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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" ]	[ "evolutionary biology", "genetics", "biology", "genomics" ]	Independent Evolution of Transcriptional Inactivation on Sex Chromosomes in Birds and Mammals	journal.pgen.1003635	null	[ [ "Vertebrates with heteromorphic sex chromosomes have either male heterogamety like humans ( XX female and XY male ) , or female heterogamety like birds ( ZZ male and ZW female ) .", "Degeneration of the non-recombining Y or W chromosome , central to the evolution of sex chromosomes , left genes on the X o...	[ "X chromosome inactivation in eutherian mammals has been thought to be tightly controlled , as expected from a mechanism that compensates for the different dosage of X-borne genes in XX females and XY males .", "However , many X genes escape inactivation in humans , inactivation of the X in marsupials is partial ...	[ "Dosage compensation is a mechanism that restores the expression of X chromosome genes back to their original level when Y homologues lose function .", "In placental and marsupial mammals this is achieved by upregulating the single X in males .", "The carry-through of overexpression to females would result in f...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "caenorhabditis", "cell biology", "developmental biology", "computational biology" ]	Predictive Modeling of Signaling Crosstalk during C. elegans Vulval Development	journal.pcbi.0030092	null	[ [ "Describing mechanistic models in biology in a formal language , especially one that is dynamic and executable by computer , has recently been shown to have various advantages ( see review [1] ) .", "A formal language comes with a rigorous semantics that goes beyond the simple positive and negative intera...	[ "Caenorhabditis elegans vulval development provides an important paradigm for studying the process of cell fate determination and pattern formation during animal development .", "Although many genes controlling vulval cell fate specification have been identified , how they orchestrate themselves to generate a rob...	[ "Systems biology aims to gain a system-level understanding of living systems .", "To achieve such an understanding , we need to establish the methodologies and techniques to understand biological systems in their full complexity .", "One such attempt is to use methods designed for the construction and analysis ...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cellular stress responses", "mechanisms of signal transduction", "microbiology", "feeback regulation", "cell differentiation", "developmental biology", "model organisms", "crosstalk", "mapk signaling cascades", "stress signaling cascade", "signal initiation", "biology", "molecular biology",...	Checkpoints in a Yeast Differentiation Pathway Coordinate Signaling during Hyperosmotic Stress	journal.pgen.1002437	null	[ [ "Eukaryotic cells commonly employ mitogen activated protein kinases ( MAPKs ) to transduce extracellular signals and evoke intracellular responses [1] .", "MAPKs are a part of an evolutionarily-conserved three-tiered signaling cascade comprised of the MAPK , a MAPK kinase ( MAPKK ) , and a MAPKK kinase ( ...	[ "All eukaryotes have the ability to detect and respond to environmental and hormonal signals .", "In many cases these signals evoke cellular changes that are incompatible and must therefore be orchestrated by the responding cell .", "In the yeast Saccharomyces cerevisiae , hyperosmotic stress and mating pheromo...	[ "All cells can detect and respond to signals in their environment .", "The ability to interpret these signals with accuracy is needed for proper growth and differentiation .", "Moreover , cells must prioritize responses when confronted with competing signals .", "However the molecular mechanisms that govern s...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry/replication and repair", "genetics and genomics/gene function" ]	Loss of Yeast Peroxiredoxin Tsa1p Induces Genome Instability through Activation of the DNA Damage Checkpoint and Elevation of dNTP Levels	journal.pgen.1000697	null	[ [ "Peroxiredoxins belong to a family of thiol-specific peroxidases widely and abundantly expressed in most living organisms [1] , [2] .", "Through one or more redox-sensitive cysteines , peroxiredoxins not only scavenge reactive oxygen species ( ROS ) including peroxides and peroxynitrite [3] , [4] , but al...	[ "Peroxiredoxins are a family of antioxidant enzymes critically involved in cellular defense and signaling .", "Particularly , yeast peroxiredoxin Tsa1p is thought to play a role in the maintenance of genome integrity , but the underlying mechanism is not understood .", "In this study , we took a genetic approac...	[ "Peroxiredoxins are a family of antioxidant enzymes highly conserved from yeast to human .", "Loss of peroxiredoxin in mice can lead to severe anemia and malignant tumors , but the underlying cause is not understood .", "One way to derive new knowledge of peroxiredoxins is through genetic analysis in yeast .", ...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "viruses", "cell biology", "microbiology", "virology" ]	Centrosomal Latency of Incoming Foamy Viruses in Resting Cells	journal.ppat.0030074	null	[ [ "After entry into their host cells , retroviruses undergo uncoating and reverse transcription , leading to the formation of pre-integration complexes , which must then gain access to the nuclear compartment and integrate the provirus into host chromosomes [1] .", "The cell cycle status is a key determinan...	[ "Completion of early stages of retrovirus infection depends on the cell cycle .", "While gammaretroviruses require mitosis for proviral integration , lentiviruses are able to replicate in post-mitotic non-dividing cells .", "Resting cells such as naive resting T lymphocytes from peripheral blood cannot be produ...	[ "Naive quiescent CD4-positive T cells or monocytes that are in the G0 stage of the cell cycle cannot be productively infected by retroviruses in vitro , but the molecular basis of this restriction remains poorly understood .", "In this report , we demonstrate that incoming foamy retroviruses remain around the cen...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "bacterial diseases", "microbial metabolism", "infectious diseases", "microbial mutation", "streptococci", "microbial evolution", "microbial pathogens", "host-pathogen interaction", "biology", "microbiology", "infectious disease modeling", "bacterial pathogens", "gram positive"...	The Role of Host and Microbial Factors in the Pathogenesis of Pneumococcal Bacteraemia Arising from a Single Bacterial Cell Bottleneck	journal.ppat.1004026	null	[ [ "Streptococcus pneumoniae , one of the major human bacterial pathogens , is also part of the normal upper respiratory tract flora , where nasopharyngeal colonisation with one or more strains often lasts weeks to months with seasonal peaks in late winter [1] , [2] .", "Carriage of S . pneumoniae ( pneumoco...	[ "The pathogenesis of bacteraemia after challenge with one million pneumococci of three isogenic variants was investigated .", "Sequential analyses of blood samples indicated that most episodes of bacteraemia were monoclonal events providing compelling evidence for a single bacterial cell bottleneck at the origin ...	[ "Decades of research on bacterial sepsis have been devoted to analysing the steps that lead from a local event , either carriage or a localised infection , to systemic disease .", "Our work analyses in depth the events determining systemic infection by one of the main human pathogens , Streptococcus pneumoniae ."...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Molecular and Functional Analyses of a Maize Autoactive NB-LRR Protein Identify Precise Structural Requirements for Activity	journal.ppat.1004674	null	[ [ "One of the main plant disease resistance mechanisms is mediated by dominant resistance ( R ) genes with a major effect [1] .", "Many R genes have been cloned from diverse plant species , most of which encode nucleotide binding leucine-rich-repeat ( NB-LRR or NLR ) proteins [2 , 3] .", "Based on the s...	[ "Plant disease resistance is often mediated by nucleotide binding-leucine rich repeat ( NLR ) proteins which remain auto-inhibited until recognition of specific pathogen-derived molecules causes their activation , triggering a rapid , localized cell death called a hypersensitive response ( HR ) .", "Three domains...	[ "The plant hypersensitive defense response ( HR ) is a rapid , localized cell death , usually occurring upon the recognition of specific pathogen-encoded molecules and consequent activation of nucleotide binding-leucine rich repeat ( NLR ) proteins .", "Rp1-D21 , a naturally-occurring mutant caused by the recombi...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "plant anatomy", "oomycetes", "medicine and health sciences", "chemical compounds", "microbiology", "nitrates", "fungi", "plant science", "nutrition", "crops", "potato", "plants", "vegetables", "crop science", "gene expression", "chemistry", "tomatoes", "leaves", "fruits", "agr...	Gene Expression and Silencing Studies in Phytophthora infestans Reveal Infection-Specific Nutrient Transporters and a Role for the Nitrate Reductase Pathway in Plant Pathogenesis	journal.ppat.1006097	null	[ [ "Successful pathogens must efficiently exploit the nutrients of their hosts to support their growth .", "Pathogens accomplish this through mechanisms that include manipulating hosts to shift nutrients to sites of infection , generating feeding structures , expressing transporters for the nutrients , and m...	[ "To help learn how phytopathogens feed from their hosts , genes for nutrient transporters from the hemibiotrophic potato and tomato pest Phytophthora infestans were annotated .", "This identified 453 genes from 19 families .", "Comparisons with a necrotrophic oomycete , Pythium ultimum var .", "ultimum , and ...	[ "Little is known of how plant pathogens adapt to different growth conditions and host tissues .", "To understand the interaction between the filamentous eukaryotic microbe Phytophthora infestans and its potato and tomato hosts , we mined the genome for genes encoding proteins involved in nutrient uptake and measu...	2016
[ "Introduction", "Materials and Methods", "Results and Discussion" ]	[ "infectious diseases/protozoal infections", "infectious diseases/tropical and travel-associated diseases", "infectious diseases/antimicrobials and drug resistance" ]	Chemosensitization of Trypanosoma congolense Strains Resistant to Isometamidium Chloride by Tetracyclines and Enrofloxacin	journal.pntd.0000828	null	[ [ "African Animal Trypanosomiasis affects about 10 million km2 of sub-Saharan Africa and is a primary cause of rural poverty and food insecurity as explicitly recognized by the African Union , FAO and others [1] .", "Tsetse and the disease they transmit will continue to be a considerable threat to livestock...	[ "Because of the development of resistance in trypanosomes to trypanocidal drugs , the livelihood of millions of livestock keepers in sub-Saharan Africa is threatened now more than ever .", "The existing compounds have become virtually useless and pharmaceutical companies are not keen on investing in the developme...	[ "African Animal Trypanosomiasis causes the death of 3 million head of cattle each year .", "The annual economic losses as a result of the disease are estimated to be 4 . 5 billion US dollars .", "Trypanosomes are transmitted by tsetse flies and can infect a wide range of hosts from wildlife to domestic animals ...	2010
[ "Introduction", "Materials and Methods", "Results/Discussion" ]	[ "computational biology/macromolecular structure analysis" ]	PoreWalker: A Novel Tool for the Identification and Characterization of Channels in Transmembrane Proteins from Their Three-Dimensional Structure	journal.pcbi.1000440	null	[ [ "Transmembrane channel proteins play pivotal roles in maintaining the homeostasis and responsiveness of cells and the cross-membrane electrochemical gradient by mediating the transport of ions and molecules through biological membranes [1] .", "For instance , aquaporins facilitate the flux of water and sm...	[ "Transmembrane channel proteins play pivotal roles in maintaining the homeostasis and responsiveness of cells and the cross-membrane electrochemical gradient by mediating the transport of ions and molecules through biological membranes .", "Therefore , computational methods which , given a set of 3D coordinates ,...	[ "Transmembrane channel proteins are responsible for the transport of ions and molecules through biological membranes and are pivotal for the physiology of the cell .", "In fact , their incorrect functioning is involved or related to several diseases ( diabetes , myotonia , Parkinson's disease , etc . ) .", "Mor...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "phosphorylation", "cryptococcus neoformans", "medicine and health sciences", "cryptococcus", "classical mechanics", "pathology and laboratory medicine", "enzymes", "pathogens", "microbiology", "sexual reproduction", "mechanical stress", "enzymology", "phosphatases", "developmental biology...	Calcineurin Targets Involved in Stress Survival and Fungal Virulence	journal.ppat.1005873	null	[ [ "Cryptococcus neoformans is an environmental fungus found ubiquitously throughout the world [1 , 2] .", "Both spores and desiccated yeast cells are infectious propagules and exposure via inhalation causes life-threatening disease [2 , 3] .", "C . neoformans is primarily an opportunistic pathogenic fun...	[ "Calcineurin governs stress survival , sexual differentiation , and virulence of the human fungal pathogen Cryptococcus neoformans .", "Calcineurin is activated by increased Ca2+ levels caused by stress , and transduces signals by dephosphorylating protein substrates .", "Herein , we identified and characterize...	[ "Calcineurin is a Ca2+/calmodulin-dependent protein phosphatase essential for stress survival , sexual development , and virulence of the human fungal pathogen Cryptococcus neoformans and other major pathogenic fungi of global human health relevance .", "However , no calcineurin substrates are known in pathogenic...	2016
[ "Introduction", "Results", "Methods", "Discussion" ]	[ "neuroscience/animal cognition", "neuroscience/theoretical neuroscience" ]	A Learning Theory for Reward-Modulated Spike-Timing-Dependent Plasticity with Application to Biofeedback	journal.pcbi.1000180	null	[ [ "Numerous experimental studies ( see [1] for a review; [2] discusses more recent", "in-vivo results ) have shown that the efficacy of synapses changes in dependence of", "the time difference", "Δt = tpost−tpre", "between the firing times tpre and", "tpost of the pre- and postsynaptic neuro...	[ "Reward-modulated spike-timing-dependent plasticity ( STDP ) has recently emerged as", "a candidate for a learning rule that could explain how behaviorally relevant", "adaptive changes in complex networks of spiking neurons could be achieved in a", "self-organizing manner through local synaptic plasticity .",...	[ "A major open problem in computational neuroscience is to explain how learning ,", "i . e . , behaviorally relevant modifications in the central nervous system , can be", "explained on the basis of experimental data on synaptic plasticity .", "Spike-timing-dependent plasticity ( STDP ) is a rule for changes i...	2008
