", "For simplicity , it is often convenient to assume these properties to b...	[ "Many cells in the body are surrounded by a 3D extracellular matrix of interconnected protein fibers .", "The density and architecture of this protein fiber network can play important roles in controlling cell behavior .", "Deregulated biophysical properties of the extracellular environment are observed in dise...	2019
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "biotechnology", "cell motility", "swimming", "medicine and health sciences", "engineering and technology", "parasite evolution", "microbiology", "parasitic diseases", "biological locomotion", "biomechanics", "parasitology", "developmental biology", "mathematical physics", "microbial growt...	Simulating the Complex Cell Design of Trypanosoma brucei and Its Motility	journal.pcbi.1003967	null	[ [ "The African trypanosome , Trypanosoma brucei , is the causative agent of the deadly nagana and sleeping sickness in livestock and humans , respectively , which still persist as a main public health and economic problem for inhabitants in sub-Saharan Africa [1]–[3] .", "Trypanosomes are protozoan parasite...	[ "The flagellate Trypanosoma brucei , which causes the sleeping sickness when infecting a mammalian host , goes through an intricate life cycle .", "It has a rather complex propulsion mechanism and swims in diverse microenvironments .", "These continuously exert selective pressure , to which the trypanosome adju...	[ "Typanosoma brucei is a uni-cellular parasite that causes the sleeping sickness , a deadly disease for humans that also occurs in livestock .", "Injected into the mammalian host by the tsetse fly , the trypanosome travels through the blood stream , where it proliferates , and ultimately can be taken up again by a...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "animal genetics", "genomics", "speciation", "gene expression", "genetics", "hybridization", "biology", "evolutionary biology", "gene networks", "evolutionary processes", "evolutionary genetics" ]	Genomic Networks of Hybrid Sterility	journal.pgen.1004162	null	[ [ "To understand patterns of biodiversity , it is essential to characterize the processes by which new species arise and are maintained in nature , including ecological specialization , population differentiation and reproductive isolation .", "Genetic dissection of reproductive isolation has proven to be a...	[ "Hybrid dysfunction , a common feature of reproductive barriers between species , is often caused by negative epistasis between loci ( “Dobzhansky-Muller incompatibilities” ) .", "The nature and complexity of hybrid incompatibilities remain poorly understood because identifying interacting loci that affect comple...	[ "New species are created when barriers to reproduction form between groups of organisms that formerly interbred freely .", "Reduced fertility or viability of hybrid offspring is a common form of reproductive isolation .", "Hybrid defects are caused by negative interactions between genes that have undergone evol...	2014
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "transfection", "flow cytometry", "parasite groups", "medicine and health sciences", "immune physiology", "enzyme-linked immunoassays", "ruminants", "293t cells", "biological cultures", "immunology", "vertebrates", "animals", "mammals", "parasitology", "apicomplexa", "molecular biology...	Assessment and optimization of Theileria parva sporozoite full-length p67 antigen expression in mammalian cells	journal.pntd.0005803	null	[ [ "Theileria parva ( T . parva ) is an intracellular protozoan belonging to the Theileria genus , order Piroplasmida and phylum Apicomplexa [1–3] .", "This parasite is the causative agent of East Cost fever ( ECF ) , an acute and often lethal disease affecting cattle in different countries of eastern , cent...	[ "Delivery of various forms of recombinant Theileria parva sporozoite antigen ( p67 ) has been shown to elicit antibody responses in cattle capable of providing protection against East Coast fever , the clinical disease caused by T . parva .", "Previous formulations of full-length and shorter recombinant versions ...	[ "East Coast fever , caused by the tick-borne protozoan parasite Theileria parva , is a disease that results in significant bovine morbidity , mortality , and production losses in regions of sub-Saharan Africa .", "Susceptible cattle develop clinical signs within a 7–14 days of exposure , which often progress to s...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Outer Hair Cell Lateral Wall Structure Constrains the Mobility of Plasma Membrane Proteins	journal.pgen.1005500	null	[ [ "The cylindrical cochlear sensory outer hair cells ( OHCs ) in the inner ear convert membrane potential changes into mechanical force at high frequencies [1 , 2] .", "This force production greatly boosts the sound-evoked displacements of the hearing organ and is therefore required for establishing the rem...	[ "Nature’s fastest motors are the cochlear outer hair cells ( OHCs ) .", "These sensory cells use a membrane protein , Slc26a5 ( prestin ) , to generate mechanical force at high frequencies , which is essential for explaining the exquisite hearing sensitivity of mammalian ears .", "Previous studies suggest that ...	[ "Nature’s fastest motor is the cochlear outer hair cell ( OHC ) in the mammalian inner ear .", "These cells can contract and elongate thousands of times per second .", "Slc26a5 ( prestin ) is the essential protein in the fast motor and resides in the plasma membrane of OHC lateral wall .", "Slc26a5 undergoes ...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "ecology and environmental sciences", "water resources", "pathology and laboratory medicine", "chemical compounds", "pathogens", "vibrio", "variant genotypes", "tropical diseases", "microbiology", "geographical locations", "salts", "genetic mapping", "health...	A prospective cohort study comparing household contact and water Vibrio cholerae isolates in households of cholera patients in rural Bangladesh	journal.pntd.0006641	null	[ [ "The World Health Organization estimates that there are 95 , 000 cholera deaths per year with 2 . 9 million cases worldwide [1] .", "Studies have identified risk factors for becoming infected with cholera such as age [2] , drinking street-vended water [3] , placing ones hands into stored household water [...	[ "Household contacts of cholera patients are at a 100 times higher risk of developing cholera than the general population .", "The objective of this study was to examine the incidence of V . cholerae infections among household contacts of cholera patients in a rural setting in Bangladesh , to identify risk factors...	[ "Household members of cholera patients are at a 100 times higher risk of developing cholera infections than the general population .", "This risk is highest during the seven days after the cholera patient presents at a health facility .", "In this study we investigated the rate of cholera transmission within ch...	2018
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "enzyme-linked immunoassays", "toxins", "pathology and laboratory medicine", "enzymes", "enzymology", "toxic agents", "toxicology", "optimization", "mathematics", "immunologic techniques", "gel electrophoresis", "pepsins", "research and analysis methods", ...	Refinement strategy for antivenom preparation of high yield and quality	journal.pntd.0007431	null	[ [ "Antivenoms prepared from hyperimmune animal plasma , mostly equine or ovine , are the only specific therapeutics for rapid counteracting post-snakebite pathophysiological manifestations .", "Although there are various well established downstream processing strategies that have been implemented into comme...	[ "Antivenoms from hyperimmune animal plasma are the only specific pharmaceuticals against snakebites .", "The improvement of downstream processing strategies is of great interest , not only in terms of purity profile , but also from yield-to-cost perspective and rational use of plasma of animal origin .", "We re...	[ "Animal plasma-derived antivenoms constitute the most important therapy against snakebite envenoming .", "Nowadays this critical treatment has been faced by severe shortage due to low sustainability of current productions , which mostly affects developing countries as those suffering from highest morbidity and mo...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "growth control", "insulin-like growth factor", "integrative physiology", "anatomy and physiology", "endocrine physiology", "developmental biology", "organism development", "genital disc", "molecular development", "morphogenesis", "limb development", "insulin", "organogenesis", "biology", ...	FOXO Regulates Organ-Specific Phenotypic Plasticity In Drosophila	journal.pgen.1002373	null	[ [ "The ability of organisms to adjust their development .", ", physiology or behavior in response to environmental conditions , called phenotypic plasticity , is a defining property of life .", "Phenotypic plasticity underlies such diverse phenomena as the relationship between childhood nutrition and ad...	[ "Phenotypic plasticity , the ability for a single genotype to generate different phenotypes in response to environmental conditions , is biologically ubiquitous , and yet almost nothing is known of the developmental mechanisms that regulate the extent of a plastic response .", "In particular , it is unclear why s...	[ "The ability of an organism to respond to its environment is a defining quality of life .", "However , why are some characteristics or individuals sensitive to environmental change while others are not ?", "We identified the mechanism that controls the response of growing organs to a particularly important envi...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunology/cellular microbiology and pathogenesis", "genetics and genomics/gene discovery", "infectious diseases", "cell biology/cellular death and stress responses", "cell biology/cell signaling", "genetics and genomics/genetics of the immune system", "cell biology", "immunology/immune response", ...	Activation of the Unfolded Protein Response Is Required for Defenses against Bacterial Pore-Forming Toxin In Vivo	journal.ppat.1000176	null	[ [ "Pore-forming toxins ( PFTs ) are the single most prevalent protein virulence factor made by disease-causing bacteria and are important for the virulence of many important human pathogens including Staphylococcus aureus , Streptococcus pyogenes , Clostridium perfringens , and Aeromonas hydrophilia [1] , [2] ....	[ "Pore-forming toxins ( PFTs ) constitute the single largest class of proteinaceous bacterial virulence factors and are made by many of the most important bacterial pathogens .", "Host responses to these toxins are complex and poorly understood .", "We find that the endoplasmic reticulum unfolded protein respons...	[ "Pore-forming toxins ( PFTs ) are bacterial toxins that form holes at the plasma membrane of cells and play an important role in the pathogenesis of many important human pathogens .", "Although PFTs comprise an important and the single largest class of bacterial protein virulence factors , how cells respond to th...	2008
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "developmental biology/molecular development", "genetics and genomics/animal genetics", "developmental biology/pattern formation", "genetics and genomics/gene expression" ]	Initiator Elements Function to Determine the Activity State of BX-C Enhancers	journal.pgen.1001260	null	[ [ "The Drosophila bithorax complex ( BX-C ) is one of two homeotic gene clusters in the fly and is responsible for determining the segmental identity of the posterior thoracic segment and each of the fly abdominal segments [1] , [2] .", "It does this by using a >300 kb cis-regulatory region to control the p...	[ "A >300 kb cis-regulatory region is required for the proper expression of the three bithorax complex ( BX-C ) homeotic genes .", "Based on genetic and transgenic analysis , a model has been proposed in which the numerous BX-C cis-regulatory elements are spatially restricted through the activation or repression of...	[ "Understanding how genes become activated is one of the primary areas of research in modern biology .", "In order to decipher the DNA components required for this process , scientists have traditionally turned to transgenic reporter assays , where DNA elements are removed from their native environment and placed ...	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "dermatology", "somatosensory system", "medicine and health sciences", "chemical compounds", "clinical research design", "pathology and laboratory medicine", "tropical diseases", "limbs (anatomy)", "neuroscience", "organic compounds", "health care", "research design", "bacterial diseases", ...	Comparison of Efficacy and Safety of Ciclosporin to Prednisolone in the Treatment of Erythema Nodosum Leprosum: Two Randomised, Double Blind, Controlled Pilot Studies in Ethiopia	journal.pntd.0004149	null	[ [ "Leprosy is a chronic granulomatous infection principally affecting the skin and peripheral nerves caused by Mycobacterium leprae [1] .", "Clinical features include skin lesions and neuropathy manifesting as loss of sensation , weakness or nerve pain .", "Delayed diagnosis or treatment may result in d...	[ "Erythema Nodosum Leprosum ( ENL ) is a serious complication of leprosy .", "It is normally treated with high dose steroids , but its recurrent nature leads to prolonged steroid usage and associated side effects .", "There is little evidence on the efficacy of alternative treatments for ENL , especially for pat...	[ "Leprosy is caused by a mycobacterium , and is curable with multi-drug therapy , a combination of antibiotics taken for 6 or 12 months .", "However , some leprosy patients develop an inflammatory condition known as erythema nodosum leprosum ( ENL ) , or Type 2 reaction .", "ENL affects multiple organs and cause...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Multiscale Embedded Gene Co-expression Network Analysis	journal.pcbi.1004574	null	[ [ "Often , complex diseases involve multiple intertwined signaling circuitries .", "Cancer is an excellent example with a number of biological machineries activated in tumor pathogenesis including proliferation , angiogenesis , avoidance of cell death , evasion of tumor suppressing mechanisms , immortality ...	[ "Gene co-expression network analysis has been shown effective in identifying functional co-expressed gene modules associated with complex human diseases .", "However , existing techniques to construct co-expression networks require some critical prior information such as predefined number of clusters , numerical ...	[ "We developed a novel co-expression network analysis framework named Multiscale Embedded Gene co-Expression Network Analysis ( MEGENA ) that can effectively and efficiently construct and analyze large scale planar filtered co-expression networks .", "Two key components of MEGENA are the parallelization of embedde...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "gram negative", "macromolecular assemblies", "host-pathogen interaction", "biology", "microbiology", "bacterial pathogens" ]	Complex Structure of OspI and Ubc13: The Molecular Basis of Ubc13 Deamidation and Convergence of Bacterial and Host E2 Recognition	journal.ppat.1003322	null	[ [ "Ubiquitination is a post-translational protein modification involved in many important cellular processes , such as signal transduction , protein degradation and vesicle trafficking [1] .", "Ubiquitination is catalyzed by a combined cascade of three enzymes: a ubiquitin-activating enzyme ( E1 ) , a ubiqu...	