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train · 24.8k rows

headings list	keywords list	title stringlengths 20 281	id stringlengths 20 20	toc stringlengths 57 522 ⌀	sections list	abstract list	summary list	year stringclasses 13 values
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "children", "cognitive neurology", "medicine and health sciences", "education", "sociology", "tropical diseases", "social sciences", "physical activity", "parasitic diseases", "neuroscience", "pediatrics", "age groups", "cognitive neuroscience", "cognitive psychology", "neglected tropica...	Associations between selective attention and soil-transmitted helminth infections, socioeconomic status, and physical fitness in disadvantaged children in Port Elizabeth, South Africa: An observational study	journal.pntd.0005573	null	[ [ "Attention skills are relevant for academic foundations and are important for learning [1] .", "Selective attention is the ability to select and focus on a particular task , while simultaneously suppressing irrelevant or distracting information .", "Competing information can occur both externally and ...	[ "Socioeconomically deprived children are at increased risk of ill-health associated with sedentary behavior , malnutrition , and helminth infection .", "The resulting reduced physical fitness , growth retardation , and impaired cognitive abilities may impede children’s capacity to pay attention .", "The present...	[ "Children growing up in challenging environments , such as townships in South Africa , are at an increased risk of ill-health associated with sedentary behavior , poor nutrition , growth retardation , and infections with parasitic worms .", "Negative factors such as limited educational resources , insufficient he...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology/germ cells", "genetics and genomics/animal genetics", "molecular biology/rna-protein interactions", "cell biology/developmental molecular mechanisms", "genetics and genomics/epigenetics", "developmental biology/developmental molecular mechanisms" ]	GASZ Is Essential for Male Meiosis and Suppression of Retrotransposon Expression in the Male Germline	journal.pgen.1000635	null	[ [ "The differentiation program of the germline is distinct from somatic cells in that resetting of the epigenome by demethylation of DNA and histones must take place for proper post-fertilization development of the embryo [1] .", "DNA demethylation occurs during primordial germ cell ( PGC ) migration as par...	[ "Nuage are amorphous ultrastructural granules in the cytoplasm of male germ cells as divergent as Drosophila , Xenopus , and Homo sapiens .", "Most nuage are cytoplasmic ribonucleoprotein structures implicated in diverse RNA metabolism including the regulation of PIWI-interacting RNA ( piRNA ) synthesis by the PI...	[ "Many aspects of RNA processing are essential for or prominent in the differentiation of germ cells .", "Some RNA metabolism in animal germ cells is associated with physical structures surrounding the cell nucleus called nuage .", "Nuage has a distinct granular appearance prior to the meiotic divisions with unc...	2009
[ "Introduction", "Models", "Results", "Discussion" ]	[ "recreation", "infographics", "interpersonal relationships", "applied mathematics", "social sciences", "mathematics", "behavioral geography", "public goods game", "human geography", "computer and information sciences", "geography", "games", "behavior", "evolutionary genetics", "game theo...	Evolutionary multiplayer games on graphs with edge diversity	journal.pcbi.1006947	null	[ [ "Understanding the emergence and persistence of cooperation in the population of egoists is an enduring challenge that has inspired a myriad of studies from biology to sociology [1] .", "Evolutionary game theory has been widely employed to investigate this cooperation conundrum at different levels of livi...	[ "Evolutionary game dynamics in structured populations has been extensively explored in past decades .", "However , most previous studies assume that payoffs of individuals are fully determined by the strategic behaviors of interacting parties , and social ties between them only serve as the indicator of the exist...	[ "The outcome of an interaction often relies on not only interactants’ strategic behaviors but also genetic and physical relationships between interactants , such as genetic similarity and geographic proximity .", "Thus when encountering different opponents who use the same strategy , an individual may derive diff...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "chemical bonding", "medicine and health sciences", "aspergillus fumigatus", "immune cells", "body fluids", "pathology and laboratory medicine", "engineering and technology", "aspergillus", "pathogens", "immunology", "microbiology", "fungi", "platelets", "fungal diseases",...	Neutrophil Interactions Stimulate Evasive Hyphal Branching by Aspergillus fumigatus	journal.ppat.1006154	null	[ [ "Aspergillus fumigatus is a filamentous , conidiating fungus ubiquitous to the environment .", "Airborne conidia are inhaled in the hundreds by individuals every day [1] and are quickly cleared by macrophages [2–4] .", "If not cleared , conidia grow into elongated hyphal structures , which present a u...	[ "Invasive aspergillosis ( IA ) , primarily caused by Aspergillus fumigatus , is an opportunistic fungal infection predominantly affecting immunocompromised and neutropenic patients that is difficult to treat and results in high mortality .", "Investigations of neutrophil-hypha interaction in vitro and in animal m...	[ "For patients who have compromised immune systems , infection with yeasts and moulds are often deadly .", "To learn more about how immune cells fight fungal infection , we developed an “infection-on-a-chip” device , which allowed us to directly image interactions in real time .", "To our surprise , when immune ...