[ "Introduction", "Materials and Methods", "Results and Discussion" ]	[ "bacterial genomics", "genetics", "biology and life sciences", "genomics", "computational biology", "microbial genomics" ]	A Taxonomy of Bacterial Microcompartment Loci Constructed by a Novel Scoring Method	journal.pcbi.1003898	null	[ [ "Membrane-bound organelles for compartmentalization of specific functions are the hallmark feature of all eukaryotic cells .", "Bacteria also have organelles , but they are not ubiquitous throughout the domain; instead they are sporadically distributed and frequently provide functions that are key to nich...	[ "Bacterial microcompartments ( BMCs ) are proteinaceous organelles involved in both autotrophic and heterotrophic metabolism .", "All BMCs share homologous shell proteins but differ in their complement of enzymes; these are typically encoded adjacent to shell protein genes in genetic loci , or operons .", "To e...	[ "Some enzymatic transformations have undesirable side reactions , produce toxic or volatile intermediates , or are inefficient; these shortcomings can be alleviated through their sequestration with their substrates in a confined space , as in the membrane-bound organelles of eukaryotes .", "Recently , it was disc...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biotechnology", "bacteriology", "small molecules", "enzymes", "gene regulation", "microbiology", "host-pathogen interaction", "molecular genetics", "microbial growth and development", "bacterial pathogens", "applied microbiology", "microbial physiology", "gene expression", "microbial path...	Necrotrophism Is a Quorum-Sensing-Regulated Lifestyle in Bacillus thuringiensis	journal.ppat.1002629	null	[ [ "Saprophytism , probably one of the most common lifestyle for micro-organisms , involves living in dead or decaying organic matter .", "For most pathogens , saprophytism is limited to necrotrophism ( the use of the host cadaver ) .", "This step of the infection process is essential for the proliferati...	[ "How pathogenic bacteria infect and kill their host is currently widely investigated .", "In comparison , the fate of pathogens after the death of their host receives less attention .", "We studied Bacillus thuringiensis ( Bt ) infection of an insect host , and show that NprR , a quorum sensor , is active after...	[ "Bacillus thuringiensis ( Bt ) is a well known entomopathogenic bacterium successfully used as a biopesticide for fifty years .", "The insecticidal properties of Bt are mainly due to specific toxins forming a crystal inclusion associated with the spore .", "After ingestion by susceptible insect larvae , toxins ...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "humoral immunity", "medicine and health sciences", "infectious disease epidemiology", "applied mathematics", "immunity to infections", "immunology", "tropical diseases", "parasitic diseases", "mathematics", "population modeling", "neglected tropical diseases", "infectious disease control", ...	Predicted Impact of Mass Drug Administration on the Development of Protective Immunity against Schistosoma haematobium	journal.pntd.0003059	null	[ [ "Urogenital schistosomiasis ( caused by the blood fluke Schistosoma haematobium ) remains a prevalent tropical disease , infecting over 100 million people in sub-Saharan Africa [1] , [2] .", "Recent control efforts have focussed upon mass drug administration ( MDA ) using the antihelminthic drug praziquan...	[ "Previous studies suggest that protective immunity against Schistosoma haematobium is primarily stimulated by antigens from dying worms .", "Praziquantel treatment kills adult worms , boosting antigen exposure and protective antibody levels .", "Current schistosomiasis control efforts use repeated mass drug adm...	[ "Urogenital schistosomiasis , caused by schistosome blood flukes , infects more than 100 million people in sub-Saharan Africa .", "Current control efforts involve regularly treating all school-aged children with the drug praziquantel , which kills schistosome worms .", "Earlier work by our group suggests that p...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "crystal structure", "split-decomposition method", "condensed matter physics", "multiple alignment calculation", "protein structure prediction", "protein structure", "crystallography", "structural genomics", "research and analysis methods", "sequence analysis", "solid state physics", "protein ...	Coevolving residues inform protein dynamics profiles and disease susceptibility of nSNVs	journal.pcbi.1006626	null	[ [ "A 3D structure is still required to computationally obtain protein dynamics , drastically limiting the extent to which conformational dynamics can be incorporated into genomic analysis .", "The reason for this is that there are exponentially more sequences than experimental structures .", "Currently ...	[ "The conformational dynamics of proteins is rarely used in methodologies used to predict the impact of genetic mutations due to the paucity of three-dimensional protein structures as compared to the vast number of available sequences .", "Until now a three-dimensional ( 3D ) structure has been required to predict...	[ "Proteins are dynamic machines that undergo atomic fluctuations , side chain rotations , and collective domain movements that are required for biological function .", "There is , therefore , a need for quantitative metrics that capture the dynamic fluctuations per position to understand the critical role of prote...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "systems biology", "computer and information sciences", "ecosystem modeling", "ecology", "network analysis", "biology and life sciences", "metabolic networks", "computational biology", "microbial ecology" ]	Emergent Biosynthetic Capacity in Simple Microbial Communities	journal.pcbi.1003695	null	[ [ "Microbes have a remarkable capacity to transform their environments , converting key nutrients and energy into accessible forms that are essential for the survival of all other organisms [1] , [2] .", "This capacity is mediated by a plethora of interactions with the environment and a complex web of metab...	[ "Microbes have an astonishing capacity to transform their environments .", "Yet , the metabolic capacity of a single species is limited and the vast majority of microorganisms form complex communities and join forces to exhibit capabilities far exceeding those achieved by any single species .", "Such enhanced m...	[ "Microbes constantly change their environment , consuming some compounds from their surroundings and secreting others .", "This microbial activity plays a crucial role in many important environmental cycles , ultimately making all life possible .", "These processes , however , are often not accomplished by a si...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Motor and Sensory Deficits in the teetering Mice Result from Mutation of the ESCRT Component HGS	journal.pgen.1005290	null	[ [ "In neurons , endosomal transport and sorting of internalized cargo affects the abundance of plasma membrane proteins and regulates a diverse group of cellular processes such as signal transduction and synaptic vesicle recycling [1–3] .", "A group of evolutionarily conserved cytosolic proteins referred to...	[ "Neurons are particularly vulnerable to perturbations in endo-lysosomal transport , as several neurological disorders are caused by a primary deficit in this pathway .", "In this report , we used positional cloning to show that the spontaneously occurring neurological mutation teetering ( tn ) is a single nucleot...	[ "Endocytic trafficking involves the internalization , endosomal sorting and lysosomal degradation of cell surface cargo .", "Many factors involved in endosomal sorting in mammalian cells have been identified , and mutations in these components are associated with a variety of neurological disorders .", "While t...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "blood cells", "medicine and health sciences", "body fluids", "fibrinogen", "fibrin", "cardiovascular medicine", "thrombosis", "elution", "platelets", "glycoproteins", "research and analysis methods", "separation processes", "coagulation disorders", "thrombin", "animal cells", "protein...	Reduced model to predict thrombin and fibrin during thrombosis on collagen/tissue factor under venous flow: Roles of γ’-fibrin and factor XIa	journal.pcbi.1007266	null	[ [ "The reaction network and kinetics of human blood clotting impact diseases such as coronary thrombosis , stroke , deep vein thrombosis , hemophilia , disseminated intravascular coagulopathy ( DIC ) , and traumatic bleeding .", "Numerous therapeutics are designed to either inhibit or catalyze reactions of ...	[ "During thrombosis , thrombin generates fibrin , however fibrin reversibly binds thrombin with low affinity E-domain sites ( KD = 2 . 8 μM ) and high affinity γ’-fibrin sites ( KD = 0 . 1 μM ) .", "For blood clotting on collagen/tissue factor ( 1 TF-molecule/μm2 ) at 200 s-1 wall shear rate , high μM-levels of in...	[ "During blood clotting events , a complex series of reaction are involved .", "Simulation gives insights to the concentration of different enzymes which are at too low of concentration to be detected .", "However , the models are often large and difficult to solve for clotting under flow conditions .", "With ...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "aspergillosis", "immune cells", "monocytes", "immunity", "innate immunity", "immune defense", "immunology", "immunity to infections", "biology", "fungal diseases" ]	Inflammatory Monocytes Orchestrate Innate Antifungal Immunity in the Lung	journal.ppat.1003940	null	[ [ "The incidence of fungal infections has been on the rise for several decades due to increased use of immunosuppressive and myeloablative therapies for malignant and non-malignant diseases [1] , [2] , [3] .", "Invasive aspergillosis ( IA ) , most commonly caused by A . fumigatus , is a frequent cause of in...	[ "Aspergillus fumigatus is an environmental fungus that causes invasive aspergillosis ( IA ) in immunocompromised patients .", "Although -CC-chemokine receptor-2 ( CCR2 ) and Ly6C-expressing inflammatory monocytes ( CCR2+Mo ) and their derivatives initiate adaptive pulmonary immune responses , their role in coordi...	[ "Despite the significant impact of fungal infections to human health our understanding of immunity to these pathogens remains incomplete .", "Human mycoses are associated with high morbidity and mortality , even with modern antifungal therapies .", "Aspergillus fumigatus is the most common etiologic agent of in...	2014
[ "Introduction", "Materials and methods", "Results and discussion" ]	[ "livestock", "medicine and health sciences", "geographical locations", "tropical diseases", "social sciences", "parasitic diseases", "social epidemiology", "farms", "crops", "africa", "agricultural production", "crop science", "epidemiology", "economics", "agriculture", "people and pla...	The impact of the Ebola virus disease (EVD) epidemic on agricultural production and livelihoods in Liberia	journal.pntd.0006580	null	[ [ "There is a plethora of evidence in the literature that epidemics such as HIV/AIDS and malaria have profound implications for the livelihoods of the affected society .", "The impact of HIV/AIDS on livelihoods has been intensively investigated and there is universal consensus that HIV/AIDS adversely affect...	[ "There is unequivocal evidence in the literature that epidemics adversely affect the livelihoods of individuals , households and communities .", "However , evidence in the literature is dominated by the socioeconomic impacts of HIV/AIDS and malaria , while evidence on the impact of the Ebola virus disease ( EVD )...	[ "Epidemics such as HIV/AIDS , malaria and Ebola virus disease ( EVD ) may adversely impact the livelihoods of the society affected by the epidemics .", "Nonetheless , the mechanism behind the effects of the epidemics may differ depending on different factors , such as the transmission mechanisms , latency , and m...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "perturbation theory", "neural networks", "neuroscience", "learning and memory", "cognitive neuroscience", "mathematics", "cognition", "network analysis", "algebra", "memory", "interneurons", "quantum mechanics", "neuronal tuning", "computer and information sciences", "animal cells", "...	Stochastic neural field model of stimulus-dependent variability in cortical neurons	journal.pcbi.1006755	null	[ [ "Consider a pair of mutually coupled ring networks labeled j = 1 , 2 .", "Let uj ( θ , t ) denote the activity at time t of a local population of cells with stimulus preference θ ∈ [−π , π ) in network j . Here θ could represent the direction preference of neurons in area-middle temporal cortex ( MT ) [10...	[ "We use stochastic neural field theory to analyze the stimulus-dependent tuning of neural variability in ring attractor networks .", "We apply perturbation methods to show how the neural field equations can be reduced to a pair of stochastic nonlinear phase equations describing the stochastic wandering of spontan...	[ "A topic of considerable current interest concerns the neural mechanisms underlying the suppression of cortical variability following the onset of a stimulus .", "Since trial-by-trial variability and noise correlations are known to affect the information capacity of neurons , such suppression could improve the ac...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell physiology", "medicine and health sciences", "pathology and laboratory medicine", "enzymes", "enzymology", "microbiology", "plasmodium falciparum", "chemical biology", "parasitic diseases", "parasitic protozoans", "parasitology", "gene function", "mutation", "mathematical computing",...	Inhibition of Plasmepsin V Activity Demonstrates Its Essential Role in Protein Export, PfEMP1 Display, and Survival of Malaria Parasites	journal.pbio.1001897	A small molecule inhibitor of the malarial protease Plasmepsin V impairs protein export and cellular remodeling, reducing parasite survival in human erythrocytes.	[ [ "Each year malaria parasites cause several hundred million infections and over 650 , 000 deaths [1] .", "Plasmodium falciparum causes the most lethal malaria and is endemic in Africa [2] .", "Plasmodium vivax causes most malarial deaths outside Africa and is associated with liver-stage hypnozoites [3]...	[ "The malaria parasite Plasmodium falciparum exports several hundred proteins into the infected erythrocyte that are involved in cellular remodeling and severe virulence .", "The export mechanism involves the Plasmodium export element ( PEXEL ) , which is a cleavage site for the parasite protease , Plasmepsin V ( ...	[ "To survive within human red blood cells , malaria parasites must export a catalog of proteins that remodel the host cell and its surface .", "This enables parasites to acquire nutrients from outside the cell and to modify the cell surface in order to evade host defenses .", "Protein export involves proteolytic...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "children", "medicine and health sciences", "education", "sociology", "geographical locations", "social sciences", "numeracy", "uganda", "neuroscience", "parasitic diseases", "pediatrics", "age groups", "academic skills", "research design", "cognitive psychology", "literacy", "survey...	The long run impact of early childhood deworming on numeracy and literacy: Evidence from Uganda	journal.pntd.0007085	null	[ [ "The theory that deworming could improve educational outcomes goes back at least as far as the 1930s [18] , but there was little rigorous research on the topic until a series of trials in the 1990s testing the impact of deworming on cognitive outcomes over short periods ( 1-7 months ) [19 , 20 , 21] , followe...	[ "Up to 1 . 45 billion people currently suffer from soil transmitted helminth infection , with the largest burden occurring in Africa and Asia .", "Safe and cost effective deworming treatment exists , but there is a debate about mass distribution of this treatment in high prevalence settings .", "While the World...	[ "Mass deworming is recommended by the World Health Organization for health benefits to communities where soil-transmitted helminth infection is endemic .", "In addition to health benefits , several recent studies find long run educational or economic benefits for cohorts dewormed as children .", "In this paper ...	2019
[ "Introduction", "Materials and Methods", "Results and Discussion" ]	[ "infectious diseases/neglected tropical diseases", "public health and epidemiology/infectious diseases", "microbiology/parasitology", "immunology/innate immunity" ]	Filarial Worms Reduce Plasmodium Infectivity in Mosquitoes	journal.pntd.0000963	null	[ [ "Malaria and lymphatic filariasis ( LF ) are two of the most important mosquito-borne diseases .", "Currently , there are 2 . 5 billion people at risk of contracting malaria , and on average , there are 300–500 million clinical cases of malaria each year causing between one and three million deaths [1]–[3...	[ "Co-occurrence of malaria and filarial worm parasites has been reported , but little is known about the interaction between filarial worm and malaria parasites with the same Anopheles vector .", "Herein , we present data evaluating the interaction between Wuchereria bancrofti and Anopheles punctulatus in Papua Ne...	[ "The parasites that cause malaria and human lymphatic filariasis are both transmitted by mosquitoes , and often times in areas where these two diseases are co-endemic , mosquitoes in the genus Anopheles transmit both parasites .", "Currently , it is unknown how parasite transmission is effected when malaria and f...	2011