[ "Ubc13 is an important ubiquitin-conjugating ( E2 ) enzyme in the NF-κB signaling pathway .", "The Shigella effector OspI targets Ubc13 and deamidates Gln100 of Ubc13 to a glutamic acid residue , leading to the inhibition of host inflammatory responses .", "Here we report the crystal structure of the OspI-Ubc13...	[ "The Gram-negative pathogenic bacterium Shigella infects human intestinal epithelium cells and causes severe inflammatory colitis ( bacillary dysentery ) .", "Shigella harbors an approximately 220-kb virulence plasmid that encodes a type III secretion system ( T3SS ) protein secretion apparatus and many effector ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/gene expression", "computational biology/systems biology", "computational biology/transcriptional regulation" ]	Invariant Distribution of Promoter Activities in Escherichia coli	journal.pcbi.1000545	null	[ [ "Bacteria face an interesting optimization problem: How to allocate limited transcriptional resources among thousands of different promoters .", "Beginning with the pioneering work of the Copenhagen school , several studies have measured the composition of the bacterial cell at different growth rates .", ...	[ "Cells need to allocate their limited resources to express a wide range of genes .", "To understand how Escherichia coli partitions its transcriptional resources between its different promoters , we employ a robotic assay using a comprehensive reporter strain library for E . coli to measure promoter activity on a...	[ "Cells respond to a changing environment by regulating the activity of genes .", "Here , we sought to understand how E . coli cells distribute their limited transcriptional resources among their target genes , and how this allocation varies with growth rate and growth conditions .", "To achieve this , we assaye...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "chronic kidney disease", "melioidosis", "pulmonology", "health care", "diabetes mellitus", "pneumonia", "bacterial diseases", "routes of administration", "endocrine disorders", "sepsis", "signs and symptoms", "pharmacolo...	The epidemiology and clinical features of melioidosis in Far North Queensland: Implications for patient management	journal.pntd.0005411	null	[ [ "Burkholderia pseudomallei , an environmental bacterium endemic to the tropics , is responsible for the disease melioidosis [1] .", "Serological studies suggest that B . pseudomallei infection is usually asymptomatic; however , it may also cause a rapidly fatal illness , particularly in those with co-morb...	[ "The epidemiology , clinical presentation and management of melioidosis vary around the world .", "It is essential to define the disease’s local features to optimise its management .", "Between 1998 and 2016 there were 197 cases of culture confirmed melioidosis in Far North Queensland; 154 ( 78% ) presented in ...	[ "Burkholderia pseudomallei is endemic to the tropics and is responsible for the disease melioidosis .", "Exposure rarely evolves to significant disease in the absence of specific comorbidities .", "Conversely , in susceptible hosts , the disease can be rapidly fatal if unrecognised .", "Patients require an ex...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "infectious disease epidemiology", "tropical diseases", "geographical locations", "age groups", "neglected tropical diseases", "infectious disease control", "public and occupational health", "infectious diseases", "serology", ...	Estimating Dengue Transmission Intensity from Case-Notification Data from Multiple Countries	journal.pntd.0004833	null	[ [ "Dengue is the most widely distributed mosquito-borne viral infection , but assessment of its geographic variation in transmission remains challenging .", "Analysis based on mapping the probability of occurrence of dengue estimated that dengue causes 390 million annual infections worldwide [1] .", "Ho...	[ "Despite being the most widely distributed mosquito-borne viral infection , estimates of dengue transmission intensity and associated burden remain ambiguous .", "With advances in the development of novel control measures , obtaining robust estimates of average dengue transmission intensity is key for assessing t...	[ "With 40% of the world’s population at risk of infection , dengue imposes a significant public health burden .", "Yet estimates of baseline transmission intensity are still sparse , making it difficult to implement efficient control programs .", "The authors used incidence data , which are abundant compared to ...	2016
[ "Introduction", "Results/Discussion", "Methods" ]	[ "systems biology", "synthetic biology", "biology", "computational biology", "signaling networks" ]	Robust Network Topologies for Generating Switch-Like Cellular Responses	journal.pcbi.1002085	null	[ [ "Signaling networks enable cells to process information from their surroundings by eliciting temporally and spatially precise responses to environmental cues .", "The complex and highly interconnected biomolecular interaction networks regulating signal transmission establish connections between specific m...	[ "Signaling networks that convert graded stimuli into binary , all-or-none cellular responses are critical in processes ranging from cell-cycle control to lineage commitment .", "To exhaustively enumerate topologies that exhibit this switch-like behavior , we simulated all possible two- and three-component network...	[ "Biomolecular signaling networks enable cells to mediate responses to extracellular and intracellular stimuli and are hence crucial for the functioning of all organisms .", "Such networks do not merely forward information , but perform signal processing: specific modules have evolved to produce complex , dynamic ...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "livestock", "medicine and health sciences", "pathology and laboratory medicine", "ruminants", "pathogens", "population dynamics", "geographical locations", "microbiology", "vertebrates", "animals", "mammals", "bacterial diseases", "population biology", "bacterial pathogens", "coxiella b...	Seroprevalence of Q fever among human and animal in Iran; A systematic review and meta-analysis	journal.pntd.0005521	null	[ [ "Q fever is a zoonosis caused by the intracellular , gram negative bacterium Coxiella burnetii .", "C . burnetii is an extremely infectious pathogen [1] .", "The extremely high infectivity , the ability to withstand harsh environmental conditions , and the potential to cause severe disease in man , ha...	[ "Q fever is a main zoonotic disease around the world .", "The aim of this meta-analysis was to estimate the overall seroprevalence of Coxiella burnetii among human and animal population in Iran .", "Major national and international databases were searched from 2005 up to August 2016 .", "We extracted the prev...	[ "Q fever is a zoonotic diseases caused by a bacterium so called Coxiella burnetii .", "Domestic ruminants ( primarily cattle , sheep and goats ) are the most important reservoir of C . burnetii in the nature .", "Q fever is mostly asymptomatic in livestock and animals .", "Clinical manifestations of Q fever i...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biotechnology", "neuroscience/cognitive neuroscience", "neuroscience/sensory systems", "computational biology/computational neuroscience" ]	Predicting Odor Pleasantness with an Electronic Nose	journal.pcbi.1000740	null	[ [ "Dravnieks envisioned an artificial ( or electronic ) nose as “an instrument that would inspect samples of odorous air and report the intensity and quality of an odor without the intervention of a human nose” [1] .", "Although eNoses have since been developed [2]–[10] , and serve in tasks of odor detectio...	[ "A primary goal for artificial nose ( eNose ) technology is to report perceptual qualities of novel odors .", "Currently , however , eNoses primarily detect and discriminate between odorants they previously “learned” .", "We tuned an eNose to human odor pleasantness estimates .", "We then used the eNose to pr...	[ "Electronic noses ( eNoses ) are devices aimed at mimicking animal noses .", "Typically , these devices contain a set of sensors that generate a pattern representing an odor .", "Application of eNoses entails first “training” the eNose to a particular odor , and once the eNose has “learned” , it can then be use...	2010
[ "Introduction", "Results", "Discussion", "Conclusions", "Methods" ]	[ "medicine and health sciences", "ecology and environmental sciences", "population genetics", "geographical locations", "tropical diseases", "uganda", "parasitic diseases", "aquatic environments", "bodies of water", "population biology", "africa", "lakes", "marine and aquatic sciences", "pe...	Genetic signatures of gene flow and malaria-driven natural selection in sub-Saharan populations of the "endemic Burkitt Lymphoma belt"	journal.pgen.1008027	null	[ [ "The endemic Burkitt Lymphoma ( eBL ) belt is a geographic area spanning 10°N-10°S and altitudes below 1500m above sea level ( Fig 1A ) in sub-Saharan Africa , where there is a high geographical correlation between malaria and eBL ( an aggressive pediatric B-cell non-Hodgkin lymphoma ) .", "This correlati...	[ "Populations in sub-Saharan Africa have historically been exposed to intense selection from chronic infection with falciparum malaria .", "Interestingly , populations with the highest malaria intensity can be identified by the increased occurrence of endemic Burkitt Lymphoma ( eBL ) , a pediatric cancer that affe...	[ "We present a genome-wide analyses of genetic structure , gene flow , and natural selection in Ghana and Northern Uganda populations , both residing in the Sub-Saharan eBL belt , a region with intense falciparum malaria transmission and high endemic Burkitt Lymphoma ( eBL ) incidence .", "These populations are fr...	2019
[ "Introduction", "Results and Discussion", "Methods" ]	[]	Crawling and Gliding: A Computational Model for Shape-Driven Cell Migration	journal.pcbi.1004280	null	[ [ "Single migrating cells fall into different morphological categories [1] .", "For example , keratocyte-like cells , named after fish epithelial cells , retain a half-moon shape and glide quite persistently , led by a lasting , thin and broad lammellipodium [2 , 3] .", "In contrast , amoeboid cells cha...	[ "Cell migration is a complex process involving many intracellular and extracellular factors , with different cell types adopting sometimes strikingly different morphologies .", "Modeling realistically behaving cells in tissues is computationally challenging because it implies dealing with multiple levels of compl...	[ "Cell migration is involved in vital processes like morphogenesis , regeneration and immune system responses , but can also play a central role in pathological processes like metastasization .", "Computational models have been successfully employed to explain how single cells migrate , and to study how diverse ce...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology/membranes and sorting" ]	Multivesicular Body Formation Requires OSBP–Related Proteins and Cholesterol	journal.pgen.1001055	null	[ [ "The multivesicular body ( MVB ) sorting pathway provides a mechanism for the lysosomal degradation of membrane proteins and has a role in many processes , including growth factor receptor down-regulation [1] , antigen presentation [2] , developmental signaling [3] , [4] , the budding of enveloped viruses [5]...	[ "In eukaryotes , different subcellular organelles have distinct cholesterol concentrations , which is thought to be critical for biological functions .", "Oxysterol-binding protein-related proteins ( ORPs ) have been assumed to mediate nonvesicular cholesterol trafficking in cells; however , their in vivo functio...	[ "The multivesicular body ( MVB ) sorting pathway provides a mechanism for the lysosomal degradation of membrane proteins , such as growth factor receptors .", "The formation of MVBs is unique in that the curvature is directed toward the lumen of the compartment rather than the cytosol .", "During MVB formation ...	2010
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "chemical bonding", "classical mechanics", "molecular dynamics", "oxygen", "potential energy", "thermodynamics", "hydrogen bonding", "polypeptides", "physical chemistry", "chemistry", "free energy", "physics", "biochemistry", "hydrogen", "molecular structure", "peptides", "biology an...	Navigating in foldonia: Using accelerated molecular dynamics to explore stability, unfolding and self-healing of the β-solenoid structure formed by a silk-like polypeptide	journal.pcbi.1005446	null	[ [ "An increasing number of functional proteins are reported to have β solenoid structure , such as antifreeze protein [1–3] , curli [4] , and carbonic anhydrase enzyme [5] .", "Formed by winding the peptide chain in a left-handed or right-handed fashion , a β solenoid structure usually has a repeat unit con...	[ "The β roll molecules with sequence ( GAGAGAGQ ) 10 stack via hydrogen bonding to form fibrils which have been themselves been used to make viral capsids of DNA strands , supramolecular nanotapes and pH-responsive gels .", "Accelerated molecular dynamics ( aMD ) simulations are used to investigate the unfolding o...	[ "Silk-inspired repeated sequences , variants of the sequence from Bombyx Mori silk , have been used to make supramolecular nanotapes , pH-responsive gels , and most importantly self-assembled coat for artificial viruses .", "Silk-inspired repeated sequences have shown great potential as promising delivery vehicle...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "dengue virus", "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "immunology", "microbiology", "viruses", "antibodies", "antibody response", "immune system proteins", "antibody specificity", "proteins", "medical microbiology", "microbial pathogens", "immu...	Dengue Viruses Are Enhanced by Distinct Populations of Serotype Cross-Reactive Antibodies in Human Immune Sera	journal.ppat.1004386	null	[ [ "Dengue is present in over 100 countries and is the most common arthropod-borne viral disease of humans [1] , [2] .", "Dengue disease is caused by dengue virus ( DENV ) , which exists as four closely-related serotypes ( DENV1-DENV4 ) .", "DENV spreads between humans through the mosquito vectors Aedes ...	[ "Dengue viruses ( DENV ) are mosquito-borne flaviviruses of global importance .", "DENV exist as four serotypes , DENV1-DENV4 .", "Following a primary infection , individuals produce DENV-specific antibodies that bind only to the serotype of infection and other antibodies that cross-react with two or more serot...	[ "The mosquito-borne dengue viruses ( DENV ) are responsible for approximately 390 million new infections worldwide each year , and an estimated 100 million of these infections lead to clinical disease .", "The presence of four different serotypes of DENV allows the same individual to experience more than one DENV...	2014