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "gene expression", "genetics", "biology", "genetics and genomics", "dna transcription" ]	Indirect DNA Readout by an H-NS Related Protein: Structure of the DNA Complex of the C-Terminal Domain of Ler	journal.ppat.1002380	null	[ [ "Enteropathogenic Escherichia coli ( EPEC ) and enterohaemorrhagic E . coli ( EHEC ) are causal agents of infectious diarrhea .", "While the former is responsible mainly for infantile diarrhea , EHEC infections are associated with hemorrhagic colitis and may produce a life-threatening complication known a...	[ "Ler , a member of the H-NS protein family , is the master regulator of the LEE pathogenicity island in virulent Escherichia coli strains .", "Here , we determined the structure of a complex between the DNA-binding domain of Ler ( CT-Ler ) and a 15-mer DNA duplex .", "CT-Ler recognizes a preexisting structural ...	[ "Pathogenic Escherichia coli strains and other enterobacteria carry genes acquired from other bacteria by a process known as horizontal gene transfer .", "Proper regulation of the genes that are expressed in a given moment is crucial for the success of the bacteria .", "The protein H-NS is a global regulator th...	2011
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "action potentials", "medicine and health sciences", "membrane potential", "electrophysiology", "neuroscience", "optimization", "ion channels", "mathematics", "research and analysis methods", "transfer functions", "mathematical functions", "animal cells", "proteins", "mathematical and stat...	Dimensions of control for subthreshold oscillations and spontaneous firing in dopamine neurons	journal.pcbi.1007375	null	[ [ "Midbrain dopaminergic neuron ( DA ) activity influences many brain functions .", "Timing of spikes and bursts in DAs signal reward prediction error [1] , and DA activity is implicated in schizophrenia and depression [2] .", "Modeling the origins of DA activity is vital for research into the neural ba...	[ "Dopaminergic neurons ( DAs ) of the rodent substantia nigra pars compacta ( SNc ) display varied electrophysiological properties in vitro .", "Despite this , projection patterns and functional inputs from DAs to other structures are conserved , so in vivo delivery of consistent , well-timed dopamine modulation t...	[ "Electrophysiological activity of the neuronal membrane and concomitant ion channel properties are highly variable within groups of neurons of the same type from the same brain region .", "Reconciliation of the mechanisms generating neuronal activity is challenging due to the complexity of the interactions betwee...	2019
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "nucleic acid synthesis", "vesicular stomatitis virus", "pathology and laboratory medicine", "pathogens", "dna-binding proteins", "microbiology", "viruses", "polymerases", "rna viruses", "protein structure", "sequence motif analysis", "rna synthesis", "chemi...	Initiation, extension, and termination of RNA synthesis by a paramyxovirus polymerase	journal.ppat.1006889	null	[ [ "Paramyxoviruses describe a family of viruses responsible for significant disease , ranging from lower respiratory disease due to parainfluenza virus and measles virus as well as emerging pathogens such as Nipah and Hendra viruses causing severe encephalitis .", "The replication machinery of these viruses...	[ "Paramyxoviruses represent a family of RNA viruses causing significant human diseases .", "These include measles virus , the most infectious virus ever reported , in addition to parainfluenza virus , and other emerging viruses .", "Paramyxoviruses likely share common replication machinery but their mechanisms o...	[ "RNA viruses replicate and transcribe their genomes using complex enzymatic machines known as RNA-dependent RNA polymerases .", "The chemical reactions driving nucleotide addition are shared among nucleic acid polymerases but the underlying mechanisms of RNA biosynthesis and the complex polymerase structures are ...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "immune physiology", "enzyme-linked immunoassays", "toxins", "pathology and laboratory medicine", "immunology", "biological cultures", "tropical diseases", "fibroblasts", "toxicology", "toxic agents", "bacterial diseases", "connective tissue cells", "neglect...	Antibody-Mediated Neutralization of the Exotoxin Mycolactone, the Main Virulence Factor Produced by Mycobacterium ulcerans	journal.pntd.0004808	null	[ [ "Mycobacterium ulcerans , the causative agent of the neglected tropical skin disease Buruli ulcer ( BU ) , produces the exotoxin mycolactone , which is responsible for the formation of chronic necrotizing skin lesions [1 , 2] .", "Early diagnosis followed by rapid initiation of the currently recommended t...	[ "Mycolactone , the macrolide exotoxin produced by Mycobacterium ulcerans , causes extensive tissue destruction by inducing apoptosis of host cells .", "In this study , we aimed at the production of antibodies that could neutralize the cytotoxic activities of mycolactone .", "Using the B cell hybridoma technolog...	[ "Mycolactones A/B ( also simply referred to as mycolactone ) are macrolide exotoxins produced by Mycobacterium ulcerans , the causative agent of the neglected tropical skin disease Buruli ulcer ( BU ) .", "The potent cytotoxic and anti-inflammatory activities of mycolactones lead to severe destruction of the subc...	2016