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "sequencing techniques", "urology", "medicine and health sciences", "immune physiology", "pathology and laboratory medicine", "pathogens", "immunology", "tropical diseases", "microbiology", "antigenic variation", "treponematoses", "bacterial diseases", "next-generation sequencing", "sexual...	Insights into the genetic variation profile of tprK in Treponema pallidum during the development of natural human syphilis infection	journal.pntd.0007621	null	[ [ "Syphilis is a complex chronic disease caused by infection with Treponema pallidum subsp .", "pallidum ( T . pallidum ) .", "Specifically , the disease has a series of highly distinct clinical stages [1] , which usually includes the localized chancre primary stage , the disseminated secondary stage , ...	[ "Although the tprK gene of Treponema pallidum are thought to play a critical role in the pathogenesis of syphilis , the profile of variations in tprK during the development of human syphilis infection have remained unclear .", "Through next-generation sequencing , we compared the tprK gene of 14 secondary syphili...	[ "Antigenic variation of the TprK antigen has been acknowledged to explain the persistence of Treponema pallidum in the host , however , the profile of variations in tprK during the development of human syphilis infection has not been well characterized .", "Here , we performed next-generation sequencing to compar...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "proteins", "gene expression", "genetics", "biology and life sciences", "epigenetics", "dna-binding proteins", "histones", "histone modification" ]	Specific Phosphorylation of Histone Demethylase KDM3A Determines Target Gene Expression in Response to Heat Shock	journal.pbio.1002026	Phosphorylation of histone demethylase KDM3A in response to thermal stress enables its specific recruitment to target genes by Stat1.	[ [ "Histone modifications , such as methylation and acetylation , regulate RNA synthesis [1] , [2] .", "Unlike the activating impact of acetylation , the methylation of lysine residues in histones can exert either an activating or a repressive effect on genes , depending on the number of methyl groups that a...	[ "Histone lysine ( K ) residues , which are modified by methyl- and acetyl-transferases , diversely regulate RNA synthesis .", "Unlike the ubiquitously activating effect of histone K acetylation , the effects of histone K methylation vary with the number of methyl groups added and with the position of these groups...	[ "Histone methylation regulates gene expression and can have drastic consequences for health if the process is defective .", "Histone lysine demethylases ( KDMs ) counteract the activity of methyl-transferases and remove methyl group ( s ) from histones .", "KDM3A is a H3K9me2/1 demethylase that performs diverse...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "developmental biology/molecular development", "genetics and genomics/genetics of disease", "neuroscience/neurodevelopment", "genetics and genomics/functional genomics" ]	Identification of Neural Crest and Glial Enhancers at the Mouse Sox10 Locus through Transgenesis in Zebrafish	journal.pgen.1000174	null	[ [ "The neural crest is a transient migratory population of cells that arise at the dorsal aspect of the neural tube as it closes and that give rise to myriad structures including , but not limited to , melanocytes , enteric nervous system ( ENS ) , and myelinating Schwann cells [1] .", "SOX10 ( SRY-box cont...	[ "Sox10 is a dynamically regulated transcription factor gene that is essential for the development of neural crest–derived and oligodendroglial populations .", "Developmental genes often require multiple regulatory sequences that integrate discrete and overlapping functions to coordinate their expression .", "To...	[ "The neural crest is a population of embryonic migratory stem cells .", "They form atop the future spinal cord and migrate throughout developing embryos and form many different cells , including the epidermal pigment cells , bone cells in the head , and nerve cells of the peripheral nervous system .", "In this ...	2008
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "computational biology/molecular dynamics", "cell biology/cell adhesion", "biophysics/theory and simulation" ]	Molecular Dynamics Simulations of Forced Unbending of Integrin αVβ3	journal.pcbi.1001086	null	[ [ "Integrins are αβ heterodimeric transmembrane receptors for cell-cell and cell-extracellular matrix adhesions [1] .", "The overall shape of an integrin ectodomain is that of a large head supported by two long legs [2] , [3] .", "The head of αA ( or αI ) domain-lacking integrins , including the integri...	[ "Integrins may undergo large conformational changes during activation , but the dynamic processes and pathways remain poorly understood .", "We used molecular dynamics to simulate forced unbending of a complete integrin αVβ3 ectodomain in both unliganded and liganded forms .", "Pulling the head of the integrin ...	[ "Proteins can regulate their functions via conformational changes .", "One example is integrins , which are transmembrane receptors mediating cell-cell and cell-matrix adhesions .", "Inactive integrins may assume a bent conformation with low affinities for ligands unable to support adhesions .", "Intracellula...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "plant science", "plant biology", "biology", "molecular cell biology" ]	The OXI1 Kinase Pathway Mediates Piriformospora indica-Induced Growth Promotion in Arabidopsis	journal.ppat.1002051	null	[ [ "The endophytic fungus Piriformospora indica , a cultivable basidiomycete of Sebacinales , colonizes the roots of many plant species including Arabidopsis [1] , [2] .", "Like other members of Sebacinales , P . indica is found worldwide in association with roots [3] , and stimulates growth , biomass and se...	[ "Piriformospora indica is an endophytic fungus that colonizes roots of many plant species and promotes growth and resistance to certain plant pathogens .", "Despite its potential use in agriculture , little is known on the molecular basis of this beneficial plant-fungal interaction .", "In a genetic screen for ...	[ "Like many root-colonizing microbes , the primitive Basidiomycete fungus Piriformospora indica colonizes the roots of many plant species and promotes their growth .", "The lack of host specificity suggests that the plant response to this endopyhte is based on general signalling processes .", "In a genetic scree...	2011
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "biology" ]	TNF-α Involvement in Insulin Resistance Induced by Experimental Scorpion Envenomation	journal.pntd.0001740	null	[ [ "Scorpion venoms induce systemic inflammation associated with an increase in cytokine release and chemokine production [1]–[3] .", "Androctonus australis hector ( Aah ) venom induces high plasma concentrations of proinflammatory cytokines including interleukin 1 beta ( IL-1β ) , interleukin 6 ( IL-6 ) and...	[ "Scorpion venom induces systemic inflammation characterized by an increase in cytokine release and chemokine production .", "There have been few experimental studies assessing the effects of scorpion venom on adipose tissue function in vivo .", "To study the adipose tissue inflammation ( ATI ) induced by Androc...	[ "Androctonus australis hector ( Aah ) is the scorpion most frequently causing serious human envenomation .", "In Algeria , Aah is responsible for approximately 50 , 000 cases of scorpion envenomation per year .", "The Aah sting causes multi-system failure that may be fatal; the manifestations include cardiopulm...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "mathematics", "biophysics/theory and simulation", "computational biology/systems biology", "physics/interdisciplinary physics" ]	Flow-Based Cytometric Analysis of Cell Cycle via Simulated Cell Populations	journal.pcbi.1000741	null	[ [ "Multiparameter flow cytometry is widely used to study the cell cycle and its perturbation in the context of both basic research and in routine clinical analysis [1]–[6] .", "Such analyses may use a wide range of fluorescent reporters that correlate to the expression of key molecular components of the cel...	[ "We present a new approach to the handling and interrogating of large flow cytometry data where cell status and function can be described , at the population level , by global descriptors such as distribution mean or co-efficient of variation experimental data .", "Here we link the “real” data to initialise a com...	[ "One of the key challenges facing cell biologists today is understanding the influence of molecular controls in shaping and controlling cell growth and proliferation .", "There is growing recognition that abnormal progression through the cell cycle and the associated effects on the growth of cell populations has ...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/epigenetics" ]	A Dominant Mutation in mediator of paramutation2, One of Three Second-Largest Subunits of a Plant-Specific RNA Polymerase, Disrupts Multiple siRNA Silencing Processes	journal.pgen.1000725	null	[ [ "Paramutation , an interaction between specific alleles that leads to a heritable change of expression of one allele , was first described for the maize red1 ( r1 ) gene [1] .", "Subsequently three more regulatory genes of the flavonoid biosynthetic pathway , b1 ( Booster1 ) , pl1 ( plant color1 ) , and p...	[ "Paramutation involves homologous sequence communication that leads to meiotically heritable transcriptional silencing .", "We demonstrate that mop2 ( mediator of paramutation2 ) , which alters paramutation at multiple loci , encodes a gene similar to Arabidopsis NRPD2/E2 , the second-largest subunit of plant-spe...	[ "How an individual's genes are activated or silenced is an essential question impacting all fields of biology .", "Usually gene expression patterns , i . e . , which genes are on and which are off in different tissues and during development , are highly reproducible; and those patterns are efficiently reset in th...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "animals", "in vitro", "infectious diseases", "microbiology" ]	TGF-β Signaling Controls Embryo Development in the Parasitic Flatworm Schistosoma mansoni	journal.ppat.0030052	null	[ [ "Amongst the Bilateria , transforming growth factor–β ( TGF-β ) signaling is recognized as playing an essential role in embryogenesis in deuterostomes and in arthropod protostomes , but its role in lophotrochozoan protostomes is unclear [1] .", "Schistosomes , the causative agents of schistosomiasis , one...	[ "Over 200 million people have , and another 600 million are at risk of contracting , schistosomiasis , one of the major neglected tropical diseases .", "Transmission of this infection , which is caused by helminth parasites of the genus Schistosoma , depends upon the release of parasite eggs from the human host ....	[ "Schistosomes are parasitic worms that infect hundreds of millions of people in developing countries .", "They cause disease by virtue of the fact that the eggs that they produce , which are intended for release from the host in order to allow transmission of infection , can become trapped in target organs such a...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Retrohoming of a Mobile Group II Intron in Human Cells Suggests How Eukaryotes Limit Group II Intron Proliferation	journal.pgen.1005422	null	[ [ "Mobile group II introns are retrotransposons that also function as self-splicing introns [1] .", "They are found in bacteria , archaea , and in the bacterial endosymbiont-derived mitochondrial and chloroplast genomes of some eukaryotes , particularly fungi and plants [2] .", "Despite their prokaryoti...	[ "Mobile bacterial group II introns are evolutionary ancestors of spliceosomal introns and retroelements in eukaryotes .", "They consist of an autocatalytic intron RNA ( a “ribozyme” ) and an intron-encoded reverse transcriptase , which function together to promote intron integration into new DNA sites by a mechan...	[ "Mobile group II introns are bacterial retrotransposons that are evolutionary ancestors of spliceosomal introns and retroelements in eukaryotes .", "They consist of an autocatalytic intron RNA ( a ribozyme ) and an intron-encoded reverse transcriptase , which together promote intron mobility to new DNA sites by a...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "hela cells", "enzymes", "cell cycle and cell division", "gene regulation", "biological cultures", "cell processes", "enzymology", "dna helicases", "chromatids", "dna replication", "cell cultures", "sequence motif analysis", "dna", "synthesis phase", "research and analysis methods", "s...	Interaction of the Warsaw breakage syndrome DNA helicase DDX11 with the replication fork-protection factor Timeless promotes sister chromatid cohesion	journal.pgen.1007622	null	[ [ "Cohesion is the process that ensures tethering of newly replicated sister chromatids until they separate in metaphase [1] .", "This process is mediated by cohesin , an evolutionarily conserved hetero-tetrameric complex ( made of Smc1 , Smc3 , Scc1 and either SA1 or SA2 subunits ) , which has a ring-like ...	[ "Establishment of sister chromatid cohesion is coupled to DNA replication , but the underlying molecular mechanisms are incompletely understood .", "DDX11 ( also named ChlR1 ) is a super-family 2 Fe-S cluster-containing DNA helicase implicated in Warsaw breakage syndrome ( WABS ) .", "Herein , we examined the r...	[ "Chromosomes are DNA molecules that contain the genetic information .", "During replication , the two sister DNA molecules covered by proteins ( sister chromatids ) are held together by many copies of a ring-like protein complex named cohesin , in a process called sister-chromatid cohesion .", "Before a cell di...	2018
[ "Introduction", "Model", "Results", "Discussion" ]	[ "circuit models", "motor systems", "nonlinear dynamics", "mathematics", "neural networks", "computational neuroscience", "biology", "computational biology", "sensory systems", "neuroscience", "neurophysiology", "coding mechanisms" ]	A Hierarchical Neuronal Model for Generation and Online Recognition of Birdsongs	journal.pcbi.1002303	null	[ [ "Songbirds are able to repeat the same , often complex songs with amazing precision .", "When male birds sing to a female repeatedly , there is on average a 1% temporal deviation across the whole song [1] , [2] .", "This combination of complexity and precision is remarkable .", "Studying the neuro...	[ "The neuronal system underlying learning , generation and recognition of song in birds is one of the best-studied systems in the neurosciences .", "Here , we use these experimental findings to derive a neurobiologically plausible , dynamic , hierarchical model of birdsong generation and transform it into a functi...	[ "How do birds communicate via their songs ?", "Investigating this question may not only lead to a better understanding of communication via birdsong , but many believe that the answer will also give us hints about how humans decode speech from complex sound wave modulations .", "In birds , the output and neuron...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics and genomics" ]	A Novel CpG Island Set Identifies Tissue-Specific Methylation at Developmental Gene Loci	journal.pbio.0060022	CpG island methylation, an epigenetic phenomenon usually associated with abnormality in disease, is little characterised in the context of "normal" human cells. Here we highlight tissue-specific CpG Island methylation, which frequently associates with developmental genes.	[ [ "DNA methylation in the mammalian genome arises due to covalent addition of a methyl group to the 5′ position of cytosine in the context of the palindromic dinucleotide , CpG .", "This modification is established and maintained by a family of DNA methyltransferases that are essential for development and v...	[ "CpG islands ( CGIs ) are dense clusters of CpG sequences that punctuate the CpG-deficient human genome and associate with many gene promoters .", "As CGIs also differ from bulk chromosomal DNA by their frequent lack of cytosine methylation , we devised a CGI enrichment method based on nonmethylated CpG affinity ...	[ "The human genome contains about 22 , 000 genes , each encoding one of the proteins required for human life .", "A particular cell type ( e . g . , blood , skin , etc . ) expresses a specific subset of protein genes and silences the remainder .", "To shed light on the mechanisms that cause genes to be activated...	2008