[ "Introduction", "Methods", "Results and discussion" ]	[ "medicine and health sciences", "toxins", "immune physiology", "pathology and laboratory medicine", "split-decomposition method", "immunology", "vertebrates", "animals", "toxicology", "toxic agents", "multiple alignment calculation", "reptiles", "antibodies", "research and analysis methods...	Cross-recognition of a pit viper (Crotalinae) polyspecific antivenom explored through high-density peptide microarray epitope mapping	journal.pntd.0005768	null	[ [ "Snakebite envenoming constitutes a serious public health problem on a global basis [1–3] .", "It primarily affects impoverished populations living in rural settings of Africa , Asia , and Latin America [4] .", "It is estimated that about 70 , 000 snakebite cases occur in Latin America every year , al...	[ "Snakebite antivenom is a 120 years old invention based on polyclonal mixtures of antibodies purified from the blood of hyper-immunized animals .", "Knowledge on antibody recognition sites ( epitopes ) on snake venom proteins is limited , but may be used to provide molecular level explanations for antivenom cross...	[ "Although snakebite antivenom is a 120-year-old invention , saving lives and limbs of thousands of snakebite victims every year , little is known about the mechanisms and molecular interactions of how antivenoms neutralize snake toxins .", "Antivenoms are produced by immunizing large animals with cocktails of sna...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular biology/dna replication", "cell biology/nuclear structure and function", "molecular biology/recombination", "cell biology/cell growth and division", "genetics and genomics/nuclear structure and function", "molecular biology/chromosome structure", "genetics and genomics/chromosome biology", ...	The SUMO Isopeptidase Ulp2p Is Required to Prevent Recombination-Induced Chromosome Segregation Lethality following DNA Replication Stress	journal.pgen.1001355	null	[ [ "As part of the DNA damage response , homologous recombination ( HR ) , particularly template switch recombination through the post-replication DNA repair pathway ( PRR ) , provides an important mechanism for restarting stalled replication forks and filling in un-replicated gaps in DNA ( reviewed in [1] , [2]...	[ "SUMO conjugation is a key regulator of the cellular response to DNA replication stress , acting in part to control recombination at stalled DNA replication forks .", "Here we examine recombination-related phenotypes in yeast mutants defective for the SUMO de-conjugating/chain-editing enzyme Ulp2p .", "We find ...	[ "DNA damage , arising from environmental stress or errors in DNA metabolism , can interfere with DNA replication .", "Cells respond by using homologous recombination to bypass the damage , resulting in DNA strand linkages between the replicated chromosomes .", "It is crucial to undo these linkages so chromosome...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "phase iii clinical investigation", "medicine and health sciences", "clinical medicine", "clinical trials", "randomized controlled trials" ]	Efficacy and Safety of Amphotericin B Emulsion versus Liposomal Formulation in Indian Patients with Visceral Leishmaniasis: A Randomized, Open-Label Study	journal.pntd.0003169	null	[ [ "Visceral leishmaniasis ( VL ) , also known as kala-azar , is a vector-borne disease transmitted to humans by the bite of an infected sandfly [1] .", "Globally , around 200 , 000–400 , 000 cases of VL occur each year of which 60% cases occur in India alone [2] .", "Kala-azar is a major public health p...	[ "India is home to 60% of the total global visceral leishmaniasis ( VL ) population .", "Use of long-term oral ( e . g . miltefosine ) and parenteral drugs , considered the mainstay for treatment of VL , is now faced with increased resistance , decreased efficacy , low compliance and safety issues .", "The autho...	[ "Visceral leishmaniasis ( VL ) is highly prevalent in northeastern India , particularly the state of Bihar and its bordering areas with Bangladesh and Nepal .", "The current standards of treatment , namely , miltefosine ( oral ) and pentavalent antimonials ( parenteral ) have long treatment durations and are face...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "zoonoses", "clinical laboratory sciences", "diagnostic medicine", "clinical immunology", "neglected tropical diseases", "brucellosis" ]	Ex Vivo Innate Immune Cytokine Signature of Enhanced Risk of Relapsing Brucellosis	journal.pntd.0002424	null	[ [ "Brucellosis in humans is a zoonotic infection caused by Gram-negative facultative intracellular bacteria of the Brucella genus .", "Four species are typically responsible for human infections , B . abortus , B . melitensis , B . suis , and B . canis , and are transmitted from animal reservoirs including ...	[ "Brucellosis , a zoonotic infection caused by one of the Gram-negative intracellular bacteria of the Brucella genus , is an ongoing public health problem in Perú .", "While most patients who receive standard antibiotic treatment recover , 5–40% suffer a brucellosis relapse .", "In this study , we examined the e...	[ "Brucellosis is a disease caused by transmission of bacteria of the Brucella genus from infected animals to humans .", "The main route of infection occurs through consumption of contaminated dairy products or contact with infected animals .", "While most patients treated with antibiotics will be cured of the in...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "population genetics", "population biology", "biology", "genomics", "evolutionary biology" ]	Balancing Selection on a Regulatory Region Exhibiting Ancient Variation That Predates Human–Neandertal Divergence	journal.pgen.1003404	null	[ [ "Most functionally important genomic loci in modern humans , including the majority of exons are under negative ( purifying ) selection and consequently show little , if any , genetic variation .", "In contrast , other forms of selection , such as balancing or directional positive selection , occur less f...	[ "Ancient population structure shaping contemporary genetic variation has been recently appreciated and has important implications regarding our understanding of the structure of modern human genomes .", "We identified a ∼36-kb DNA segment in the human genome that displays an ancient substructure .", "The variat...	[ "Natural selection shapes the genome in a non-random way , as an allele that contributes more to the reproductive fitness of a species increases in frequency within the population .", "Under balancing selection , a particular kind of natural selection , more than one allele increases in frequency in the populatio...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "bacteriology", "bacterial diseases", "infectious diseases", "medicine and health sciences", "biology and life sciences", "microbiology", "opportunistic infections", "healthcare-associated infections" ]	The Pseudomonas aeruginosa Type III Translocon Is Required for Biofilm Formation at the Epithelial Barrier	journal.ppat.1004479	null	[ [ "For Pseudomonas aeruginosa and many other human pathogens , biofilms are an important mode of growth in a wide variety of clinically significant infections , including lung infections in cystic fibrosis patients , endocarditis , and periodontitis [1] , [2] .", "A widely accepted and core definition of a ...	[ "Clinical infections by Pseudomonas aeruginosa , a deadly Gram-negative , opportunistic pathogen of immunocompromised hosts , often involve the formation of antibiotic-resistant biofilms .", "Although biofilm formation has been extensively studied in vitro on glass or plastic surfaces , much less is known about b...	[ "Clinical infections by Pseudomonas aeruginosa , a deadly Gram-negative , opportunistic pathogen of immunocompromised patients , involve the formation of antibiotic-resistant biofilms .", "Although P . aeruginosa biofilm formation has been extensively studied on glass or plastic surfaces , less is known about bio...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "proteins", "protein structure", "macromolecular assemblies", "salmonella", "biology", "microbiology", "host-pathogen interaction", "bacterial pathogens" ]	A Refined Model of the Prototypical Salmonella SPI-1 T3SS Basal Body Reveals the Molecular Basis for Its Assembly	journal.ppat.1003307	null	[ [ "The bacterial injectisome , or type III secretion system ( T3SS ) , is a specialized syringe-shaped protein-export system utilized by many pathogenic Gram-negative bacteria for the injection of virulence proteins ( effectors ) into host cells .", "Bacterial proteins destined for both needle assembly and ...	[ "The T3SS injectisome is a syringe-shaped macromolecular assembly found in pathogenic Gram-negative bacteria that allows for the direct delivery of virulence effectors into host cells .", "It is composed of a “basal body” , a lock-nut structure spanning both bacterial membranes , and a “needle” that protrudes awa...	[ "Gram-negative bacteria such as E . coli , Salmonella , Shigella , Pseudomonas aeruginosa , and Yersinia pestis are responsible for a wide range of diseases , from pneumonia to lethal diarrhea and plague .", "A common trait shared by these bacteria is their capacity to inject toxins directly inside the cells of i...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Neisseria meningitidis Type IV Pili Composed of Sequence Invariable Pilins Are Masked by Multisite Glycosylation	journal.ppat.1005162	null	[ [ "Members of the Neisseria genus are Gram-negative proteobacteria that include several commensals such as N . sicca , N . lactamica or N . elongata and two human pathogens , N . gonorrheae and N . meningitidis .", "Both of these are highly adapted for interaction with humans , their unique host .", "N ...	[ "The ability of pathogens to cause disease depends on their aptitude to escape the immune system .", "Type IV pili are extracellular filamentous virulence factors composed of pilin monomers and frequently expressed by bacterial pathogens .", "As such they are major targets for the host immune system .", "In t...	[ "During infection pathogens and their host engage in a series of measures and counter-measures to promote their own survival: pathogens express virulence factors , the immune system targets these surface structures and pathogens modify them to evade detection .", "Like numerous bacterial pathogens , Neisseria men...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "genome-wide association studies", "medicine and health sciences", "body fluids", "vegf signaling", "genomic databases", "mathematics", "statistics (mathematics)", "genome analysis", "platelets", "research and analysis methods", "genome complexity", "chromosome biology", "an...	Six Novel Loci Associated with Circulating VEGF Levels Identified by a Meta-analysis of Genome-Wide Association Studies	journal.pgen.1005874	null	[ [ "Vascular Endothelial Growth Factor ( VEGF ) is secreted largely by endothelial cells and plays a key role in several physiological and pathological conditions .", "During growth , development , and maintenance of the circulatory system , VEGF is the principal pro-angiogenic factor and it has additionally...	[ "Vascular endothelial growth factor ( VEGF ) is an angiogenic and neurotrophic factor , secreted by endothelial cells , known to impact various physiological and disease processes from cancer to cardiovascular disease and to be pharmacologically modifiable .", "We sought to identify novel loci associated with cir...	[ "Vascular Endothelial Growth Factor ( VEGF ) is a protein with a fundamental role in development of vascular system .", "The protein , produced by many types of cells , is released in the blood .", "High levels of VEGF have been observed in different pathological conditions especially in cancer , cardiovascular...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "bacteriology", "animal models of infection", "bacterial diseases", "infectious diseases", "microbial mutation", "medicine and health sciences", "population modeling", "neglected tropical diseases", "biology and life sciences", "tropical diseases", "microbiology", "infectious disease modeling"...	Type 3 Secretion System Cluster 3 Is a Critical Virulence Determinant for Lung-Specific Melioidosis	journal.pntd.0003441	null	[ [ "Burkholderia pseudomallei is the Tier 1 Select Agent bacterial pathogen responsible for the disease melioidosis .", "B . pseudomallei is found in moist tropical soils worldwide , but has been long characterized to be endemic to Southeast Asia and northern Australia [1] .", "Naturally acquired disease...	[ "Burkholderia pseudomallei , the bacterial agent of melioidosis , causes disease through inhalation of infectious particles , and is classified as a Tier 1 Select Agent .", "Optical diagnostic imaging has demonstrated that murine respiratory disease models are subject to significant upper respiratory tract ( URT ...	[ "Respiratory melioidosis is a lethal disease presentation of the bacterium Burkholderia pseudomallei , which is found in tropical regions worldwide .", "Respiratory melioidosis has also been highlighted as a concern in the biodefense community given the potential for weaponization of B . pseudomallei .", "This ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "bacteriology", "medicine and health sciences", "pathology and laboratory medicine", "microbiology", "escherichia coli", "bacterial pathogens", "immune system proteins", "proteins", "medical microbiology", "metabolic pathways", "microbial pathogens", "pathogenesis", "systems biology", "bio...	Combined Systems Approaches Reveal Highly Plastic Responses to Antimicrobial Peptide Challenge in Escherichia coli	journal.ppat.1004104	null	[ [ "The isolation of cecropins [1] , magainins [2] and defensins [3] from insects , amphibians and mammals in the late 1980's and early 1990's , highlighted the potential of host defence peptides as sources of novel antibiotics [4] .", "This novel antibiotic potential encouraged researchers to develop struct...	[ "Obtaining an in-depth understanding of the arms races between peptides comprising the innate immune response and bacterial pathogens is of fundamental interest and will inform the development of new antibacterial therapeutics .", "We investigated whether a whole organism view of antimicrobial peptide ( AMP ) cha...	[ "Antimicrobial peptides ( AMP ) are small proteins with often potent antibacterial activity found in a variety of organisms , including humans .", "Understanding how these antibiotics operate is challenging and often controversial since many studies have necessarily focussed on identifying a single major cause of...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Deletion of an X-Inactivation Boundary Disrupts Adjacent Gene Silencing	journal.pgen.1003952	null	[ [ "Recent annotation of the human and mouse genomes has revealed chromosome domains that are distinguished by sequence and gene content , regulatory-factor binding , replication dynamics , chromatin composition , or nuclear location .", "Many of these domains overlap and can functionally segregate active an...	[ "In mammalian females , genes on one X are largely silenced by X-chromosome inactivation ( XCI ) , although some “escape” XCI and are expressed from both Xs .", "Escapees can closely juxtapose X-inactivated genes and provide a tractable model for assessing boundary function at epigenetically regulated loci .", ...	[ "Early in mammalian female development , one X chromosome is largely silenced to equalize X-linked gene expression between the sexes .", "Nevertheless , some genes “escape” this silencing and therefore are expressed from both X chromosomes .", "Understanding how these escape genes are regulated , particularly w...