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "ecology and environmental sciences", "medicine and health sciences", "infectious disease epidemiology", "parasitic protozoans", "plant science", "protozoans", "plant pathology", "population biology", "genetic epidemiology", "infectious diseases", "environmental epidemiology", "epidemiology", ...	Hunting, Swimming, and Worshiping: Human Cultural Practices Illuminate the Blood Meal Sources of Cave Dwelling Chagas Vectors (Triatoma dimidiata) in Guatemala and Belize	journal.pntd.0003047	null	[ [ "Humans have been attracted to caves for much of our history for purposes as varied as religious ceremonies to simply shelter .", "In Guatemala people use caves for several cultural practices including religious ceremonies , tourism , and shelter [1] .", "In the department of Petén in northern Guatema...	[ "Triatoma dimidiata , currently the major Central American vector of Trypanosoma cruzi , the parasite that causes Chagas disease , inhabits caves throughout the region .", "This research investigates the possibility that cave dwelling T . dimidiata might transmit the parasite to humans and links the blood meal so...	[ "Caves have enduring appeal to humans , and their lure in Central America includes tourism , religious ceremonies and shelter .", "The major Chagas disease vector in this region , Triatoma dimidiata , inhabits caves throughout its range .", "We challenge the assumption that cave-dwelling vectors are not importa...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "plant anatomy", "medicine and health sciences", "pathology and laboratory medicine", "immunology", "brassica", "alleles", "plant science", "model organisms", "signs and symptoms", "experimental organism systems", "plants", "arabidopsis thaliana", "research and analysis methods", "sequence...	Modulation of ACD6 dependent hyperimmunity by natural alleles of an Arabidopsis thaliana NLR resistance gene	journal.pgen.1007628	null	[ [ "Plants rely on a sophisticated immune system to defend themselves against pathogens .", "A central challenge for plants is how to achieve a fast , effective response upon pathogen attack , while at the same time preventing spontaneous firing of the signaling machinery in the absence of danger [1] .", ...	[ "Plants defend themselves against pathogens by activating an array of immune responses .", "Unfortunately , immunity programs may also cause unintended collateral damage to the plant itself .", "The quantitative disease resistance gene ACCELERATED CELL DEATH 6 ( ACD6 ) serves to balance growth and pathogen resi...	[ "Plants defend themselves against pathogens by activating immune responses .", "Unfortunately , these can cause unintended collateral damage to the plant itself .", "Nevertheless , some wild plants have genetic variants that confer a low threshold for the activation of immunity .", "While these enable a plant...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "genome-wide association studies", "variant genotypes", "alleles", "genetic mapping", "genome analysis", "research and analysis methods", "sequence analysis", "sequence alignment", "bioinformatics", "gene expression", "genetic loci", "haplotypes", "heredity", "database and informatics meth...	Expression estimation and eQTL mapping for HLA genes with a personalized pipeline	journal.pgen.1008091	null	[ [ "The HLA region is the most polymorphic in the genome , and also shows the greatest number of disease associations , which has made it very well characterized at the genomic , population and functional levels [1 , 2] .", "Decades of research have also shown that the HLA genes are targets of natural select...	[ "The HLA ( Human Leukocyte Antigens ) genes are well-documented targets of balancing selection , and variation at these loci is associated with many disease phenotypes .", "Variation in expression levels also influences disease susceptibility and resistance , but little information exists about the regulation and...	[ "The level at which a gene is expressed can have important influence on the phenotype of an organism , including its predisposition to develop diseases .", "One way to estimate gene expression is by quantifying the abundance of RNA .", "RNA-seq has become the method of choice to provide such estimates at the ge...	2019
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "sequencing techniques", "organismal evolution", "comparative sequence analysis", "medicine and health sciences", "viral classification", "emerging viral diseases", "vector-borne diseases", "microbiology", "viruses", "microbial evolution", "molecular biology techniques", "bunyaviruses", "seq...	Molecular Characterization of Human Pathogenic Bunyaviruses of the Nyando and Bwamba/Pongola Virus Groups Leads to the Genetic Identification of Mojuí dos Campos and Kaeng Khoi Virus	journal.pntd.0003147	null	[ [ "The Bunyaviridae are a large , diverse group of more than 350 viruses divided into 5 genera , of which more than 150 belong to the genus Orthobunyavirus [1] .", "Importantly , these viruses represent a significant cause of arthropod-borne human disease worldwide , with infection often associated with a f...	[ "Human infection with Bwamba virus ( BWAV ) and the closely related Pongola virus ( PGAV ) , as well as Nyando virus ( NDV ) , are important causes of febrile illness in Africa .", "However , despite seroprevalence studies that indicate high rates of infection in many countries , these viruses remain relatively u...	[ "Bunyavirus infections cause febrile illnesses of varying severity worldwide; however , despite their public health importance most remain relatively unstudied .", "In order to clarify the genetic relationships among African orthobunyaviruses associated with human infection , we have sequenced multiple strains of...	2014
[ "Introduction", "Material and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "microbiology", "sequence assembly tools", "membrane proteins", "outer membrane proteins", "genome analysis", "sequence motif analysis", "cellular structures and organelles", "bacterial pathogens", "research and ...	Complete genome sequences of two strains of Treponema pallidum subsp. pertenue from Indonesia: Modular structure of several treponemal genes	journal.pntd.0006867	null	[ [ "The infectious agent of yaws , Treponema pallidum subsp .", "pertenue ( TPE ) , causes chronic infections in children and young adults , which is characterized by skin lesions including nodules and ulcerations of the skin , which is later accompanied by joint , soft tissue , and bone manifestations ( rev...	[ "Treponema pallidum subsp .", "pertenue ( TPE ) is the causative agent of yaws , a multistage disease endemic in tropical regions in Africa , Asia , Oceania , and South America .", "To date , seven TPE strains have been completely sequenced and analyzed including five TPE strains of human origin ( CDC-2 , CDC 2...	[ "Treponema pallidum subsp .", "pertenue ( TPE ) is the causative agent of yaws , a multi-stage disease that is endemic in tropical regions of Africa , Asia , Oceania , and South America .", "TPE belongs to the pathogenic treponemes and causes several human and animal infections .", "Whole genome sequences of ...	2018
[ "Introduction", "Results", "Discussion", "Material and methods" ]	[ "blood cells", "t helper cells", "innate immune system", "medicine and health sciences", "immune cells", "immune physiology", "cytokines", "immunology", "tropical diseases", "cell-mediated immunity", "cloning", "bacterial diseases", "developmental biology", "molecular development", "mole...	Engaging the CD40-CD40L pathway augments T-helper cell responses and improves control of Mycobacterium tuberculosis infection	journal.ppat.1006530	null	[ [ "Critical to the success of Mycobacterium tuberculosis ( Mtb ) as a pathogen is its ability to manipulate host innate and adaptive immune responses to its benefit .", "Despite the development of antigen-specific T cell responses following infection , Mtb is able to persist within the host , indicating tha...	[ "Mycobacterium tuberculosis ( Mtb ) impairs dendritic cell ( DC ) functions and induces suboptimal antigen-specific CD4 T cell immune responses that are poorly protective .", "Mucosal T-helper cells producing IFN-γ ( Th1 ) and IL-17 ( Th17 ) are important for protecting against tuberculosis ( TB ) , but the mecha...	[ "Tuberculosis ( TB ) remains a serious global health problem and understanding how to induce protective immunity to M . tuberculosis ( Mtb ) remains a major challenge .", "While antigen-specific CD4 T cells and IFN-γ are important for controlling Mtb infection , they are not sufficient for protecting against TB ....	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "voltage-gated ion channels", "uterus", "calcium-activated potassium channels", "medicine and health sciences", "reproductive system", "membrane potential", "electrophysiology", "neuroscience", "ion channels", "cellular structures and organelles", "proteins", "calcium channels", "biophysics"...	Reconstruction of Cell Surface Densities of Ion Pumps, Exchangers, and Channels from mRNA Expression, Conductance Kinetics, Whole-Cell Calcium, and Current-Clamp Voltage Recordings, with an Application to Human Uterine Smooth Muscle Cells	journal.pcbi.1004828	null	[ [ "The human genome contains a large number of distinct ion channels , each of which may be assembled into multimeric complexes that modulate the electrical activity of the cell in a subtly different way [1] .", "Determination of the total ion channel repertoire of a given cell ( its ‘conductance repertoire...	[ "Uterine smooth muscle cells remain quiescent throughout most of gestation , only generating spontaneous action potentials immediately prior to , and during , labor .", "This study presents a method that combines transcriptomics with biophysical recordings to characterise the conductance repertoire of these cells...	[ "A well-known problem in electrophysiologal modeling is that the parameters of the gating kinetics of the ion channels cannot be uniquely determined from observed behavior at the cellular level .", "One solution is to employ simplified “macroscopic” currents that mimic the behavior of aggregates of distinct entit...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[]	Schwann cells ER-associated degradation contributes to myelin maintenance in adult nerves and limits demyelination in CMT1B mice	journal.pgen.1008069	null	[ [ "In the peripheral nervous system ( PNS ) , Schwann cells discontinuously myelinate axons to promote the fast saltatory conduction of the nerve impulses .", "During myelin biogenesis , large amounts of both lipids and proteins are produced .", "After the completion of myelination , the maintenance of ...	[ "In the peripheral nervous system ( PNS ) myelinating Schwann cells synthesize large amounts of myelin protein zero ( P0 ) glycoprotein , an abundant component of peripheral nerve myelin .", "In humans , mutations in P0 cause the demyelinating Charcot-Marie-Tooth 1B ( CMT1B ) neuropathy , one of the most diffused...	[ "Charcot-Marie-Tooth neuropathies are a large family of peripheral nerve disorders , showing extensive clinical and genetic heterogeneity .", "Although strong advances have been made in the identification of genes and mutations involved , effective therapies are still lacking .", "Intracellular retention of abn...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "helminth infections", "infectious diseases", "schistosomiasis", "medicine and health sciences", "neglected tropical diseases", "tropical diseases", "parasitic diseases" ]	Praziquantel, Mefloquine-Praziquantel, and Mefloquine-Artesunate-Praziquantel against Schistosoma haematobium: A Randomized, Exploratory, Open-Label Trial	journal.pntd.0002975	null	[ [ "Schistosomiasis is a neglected tropical disease caused by a chronic infection with blood-dwelling parasitic flatworms of the genus Schistosoma [1] .", "More than 230 million people in the tropics and subtropics are infected and the global burden of schistosomiasis is estimated at 3 . 3 million disability...	[ "Treatment and morbidity control of schistosomiasis relies on a single drug , praziquantel .", "Hence , there is a pressing need to develop additional therapeutics against schistosomiasis .", "The antimalarial drug mefloquine shows antischistosomal activity in animal models and clinical trials , which calls for...	[ "The antimalarial drug mefloquine shows activity against blood flukes that cause the disease schistosomiasis .", "In animal studies it has been found that a mefloquine-praziquantel combination kills blood flukes more effectively than praziquantel alone .", "Combining praziquantel with another drug might therefo...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	A Conserved NS3 Surface Patch Orchestrates NS2 Protease Stimulation, NS5A Hyperphosphorylation and HCV Genome Replication	journal.ppat.1004736	null	[ [ "Hepatitis C virus ( HCV ) is a single-stranded positive-sense RNA virus belonging to the family Flaviviridae and is with 170 million infected individuals worldwide an important cause of chronic liver disease [1] .", "The positive sense RNA genome contains a 5’-untranslated region ( UTR ) , a single open ...	[ "Hepatitis C virus ( HCV ) infection is a leading cause of liver disease worldwide .", "The HCV RNA genome is translated into a single polyprotein .", "Most of the cleavage sites in the non-structural ( NS ) polyprotein region are processed by the NS3/NS4A serine protease .", "The vital NS2-NS3 cleavage is ca...	[ "Hepatitis C virus ( HCV ) replicates its genome in close association to cellular membranes which serve as assembly site of multi-subunit replication complexes .", "The process of replication complex maturation must be properly controlled to prevent the non-functional maturation/assembly of these complexes .", ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "body fluids", "granulomas", "immunology", "tropical diseases", "biomarkers", "bacterial diseases", "cytotoxic t cells", "bacteria", "infectious diseases", "white blood cells", "memory t cells", "animal cells", "tuberculosi...	Computational and Empirical Studies Predict Mycobacterium tuberculosis-Specific T Cells as a Biomarker for Infection Outcome	journal.pcbi.1004804	null	[ [ "Mycobacterium tuberculosis ( Mtb ) continues to be a global public health threat , responsible for 1 . 3 million deaths due to tuberculosis ( TB ) and 8 . 6 million new infections in 2013 [1] .", "While only 10% of infected individuals develop clinically active TB , the other 90% harbor bacteria and are ...	[ "Identifying biomarkers for tuberculosis ( TB ) is an ongoing challenge in developing immunological correlates of infection outcome and protection .", "Biomarker discovery is also necessary for aiding design and testing of new treatments and vaccines .", "To effectively predict biomarkers for infection progress...	[ "Tuberculosis ( TB ) is a disease that is caused by infection after inhaling the bacterium Mycobacterium tuberculosis .", "Not everyone infected with TB bacteria becomes sick .", "As a result , two TB-related conditions have been categorized: latent TB infection ( not sick but still harboring the bacteria ) and...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	CR3 and Dectin-1 Collaborate in Macrophage Cytokine Response through Association on Lipid Rafts and Activation of Syk-JNK-AP-1 Pathway	journal.ppat.1004985	null	[ [ "Diseases caused by fungal pathogens have become an important cause of morbidity and mortality over the last decades due to the increasing number of immunocompromised patients [1] .", "To reveal the cellular and molecular mechanisms of the interaction between host and fungal pathogens will be helpful for ...	[ "Collaboration between heterogeneous pattern recognition receptors ( PRRs ) leading to synergistic coordination of immune response is important for the host to fight against invading pathogens .", "Although complement receptor 3 ( CR3 ) and Dectin-1 are major PRRs to detect fungi , crosstalk between these two rec...	[ "The incidence of life-threatening fungal infections is increasing during the last decades .", "A better understanding of the interactions between fungal pathogen and its host cell is important to the development of new therapeutic strategies against fungal infections .", "Dimorphic fungus Histoplasma capsulatu...	2015