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "bacteriology", "periplasm", "biochemistry", "proteins", "protein structure", "biology and life sciences", "molecular biology techniques", "microbiology", "molecular biology", "macromolecular structure analysis" ]	Structure of CfaA Suggests a New Family of Chaperones Essential for Assembly of Class 5 Fimbriae	journal.ppat.1004316	null	[ [ "Bacteria assemble filamentous projections on their surface to facilitate adhesion to other bacteria , eukaryotic cells and abiotic substrates .", "These macromolecular organelles are composed of protein polymers and can appear as regular , rod-like pili ( or fimbriae ) , irregular , thin fibrils or indis...	[ "Adhesive pili on the surface of pathogenic bacteria comprise polymerized pilin subunits and are essential for initiation of infections .", "Pili assembled by the chaperone-usher pathway ( CUP ) require periplasmic chaperones that assist subunit folding , maintain their stability , and escort them to the site of ...	[ "Bacterial infection begins with microbial adhesion to host cells .", "For gram-negative bacteria , adhesion is often mediated by pili , proteinaceous polymers that protrude from the bacterial surface and recognize host receptors .", "During assembly , each pilus protein subunit is assisted in folding by a chap...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "meiosis", "cell biology", "chromosome biology", "cell cycle and cell division", "biology and life sciences", "cell processes", "molecular cell biology" ]	Meiosis-Specific Cohesin Component, Stag3 Is Essential for Maintaining Centromere Chromatid Cohesion, and Required for DNA Repair and Synapsis between Homologous Chromosomes	journal.pgen.1004413	null	[ [ "During mitosis , chromosomes are replicated and the resulting sister chromatids are segregated , generating two genetically identical daughter cells .", "Meiosis , on the other hand , is a specialized cell division that involves chromosome replication and two rounds of chromosome segregation ( meiosis I ...	[ "Cohesins are important for chromosome structure and chromosome segregation during mitosis and meiosis .", "Cohesins are composed of two structural maintenance of chromosomes ( SMC1-SMC3 ) proteins that form a V-shaped heterodimer structure , which is bridged by a α-kleisin protein and a stromal antigen ( STAG ) ...	[ "Meiosis is a specialized cell division required for the formation of gametes ( sperm and egg ) .", "Early in meiosis , the chromosome pairs that we inherit from our mother and father become linked and genetic material is exchanged .", "This is a remarkable process as every gamete that we make is unique , and t...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "neuroscience/theoretical neuroscience" ]	From Spiking Neuron Models to Linear-Nonlinear Models	journal.pcbi.1001056	null	[ [ "Neurons encode stimuli by emitting trains of actions potentials in response to sensory inputs .", "To uncover the corresponding neural code , the mapping between sensory inputs and output action potentials needs to be described with the help of a quantitative model [1] .", "In the recent years , gene...	[ "Neurons transform time-varying inputs into action potentials emitted stochastically at a time dependent rate .", "The mapping from current input to output firing rate is often represented with the help of phenomenological models such as the linear-nonlinear ( LN ) cascade , in which the output firing rate is est...	[ "Deciphering the encoding of information in the brain implies understanding how individual neurons emit action potentials ( APs ) in response to time-varying stimuli .", "This task is made difficult by two facts:", "( i ) although the biophysics of AP generation are well understood , the dynamics of the membran...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology/cell signaling", "cell biology/morphogenesis and cell biology", "mathematics", "biophysics/theory and simulation", "cell biology/microbial growth and development", "computational biology" ]	Mathematical Description of Bacterial Traveling Pulses	journal.pcbi.1000890	null	[ [ "Since Adler's seminal paper [1] , several groups have reported the formation and the propagation of concentration waves in bacteria suspensions [2] , [3] .", "Typically , a suspension of swimming bacteria such as E . coli self-concentrates in regions where the environment is slightly different such as th...	[ "The Keller-Segel system has been widely proposed as a model for bacterial waves driven by chemotactic processes .", "Current experiments on Escherichia coli have shown the precise structure of traveling pulses .", "We present here an alternative mathematical description of traveling pulses at the macroscopic s...	[ "Modeling chemotaxis has raised a lot of interest in the applied mathematics community in past decades .", "The precise description of bacterial pulses traveling in a narrow channel is a challenging issue in the self-organization of cells .", "Indeed , our biological knowledge of signal integration in E . coli ...	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "behavioral and social aspects of health", "tropical diseases", "cancers and neoplasms", "parasitic diseases", "cardiovascular medicine", "health care", "oncology", "bacterial diseases", "neglected tropical diseases", "public and occupational health", "infectiou...	Diseases Neglected by the Media in Espírito Santo, Brazil in 2011–2012	journal.pntd.0004662	null	[ [ "In the contemporary sociopolitical landscape , mass media operates in three dimensions , lending them a unique importance .", "It acts as a vehicle for the social dissemination of relevant information on health as a system that allows the introduction of social themes and issues to the public [1] and as ...	[ "The aims of the present study were to identify and analyse the Diseases Neglected by the Media ( DNMs ) via a comparison between the most important health issues to the population of Espírito Santo , Brazil , from the epidemiological perspective ( health value ) and their effective coverage by the print media , an...	[ "The Diseases Neglected by the Media ( DNMs ) are those diseases without media visibility due to their low newsworthiness level .", "In most cases , these diseases affect deprived social groups .", "This study analyses the DNMs by comparing the space achieved by the most important health problems for the popula...	2016
[ "Introduction", "Results", "Discussion and future work", "Methods" ]	[ "phosphorylation", "medicine and health sciences", "breast tumors", "statistics", "cancers and neoplasms", "signaling networks", "enzymology", "oncology", "mathematics", "forecasting", "network analysis", "sequence motif analysis", "enzyme inhibitors", "discrete mathematics", "combinator...	CoPhosK: A method for comprehensive kinase substrate annotation using co-phosphorylation analysis	journal.pcbi.1006678	null	[ [ "Protein phosphorylation ( PP ) is a post-translational modification that is central to cellular signalling where networks composed of kinases , phosphatases , and their substrates regulate the sites and levels of phosphorylation at the molecular level .", "MS-based approaches based on phosphopeptide enri...	[ "We present CoPhosK to predict kinase-substrate associations for phosphopeptide substrates detected by mass spectrometry ( MS ) .", "The tool utilizes a Naïve Bayes framework with priors of known kinase-substrate associations ( KSAs ) to generate its predictions .", "Through the mining of MS data for the collec...	[ "Kinases play an important role in cellular regulation and have emerged as an important class of drug targets for many diseases , particularly cancers .", "Comprehensive identification of the links between kinases and their substrates enhances our ability to understand the underlying mechanism of diseases and sig...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "animal genetics", "animal models", "developmental biology", "caenorhabditis elegans", "model organisms", "molecular development", "morphogenesis", "proteins", "biology", "biochemistry", "cytoskeletal proteins", "signaling", "cell migration", "genetics", "genetics and genomics" ]	SLI-1 Cbl Inhibits the Engulfment of Apoptotic Cells in C. elegans through a Ligase-Independent Function	journal.pgen.1003115	null	[ [ "The engulfment of apoptotic cells requires at least two processes to occur in the engulfing cell at the interface with the dying cell .", "Actin cytoskeletal elements need to be reorganized and membrane needs to be recruited .", "Together , these two processes result in the engulfing cell surrounding...	[ "The engulfment of apoptotic cells is required for normal metazoan development and tissue remodeling .", "In Caenorhabditis elegans , two parallel and partially redundant conserved pathways act in cell-corpse engulfment .", "One pathway , which includes the small GTPase CED-10 Rac and the cytoskeletal regulator...	[ "Cell death is a normal part of organismal development .", "When cells die , other cells engulf them .", "In the roundworm C . elegans , engulfment is facilitated by one pathway that rearranges the actin cytoskeleton and another that recruits membrane .", "Together they cause the formation of cellular extensi...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "density", "neural networks", "nervous system", "vertebrates", "mice", "neuroscience", "animals", "mammals", "primates", "animal anatomy", "materials science", "brain mapping", "materials physics", "nerve fibers", "zoology", "old world monkeys", "com...	Statistical Analysis of Tract-Tracing Experiments Demonstrates a Dense, Complex Cortical Network in the Mouse	journal.pcbi.1005104	null	[ [ "Recently , there has been much interest in the connectome perspective of the brain , which aims to map the entire set of connections or interactions between brain regions , rather than the more traditional focus on individual regions and their connectivity [1 , 2] .", "This view may offer new insights bo...	[ "Anatomical tract tracing methods are the gold standard for estimating the weight of axonal connectivity between a pair of pre-defined brain regions .", "Large studies , comprising hundreds of experiments , have become feasible by automated methods .", "However , this comes at the cost of positive-mean noise ma...	[ "Tract-tracing depends on active axonal transport of tracers between nerve cells , indicating the anatomical connectivity between areas of the brain .", "Recent advances in tract-tracing technology have enabled reconstruction of the connectome or wiring diagram of mammalian cerebral cortex .", "Here , we propos...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "access to consciousness", "social sciences", "neuroscience", "multivariate analysis", "cognitive neuroscience", "systems science", "mathematics", "statistics (mathematics)", "brain mapping", "vision", "discrete mathematics", "neuroimaging", "combinatorics", "research and analysis methods"...	Initial-state-dependent, robust, transient neural dynamics encode conscious visual perception	journal.pcbi.1005806	null	[ [ "Identical sensory input can be processed by the brain consciously or unconsciously [1 , 2] .", "What determines whether a sensory stimulus gains conscious access or not ?", "And what distinguishes neural activity underlying conscious and unconscious processing ?", "Traditionally , neuroscientists...	[ "Recent research has identified late-latency , long-lasting neural activity as a robust correlate of conscious perception .", "Yet , the dynamical nature of this activity is poorly understood , and the mechanisms governing its presence or absence and the associated conscious perception remain elusive .", "We ap...	[ "What brain mechanisms underlie conscious perception ?", "A commonly adopted paradigm for studying this question is to present human subjects with threshold-level stimuli .", "When shown repeatedly , the same stimulus is sometimes consciously perceived , sometimes not .", "Using magnetoencephalography , we sh...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/neglected tropical diseases", "cell biology", "cell biology/membranes and sorting", "microbiology/parasitology", "infectious diseases/protozoal infections", "cell biology/cytoskeleton" ]	Rab11A-Controlled Assembly of the Inner Membrane Complex Is Required for Completion of Apicomplexan Cytokinesis	journal.ppat.1000270	null	[ [ "Cytokinesis , the final step during cell division , has been extensively studied in eukaryotes .", "Whereas in animal cells cytokinesis is dependent on the formation of an actin/myosin-based contractile ring that forms in the middle of the anaphase spindle [1] , [2] , in plants the phragmoplast ( a speci...	[ "The final step during cell division is the separation of daughter cells , a process that requires the coordinated delivery and assembly of new membrane to the cleavage furrow .", "While most eukaryotic cells replicate by binary fission , replication of apicomplexan parasites involves the assembly of daughters ( ...	[ "Apicomplexan parasites are unusual in that they replicate by assembling daughter parasites within the mother cell .", "This involves the ordered assembly of an Inner Membrane Complex ( IMC ) , a scaffold consisting of flattened membrane cisternae and a subpellicular network made up of microtubules and scaffold p...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Identifying the Role of E2 Domains on Alphavirus Neutralization and Protective Immune Responses	journal.pntd.0004163	null	[ [ "Alphaviruses are a diverse group of arthropod-borne viruses ( arbovirus ) that are distributed worldwide [1] .", "Chikungunya virus ( CHIKV ) has been the cause of several recent outbreaks of arthritic disease and has now spread into the Caribbean and Central/South America , with at least 44 countries in...	[ "Chikungunya virus ( CHIKV ) and other alphaviruses are the etiologic agents of numerous diseases in both humans and animals .", "Despite this , the viral mediators of protective immunity against alphaviruses are poorly understood , highlighted by the lack of a licensed human vaccine for any member of this virus ...	[ "Chikungunya virus ( CHIKV ) is the cause of an ongoing explosive outbreak of arthritic disease in the Americas .", "Related alphaviruses cause human/animal disease globally , yet no vaccines or antivirals exist for human use .", "Although numerous candidate vaccines and therapies are being developed , little i...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "taxonomy", "ecology and environmental sciences", "medicine and health sciences", "immunology", "tropical diseases", "microbiology", "rabies", "clinical medicine", "neglected tropical diseases", "veterinary science", "public and occupational health", "infectious diseases", "veterinary diseas...	Re-emergence of Rabies in the Guangxi Province of Southern China	journal.pntd.0003114	null	[ [ "Rabies is a fatal enzootic viral infection of the central nervous system .", "The disease is widespread throughout the world , and is a serious public health problem in developing countries .", "The WHO reported that human mortality from endemic canine rabies is estimated to be 55000 deaths per year ...	[ "Human rabies cases in the Guangxi province of China decreased from 839 in 1982 to 24 in 1995 , but subsequently underwent a sharp increase , and has since maintained a high level .", "3 , 040 brain samples from normal dogs and cats were collected from 14 districts of Guangxi and assessed by RT-PCR .", "The bra...	[ "Rabies is a worldwide zoonosis disease and is of considerable public health threat and hazard .", "The Guangxi province of southern China is a severe rabies epidemic region .", "Human rabies cases decreased from 839 in 1982 to 24 in 1995 in Guangxi as a result of a dog vaccination campaign .", "However , the...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "cellular structures", "molecular neuroscience", "anatomy and physiology", "neuroscience", "biology", "proteomics", "biochemistry", "cellular neuroscience", "cell biology", "neurological disorders", "neurology", "physiology", "cellular types", "molecular cell biology" ]	GTPase Activity and Neuronal Toxicity of Parkinson's Disease–Associated LRRK2 Is Regulated by ArfGAP1	journal.pgen.1002526	null	[ [ "Mutations in the leucine-rich repeat kinase 2 gene ( LRRK2 , PARK8 , OMIM 607060 ) cause late-onset , autosomal dominant Parkinson's disease ( PD ) that is clinically and neurochemically indistinguishable from idiopathic PD [1] , [2] , [3] .", "LRRK2 mutations that clearly segregate with disease include ...	[ "Mutations in the leucine-rich repeat kinase 2 ( LRRK2 ) gene are the most common cause of autosomal dominant familial Parkinson's disease ( PD ) and also contribute to idiopathic PD .", "LRRK2 encodes a large multi-domain protein with GTPase and kinase activity .", "Initial data indicates that an intact functi...	[ "Parkinson's disease ( PD ) is the most common neurodegenerative movement disorder .", "Current therapies for treating PD are symptomatic and rely on restoring dopamine signaling .", "There is presently no cure for PD .", "PD is typically a sporadic disease , although 5%–10% of cases are known to have a famil...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "atmospheric science", "geographical locations", "tropical diseases", "animals", "neglected tropical diseases", "infectious disease control", "insect vectors", "zoology", "africa", "infectious diseases", "aedes aegypti", "epidemiology", "d...	Dengue Outbreak in Mombasa City, Kenya, 2013–2014: Entomologic Investigations	journal.pntd.0004981	null	[ [ "Dengue virus ( DENV ) is a member of the genus flavivirus ( family Flaviviridae ) that is transmitted principally by Aedes aegypti mosquitoes in an Ae .", "aegypti-human cycle [1] , sometimes resulting in epidemics .", "Although the presence of other Stegomyia spp .", "including Ae .", "simps...	[ "Dengue outbreaks were first reported in East Africa in the late 1970s to early 1980s including the 1982 outbreak on the Kenyan coast .", "In 2011 , dengue outbreaks occurred in Mandera in northern Kenya and subsequently in Mombasa city along the Kenyan coast in 2013–2014 .", "Following laboratory confirmation ...	[ "The first dengue outbreak in Kenya was reported in 1982 in the coastal region .", "This was followed almost 30 years later by the 2011 dengue outbreak in Mandera , northern Kenya and subsequently in Mombasa city in the coastal region ( 2013–2014 ) .", "An entomologic investigation was conducted to establish th...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "body fluids", "pathology and laboratory medicine", "redox signaling", "oxidative stress", "enzymes", "pathogens", "immunology", "microbiology", "enzymology", "dismutases", "animal models", "fungi", "clinical medicine", "...	Intersection of phosphate transport, oxidative stress and TOR signalling in Candida albicans virulence	journal.ppat.1007076	null	[ [ "Candida albicans is the most common invasive human fungal pathogen , whose infections carry a high mortality rate [1] .", "It is also a widespread commensal , colonizing gastrointestinal mucous membranes of around half of healthy humans [2] and competing with myriad bacteria for nutrients shed by the hos...	[ "Phosphate is an essential macronutrient required for cell growth and division .", "Pho84 is the major high-affinity cell-surface phosphate importer of Saccharomyces cerevisiae and a crucial element in the phosphate homeostatic system of this model yeast .", "We found that loss of Candida albicans Pho84 attenua...	[ "Candida albicans is the species most often isolated from patients with invasive fungal disease , and is also a common colonizer of healthy people .", "It is well equipped to compete for nutrients with bacteria co-inhabiting human gastrointestinal mucous membranes , since it possesses multiple transporters to int...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "flow cytometry", "phosphorylation", "g1 phase", "condensation", "cell cycle and cell division", "cell processes", "condensed matter physics", "mitosis", "epigenetics", "chromatin", "research and analysis methods", "chromosome biology", "proteins", "gene expression", "phase transitions",...	Levels of Ycg1 Limit Condensin Function during the Cell Cycle	journal.pgen.1006216	null	[ [ "The eukaryotic cell cycle is divided into two distinct parts: interphase , when cell growth and DNA replication occur , and mitosis , when chromosomes are segregated into daughter cells .", "One major phenotypic difference between these phases is chromosome conformation .", "Specifically , interphase...	[ "During mitosis chromosomes are condensed to facilitate their segregation , through a process mediated by the condensin complex .", "Although several factors that promote maximal condensin activity during mitosis have been identified , the mechanisms that downregulate condensin activity during interphase are larg...	[ "Chromosome conformation is cell cycle-regulated so that chromosomes are highly compacted to facilitate their segregation during mitosis , and decondensed during interphase to facilitate DNA-dependent processes such as replication and transcription .", "Understanding how chromosomes transition between these diffe...	2016
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "genome evolution", "human genomics", "genome analysis", "genetic elements", "genome annotation", "mammalian genomics", "dna", "mobile genetic elements", "molecular evolution", "comparative genomics", "animal genomics", "biochemistry", "bird genomics", "nucleic acids", "genetics", "tra...	Divergent genome evolution caused by regional variation in DNA gain and loss between human and mouse	journal.pcbi.1006091	null	[ [ "Evolution as a result of natural selection has led to many streamlined forms which follow directly from their function .", "However , in the case of genome evolution of complex organisms this connection is not quite so direct .", "One example is the evolution of genome size .", "In vertebrates , ...	[ "The forces driving the accumulation and removal of non-coding DNA and ultimately the evolution of genome size in complex organisms are intimately linked to genome structure and organisation .", "Our analysis provides a novel method for capturing the regional variation of lineage-specific DNA gain and loss events...	[ "Approximately 2% of a mammalian genome is protein-coding DNA , the remainder is non-coding DNA .", "In mammals , this non-coding DNA fraction has undergone large amounts of turnover since placental mammals diverged from a common ancestor .", "For example , human and mouse , two species who diverged approximate...	2018
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "ecology and environmental sciences", "gut bacteria", "microbiome", "pathology and laboratory medicine", "pathogens", "microbiology", "animals", "wolbachia", "infectious disease control", "insect vectors", "bacteria", "microbial genomics", ...	Comparative analysis of gut microbiota of mosquito communities in central Illinois	journal.pntd.0005377	null	[ [ "Mosquitoes transmit a wide range of pathogens that cause diseases in humans and other animals .", "The majority of mosquito-borne pathogens were previously confined to small geographic regions in the tropics but have recently emerged as a worldwide threat to human and animal health .", "Recent exampl...	[ "The composition and structure of microbial communities that inhabit the mosquito midguts are poorly understood despite their well-documented potential to impede pathogen transmission .", "We used MiSeq sequencing of the 16S rRNA gene to characterize the bacterial communities of field-collected populations of 12 ...	[ "The microbial communities that reside in mosquito midguts can impact transmission of mosquito-borne pathogens .", "We used high throughput next generation sequencing to characterize the midgut microbial communities of 12 mosquito species collected in urban residential areas in Champaign County , Illinois .", "...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "infectious diseases/protozoal infections", "microbiology/microbial evolution and genomics", "microbiology/parasitology" ]	A Broad Distribution of the Alternative Oxidase in Microsporidian Parasites	journal.ppat.1000761	null	[ [ "Microsporidia are a large and diverse group of eukaryotic intracellular parasites that infect a wide variety of animal lineages , including humans [1] .", "Although once thought to be early branching eukaryotes , they are now widely accepted to be very atypical parasitic fungi [2] , [3] , [4] , [5] .", ...	[ "Microsporidia are a group of obligate intracellular parasitic eukaryotes that were considered to be amitochondriate until the recent discovery of highly reduced mitochondrial organelles called mitosomes .", "Analysis of the complete genome of Encephalitozoon cuniculi revealed a highly reduced set of proteins in ...	[ "Microsporidia are obligate intracellular parasites responsible for a number of diseases in commercially important animals ( e . g . bees ) and of significant medical concern , in particular in immunocompromised humans .", "Though related to fungi , microsporidia have undergone a rapid phase of adaption to the in...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology/virus evolution and symbiosis", "immunology/immune response", "virology/new therapies, including antivirals and immunotherapy", "virology", "virology/emerging viral diseases", "infectious diseases/viral infections", "immunology", "virology/immune evasion", "immunology/immunity to infection...	Broadening of Neutralization Activity to Directly Block a Dominant Antibody-Driven SARS-Coronavirus Evolution Pathway	journal.ppat.1000197	null	[ [ "A novel coronavirus ( CoV ) , severe acute respiratory syndrome coronavirus ( SARS-CoV ) , caused a worldwide epidemic of SARS with a fatality rate of 9 . 6% in 2002/03 and later reemerged and resulted in infection of four individuals with full recovery in the winter of 2003/04 [1]–[5] .", "SARS-CoV has ...	[ "Phylogenetic analyses have provided strong evidence that amino acid changes in spike ( S ) protein of animal and human SARS coronaviruses ( SARS-CoVs ) during and between two zoonotic transfers ( 2002/03 and 2003/04 ) are the result of positive selection .", "While several studies support that some amino acid ch...	[ "The SARS-CoV caused a worldwide epidemic of SARS in 2002/03 and was responsible for this zoonotic infectious disease .", "The role of neutralizing antibody ( nAb ) mediated immune pressure in the evolution of SARS-CoV during the 2002/03 outbreak and a second 2003/04 zoonotic transmission is unknown .", "Here w...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "plant science", "plant growth and development", "plant biology", "genetics", "plant genetics", "epigenetics", "biology", "dna modification", "genetics and genomics", "histone modification" ]	Arabidopsis Homologs of Retinoblastoma-Associated Protein 46/48 Associate with a Histone Deacetylase to Act Redundantly in Chromatin Silencing	journal.pgen.1002366	null	[ [ "Cytosine DNA methylation is critical for stable silencing of transposable elements ( TE ) and repetitive sequences and for epigenetic regulation of endogenous gene expression in eukaryotes [1]–[3] .", "DNA methylation is thought to play an ancestral role in the defense against invasive DNA elements to ma...	[ "RNA molecules such as small-interfering RNAs ( siRNAs ) and antisense RNAs ( asRNAs ) trigger chromatin silencing of target loci .", "In the model plant Arabidopsis , RNA–triggered chromatin silencing involves repressive histone modifications such as histone deacetylation , histone H3 lysine-9 methylation , and ...	[ "Chromatin , made of histones and DNA , is often covalently modified in the nucleus , and modifications can regulate gene transcription .", "RNA molecules such as small-interfering or silencing RNAs ( siRNAs ) and antisense RNAs ( asRNAs ) can trigger silencing of gene expression in eukaryotes .", "We have foun...	2011
[ "Introduction", "Results", "Discussion" ]	[]	FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants	journal.pcbi.1004556	null	[ [ "Proteins are increasingly used in biotechnological applications as therapeutics [1] , diagnostics [2] , nanomaterials [1] and biocatalysts [3] .", "Despite numerous advantages , the utility of proteins is frequently restricted by their limited stability under practical conditions , such as high temperatu...	[ "There is great interest in increasing proteins’ stability to enhance their utility as biocatalysts , therapeutics , diagnostics and nanomaterials .", "Directed evolution is a powerful , but experimentally strenuous approach .", "Computational methods offer attractive alternatives .", "However , due to the li...	[ "Proteins are increasingly used in numerous biotechnological applications .", "A key property determining proteins’ applicability is their stability under operating conditions .", "Natural proteins can be stabilized by modification of their structure .", "Methods of molecular biology allow introduction of mod...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "cell biology/neuronal and glial cell biology", "developmental biology/aging", "neurological disorders/movement disorders", "genetics and genomics/genetics of disease", "genetics and genomics/gene function", "neuroscience/neurobiology of disease and regeneration" ]	Deletion of the Huntingtin Polyglutamine Stretch Enhances Neuronal Autophagy and Longevity in Mice	journal.pgen.1000838	null	[ [ "In vertebrates , the polyQ stretch within htt is located close to the protein's N-terminus , and separates a highly conserved 17 amino acid N-terminal domain ( N1–17 ) that can act as a membrane association signal [1] , from a proline-rich region that is implicated in protein-protein interactions [2]–[4] .",...	[ "Expansion of a stretch of polyglutamine in huntingtin ( htt ) , the protein product of the IT15 gene , causes Huntington's disease ( HD ) .", "Previous investigations into the role of the polyglutamine stretch ( polyQ ) in htt function have suggested that its length may modulate a normal htt function involved in...	[ "Expansion of a stretch of glutamines near the amino-terminus of huntingtin ( htt ) , the protein product of the IT15 gene , is a deleterious mutation that causes Huntington's disease ( HD ) .", "Here we show , in contrast , that deletion of htt's normal polyglutamine stretch ( ΔQ-htt ) is a potentially beneficia...	2010