[ "Introduction", "Discussion", "Materials and Methods" ]	[]	A Recessive Founder Mutation in Regulator of Telomere Elongation Helicase 1, RTEL1, Underlies Severe Immunodeficiency and Features of Hoyeraal Hreidarsson Syndrome	journal.pgen.1003695	null	[ [ "Hoyeraal Hreidarsson syndrome ( HH ) is a clinically severe variant of the telomere biology disorder dyskeratosis congenita ( DC ) [1] .", "DC is a heterogeneous inherited bone marrow failure syndrome ( IBMFS ) diagnosed by the presence of the classic triad of dysplastic nails , abnormal skin pigmentatio...	[ "Dyskeratosis congenita ( DC ) is a heterogeneous inherited bone marrow failure and cancer predisposition syndrome in which germline mutations in telomere biology genes account for approximately one-half of known families .", "Hoyeraal Hreidarsson syndrome ( HH ) is a clinically severe variant of DC in which pati...	[ "Patients with dyskeratosis congenita ( DC ) , a rare inherited disease , are at very high risk of developing cancer and bone marrow failure .", "The clinical features of DC include nail abnormalities , skin discoloration , and white spots in the mouth .", "Patients with Hoyeraal-Hreidarsson syndrome ( HH ) hav...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "chromosome structure and function", "cell cycle and cell division", "cell processes", "dna replication", "forms of dna", "circular dna", "dna", "homologous recombination", "chromosome biology", "genetic loci", "biochemistry", "cell biology", "nucleic acids", "heredity", "genetics", "b...	Broken replication forks trigger heritable DNA breaks in the terminus of a circular chromosome	journal.pgen.1007256	null	[ [ "The bidirectional replication of the Escherichia coli circular chromosome starts at the replication origin oriC and ends when forks meet in the opposite region , the chromosome terminus .", "Replication forks are arrested in the terminus region by specific sites called ter where binding of the Tus protei...	[ "It was recently reported that the recBC mutants of Escherichia coli , deficient for DNA double-strand break ( DSB ) repair , have a decreased copy number of their terminus region .", "We previously showed that this deficit resulted from DNA loss after post-replicative breakage of one of the two sister-chromosome...	[ "The Escherichia coli recBC mutant , deficient for DNA double-strand break ( DSB ) repair , shows a viability defect and a specific deficit in the level of chromosome terminus DNA sequences .", "We previously showed that this deficit results from heritable terminus DNA loss , owing to cell-division dependent DSBs...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "systems biology", "biochemistry", "computer science", "model organisms", "molecular cell biology", "genetics", "chemistry", "biology", "genomics", "microbiology", "genetics and genomics", "toxicology" ]	The Amidation Step of Diphthamide Biosynthesis in Yeast Requires DPH6, a Gene Identified through Mining the DPH1-DPH5 Interaction Network	journal.pgen.1003334	null	[ [ "Regulation of biological processes by posttranslational modification can involve the function , distribution and interaction capabilities of the modified protein [1]–[3] .", "Though most modification pathways such as phosphorylation and ubiquitin conjugation target many different proteins , some exceptio...	[ "Diphthamide is a highly modified histidine residue in eukaryal translation elongation factor 2 ( eEF2 ) that is the target for irreversible ADP ribosylation by diphtheria toxin ( DT ) .", "In Saccharomyces cerevisiae , the initial steps of diphthamide biosynthesis are well characterized and require the DPH1-DPH5...	[ "Diphthamide is an unusual modified amino acid found uniquely in a single protein , eEF2 , which is required for cells to synthesize new proteins .", "The name refers to its target function for eEF2 inactivation by diphtheria toxin , the disease-inducing agent produced by the pathogen Corynebacterium diphtheriae ...	2013
[ "Introduction", "Results", "Discussion", "Material and Methods" ]	[ "immunity", "innate immunity", "immunology", "biology" ]	Toll-8/Tollo Negatively Regulates Antimicrobial Response in the Drosophila Respiratory Epithelium	journal.ppat.1002319	null	[ [ "Although the innate immune system is a primitive host defense mechanism , it involves a sophisticated repertoire of humoral and cellular responses both acting systemically and locally [1] .", "In recent years , the Drosophila model organism has proven to be an invaluable system in dissecting in great det...	[ "Barrier epithelia that are persistently exposed to microbes have evolved potent immune tools to eliminate such pathogens .", "If mechanisms that control Drosophila systemic responses are well-characterized , the epithelial immune responses remain poorly understood .", "Here , we performed a genetic dissection ...	[ "Invertebrates solely rely on innate immune responses for defense against microbial infections .", "Taking advantage of its powerful genetics , the fly Drosophila melanogaster has been extensively used as a model system to dissect the molecular mechanisms that control innate immunity .", "This work led to the d...	2011
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "transfection", "learning", "neural networks", "engineering and technology", "gene regulation", "social sciences", "neuroscience", "learning and memory", "artificial neural networks", "micrornas", "cognitive psychology", "mathematics", "nuclear engineering", "forecasting", "statistics (m...	miRAW: A deep learning-based approach to predict microRNA targets by analyzing whole microRNA transcripts	journal.pcbi.1006185	null	[ [ "MicroRNAs ( miRNAs ) are a family of ∼22-nucleotide ( nt ) small RNAs that regulate gene expression at the post-transcriptional level .", "They act by binding to partially complementary sites on target genes to induce cleavage or repression of productive translation , preventing the target gene from prod...	[ "MicroRNAs ( miRNAs ) are small non-coding RNAs that regulate gene expression by binding to partially complementary regions within the 3’UTR of their target genes .", "Computational methods play an important role in target prediction and assume that the miRNA “seed region” ( nt 2 to 8 ) is required for functional...	[ "microRNAs are small RNA molecules that regulate biological processes by binding to the 3’UTR of a gene and their dysregulation is associated with several diseases .", "Computationally predicting these targets remains a challenge as they only partially match their target and so there can be hundreds of targets fo...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "public health and epidemiology/global health", "public health and epidemiology/occupational and industrial medicine" ]	Randomised Controlled Double-Blind Non-Inferiority Trial of Two Antivenoms for Saw-Scaled or Carpet Viper (Echis ocellatus) Envenoming in Nigeria	journal.pntd.0000767	null	[ [ "Bites by saw-scaled or carpet vipers ( Echis ocellatus ) are frequent in the savanna region of West Africa , where agricultural workers and their children are at greatest risk [1]–[6] .", "Systemic haemorrhage , consumption coagulopathy , shock and debilitating local tissue necrosis may ensue [6] .", ...	[ "In West Africa , envenoming by saw-scaled or carpet vipers ( Echis ocellatus ) causes great morbidity and mortality , but there is a crisis in supply of effective and affordable antivenom ( ISRCTN01257358 ) .", "In a randomised , double-blind , controlled , non-inferiority trial , “EchiTAb Plus-ICP” ( ET-Plus ) ...	[ "Snake bite threatens millions of poor rural folk throughout Africa .", "In Nigeria , as in many countries of sub-Saharan Africa , it takes a terrible toll on human life and limb .", "Over the years , the news for those exposed to snake bite has been generally bad: withdrawal of antivenom manufacturers , increa...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biotechnology", "biochemistry", "lipids", "enzymes", "genetics", "biology", "genomics", "microbiology", "metabolism", "genetics and genomics" ]	Comparative and Functional Genomics of Rhodococcus opacus PD630 for Biofuels Development	journal.pgen.1002219	null	[ [ "Bio-Diesel is an energy-rich portable fuel derived mainly from triacylglycerols ( TAGs ) .", "Biodiesel and related fuels are extracted from oleaginous organisms , both photosynthetic and non-photosynthetic , that use available energy sources to fix carbon into high levels of stored lipids .", "In ch...	[ "The Actinomycetales bacteria Rhodococcus opacus PD630 and Rhodococcus jostii RHA1 bioconvert a diverse range of organic substrates through lipid biosynthesis into large quantities of energy-rich triacylglycerols ( TAGs ) .", "To describe the genetic basis of the Rhodococcus oleaginous metabolism , we sequenced a...	[ "Biofuels research is focused on understanding the energy-related metabolic capabilities of a broad range of biological species .", "To this end we sequenced the genome of Rhodococcus opacus PD630 , a bacterium that accumulates close to 80% of its cellular dry weight in oil , a rare trait in the prokaryotic and e...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Huntington's Disease Induced Cardiac Amyloidosis Is Reversed by Modulating Protein Folding and Oxidative Stress Pathways in the Drosophila Heart	journal.pgen.1004024	null	[ [ "Amyloidosis constitutes a large group of diseases characterized by the misfolding of proteins and the accumulation of protein aggregates in different tissues [1]–[3] .", "Huntington's disease ( HD ) is an inherited neurodegenerative disorder caused by mutations in the Huntingtin ( HTT ) protein which res...	[ "Amyloid-like inclusions have been associated with Huntington's disease ( HD ) , which is caused by expanded polyglutamine repeats in the Huntingtin protein .", "HD patients exhibit a high incidence of cardiovascular events , presumably as a result of accumulation of toxic amyloid-like inclusions .", "We have g...	[ "Huntington's disease ( HD ) is associated with amyloid-like inclusions in the brain and heart , and accumulation of amyloid protein is associated with neurodegeneration and cardiomyopathy .", "Recent studies suggest that HD patients show increased susceptibility to cardiac failure .", "However , the mechanisms...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "embryology", "organism development", "stem cells", "embryonic stem cells", "genetic screens", "genetics", "organogenesis", "biology", "genetics and genomics" ]	Ror2 Enhances Polarity and Directional Migration of Primordial Germ Cells	journal.pgen.1002428	null	[ [ "Primordial germ cells ( PGCs ) are embryonic precursors of the gametes that arise before other major cell lineages in most multicellular animals [1] .", "This early specification necessitates a lengthy migration through the developing embryo in order to reach the nascent ovaries or testes .", "In mic...	[ "The trafficking of primordial germ cells ( PGCs ) across multiple embryonic structures to the nascent gonads ensures the transmission of genetic information to the next generation through the gametes , yet our understanding of the mechanisms underlying PGC migration remains incomplete .", "Here we identify a rol...	[ "Egg and sperm derive from precursors in the early embryo called primordial germ cells ( PGCs ) .", "The mechanisms underlying the migration of PGCs through the embryo to the forming gonads remain unclear .", "In a genetic screen , we identified a role for the receptor Ror2 and its ligand Wnt5a in promoting PGC...	2011
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases/protozoal infections", "infectious diseases/neglected tropical diseases", "molecular biology", "microbiology/parasitology" ]	International Study to Evaluate PCR Methods for Detection of Trypanosoma cruzi DNA in Blood Samples from Chagas Disease Patients	journal.pntd.0000931	null	[ [ "A century after its discovery [1] Chagas disease still represents a health threat to an estimated 28 million people in the Americas , being the second highest illness burden among neglected tropical diseases [2]–[3] .", "The infection by the protozoan Trypanosoma cruzi can be acquired from blood-sucking ...	[ "A century after its discovery , Chagas disease still represents a major neglected tropical threat .", "Accurate diagnostics tools as well as surrogate markers of parasitological response to treatment are research priorities in the field .", "The purpose of this study was to evaluate the performance of PCR meth...	[ "A century after its discovery , Chagas disease , caused by the parasite Trypanosoma cruzi , still represents a major neglected tropical threat .", "Accurate diagnostics tools as well as surrogate markers of parasitological response to treatment are research priorities in the field .", "The polymerase chain rea...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience/neuronal signaling mechanisms", "biophysics/theory and simulation", "neuroscience/theoretical neuroscience", "computational biology/computational neuroscience" ]	Stochastic Ion Channel Gating in Dendritic Neurons: Morphology Dependence and Probabilistic Synaptic Activation of Dendritic Spikes	journal.pcbi.1000886	null	[ [ "The appropriate level of physical detail required to understand how complex processes such as cognition and behavior emerge from more simple biological structures is unclear [1] , [2] .", "For example , while it is possible to account for certain aspects of nervous system function using models that repre...	[ "Neuronal activity is mediated through changes in the probability of stochastic transitions between open and closed states of ion channels .", "While differences in morphology define neuronal cell types and may underlie neurological disorders , very little is known about influences of stochastic ion channel gatin...	[ "The activity of neurons in the brain is mediated through changes in the probability of random transitions between open and closed states of ion channels .", "Since differences in morphology define distinct types of neuron and may underlie neurological disorders , it is important to understand how morphology infl...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "host-pathogen interaction", "biology", "microbiology" ]	Mycobacterium tuberculosis Nucleoside Diphosphate Kinase Inactivates Small GTPases Leading to Evasion of Innate Immunity	journal.ppat.1003499	null	[ [ "The ability of Mycobacterium tuberculosis ( Mtb ) to adapt and thrive intracellularly relies on a variety of strategies to alter mechanisms of the host innate immunity .", "In particular , interference with phagosome biogenesis was highlighted as a significant aspect of Mtb persistence and replication wi...	[ "Defining the mechanisms of Mycobacterium tuberculosis ( Mtb ) persistence in the host macrophage and identifying mycobacterial factors responsible for it are keys to better understand tuberculosis pathogenesis .", "The emerging picture from ongoing studies of macrophage deactivation by Mtb suggests that ingested...	[ "Mycobacterium tuberculosis ( Mtb ) is a very successful intracellular pathogen that infects lung macrophages .", "Its resistance to intracellular killing has been linked to the development of pulmonary tuberculosis ( TB ) in humans .", "Thus , understanding the mechanism by which Mycobacterium tuberculosis ( M...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Cell Interactions and Patterned Intercalations Shape and Link Epithelial Tubes in C. elegans	journal.pgen.1003772	null	[ [ "Epithelial tubes are fundamental components of animal organs , and perform many functions such as the transport of liquids , gases or food ( reviewed in [1] ) .", "Epithelial tubes range in shape from simple cylinders to the branched , convoluted structures of the Drosophila trachea or mammalian kidney (...	[ "Many animal organs are composed largely or entirely of polarized epithelial tubes , and the formation of complex organ systems , such as the digestive or vascular systems , requires that separate tubes link with a common polarity .", "The Caenorhabditis elegans digestive tract consists primarily of three interco...	