[ "Introduction", "Results/Discussion", "Methods" ]	[ "medicine", "genome evolution", "viral classification", "immunology", "dna-binding proteins", "microbiology", "vaccines", "genome sequencing", "dna viruses", "microbial evolution", "veterinary science", "vaccination", "infectious diseases", "genome complexity", "veterinary diseases", "...	A Wide Extent of Inter-Strain Diversity in Virulent and Vaccine Strains of Alphaherpesviruses	journal.ppat.1002282	null	[ [ "Alphaherpesviruses are widespread in the human population , with herpes simplex virus 1 ( HSV1 ) and 2 causing oral and genital lesions , respectively , while varicella zoster virus ( VZV ) causes chicken pox and shingles [1]–[3] .", "In the agricultural industry , a related veterinary alphaherpesvirus ,...	[ "Alphaherpesviruses are widespread in the human population , and include herpes simplex virus 1 ( HSV-1 ) and 2 , and varicella zoster virus ( VZV ) .", "These viral pathogens cause epithelial lesions , and then infect the nervous system to cause lifelong latency , reactivation , and spread .", "A related veter...	[ "Alphaherpesviruses such as herpes simplex virus ( HSV ) are ubiquitous in the human population .", "HSV causes oral and genital lesions , and has co-morbidities in acquisition and spread of human immunodeficiency virus ( HIV ) .", "The lack of a vaccine for HSV hinders medical progress for both of these infect...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "biochemical simulations", "protein interactions", "proteins", "biophysic al simulations", "biology", "computational biology", "biophysics simulations", "biophysics" ]	Quantifying the Molecular Origins of Opposite Solvent Effects on Protein-Protein Interactions	journal.pcbi.1003072	null	[ [ "Cosolvents such as denaturants , salts , amino acids and polyols play an important role in many protein processes as they modify the strength of intra- and intermolecular interactions of proteins in various cellular and biochemical environments [1]–[5] .", "Cosolvents that strengthen protein-protein inte...	[ "Although the nature of solvent-protein interactions is generally weak and non-specific , addition of cosolvents such as denaturants and osmolytes strengthens protein-protein interactions for some proteins , whereas it weakens protein-protein interactions for others .", "This is exemplified by the puzzling observ...	[ "Solvents play a fundamental role in living systems where they mediate the interactions between proteins and other biomolecules .", "Besides water , biological solvents often contain high concentrations of small molecular compounds known as cosolvents .", "Although many studies have reported specific and opposi...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	TRAF4 Is a Novel Phosphoinositide-Binding Protein Modulating Tight Junctions and Favoring Cell Migration	journal.pbio.1001726	The cancer-associated TRAF4 protein has a TRAF domain that is a bona fide phosphoinositide-binding domain and involved in the modulation of tight junctions and cell migration.	[ [ "Tumor necrosis factor receptor-associated factor 4 ( TRAF4 ) was originally identified as a gene overexpressed in breast carcinoma [1] , [2] .", "Interestingly , TRAF4 overexpression is not restricted to breast cancer and extends to a variety of different carcinomas [3] , [4] .", "TRAF4 belongs to th...	[ "Tumor necrosis factor ( TNF ) receptor-associated factor 4 ( TRAF4 ) is frequently overexpressed in carcinomas , suggesting a specific role in cancer .", "Although TRAF4 protein is predominantly found at tight junctions ( TJs ) in normal mammary epithelial cells ( MECs ) , it accumulates in the cytoplasm of mali...	[ "Tumor necrosis factor ( TNF ) receptor-associated factor 4 , also known as TRAF4 , is an unusual member of the TRAF protein family .", "While TRAFs are primarily known as regulators of inflammation , antiviral responses , and apoptosis , research on TRAF4 has identified its involvement in development and cancer ...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "neuroscience/behavioral neuroscience", "mathematics", "neuroscience/cognitive neuroscience", "neuroscience/experimental psychology" ]	What Do Transitive Inference and Class Inclusion Have in Common? Categorical (Co)Products and Cognitive Development	journal.pcbi.1000599	null	[ [ "Children acquire various reasoning skills over remarkably similar periods of development .", "Transitive Inference and Class Inclusion are two behaviours among a suite of inferential abilities that have strikingly similar developmental profiles—all are acquired around the age of five years [1] .", "F...	[ "Transitive inference , class inclusion and a variety of other inferential abilities have strikingly similar developmental profiles—all are acquired around the age of five .", "Yet , little is known about the reasons for this correspondence .", "Category theory was invented as a formal means of establishing com...	[ "Children acquire various reasoning skills during a remarkably similar period of development .", "Yet , the reasons for these similarities are a mystery .", "Two examples are Transitive Inference and Class Inclusion , which develop around five years of age .", "Older children understand that if John is taller...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/protozoal infections" ]	Adenylyl Cyclase α and cAMP Signaling Mediate Plasmodium Sporozoite Apical Regulated Exocytosis and Hepatocyte Infection	journal.ppat.1000008	null	[ [ "Plasmodium , the causative agent of malaria , is transmitted by the bite of infected mosquitoes that inoculate the sporozoite form of the parasite in the host .", "Sporozoites rapidly migrate to the liver , where they infect hepatocytes , replicate and develop into merozoites , the blood-stage form of th...	[ "Malaria starts with the infection of the liver of the host by Plasmodium sporozoites , the parasite form transmitted by infected mosquitoes .", "Sporozoites migrate through several hepatocytes by breaching their plasma membranes before finally infecting one with the formation of an internalization vacuole .", ...	[ "Malaria is transmitted through the bite of an infected mosquito that deposits Plasmodium sporozoites under the skin .", "These sporozoites migrate from the skin into the circulation and then enter the liver to start a new infection inside hepatocytes .", "Sporozoites have the capacity to traverse mammalian cel...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "rna", "rna processing", "cell biology", "nucleic acids", "protein translation", "gene expression", "genetics", "biology and life sciences", "molecular cell biology", "rna stability" ]	The Cytoplasmic Capping Complex Assembles on Adapter Protein Nck1 Bound to the Proline-Rich C-Terminus of Mammalian Capping Enzyme	journal.pbio.1001933	mRNA capping and decapping requires a cytoplasmic complex to maintain and/or restore the 5′ cap on a subset of the mammalian transcriptome; Nck1, an SH2/SH3 adapter, creates a scaffold upon which the cytoplasmic capping complex forms.	[ [ "The 7-methylguanosine “cap” is a defining feature of all eukaryotic mRNAs , and the cap plays a role in almost every step of mRNA metabolism .", "In the nucleus , the cap is bound by a heterodimer of CBP80-CBP20 , and its interaction with other proteins coordinates many of the subsequent steps in pre-mRN...	[ "Cytoplasmic capping is catalyzed by a complex that contains capping enzyme ( CE ) and a kinase that converts RNA with a 5′-monophosphate end to a 5′ diphosphate for subsequent addition of guanylic acid ( GMP ) .", "We identify the proline-rich C-terminus as a new domain of CE that is required for its participati...	[ "We previously described a cyclical process of mRNA decapping and recapping termed “cap homeostasis . ”", "Recapping is catalyzed by a complex of cytoplasmic proteins that includes the enzyme known to catalyze nuclear capping , and a kinase that converts RNA with a 5′-monophosphate end to a 5′-diphosphate capping...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Simian Immunodeficiency Virus Infection of Chimpanzees (Pan troglodytes) Shares Features of Both Pathogenic and Non-pathogenic Lentiviral Infections	journal.ppat.1005146	null	[ [ "Over 40 different African primate species are naturally infected with a species-specific simian immunodeficiency virus ( SIV ) [1] .", "To date , studies into the outcome of SIV infection have been limited to only a few species , in particular African green monkeys ( Chlorocebus genus ) and sooty mangabe...	[ "The virus-host relationship in simian immunodeficiency virus ( SIV ) infected chimpanzees is thought to be different from that found in other SIV infected African primates .", "However , studies of captive SIVcpz infected chimpanzees are limited .", "Previously , the natural SIVcpz infection of one chimpanzee ...	[ "The HIV-1/AIDS pandemic is the result of cross-species transmission of simian immunodeficiency virus ( SIVcpz ) from chimpanzees to humans .", "Many African primates are infected with SIV , but those studied in captivity generally do not develop disease .", "However , wild chimpanzees infected with SIVcpz are ...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "blood cells", "medicine and health sciences", "immune cells", "immune physiology", "spleen", "immunology", "animal models", "model organisms", "experimental organism systems", "cytotoxic t cells", "antibodies", "research and analysis methods", "immune system proteins", "specimen preparati...	CD8 T cells protect adult naive mice from JEV-induced morbidity via lytic function	journal.pntd.0005329	null	[ [ "Japanese encephalitis virus ( JEV ) is a mosquito-borne flavivirus .", "JEV-mediated encephalitis is commonly found in South and Southeast Asia [1–4] .", "Although the ratio of clinical to subclinical illness is very low an estimated 67 , 900 cases are reported in Asia with 20–30% mortality [5] .", ...	[ "Following Japanese encephalitis virus ( JEV ) infection neutralizing antibodies are shown to provide protection in a significant proportion of cases , but not all , suggesting additional components of immune system might also contribute to elicit protective immune response .", "Here we have characterized the rol...	[ "Japanese encephalitis virus ( JEV ) commonly infects human beings in developing countries including those in Southeast Asia .", "While the majority of the infected people suffer from mild illness , a minority suffers from encephalitis which may lead to death .", "The virus is transmitted by mosquito bites and ...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunopathology", "immune cells", "cytokines", "t cells", "immunology", "biology", "immune response", "immune system" ]	CD8+ T-Cells Expressing Interferon Gamma or Perforin Play Antagonistic Roles in Heart Injury in Experimental Trypanosoma Cruzi-Elicited Cardiomyopathy	journal.ppat.1002645	null	[ [ "Trypanosoma cruzi is the intracellular protozoan that causes American trypanosomiasis , which is also known as Chagas disease .", "In Latin America , 8–15 million people are estimated to currently be infected with this organism [1] .", "While 50% of T . cruzi-infected individuals suffer from an indet...	[ "In Chagas disease , CD8+ T-cells are critical for the control of Trypanosoma cruzi during acute infection .", "Conversely , CD8+ T-cell accumulation in the myocardium during chronic infection may cause tissue injury leading to chronic chagasic cardiomyopathy ( CCC ) .", "Here we explored the role of CD8+ T-cel...	[ "Chagas disease , a neglected tropical disease that is caused by Trypanosoma cruzi , afflicts between 8 and 15 million people in Latin America .", "Anti-parasite immunity allows for acute phase survival; however , approximately 30% of patients present chronic chagasic cardiomyopathy ( CCC ) with parasite persiste...	2012
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "gene regulation", "animals", "invertebrate genomics", "dna transcription", "developmental biology", "epigenetics", "dna", "dna methylation", "chromatin", "chromosome biology", "gene expression", "oysters", "molluscs", "chromatin modification", "dna modification", "a...	Dynamics of DNA methylomes underlie oyster development	journal.pgen.1006807	null	[ [ "The methylation of DNA is a prevalent epigenetic mark that is deeply rooted in evolution and found from bacteria to mammals .", "Despite that metazoan organisms display methylation on cytosines , great variations exist in the amount and distribution of methylcytosines ( meCs ) across taxa .", "DNA me...	[ "DNA methylation is a critical epigenetic regulator of development in mammals and social insects , but its significance in development outside these groups is not understood .", "Here we investigated the genome-wide dynamics of DNA methylation in a mollusc model , the oyster Crassostrea gigas , from the egg to th...	[ "Elucidating the mechanisms which govern the development of multicellular animals and their evolution is a fundamental task .", "Epigenetic mechanisms like DNA methylation have recently emerged as critical regulators of mammalian development through the control of genes that determine the identity of cells and th...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "bacteriology", "chemical bonding", "medicine and health sciences", "leptospira", "pathology and laboratory medicine", "fibrinogen", "pathogens", "microbiology", "fibrin", "signs and symptoms", "glycoproteins", "bacteria", "bacterial pathogens", "physical chemistry", "adhesins", "throm...	Leptospira Immunoglobulin-Like Protein B (LigB) Binds to Both the C-Terminal 23 Amino Acids of Fibrinogen αC Domain and Factor XIII: Insight into the Mechanism of LigB-Mediated Blockage of Fibrinogen α Chain Cross-Linking	journal.pntd.0004974	null	[ [ "Leptospira spp are pathogenic spirochetes that cause the most widespread zoonotic disease in the world [1 , 2] .", "Leptospirosis is reported regularly in tropical nations and is reemerging in the United States [3 , 4] .", "Numerous mammalian hosts , including incidental hosts like humans , can be in...	[ "The coagulation system provides a primitive but effective defense against hemorrhage .", "Soluble fibrinogen ( Fg ) monomers , composed of α , β and γ chains , are recruited to provide structural support for the formation of a hemostatic plug .", "Fg binds to platelets and is processed into a cross-linked fibr...	[ "Leptospirosis , caused by pathogenic Leptospira spp .", ", has been increasingly recognized as an emerging zoonosis worldwide .", "In human cases , clinical presentation can vary from a mild flu-like syndrome to severe multi-organ failure including hepatitis , nephritis and occasionally meningitis .", "Parti...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetic networks", "gene regulation", "applied mathematics", "protein interaction networks", "enzymes", "enzymology", "simulation and modeling", "algorithms", "methylation", "mathematics", "network analysis", "enzyme chemistry", "research and analysis methods", "computer and information s...	m6A-Driver: Identifying Context-Specific mRNA m6A Methylation-Driven Gene Interaction Networks	journal.pcbi.1005287	null	[ [ "Methylation , as a significant epigenetic modification of nucleic acids , regulates gene expression , influences grows and development of plants and animals , and is closely related to the occurrence and development of disease .", "The epigenetic regulatory mechanisms and physiological functions of DNA m...	[ "As the most prevalent mammalian mRNA epigenetic modification , N6-methyladenosine ( m6A ) has been shown to possess important post-transcriptional regulatory functions .", "However , the regulatory mechanisms and functional circuits of m6A are still largely elusive .", "To help unveil the regulatory circuitry ...	[ "Powered by methylated RNA immunoprecipitation sequencing ( MeRIP-Seq ) technology , recent studies have revealed a new mode of post transcriptional regulation mediated by mRNA N6-methyladenosine ( m6A ) .", "Currently , the analysis of m6A focuses mostly on prediction of m6A sites as well as differential m6A met...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "cancer genetics", "genome evolution", "animal models", "model organisms", "comparative genomics", "biology", "mouse", "evolutionary genetics", "genetics", "genomics", "evolutionary biology", "gene networks", "rat", "genetics and genomics" ]	Fuzzy Tandem Repeats Containing p53 Response Elements May Define Species-Specific p53 Target Genes	journal.pgen.1002731	null	[ [ "Retinoblastoma is the most common pediatric intraocular tumor , that may arise in an unilateral or bilateral form .", "In human bilateral retinoblastoma , a germline mutation in one RB1 allele is typically observed , and the second allele undergoes somatic mutation , in agreement with Knudson's «two-hit ...	[ "Evolutionary forces that shape regulatory networks remain poorly understood .", "In mammals , the Rb pathway is a classic example of species-specific gene regulation , as a germline mutation in one Rb allele promotes retinoblastoma in humans , but not in mice .", "Here we show that p53 transactivates the Retin...	[ "TP53 , the gene encoding p53 , is mutated in more than half of human cancers .", "Consequently , p53 is one of the most studied transcription factors , shown to directly regulate more than 150 genes .", "The mouse is a model of choice to study p53 mutants and cancer .", "However , differences were found betw...	2012