[ "Tubes composed of epithelial cells are universal building blocks of animal organs , and complex organs typically contain multiple interconnected tubes , such as in the digestive tract or vascular system .", "The nematode Caenorhabditis elegans provides a simple genetic system to study how tubes form and link .",...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "ecology and environmental sciences", "medicine and health sciences", "infectious disease epidemiology", "tropical diseases", "microbiology", "bacterial diseases", "plant science", "yersinia", "global health", "plant pathology", "neglected tropical diseases", "bacterial pathogens", "public a...	A Non-Stationary Relationship between Global Climate Phenomena and Human Plague Incidence in Madagascar	journal.pntd.0003155	null	[ [ "Plague is a vector-borne , highly virulent zoonotic disease present today in the Americas , Asia and Africa .", "It is caused by infection with the bacterium Yersinia pestis , which triggers serious illness with up to seventy percent case fatality in human populations if left untreated .", "The infec...	[ "Plague , a zoonosis caused by Yersinia pestis , is found in Asia and the Americas , but predominantly in Africa , with the island of Madagascar reporting almost one third of human cases worldwide .", "Plague's occurrence is affected by local climate factors which in turn are influenced by large-scale climate phe...	[ "Plague is a vector-borne bacterial infection with rodents and their fleas as its principal hosts .", "Transmission to humans occurs via the bite of an infected flea .", "In the highlands of Madagascar , plague is endemic and more than one hundred human cases are reported every year .", "Global climate is kno...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "methods and resources", "diagnostic radiology", "functional magnetic resonance imaging", "neural networks", "social sciences", "problem solving", "neuroscience", "magnetic resonance imaging", "cognitive psychology", "mathematics", "brain mapping", "intelligen...	Performing group-level functional image analyses based on homologous functional regions mapped in individuals	journal.pbio.2007032	null	[ [ "In functional MRI ( fMRI ) studies , comparing functional characteristics between subjects or groups requires aligning the individual’s data to an “average brain” based on global brain morphology [1] .", "It is becoming increasingly recognized that interindividual variability exists not only in macroscop...	[ "Functional MRI ( fMRI ) studies have traditionally relied on intersubject normalization based on global brain morphology , which cannot establish proper functional correspondence between subjects due to substantial intersubject variability in functional organization .", "Here , we reliably identified a set of di...	[ "No two individuals are alike .", "The size , shape , position , and connectivity patterns of brain functional regions can vary drastically between individuals .", "While interindividual differences in functional organization are well recognized , to date , standard procedures for functional neuroimaging resear...	2019
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "blood cells", "cell death", "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "endothelial cells", "cell processes", "immunology", "tropical diseases", "macroglial cells", "fibroblasts", "toxicology", "epithelial cells", "animal models", "bacterial dis...	Mycolactone cytotoxicity in Schwann cells could explain nerve damage in Buruli ulcer	journal.pntd.0005834	null	[ [ "Buruli ulcer is a disease characterized by the painless nature of its lesion .", "The disease is basically characterized by the ulcer without pain [1] , but some pain is noted at the wound care dressing service [2] .", "These studies suggest that Buruli ulcer lesions are initially painless , but the ...	[ "Buruli ulcer is a chronic painless skin disease caused by Mycobacterium ulcerans .", "The local nerve damage induced by M . ulcerans invasion is similar to the nerve damage evoked by the injection of mycolactone in a Buruli ulcer mouse model .", "In order to elucidate the mechanism of this nerve damage , we te...	[ "Buruli ulcer is a chronic skin disease caused by Mycobacterium ulcerans , and the disease is characterized by the painless nature of its lesion .", "Similar to leprosy , loss of pain often hinders the patients from taking proper medical care , resulting in gross deformities .", "A toxic lipid mycolactone produ...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "vaccines", "medicine", "vaccination", "infectious diseases", "rabies", "clinical immunology", "immunity", "travel-associated diseases", "neglected tropical diseases", "immunology" ]	Using Serology to Assist with Complicated Post-Exposure Prophylaxis for Rabies and Australian Bat Lyssavirus	journal.pntd.0002066	null	[ [ "Without appropriate management , infection with rabies virus or with Australian bat lyssavirus can lead to progressive , fatal neurologic illness .", "Whilst Australia is free of classical rabies , Australian bat lyssavirus ( ABLV ) is endemic in local bat populations [1] .", "Further , Australians a...	[ "Australia uses a protocol combining human rabies immunoglobulin ( HRIG ) and rabies vaccine for post-exposure prophylaxis ( PEP ) of rabies and Australian bat lyssavirus ( ABLV ) , with the aim of achieving an antibody titre of ≥0 . 5 IU/ml , as per World Health Organization ( WHO ) guidelines , as soon as possibl...	[ "In Australia , the administration of rabies post-exposure prophylaxis ( PEP ) occurs for potentially exposed returned travellers from endemic regions or for potential local exposure to Australian Bat Lyssavirus .", "For Australian tourists , delays in commencing PEP or not receiving HRIG or all recommended doses...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	HIF1A Reduces Acute Lung Injury by Optimizing Carbohydrate Metabolism in the Alveolar Epithelium	journal.pbio.1001665	A study of acute lung injury reveals the involvement of transcription factor HIF1A in lung protection, where normoxic HIF1A stabilization functions to control alveolar epithelial glucose metabolism.	[ [ "Acute lung injury ( ALI ) is an inflammatory disease of the lungs that is characterized by hypoxemic respiratory failure with bilateral pulmonary infiltrates , not attributable to left heart failure [1]–[4] .", "Among the hallmarks of ALI are severe arterial hypoxemia and uncontrolled accumulation of inf...	[ "While acute lung injury ( ALI ) contributes significantly to critical illness , it resolves spontaneously in many instances .", "The majority of patients experiencing ALI require mechanical ventilation .", "Therefore , we hypothesized that mechanical ventilation and concomitant stretch-exposure of pulmonary ep...	[ "Acute lung injury is a devastating lung disease caused by injuries or acute infections to the lung .", "In patients it manifests itself as acute respiratory distress syndrome .", "Severe pulmonary edema and uncontrolled lung inflammation are typical symptoms of acute lung injury , which make it hard for patien...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "protein interactions", "brassica", "plant physiology", "plasmid construction", "fungi", "plant science", "model organisms", "experimental organism systems", "plant pathology", "sequence motif analysis", "molecular biology techniques", "dna construction", "plants", "arabidopsis thaliana", ...	Perturbations of the ZED1 pseudokinase activate plant immunity	journal.ppat.1007900	null	[ [ "Both plants and animals use cell membrane-spanning receptor kinases to sense extracellular molecular patterns produced by invading pathogens .", "While agonists of these receptors can trigger signal cascades that result in protective host immune responses ( pattern-triggered immunity , or PTI ) , Gram-ne...	[ "The Pseudomonas syringae acetyltransferase HopZ1a is delivered into host cells by the type III secretion system to promote bacterial growth .", "However , in the model plant host Arabidopsis thaliana , HopZ1a activity results in an effector-triggered immune response ( ETI ) that limits bacterial proliferation ."...	[ "All plants must ward off potentially infectious microbes , and those grown in large-scale crop operations are especially vulnerable to the rapid spread of disease by successful pathogens .", "Although many bacteria and fungi can supress plant immune responses by producing specialized virulence proteins called ‘e...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	ALIX and ESCRT-III Coordinately Control Cytokinetic Abscission during Germline Stem Cell Division In Vivo	journal.pgen.1004904	null	[ [ "Cytokinesis is the final step of cell division that leads to the physical separation of the two daughter cells .", "It is tightly controlled in space and time and proceeds in multiple steps via sequential specification of the cleavage plane , assembly and constriction of the actomyosin-based contractile ...	[ "Abscission is the final step of cytokinesis that involves the cleavage of the intercellular bridge connecting the two daughter cells .", "Recent studies have given novel insight into the spatiotemporal regulation and molecular mechanisms controlling abscission in cultured yeast and human cells .", "The mechani...	[ "Cytokinesis , the final step of cell division , concludes with a process termed abscission , during which the two daughter cells physically separate .", "In spite of their importance , the molecular machineries controlling abscission are poorly characterized especially in the context of living metazoan tissues ....	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "nucleic acids", "gene regulation", "genetics", "gene expression", "dna", "molecular genetics", "biology", "computational biology", "molecular cell biology", "synthetic biology", "biophysics", "dna transcription" ]	Transcription-Factor-Mediated DNA Looping Probed by High-Resolution, Single-Molecule Imaging in Live E. coli Cells	journal.pbio.1001591	A high-resolution, single-molecule study directly assesses the prevalence and dynamics of DNA looping in gene regulation in live E. coli cells.	[ [ "Looping between two DNA sites , mediated by transcription factors , is a ubiquitous mechanism in prokaryotic transcription regulation [1] .", "DNA looping brings two distal DNA sites into close proximity , enhancing interactions between transcription factors bound at separate sites or bringing transcript...	[ "DNA looping mediated by transcription factors plays critical roles in prokaryotic gene regulation .", "The “genetic switch” of bacteriophage λ determines whether a prophage stays incorporated in the E . coli chromosome or enters the lytic cycle of phage propagation and cell lysis .", "Past studies have shown t...	[ "One mechanism cells use to regulate gene expression is DNA looping , whereby two distant DNA sites are brought together by regulatory proteins .", "The looping then either enhances interactions between other regulatory proteins bound at the separate sites or brings those regulatory proteins close to RNA polymera...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "signal transduction", "mycology", "signaling in cellular processes", "model organisms", "molecular cell biology", "cellular stress responses", "cell biology", "microbial pathogens", "yeast and fungal models", "biology", "microbiology", "fungal physiology", "candida albicans" ]	Hsp90 Orchestrates Transcriptional Regulation by Hsf1 and Cell Wall Remodelling by MAPK Signalling during Thermal Adaptation in a Pathogenic Yeast	journal.ppat.1003069	null	[ [ "Microorganisms inhabit dynamic environments and are continually challenged with environmental stimuli and stresses .", "Microbial survival depends upon effective environmental response strategies that have been elaborated over evolutionary time .", "These cellular strategies have been intensively stu...	[ "Thermal adaptation is essential in all organisms .", "In yeasts , the heat shock response is commanded by the heat shock transcription factor Hsf1 .", "Here we have integrated unbiased genetic screens with directed molecular dissection to demonstrate that multiple signalling cascades contribute to thermal adap...	[ "Candida albicans is one of the most persistent yeast pathogens known to man , causing frequent mucosal infections ( thrush ) in otherwise healthy individuals , and potentially fatal bloodstream infections in immunocompromised patients .", "C . albicans colonises warm-blooded animals and occupies thermally buffer...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases/protozoal infections", "infectious diseases/neglected tropical diseases", "immunology/immunity to infections" ]	Profile of Central and Effector Memory T Cells in the Progression of Chronic Human Chagas Disease	journal.pntd.0000512	null	[ [ "Infection with the protozoan Trypanosoma cruzi is a major cause of morbidity and mortality in Central and South America , accounting for 12 . 500 deaths per year [1] , [2] .", "The acute phase of infection is characterized by intense and evident blood parasitemia and may result in death .", "Upon inf...	[ "Chronic Chagas disease presents several different clinical manifestations ranging from asymptomatic to severe cardiac and/or digestive clinical forms .", "Several studies have demonstrated that immunoregulatory mechanisms are important processes for the control of the intense immune activity observed in the chro...	[ "Chagas disease is a parasitic infection caused by protozoan Trypanosoma cruzi that affects approximately 11 million people in Latin America .", "The involvement of the host's immune response on the development of severe forms of Chagas disease has not been fully elucidated .", "Studies on the immune response a...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell motility", "actin filaments", "biophysic al simulations", "biology", "cell mechanics", "computational biology", "biophysics", "biomechanics" ]	Mesoscopic Model of Actin-Based Propulsion	journal.pcbi.1002764	null	[ [ "Cell migration is a fundamental phenomenon underlying wound healing and morphogenesis [1] .", "The first step of migration is protrusion – actin-based extension of the cell's leading edge [2] .", "Lamellipodial motility [3] and intracellular motility of the bacterium Listeria monocytogenes [4] are tw...	[ "Two theoretical models dominate current understanding of actin-based propulsion: microscopic polymerization ratchet model predicts that growing and writhing actin filaments generate forces and movements , while macroscopic elastic propulsion model suggests that deformation and stress of growing actin gel are respo...	[ "There are two major ideas about how actin networks generate force against an obstacle: one is that the force comes directly from the elongation and bending of individual actin filaments against the surface of the obstacle; the other is that a growing actin gel can build up stress around the obstacle to squeeze it ...	2012
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "bacteriology", "medicine and health sciences", "gut bacteria", "animal models of disease", "microbiology", "animal models", "mutation", "model organisms", "gastroenterology and hepatology", "experimental organism systems", "bacteria", "extraction techniques", "digestive system", "research...	Clostridium sordellii outer spore proteins maintain spore structural integrity and promote bacterial clearance from the gastrointestinal tract	journal.ppat.1007004	null	[ [ "Bacillus and Clostridium bacterial species produce spores as a survival mechanism , in response to adverse conditions such as nutrient starvation [1 , 2] .", "Spores are resistant in environmentally unfavourable conditions and allow bacteria to persist in conditions that do not allow the survival of meta...	[ "Bacterial spores play an important role in disease initiation , transmission and persistence .", "In some species , the exosporium forms the outermost structure of the spore and provides the first point of contact between the spore and the environment .", "The exosporium may also be involved in spore adherence...	[ "Clostridium sordellii is a lethal pathogen in humans and animals and its spores are critical for initiating infection .", "Outer spore proteins in Bacillus and Clostridium species are important for spore fitness and pathogenesis , however , equivalent proteins in C . sordellii have not been identified and their ...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "viruses", "infectious diseases", "cell biology", "virology", "immunology", "homo (human)" ]	HIV-1 Buds Predominantly at the Plasma Membrane of Primary Human Macrophages	journal.ppat.0030036	null	[ [ "HIV-1 is an enveloped retrovirus that acquires its envelope by budding through limiting membranes .", "CD4+ T cells and macrophages are the primary targets of HIV-1 and are commonly used to study virus replication in tissue culture .", "Infected macrophages constitute a long-lived reservoir for HIV p...	[ "HIV-1 assembly and release are believed to occur at the plasma membrane in most host cells with the exception of primary macrophages , for which exclusive budding at late endosomes has been reported .", "Here , we applied a novel ultrastructural approach to assess HIV-1 budding in primary macrophages in an immun...	[ "Macrophages are one of the major target cells for HIV-1 infection and play an important role in viral pathogenesis .", "Previous studies indicated that the pathway of HIV-1 particle morphogenesis is distinct in primary human macrophages , and this has been suggested to play a role in viral persistence .", "Ear...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "gene function", "animal models", "signal transduction", "developmental biology", "model organisms", "animal genetics", "organism development", "cell biology", "cell growth", "gene expression", "genetics", "biology and life sciences", "cell processes", "molecular genetics", "molecular ce...	Transcriptional Control of Steroid Biosynthesis Genes in the Drosophila Prothoracic Gland by Ventral Veins Lacking and Knirps	journal.pgen.1004343	null	[ [ "Steroid hormones have a conserved role in the regulation of developmental transitions , growth , metabolism and reproduction in animals [1]-[3] .", "Specialized endocrine tissues with cell-type specific complements of enzymes that form biochemical pathways mediate the biosynthesis of steroids .", "In...	[ "Specialized endocrine cells produce and release steroid hormones that govern development , metabolism and reproduction .", "In order to synthesize steroids , all the genes in the biosynthetic pathway must be coordinately turned on in steroidogenic cells .", "In Drosophila , the steroid producing endocrine cell...	[ "Steroid hormones play important roles in physiology and disease .", "These hormones are molecules produced and secreted by endocrine cells in the body and control sexual maturation , metabolism and reproduction .", "We found transcriptional regulators that underlie the specialized function of endocrine steroid...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "computational biology/signaling networks", "biochemistry/cell signaling and trafficking structures", "biochemistry/theory and simulation", "cell biology/cell signaling" ]	A Hidden Feedback in Signaling Cascades Is Revealed	journal.pcbi.1000041	null	[ [ "Covalent modification cycles are one of the major intracellular signaling mechanisms , both in prokaryotic and eukaryotic organisms [1] .", "Complex signaling occurs through networks of signaling pathways made up of chains or cascades of such cycles , in which the activated protein in one cycle promotes ...	[ "Cycles involving covalent modification of proteins are key components of the intracellular signaling machinery .", "Each cycle is comprised of two interconvertable forms of a particular protein .", "A classic signaling pathway is structured by a chain or cascade of basic cycle units in such a way that the acti...	[ "Cellular signaling is carried out by a complex network of interactions .", "A structure that is found commonly in signaling pathways is a sequence of on-off cycles between two states of the same protein , referred to as a cascade .", "By analyzing and reducing the basic kinetic equations of this system , we ha...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "genetics", "biology", "genomics", "evolutionary biology", "genetics and genomics" ]	Structural and Functional Differences in the Long Non-Coding RNA Hotair in Mouse and Human	journal.pgen.1002071	null	[ [ "Genomes contain a large number of RNAs , which do not encode any protein [1]–[5] .", "While some of", "these non-coding RNAs such as XIST , TSIX and AIR associate with epigenetic modifying", "complexes [6]–[11] , the functions of others remain poorly understood .", "Many", "of the predict...	[ "Long non-coding RNAs regulate various biological processes such as dosage", "compensation , imprinting , and chromatin organization .", "HOTAIR , a paradigm of this", "new class of RNAs , is localized within the human HOXC gene", "cluster and was shown , in human cells , to regulate HOXD genes", "in tran...	[ "Long non-coding RNAs ( lincRNA ) have recently become a new paradigm for gene", "regulation via chromatin remodeling in a variety of biological", "processes , including during embryonic development .", "HOTAIR , a human lincRNA", "localized within the HOXC cluster was shown to help silence", "HOXD cluste...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology/morphogenesis and cell biology", "molecular biology/translational regulation", "molecular biology/rna-protein interactions", "biochemistry/macromolecular assemblies and machines" ]	A Cytoplasmic Complex Mediates Specific mRNA Recognition and Localization in Yeast	journal.pbio.1000611	The localization of ash mRNA in yeast requires the binding of She2p and the myosin adaptor protein She3p to its localization element, which is highly specific and leads to the assembly of stable transport complexes.	[ [ "In eukaryotes , directional transport and localization of mRNA is widely used to regulate gene expression on a temporal and spatial level .", "mRNA localization is involved in diverse processes such as inducing cellular asymmetry , guiding key events during embryonic development , and supporting synaptic...	[ "In eukaryotes , hundreds of mRNAs are localized by specialized transport complexes .", "For localization , transcripts are recognized by RNA-binding proteins and incorporated into motor-containing messenger ribonucleoprotein particles ( mRNPs ) .", "To date , the molecular assembly of such mRNPs is not well un...	[ "In eukaryotes , the majority of cells are asymmetric and a way to establish such polarity is directional transport of macromolecules along cytoskeletal filaments .", "Among the cargoes transported , mRNAs play an essential role , as their localized translation contributes significantly to the generation of asymm...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "genome-wide association studies", "dna-binding proteins", "social sciences", "simulation and modeling", "probability distribution", "mathematics", "genome analysis", "epigenetics", "molecular genetics", "chromatin", "research and analysis methods", "economic models", "chromosome biology", ...	Methods for fine-mapping with chromatin and expression data	journal.pgen.1007240	null	[ [ "Discerning the genetic and molecular basis of complex traits is a fundamental problem in biology .", "Genome-wide association studies have revealed that the majority of variants associated with disease lie in noncoding regulatory sequences [1 , 2] .", "Identifying the target genes of these variants a...	[ "Recent studies have identified thousands of regions in the genome associated with chromatin modifications , which may in turn be affecting gene expression .", "Existing works have used heuristic methods to investigate the relationships between genome , epigenome , and gene expression , but , to our knowledge , n...	[ "Genome-wide association studies ( GWAS ) have revealed that the majority of variants associated with complex disease lie in noncoding regulatory sequences .", "More recent studies have identified thousands of quantitative trait loci ( QTLs ) associated with chromatin modifications , which in turn are associated ...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "inflammatory diseases", "innate immune system", "medicine and health sciences", "immune physiology", "cytokines", "pathology and laboratory medicine", "pig models", "gene regulation", "immunology", "vertebrates", "animals", "mammals", "animal models", "developmental biology", "signs and...	TNF-α blockade suppresses pericystic inflammation following anthelmintic treatment in porcine neurocysticercosis	journal.pntd.0006059	null	[ [ "Neurocysticercosis ( NCC ) , an infection of the central nervous system ( CNS ) by the larval stage ( cysticercus ) of the parasitic cestode Taenia solium , is a major cause of epilepsy in developing countries and a serious public health burden [1–4] .", "The disease is endemic to regions across the worl...	[ "Neurocysticercosis ( NCC ) is an infection of the brain with the larval cyst of the tapeworm , Taenia solium .", "Cysticidal treatment induces parasite killing resulting in a post inflammatory response and seizures , which generally requires corticosteroid treatment to control inflammation .", "The nature of t...	[ "Infection of the brain with larvae of the tapeworm Taenia solium is called neurocysticercosis ( NCC ) , a disease with varied and serious neurological symptoms .", "Therapy requires antiparasitic drugs and corticosteroids to prevent seizures caused by treatment due to inflammation around dying parasites .", "T...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The Neuroglial Potassium Cycle during Neurotransmission: Role of Kir4.1 Channels	journal.pcbi.1004137	null	[ [ "Astrocytic processes enwrap more than half of CA1 hippocampal synapses to form tripartite synapses [1 , 2] .", "Perisynaptic astroglial processes are enriched in ionic channels , neurotransmitter receptors and transporters , enabling astrocytes to detect neuronal activity via calcium signaling [3] and io...	[ "Neuronal excitability relies on inward sodium and outward potassium fluxes during action potentials .", "To prevent neuronal hyperexcitability , potassium ions have to be taken up quickly .", "However , the dynamics of the activity-dependent potassium fluxes and the molecular pathways underlying extracellular ...	[ "Neural excitability relies on precise inward and outward ionic fluxes .", "In particular , potassium ions , released by neurons during activity , have to be taken up efficiently to prevent hyperexcitability .", "Astrocytes , the third element of the synapse , play a prominent role in extracellular potassium ho...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "plant anatomy", "medicine and health sciences", "cell cycle and cell division", "cell processes", "brassica", "animals", "animal models", "developmental biology", "drosophila melanogaster", "model organisms", "plant science", "experimental organism systems", "embryos", ...	TCTP and CSN4 control cell cycle progression and development by regulating CULLIN1 neddylation in plants and animals	journal.pgen.1007899	null	[ [ "The correct implementation of organs with unique shape , size and function is fundamental to the development of all multicellular organisms and is the result of coordinated cellular processes requiring key molecular actors .", "One such key player in eukaryotes is the Translationally Controlled Tumor Pro...	[ "Translationally Controlled Tumor Protein ( TCTP ) controls growth by regulating the G1/S transition during cell cycle progression .", "Our genetic interaction studies show that TCTP fulfills this role by interacting with CSN4 , a subunit of the COP9 Signalosome complex , known to influence CULLIN-RING ubiquitin ...	[ "During organism development , the correct implementation of organs with unique shape , size and function , is the result of coordinated cellular processes , such as cell proliferation and expansion .", "Deregulation of these processes affect human health and can lead to severe diseases .", "While plants and an...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics", "developmental biology/aging" ]	Deletion of the Mitochondrial Superoxide Dismutase sod-2 Extends Lifespan in Caenorhabditis elegans	journal.pgen.1000361	null	[ [ "The oxidative stress theory of aging proposes that reactive oxygen species ( ROS ) generated by normal metabolism cause damage to macromolecules within the cell and that the accumulation of this damage over time leads to cellular dysfunction and eventually organismal death [1]–[3] .", "The majority of RO...	[ "The oxidative stress theory of aging postulates that aging results from the accumulation of molecular damage caused by reactive oxygen species ( ROS ) generated during normal metabolism .", "Superoxide dismutases ( SODs ) counteract this process by detoxifying superoxide .", "It has previously been shown that ...	[ "In this paper , we examine the oxidative stress theory of aging using C . elegans as a model system .", "This theory proposes that aging results from the accumulation of molecular damage caused by reactive oxygen species ( ROS ) .", "To test this theory , we examined the effect of deleting each of the five ind...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/animal genetics", "cell biology/cellular death and stress responses", "biotechnology/plant biotechnology", "biochemistry/biomacromolecule-ligand interactions" ]	An ABC Transporter Mutation Is Correlated with Insect Resistance to Bacillus thuringiensis Cry1Ac Toxin	journal.pgen.1001248	null	[ [ "Insecticidal protein toxins of the Cry1A family produced by certain strains of the gram-positive bacterium Bacillus thuringiensis ( Bt ) are highly active against many Lepidoptera but nontoxic to most other animal species .", "Transgenic cotton producing Cry1Ac and transgenic maize producing Cry1Ab have ...	[ "Transgenic crops producing insecticidal toxins from Bacillus thuringiensis ( Bt ) are commercially successful in reducing pest damage , yet knowledge of resistance mechanisms that threaten their sustainability is incomplete .", "Insect resistance to the pore-forming Cry1Ac toxin is correlated with the loss of hi...	[ "Crystal toxin proteins from Bacillus thuringiensis ( Bt ) make ideal bioinsecticides because of their high potency against certain insects and lack of activity against most other species .", "Transgenic cotton and maize expressing pore-forming Cry1A Bt-toxins are now widely used in agriculture , enabling substan...	2010