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "bacteriology", "organismal evolution", "chemical compounds", "microbiology", "organic compounds", "microbial evolution", "amino acids", "sequence motif analysis", "cellular structures and organelles", "research and analysis methods", "sequence analysis", "bioinformatics", "proteins", "gen...	Evolutionary analysis of polyproline motifs in Escherichia coli reveals their regulatory role in translation	journal.pcbi.1005987	null	[ [ "Ribosomes facilitate the synthesis of proteins by translating the nucleotide sequence from an mRNA template .", "The speed of mRNA translation significantly varies and strongly depends on the amino acids to be incorporated into the growing polypeptide chain [1] .", "Especially slow is the incorporati...	[ "Translation of consecutive prolines causes ribosome stalling , which is alleviated but cannot be fully compensated by the elongation factor P . However , the presence of polyproline motifs in about one third of the E . coli proteins underlines their potential functional importance , which remains largely unexplore...	[ "Polyproline motifs induce ribosome stalling during translation , but the functional significance of this effect remains unclear .", "Our evolutionary analysis of polyproline motifs reveals that they are disfavored in E . coli proteomes as a consequence of the reduced translation efficiency , supporting the conje...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Optimal Strategies for Controlling Riverine Tsetse Flies Using Targets: A Modelling Study	journal.pntd.0003615	null	[ [ "Tsetse flies ( Glossina spp . ) occur in 36 countries of Africa where they transmit species of Trypanosoma which cause the potentially fatal diseases of sleeping sickness in humans and nagana in domestic stock [1 , 2] .", "Vector control can be important in managing these diseases [2] .", "Of the sev...	[ "Tsetse flies occur in much of sub-Saharan Africa where they transmit the trypanosomes that cause the diseases of sleeping sickness in humans and nagana in livestock .", "One of the most economical and effective methods of tsetse control is the use of insecticide-treated screens , called targets , that simulate h...	[ "We employed a deterministic model to simulate the efficacy of various ways of using the tiny , ~0 . 06m2 , insecticide-treated targets recently recommended as replacements for the larger , ~1m2 , types previously used to control riverine species of tsetse fly , the main vectors of sleeping sickness in humans .", ...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "meiosis", "invertebrates", "chromosome staining", "medicine and health sciences", "reproductive system", "rna interference", "gonads", "chromosome structure and function", "caenorhabditis", "cell cycle and cell division", "cell processes", "chromatids", "animals", "animal models", "caen...	Condensin I protects meiotic cohesin from WAPL-1 mediated removal	journal.pgen.1007382	null	[ [ "Meiosis is a specialized form of cell division in which one round of DNA replication is followed by two rounds of chromosome segregation to produce haploid gametes .", "Critical to this process is the timely establishment and sequential release of connections between homologous chromosomes and sister chr...	[ "Condensin complexes are key determinants of higher-order chromatin structure and are required for mitotic and meiotic chromosome compaction and segregation .", "We identified a new role for condensin in the maintenance of sister chromatid cohesion during C . elegans meiosis .", "Using conventional and stimulat...	[ "During the early stages of meiosis , duplicated copies of chromosomes must be held together , and homologous chromosomes must pair to ensure formation of sperm and oocytes with the correct number of chromosomes .", "A protein complex called cohesin is essential for this process .", "A related complex called co...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "virology/immunodeficiency viruses", "virology/animal models of infection", "virology/immune evasion" ]	In Vivo CD8+ T-Cell Suppression of SIV Viremia Is Not Mediated by CTL Clearance of Productively Infected Cells	journal.ppat.1000748	null	[ [ "The capacity and limits of host immunity in containing lentiviral infection are fundamental to the understanding of Human Immunodeficiency Virus ( HIV ) and SIV pathogenesis yet are incompletely understood .", "Previous studies support effects of host immunity in modulating HIV disease progression [1] , ...	[ "The CD8+ T-cell is a key mediator of antiviral immunity , potentially contributing to control of pathogenic lentiviral infection through both innate and adaptive mechanisms .", "We studied viral dynamics during antiretroviral treatment of simian immunodeficiency virus ( SIV ) infected rhesus macaques following C...	[ "The recognition and elimination of infected host cells by CD8+ T-lymphocytes is held to be a key component of the immune response against viral pathogens .", "However , this basic tenet of viral immunology may not hold true for HIV and the related SIV .", "In the current work , we eliminated CD8+ T-cells by tr...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunology/cellular microbiology and pathogenesis" ]	Antibodies Targeting the PfRH1 Binding Domain Inhibit Invasion of Plasmodium falciparum Merozoites	journal.ppat.1000104	null	[ [ "Malaria is caused by parasites of the genus Plasmodium with an estimated 300–500 million clinical cases and 1–3 million deaths annually [1] , [2] .", "Plasmodium falciparum is the most prevalent and is responsible for a large proportion of the mortality associated with this disease .", "An essential ...	[ "Invasion by the malaria merozoite depends on recognition of specific erythrocyte surface receptors by parasite ligands .", "Plasmodium falciparum uses multiple ligands , including at least two gene families , reticulocyte binding protein homologues ( RBLs ) and erythrocyte binding proteins/ligands ( EBLs ) .", ...	[ "Plasmodium falciparum causes the most virulent form of human malaria .", "The pathology of the disease is associated with the invasion , replication and subsequent destruction of the erythrocyte by the parasite .", "Invasion of the host erythrocyte by the invasive form of the parasite , the merozoite , is a ke...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "livestock", "medicine and health sciences", "vesicles", "immune cells", "immunology", "microbiology", "vertebrates", "viral structure", "animals", "mammals", "cellular structures and organelles", "endosomes", "swine", "white blood cells", "viral core", "animal cells",...	African Swine Fever Virus Undergoes Outer Envelope Disruption, Capsid Disassembly and Inner Envelope Fusion before Core Release from Multivesicular Endosomes	journal.ppat.1005595	null	[ [ "Most viruses take advantage of existing cellular endocytic pathways to enter their host cells [1–4] .", "Once internalized , virus particles move through a dynamic network of endocytic vesicles , which undergo gradual sorting and complex maturation events .", "Endosome maturation , in turn , triggers...	[ "African swine fever virus ( ASFV ) is a nucleocytoplasmic large DNA virus ( NCLDV ) that causes a highly lethal disease in domestic pigs .", "As other NCLDVs , the extracellular form of ASFV possesses a multilayered structure consisting of a genome-containing nucleoid successively wrapped by a thick protein core...	[ "Virus entry is a crucial initial event for productive infection , being therefore a potential target for antiviral strategies .", "African swine fever virus ( ASFV ) is the causative agent of a frequently fatal swine disease for which there is no vaccine .", "ASFV belongs to the superfamily of nucleocytoplasmi...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "urology", "medicine and health sciences", "body fluids", "diagnostic radiology", "ultrasound imaging", "helminths", "bladder", "parasitic diseases", "animals", "health care", "urine", "morbidity", "research and analysis methods", "imaging techniques", ...	Ultrasonographic evaluation of urinary tract morbidity in school-aged and preschool-aged children infected with Schistosoma haematobium and its evolution after praziquantel treatment: A randomized controlled trial	journal.pntd.0005400	null	[ [ "Schistosomiasis primarily caused by Schistosoma haematobium , S . japonicum and S . mansoni is a significant public health problem in low-income tropical and subtropical countries .", "It is an ancient disease with first reports on schistosomiasis dating back 4000 years ago [1] .", "Yet , still today...	[ "Schistosoma haematobium infections are responsible for significant urinary tract ( UT ) complications .", "Schistosomiasis control programs aim to reduce morbidity , yet the extent of morbidity in preschool-aged children and the impact of treatment on morbidity reduction are not well studied .", "Our study was...	[ "Schistosoma haematobium is a parasite that infects the human genito-urinary tract .", "People get infected with the parasite through contact with fresh water and children are at major risk .", "The complications linked to this infection are due to an inflammation caused by accumulation of the eggs in peri-blad...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "medicine and health sciences", "neurochemistry", "immune cells", "nuclear staining", "eicosanoids", "immunology", "neuroscience", "lipid inclusions", "bacteria", "research and analysis methods", "specimen preparation and treatment", "staining", "lipids", "white blood cell...	Lipid droplet formation in Mycobacterium tuberculosis infected macrophages requires IFN-γ/HIF-1α signaling and supports host defense	journal.ppat.1006874	null	[ [ "Mycobacterium tuberculosis remains a global scourge , causing more than one million deaths annually [1] .", "Tuberculosis is a disease characterized by long periods of latency , with viable M . tuberculosis remaining dormant in the lungs of infected patients for years to decades [2] .", "One of the c...	[ "Lipid droplet ( LD ) formation occurs during infection of macrophages with numerous intracellular pathogens , including Mycobacterium tuberculosis .", "It is believed that M . tuberculosis and other bacteria specifically provoke LD formation as a pathogenic strategy in order to create a depot of host lipids for ...	[ "Mycobacterium tuberculosis , the causative agent of the disease tuberculosis , causes more deaths annually than any other single bacterial pathogen .", "M . tuberculosis primarily lives in macrophages , immune cells which specialize in phagocytosing and killing pathogens .", "In order to survive this inhospita...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "cellular structures", "subcellular organelles", "model organisms", "molecular cell biology", "genetic screens", "genetics", "gene duplication", "molecular genetics", "biology", "yeast and fungal models", "saccharomyces cerevisiae", "gene networks" ]	A Highly Redundant Gene Network Controls Assembly of the Outer Spore Wall in S. cerevisiae	journal.pgen.1003700	null	[ [ "All cells surround themselves with some form of extracellular matrix that provides structural integrity to the cell and protection from the environment .", "While the composition of these extracellular matrices varies , they present all cells with a common problem – how to assemble a complex macromolecul...	[ "The spore wall of Saccharomyces cerevisiae is a multilaminar extracellular structure that is formed de novo in the course of sporulation .", "The outer layers of the spore wall provide spores with resistance to a wide variety of environmental stresses .", "The major components of the outer spore wall are the p...	[ "The cell wall of fungi is a complex extracellular matrix and an important target for antifungal drugs .", "Assembly of the wall during spore formation in baker's yeast is a useful model for fungal wall development .", "The outermost layers of the spore wall are composed of a polymer of dityrosine connected to ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "neuroscience/behavioral neuroscience", "neuroscience/animal cognition", "neuroscience/theoretical neuroscience", "neuroscience/cognitive neuroscience" ]	Modeling the Violation of Reward Maximization and Invariance in Reinforcement Schedules	journal.pcbi.1000131	null	[ [ "In studying reward-seeking behavior it is often assumed that animals attempt to maximize long term returns .", "This postulate often forms the basis of normative models of decision making [1] , choice behavior [2]–[4] , and motivation [5] , and plays a prominent role in the field of Reinforcement Learnin...	[ "It is often assumed that animals and people adjust their behavior to maximize reward acquisition .", "In visually cued reinforcement schedules , monkeys make errors in trials that are not immediately rewarded , despite having to repeat error trials .", "Here we show that error rates are typically smaller in tr...	[ "Theories of rational behavior are built on a number of principles , including the assumption that subjects adjust their behavior to maximize their long-term returns and that they should work equally hard to obtain a reward in situations where the effort to obtain reward is the same ( called the invariance principl...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "biochemistry", "autosomal recessive", "dna replication", "nucleic acids", "genetics", "dna", "biology", "human genetics", "genetics and genomics", "clinical genetics" ]	Deficiency in Origin Licensing Proteins Impairs Cilia Formation: Implications for the Aetiology of Meier-Gorlin Syndrome	journal.pgen.1003360	null	[ [ "Replication in S phase initiates from replication origins , which become “licensed” during G1 phase of the cell cycle [1] , [2] , [3] , [4] .", "Licensing commences with binding of the origin recognition complex ( ORC ) followed by recruitment of the pre-replication complex ( pre-RC ) proteins , CDC6 , C...	[ "Mutations in ORC1 , ORC4 , ORC6 , CDT1 , and CDC6 , which encode proteins required for DNA replication origin licensing , cause Meier-Gorlin syndrome ( MGS ) , a disorder conferring microcephaly , primordial dwarfism , underdeveloped ears , and skeletal abnormalities .", "Mutations in ATR , which also functions ...	[ "Meier-Gorlin syndrome ( MGS ) is a rare disorder conferring small head circumference , primordial dwarfism , underdeveloped ears , and skeletal abnormalities .", "Our previous findings suggest that impaired DNA replication could cause the developmental defects in these disorders .", "Here we expand on those fi...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "microbiology/parasitology", "infectious diseases/protozoal infections", "molecular biology", "microbiology/cellular microbiology and pathogenesis" ]	The Glutathione Biosynthetic Pathway of Plasmodium Is Essential for Mosquito Transmission	journal.ppat.1000302	null	[ [ "Plasmodium infection leads to increased oxidative stress in both the vertebrate and mosquito hosts .", "The high proliferation rate of parasites results in the production of large quantities of toxic redox-active by-products .", "Reactive oxygen species ( ROS ) are generated within the infected RBC (...	[ "Infection of red blood cells ( RBC ) subjects the malaria parasite to oxidative stress .", "Therefore , efficient antioxidant and redox systems are required to prevent damage by reactive oxygen species .", "Plasmodium spp .", "have thioredoxin and glutathione ( GSH ) systems that are thought to play a major ...	[ "The antioxidant systems of malaria parasites ( Plasmodium spp . ) are potential targets for the development of antimalarials .", "The glutathione ( GSH ) redox system constitutes one of the Plasmodium primary lines of defense against damage caused by reactive oxygen species and other forms of chemical stress .",...	2009