[ "Introduction", "Models", "Results", "Discussion" ]	[ "invertebrates", "markov models", "particle physics", "applied mathematics", "social sciences", "light", "neuroscience", "animals", "electromagnetic radiation", "simulation and modeling", "algorithms", "photons", "mathematics", "vision", "cellular structures and organelles", "research ...	Point process analysis of noise in early invertebrate vision	journal.pcbi.1005687	null	[ [ "The phototransduction cascade consists of a series of chemical reactions which convert light inputs into usable current signals at the retina .", "As it serves as the front end to the visual system , it should be capable of extracting information from environmental inputs with high accuracy [1] .", "...	[ "Noise is a prevalent and sometimes even dominant aspect of many biological processes .", "While many natural systems have adapted to attenuate or even usefully integrate noise , the variability it introduces often still delimits the achievable precision across biological functions .", "This is particularly so ...	[ "The invertebrate phototransduction system captures and converts environmental light inputs into electrical signals for use in later visual processing .", "Consequently , one would expect it to be optimised in some way to ensure that only a minimal amount of environmental information is lost during conversion .",...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The Entamoeba histolytica, Arp2/3 Complex Is Recruited to Phagocytic Cups through an Atypical Kinase EhAK1	journal.ppat.1005310	null	[ [ "Phagocytosis plays a critical role in invasion and pathogenesis of the parasite Entamoeba histolytica , the causative agent of amoebiasis , and a major cause of morbidity and mortality in developing countries .", "Phagocytosis is an essential process in E . histolytica as blocking this process leads to a...	[ "The parasite Entamoeba histolytica is the etiological agent of amoebiasis and phagocytosis plays a key role in virulence of this organism .", "Signaling pathways involved in activation of cytoskeletal dynamics required for phagocytosis remain to be elucidated .", "Phagocytosis is initiated with sequential recr...	[ "E . histolytica is the causative agent of amoebiasis and leads to morbidity and mortality in developing countries .", "It is known to phagocytose immune and non-immune cells , epithelial tissue , erythrocytes and commensal bacteria .", "The high rate of phagocytosis in this protist parasite provides a unique s...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "milk", "body fluids", "toxins", "pathology and laboratory medicine", "crystal structure", "immune physiology", "immunology", "tropical diseases", "condensed matter physics", "blood groups", "toxic agents", "toxicology", "bacterial diseases", "neglected tr...	High-Resolution Crystal Structures Elucidate the Molecular Basis of Cholera Blood Group Dependence	journal.ppat.1005567	null	[ [ "Cholera is a severe diarrheal disease caused by the pathogen Vibrio cholerae [1] .", "It originated in the Ganges delta , but is now widespread across the world .", "Caused by contaminated drinking water , severe cholera outbreaks often occur in war zones or in the aftermath of natural disasters .", ...	[ "Cholera is the prime example of blood-group-dependent diseases , with individuals of blood group O experiencing the most severe symptoms .", "The cholera toxin is the main suspect to cause this relationship .", "We report the high-resolution crystal structures ( 1 . 1–1 . 6 Å ) of the native cholera toxin B-pe...	[ "Cholera is a severe diarrheal disease that kills a hundred thousand people per year .", "With climate change , the number of cases is predicted to increase to millions .", "Individuals with blood group O are particularly at risk .", "Here we report high-resolution crystal structures of the native cholera tox...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The Pif1 Helicase, a Negative Regulator of Telomerase, Acts Preferentially at Long Telomeres	journal.pgen.1005186	null	[ [ "Telomerase is a specialized reverse transcriptase that extends the G-strand of telomeric DNA using its RNA subunit as a template .", "In Saccharomyces cerevisiae , telomerase consists minimally of Est2 , the catalytic reverse transcriptase , TLC1 , the templating telomerase RNA , and Est1 and Est3 , two ...	[ "Telomerase , the enzyme that maintains telomeres , preferentially lengthens short telomeres .", "The S . cerevisiae Pif1 DNA helicase inhibits both telomerase-mediated telomere lengthening and de novo telomere addition at double strand breaks ( DSB ) .", "Here , we report that the association of the telomerase...	[ "Telomerase , the enzyme that maintains telomeres , preferentially lengthens short telomeres .", "The baker’s yeast Pif1 DNA helicase inhibits both telomerase-mediated lengthening of existing telomeres and the formation of new telomeres at double strand breaks .", "By virtue of its ATPase activity , Pif1 reduce...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "velocity", "collective animal behavior", "fish", "swimming", "medicine and health sciences", "classical mechanics", "reaction time", "vertebrates", "mathematical models", "neuroscience", "biological locomotion", "animals", "cognitive neuroscience", "animal behavior", "zoology", "resea...	Identifying influential neighbors in animal flocking	journal.pcbi.1005822	null	[ [ "Collective motion phenomena such as swarming , flocking and schooling behavior have been observed in a large variety of animal species ranging from bacteria to humans [1] .", "Several theoretical models have been proposed to explain how such large scale coordination patterns emerge from “microscopic leve...	[ "Schools of fish and flocks of birds can move together in synchrony and decide on new directions of movement in a seamless way .", "This is possible because group members constantly share directional information with their neighbors .", "Although detecting the directionality of other group members is known to b...	[ "Schooling fish exhibit impressive group-level coordination in which multiple individuals move together in a seamless way .", "This is possible because each individual in the group responds to the movement of other group members .", "But how many individuals does each fish pay attention to ?", "Which are the ...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "clinical immunology", "genetics", "immunology", "biology", "microbiology", "clinical genetics" ]	TLR9 Activation Dampens the Early Inflammatory Response to Paracoccidioides brasiliensis, Impacting Host Survival	journal.pntd.0002317	null	[ [ "Paracoccidioides brasiliensis is a causative agent of paracoccidioidomycosis ( PCM ) , one of the most prevalent systemic mycosis in Latin America [1] .", "One of P . brasiliensis biological hallmarks is its particular temperature-dependent morphological dimorphism .", "This fungus switches from the ...	[ "Paracoccidioides brasiliensis causes paracoccidioidomycosis , one of the most prevalent systemic mycosis in Latin America .", "Thus , understanding the characteristics of the protective immune response to P . brasiliensis is of interest , as it may reveal targets for disease control .", "The initiation of the ...	[ "Paracoccidioides brasiliensis is an etiological agent of paracoccidioidomycosis , one of the most prevalent systemic mycosis in South America , affecting over 10 million people .", "One of the hallmark features of this fungus is its multinucleated nature , where a single P . brasiliensis cell can have from one t...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "ecology and environmental sciences", "helminths", "grasslands", "tropical diseases", "hookworms", "geographical locations", "plant communities", "parasitic diseases", "animals", "necator americanus", "plant science", "ascaris", "ascaris l...	An environmental assessment and risk map of Ascaris lumbricoides and Necator americanus distributions in Manufahi District, Timor-Leste	journal.pntd.0005565	null	[ [ "Soil-transmitted helminth ( STH ) infections are predominantly a disease of poverty , typically prevalent in poor tropical and subtropical regions .", "[1] In 2010 , the four main species of human STH were estimated to infect 1 . 5 billion people worldwide; with whipworm ( Trichuris trichiura ) , roundwo...	[ "In Timor-Leste there have been intermittent and ineffective soil-transmitted helminth ( STH ) deworming programs since 2004 .", "In a resource-constrained setting , having information on the geographic distribution of STH can aid in prioritising high risk communities for intervention .", "This study aimed to q...	[ "The majority of soil-transmitted helminth ( STH ) infections have long-term ramifications on an individual’s health and productivity , contributing to malnutrition , anaemia , and impaired childhood growth .", "In Timor-Leste there have been intermittent and ineffective STH control programs since 2004 .", "Whe...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Dynamical Localization of DivL and PleC in the Asymmetric Division Cycle of Caulobacter crescentus: A Theoretical Investigation of Alternative Models	journal.pcbi.1004348	null	[ [ "The asymmetric localization of proteins is critical for cell and/or tissue development in eukaryotic systems as diverse as S . cerevisiae [1] , C . elegans [2] , A . thaliana [3] , and D . melanogaster [4] .", "For years , spatial organization of cellular components was thought to be an exclusive feature...	[ "Cell-fate asymmetry in the predivisional cell of Caulobacter crescentus requires that the regulatory protein DivL localizes to the new pole of the cell where it up-regulates CckA kinase , resulting in a gradient of CtrA~P across the cell .", "In the preceding stage of the cell cycle ( the “stalked” cell ) , DivL...	[ "The aquatic bacterium , Caulobacter crescentus , divides asymmetrically into a non-motile “stalked” cell that stays at its place of birth , and a motile “swarmer” cell that disperses to a different locale .", "Prior to cell division , the cell passes through a “predivisional” stage , when it has a stalk at its “...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "dermatology", "public health and epidemiology", "mental health", "science policy", "evidence-based healthcare", "neurological disorders", "anesthesiology and pain management", "infectious diseases/bacterial infections", "neuroscience" ]	Neuropathic Pain and Psychological Morbidity in Patients with Treated Leprosy: A Cross-Sectional Prevalence Study in Mumbai	journal.pntd.0000981	null	[ [ "Leprosy is a chronic granulomatous disease caused by Mycobacterium leprae that principally affects skin and peripheral nerves . [1]", "Leprosy is still present throughout the tropics and sub-tropics .", "Worldwide 249 , 007 new cases were registered in 2008 with India registering 134 , 184 . [2] Lepr...	[ "Neuropathic pain has been little studied in leprosy .", "We assessed the prevalence and clinical characteristics of neuropathic pain and the validity of the Douleur Neuropathique 4 questionnaire as a screening tool for neuropathic pain in patients with treated leprosy .", "The association of neuropathic pain w...	[ "Neuropathic pain has only recently been recognised as a complication of leprosy .", "We assessed 101 treated leprosy patients in Mumbai and found that 22 of them had neuropathic pain .", "The pain occurred as numbness 86% , tingling 68% , and decreased sensation to light touch 81% .", "This pain was signific...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell death", "autophagic cell death", "medicine and health sciences", "antiviral immune response", "viral transmission and infection", "cell processes", "immunology", "microbiology", "vertebrates", "animals", "animal models", "osteichthyes", "developmental biology", "model organisms", "...	TNFα Impairs Rhabdoviral Clearance by Inhibiting the Host Autophagic Antiviral Response	journal.ppat.1005699	null	[ [ "Tumor necrosis factor alpha ( TNFα ) is one of the main pro-inflammatory cytokines produced in response to a broad type of bacterial , viral and fungal infections [1] .", "TNFα has a crucial role in activating and orchestrating the immune response in order to protect the host organism from pathogens .", ...	[ "TNFα is a pleiotropic pro-inflammatory cytokine with a key role in the activation of the immune system to fight viral infections .", "Despite its antiviral role , a few viruses might utilize the host produced TNFα to their benefit .", "Some recent reports have shown that anti-TNFα therapies could be utilized t...	[ "Tumor necrosis factor alpha ( TNFα ) is one of the main pro-inflammatory cytokines produced in response to a broad type of infections [1] .", "Although TNFα has a crucial role in protecting the host organism from pathogens , its deregulation can promote susceptibility to pathogens by impairing pathogen clearance...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "integrative physiology", "anatomy and physiology", "cardiovascular", "mathematics", "circulatory physiology", "stroke", "medical physics", "biology", "nonlinear dynamics", "cardiovascular system", "physics", "cerebrovascular diseases", "ischemic stroke", "neurological disord...	A Nonlinear Dynamic Approach Reveals a Long-Term Stroke Effect on Cerebral Blood Flow Regulation at Multiple Time Scales	journal.pcbi.1002601	null	[ [ "Cerebral blood flow ( CBF ) is regulated to provide adequate blood supply to brain .", "One of the important CBF control mechanisms is cerebral autoregulation ( CA ) [1] .", "Involving dilation and constriction of cerebral arterioles through myogenic and neurogenic regulation , CA allows to maintain ...	[ "Cerebral autoregulation ( CA ) is an important vascular control mechanism responsible for relatively stable cerebral blood flow despite changes of systemic blood pressure ( BP ) .", "Impaired CA may leave brain tissue unprotected against potentially harmful effects of BP fluctuations .", "It is generally accep...	[ "Cerebral autoregulation is an important mechanism that regulates blood supply to brain tissue to match metabolic demands during daily activities .", "Impaired cerebral autoregulation increases the dependence of cerebral blood flow on systemic blood pressure , and is associated with fatal outcomes in patients aft...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Calorie Restriction-Mediated Replicative Lifespan Extension in Yeast Is Non-Cell Autonomous	journal.pbio.1002048	Calorie-restriction extends lifespan in many multicellular organisms; here substances secreted by calorie-restricted yeast are found to induce longer life in other yeast cells, suggesting that cellular communication is a component of this phenomenon even in a single-celled organism.	[ [ "Calorie restriction ( CR ) extends lifespan and healthspan in several model organisms [1 , 2] .", "Although inconsistent results have been obtained on lifespan extension in primates , the beneficial effects on healthspan are widely observed [3 , 4] .", "Thus , dissecting the underlying mechanism of h...	[ "In laboratory yeast strains with Sir2 and Fob1 function , wild-type NAD+ salvage is required for calorie restriction ( CR ) to extend replicative lifespan .", "CR does not significantly alter steady state levels of intracellular NAD+ metabolites .", "However , levels of Sir2 and Pnc1 , two enzymes that sequent...	[ "Though calorie restriction extends lifespan and healthspan in multiple model organisms , the intrinsic mechanisms remain unclear .", "In budding yeast Saccharomyces cerevisiae , manipulation of nicotinamide adenine dinucleotide ( NAD+ ) —a central metabolic cofactor—can restrict or extend replicative lifespan , ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "bacteriology", "organismal evolution", "microbiology", "cloning", "plant science", "genome analysis", "microbial evolution", "crops", "plant pathology", "molecular biology techniques", "plants", "research and analysis methods", "legumes", "genomics", "crop science", "beans", "plant ...	Enhanced in planta Fitness through Adaptive Mutations in EfpR, a Dual Regulator of Virulence and Metabolic Functions in the Plant Pathogen Ralstonia solanacearum	journal.ppat.1006044	null	[ [ "Bacterial plant pathogens constitute a major threat to crop production .", "In addition , disease emergence can occur through rapid adaptation of many pathogens to new hosts [1 , 2] .", "Understanding how pathogens are adapting to new hosts is crucial for unraveling the mechanisms that drive disease ...	[ "Experimental evolution of the plant pathogen Ralstonia solanacearum , where bacteria were maintained on plant lineages for more than 300 generations , revealed that several independent single mutations in the efpR gene from populations propagated on beans were associated with fitness gain on bean .", "In the pre...	[ "Among plant pathogens of major economic and food crops , Ralstonia solanacearum , the causal agent of bacterial wilt , is recognized as one of the most destructive plant bacterial diseases .", "In addition , the emergence of new pathotypes , more aggressive and adapted to new hosts , has been reported .", "Dur...	2016
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "infectious diseases", "none (leishmania)", "microbiology", "mus (mouse)", "insects" ]	Leishmania Manipulation of Sand Fly Feeding Behavior Results in Enhanced Transmission	journal.ppat.0030091	null	[ [ "Parasites exhibit myriad adaptations to ensure their survival and transmission from host to host .", "These include manipulation , where infection elicits a specific behavioral response from the host of selective benefit to the parasite [1–3] .", "For vector-borne diseases like leishmaniasis there ar...	[ "In nature the prevalence of Leishmania infection in whole sand fly populations can be very low ( <0 . 1% ) , even in areas of endemicity and high transmission .", "It has long since been assumed that the protozoan parasite Leishmania can manipulate the feeding behavior of its sand fly vector , thus enhancing tra...	[ "Leishmaniasis is a human parasitic disease that can result in destructive skin lesions or sometimes in fatal visceral involvement if left untreated .", "Infections are acquired via the bites of female sand flies , small blood-feeding insects .", "In this experimental study using mice , we show that Leishmania ...	2007

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