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "viral vaccines", "medicine and health sciences", "ecology and environmental sciences", "influenza", "population dynamics", "immunology", "microbiology", "vaccines", "preventive medicine", "systems science", "mathematics", "population biology", "infectious disease control", "vaccination an...	Long-term dynamics of measles in London: Titrating the impact of wars, the 1918 pandemic, and vaccination	journal.pcbi.1007305	null	[ [ "Predicting transitions between dynamic attractors is a fundamental question in ecology [1]; in particular , how external forcing impacts intrinsic oscillatory dynamics .", "Phase transitions in nonlinear systems have been extensively studied theoretically [2] .", "However , examples of systems underg...	[ "A key question in ecology is the relative impact of internal nonlinear dynamics and external perturbations on the long-term trajectories of natural systems .", "Measles has been analyzed extensively as a paradigm for consumer-resource dynamics due to the oscillatory nature of the host-pathogen life cycle , the a...	[ "The impact of intrinsic versus external drivers of transmission on long-term dynamics is an open question in complex systems studies .", "In particular , when and where dynamics become chaotic has crucial implications for control efforts .", "Here , we extended the well-studied London measles data to include n...	2019
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "genetics and genomics/complex traits", "genetics and genomics/animal genetics", "genetics and genomics/bioinformatics", "genetics and genomics/gene expression" ]	Genome-Wide Assessments Reveal Extremely High Levels of Polymorphism of Two Active Families of Mouse Endogenous Retroviral Elements	journal.pgen.1000007	null	[ [ "The laboratory mouse is the model of choice for mammalian biological research and a plethora of mouse genomic resources and databases now exist [1] .", "Notably , fueled by availability of genomic sequence for the common strain C57BL/6J ( B6 ) [2] , several groups have documented genetic variation among ...	[ "Endogenous retroviral elements ( ERVs ) in mice are significant genomic mutagens , causing ∼10% of all reported spontaneous germ line mutations in laboratory strains .", "The majority of these mutations are due to insertions of two high copy ERV families , the IAP and ETn/MusD elements .", "This significant le...	[ "The laboratory mouse is the most widely used mammal for biological research .", "Hundreds of inbred mouse strains have been developed that vary in characteristics such as susceptibility to cancer or other diseases .", "There is much interest in uncovering differences between strains that result in different tr...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Staphylococcus aureus Leukocidin A/B (LukAB) Kills Human Monocytes via Host NLRP3 and ASC when Extracellular, but Not Intracellular	journal.ppat.1004970	null	[ [ "S . aureus is one of the most commonly identified causes of infection , and is responsible for a significant health and economic burden including approximately 100 , 000 life-threatening infections per year in the United States [1] .", "S . aureus can cause a variety of diseases that range from recurrent...	[ "Staphylococcus aureus infections are a growing health burden worldwide , and paramount to this bacterium’s pathogenesis is the production of virulence factors , including pore-forming leukotoxins .", "Leukocidin A/B ( LukAB ) is a recently discovered toxin that kills primary human phagocytes , though the underly...	[ "Staphylococcus aureus infections are becoming increasingly common , aggressive , and difficult to manage clinically .", "S . aureus produces a number of pore-forming toxins that target and kill immune cells .", "In this study , we demonstrate that LukAB is primarily responsible for S . aureus-mediated targetin...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "signal transduction", "biology", "microbiology", "molecular cell biology", "proteomics", "parasitology" ]	LmaPA2G4, a Homolog of Human Ebp1, Is an Essential Gene and Inhibits Cell Proliferation in L. major	journal.pntd.0002646	null	[ [ "Protozoan parasites of the genus Leishmania are the causative agents of leishmaniasis , a disease that is characterized by a spectrum of clinical manifestations ranging from ulcerative skin lesions to fatal visceral infections [1] .", "Leishmaniasis is a poverty-related disease and is associated with mal...	[ "We have identified LmaPA2G4 , a homolog of the human proliferation-associated 2G4 protein ( also termed Ebp1 ) , in a phosphoproteomic screening .", "Multiple sequence alignment and cluster analysis revealed that LmaPA2G4 is a non-peptidase member of the M24 family of metallopeptidases .", "This pseudoenzyme i...	[ "Leishmaniasis is a disease caused by protozoan parasites of the genus Leishmania .", "Its clinical manifestations are widespread , ranging from ulcerative skin lesions to life-threatening visceral infections .", "Approximately 1 . 5–2 million new cases of leishmaniasis are reported each year with an estimated ...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "biotechnology", "digital video imaging microscopy", "engineering and technology", "biological cultures", "light microscopy", "biological locomotion", "biomechanics", "parasitology", "microscopy", "computer based imaging", "cell cultures", "quantitative parasitology", "research and analysis ...	An Integrated In Vitro Imaging Platform for Characterizing Filarial Parasite Behavior within a Multicellular Microenvironment	journal.pntd.0003305	null	[ [ "Lymphatic Filariasis ( LF ) is the single largest world-wide source of secondary lymphedema [1] and is caused by adult parasitic nematodes that target and dwell in the lymphatic system .", "An estimated 120 million people in 73 countries are currently infected , and a further 1 . 4 billion live in areas ...	[ "Lymphatic Filariasis , a Neglected Tropical Disease , is caused by thread-like parasitic worms , including B . malayi , which migrate to the human lymphatic system following transmission .", "The parasites reside in collecting lymphatic vessels and lymph nodes for years , often resulting in lymphedema , elephant...	[ "Lymphatic Filariasis is the largest world-wide source of secondary lymphedema and is caused by parasitic nematodes that migrate to and dwell in the lymphatic system .", "The World Health Organization estimates that over 120 million people in 73 countries are currently infected , and a further 1 . 4 billion live ...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases", "vector-borne diseases", "medicine and health sciences" ]	Quantitative PCR in Epidemiology for Early Detection of Visceral Leishmaniasis Cases in India	journal.pntd.0003366	null	[ [ "The Leishmania spp .", "parasites of humans are endemic in 98 countries , and more than 350 million people are at risk of infection [1] .", "Leishmaniasis is a neglected tropical disease , and the most severe form visceral leishmaniasis ( VL , also known as kala-azar ) is fatal if untreated .", "...	[ "Studies employing serological , DTH or conventional PCR techniques suggest a vast proportion of Leishmania infected individuals living in regions endemic for Visceral Leishmaniasis ( VL ) remain asymptomatic .", "This study was designed to assess whether quantitative PCR ( qPCR ) can be used for detection of asy...	[ "Anthroponotic VL caused by Leishmania donovani in the Indian subcontinent accounts for 70% of the world burden of VL .", "Among the estimated 100 , 000 cases of VL acquired annually in India , 90% occur in the state of Bihar .", "Leishmania infection can result in either symptomatic or asymptomatic infection ....	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biophysics", "biochemistry", "biochemistry/membrane proteins and energy transduction" ]	S. aureus MscL Is a Pentamer In Vivo but of Variable Stoichiometries In Vitro: Implications for Detergent-Solubilized Membrane Proteins	journal.pbio.1000555	Detergent-induced rearrangements of membrane-protein subunits explain why two MscL channel stoichiometries have been resolved by X-ray crystallography - but S. aureus MscL is truly a pentamer in vivo.	[ [ "The bacterial mechanosensitive channel MscL serves as a biological “emergency release valve , ” allowing rapid loss of solutes in response to a sudden decrease in the osmolarity of a bacterium's environment [1] .", "It is perhaps the best characterized mechanosensor [2] , thus serving as a paradigm of ho...	[ "While the bacterial mechanosensitive channel of large conductance ( MscL ) is the best studied biological mechanosensor and serves as a paradigm for how a protein can sense and respond to membrane tension , the simple matter of its oligomeric state has led to debate , with models ranging from tetramers to hexamers...	[ "The ability to detect mechanical forces is at the basis of not only the senses of touch hearing and balance but also cardiovascular and osmotic regulation .", "One of the primary ways that organisms detect forces is through mechanosensitive channels , and mechanosensation is so vital that essentially all organis...	2010
[ "Introduction", "Results and Discussion", "Materials and Methods" ]	[ "invertebrates", "medicine and health sciences", "ixodes", "pathology and laboratory medicine", "pathogens", "population genetics", "vertebrates", "animals", "alleles", "developmental biology", "nymphs", "ticks", "population biology", "epidemiology", "evolutionary genetics", "disease v...	Vectors as Epidemiological Sentinels: Patterns of Within-Tick Borrelia burgdorferi Diversity	journal.ppat.1005759	null	[ [ "Hosts including humans , other vertebrates , and arthropods , are frequently co-infected with multiple pathogen species in addition to diverse populations of pathogens of the same species .", "Within-host pathogen diversity may have important implications for human health and disease epidemiology as comp...	[ "Hosts including humans , other vertebrates , and arthropods , are frequently infected with heterogeneous populations of pathogens .", "Within-host pathogen diversity has major implications for human health , epidemiology , and pathogen evolution .", "However , pathogen diversity within-hosts is difficult to ch...	[ "Lyme disease , caused by a bacteria carried by deer ticks , is the most common vector-borne disease in North America and over 30 , 000 cases are reported each year in the United States .", "Ticks may be infected with multiple strains of the Lyme disease bacteria , which differ in transmissibility and the harm th...	2016
[ "Introduction", "Results/Discussion", "Material and Methods" ]	[ "genetics and genomics/gene expression", "evolutionary biology/genomics" ]	Stage-Specific Expression Profiling of Drosophila Spermatogenesis Suggests that Meiotic Sex Chromosome Inactivation Drives Genomic Relocation of Testis-Expressed Genes	journal.pgen.1000731	null	[ [ "Sex chromosomes evolve differently than autosomes due to their distinct characteristics such as a lack of recombination between the homologues ( X and Y ) , a different number of chromosome copies between sexes , and the proportion of heterochromatin [1] .", "Genomic and proteomic studies in Drosophila ,...	[ "In Drosophila , genes expressed in males tend to accumulate on autosomes and are underrepresented on the X chromosome .", "In particular , genes expressed in testis have been observed to frequently relocate from the X chromosome to the autosomes .", "The inactivation of X-linked genes during male meiosis ( i ....	[ "During the course of Drosophila evolution , genes expressed in males have accumulated on the autosomes .", "Meiotic sex chromosome X inactivation in males was proposed , among other hypotheses , as a selective force favoring the accumulation of testis-expressed genes on the autosomes .", "Under such a model , ...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "systems biology", "biology", "neuroscience", "genetics and genomics" ]	Specific Contributions of Ventromedial, Anterior Cingulate, and Lateral Prefrontal Cortex for Attentional Selection and Stimulus Valuation	journal.pbio.1001224	Functional clusters of neurons in the monkey prefrontal and anterior cingulate cortex are involved in guiding attention to the most valuable objects in a scene.	[ [ "Selective attention prioritizes the processing of behaviorally relevant stimuli , at the expense of processing irrelevant stimuli [1] .", "Identifying the relevance of a stimulus requires neuronal circuitry to signal its associated value or reward outcome , in a given context .", "Recent evidence sug...	[ "Attentional control ensures that neuronal processes prioritize the most relevant stimulus in a given environment .", "Controlling which stimulus is attended thus originates from neurons encoding the relevance of stimuli , i . e . their expected value , in hand with neurons encoding contextual information about s...	[ "To navigate within an environment filled with sensory stimuli , the brain must selectively process only the most relevant sensory information .", "Identifying and shifting attention to the most relevant sensory stimulus requires integrating information about its sensory features as well as its relative value , t...	2011

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