[ "Introduction", "Results and discussion", "Materials and methods" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "biological cultures", "tropical diseases", "parasitic diseases", "parasitic protozoans", "parasitology", "toxicology", "parasitemia", "trypanosoma brucei", "toxicity", "protozoans", "neglected tropical diseases", "quanti...	Anilinoquinoline based inhibitors of trypanosomatid proliferation	journal.pntd.0006834	null	[ [ "Neglected tropical diseases ( NTDs ) are a collection of 20 communicable diseases [1] .", "Though mostly treatable and/or preventable , NTDs remain a leading cause of morbidity and mortality affecting over 1 billion people worldwide .", "Many of the current treatments have significant side effects , ...	[ "We recently reported the medicinal chemistry re-optimization of a series of compounds derived from the human tyrosine kinase inhibitor , lapatinib , for activity against Plasmodium falciparum .", "From this same library of compounds , we now report potent compounds against Trypanosoma brucei brucei ( which cause...	[ "As part of our efforts to identify compounds that are active against the parasite that causes malaria ( P . falciparum ) , we employed a “parasite hopping” approach in our drug discovery efforts .", "This involved screening a library of demonstrated antiparasitic agents against other parasites responsible for a ...	2018
[ "Introduction", "Results", "Discussion" ]	[ "acoustics", "medicine and health sciences", "sine waves", "engineering and technology", "signal processing", "vertebrates", "electrophysiology", "neuroscience", "animals", "mammals", "signal filtering", "bandwidth (signal processing)", "research and analysis methods", "mathematical functi...	Non-linear auto-regressive models for cross-frequency coupling in neural time series	journal.pcbi.1005893	null	[ [ "We note y the signal containing the high-frequency activity , and x the signal with slow frequency oscillations , also called the exogenous driver .", "When a signal x results from a band-pass filtering step , we note the central frequency of the filter fx and the bandwidth Δfx .", "The value of the ...	[ "We address the issue of reliably detecting and quantifying cross-frequency coupling ( CFC ) in neural time series .", "Based on non-linear auto-regressive models , the proposed method provides a generative and parametric model of the time-varying spectral content of the signals .", "As this method models the e...	[ "Neural oscillations synchronize information across brain areas at various anatomical and temporal scales .", "Of particular relevance , slow fluctuations of brain activity have been shown to affect high frequency neural activity , by regulating the excitability level of neural populations .", "Such cross-frequ...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma mansoni", "medicine and health sciences", "ecology and environmental sciences", "education", "helminths", "sociology", "tropical diseases", "geographical locations", "social sciences", "parasitic diseases", "animals", "tanzania", "aquatic envi...	Estimating the prevalence and intensity of Schistosoma mansoni infection among rural communities in Western Tanzania: The influence of sampling strategy and statistical approach	journal.pntd.0005937	null	[ [ "Schistosomiasis , which is caused by trematode parasites in the genus Schistosoma , is a typically chronic disease that can result in debilitation and severe pathology in infected patients [1] .", "Infection with the parasite can also be asymptomatic and can remain undetected for a long period of time [2...	[ "Schistosoma mansoni is a parasite of major public health importance in developing countries , where it causes a neglected tropical disease known as intestinal schistosomiasis .", "However , the distribution of the parasite within many endemic regions is currently unknown , which hinders effective control .", "...	[ "Schistosomiasis constitutes a major public health problem in Tanzania , with up to 80% prevalence of infection in some areas .", "Infection with the disease causes abdominal pain , diarrhoea , stunted growth and impaired cognitive abilities in children .", "Accurate information on the distribution of schistoso...	2017
[ "Introduction", "Model", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "respiratory infections", "influenza", "pathogens", "immunology", "microbiology", "orthomyxoviruses", "pulmonology", "viruses", "preventive medicine", "seasons", "probability distribution", "mathematics", "rna viruses",...	Characterising seasonal influenza epidemiology using primary care surveillance data	journal.pcbi.1006377	null	[ [ "Influenza is a highly contagious , rapidly evolving respiratory virus that circulates globally on a seasonal basis [1 , 2] .", "It can cause death in at-risk groups , and places a high burden on health systems ( e . g . , emergency room ( ER ) and general practitioner ( GP ) services ) .", "In some c...	[ "Understanding the epidemiology of seasonal influenza is critical for healthcare resource allocation and early detection of anomalous seasons .", "It can be challenging to obtain high-quality data of influenza cases specifically , as clinical presentations with influenza-like symptoms may instead be cases of one ...	[ "When patients present to their doctor with influenza-like symptoms , they may have influenza , or some other respiratory virus .", "The only way to discriminate between these viruses is with an expensive test , which is not performed in many cases .", "Additionally , results other than influenza may not be rep...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology and life sciences" ]	mir-233 Modulates the Unfolded Protein Response in C. elegans during Pseudomonas aeruginosa Infection	journal.ppat.1004606	null	[ [ "The innate immune system , the first line of defense against microbial infection , is evolutionarily conserved in both vertebrate and invertebrate animals .", "Activation of the innate immune system upon pathogen infection results in a definitive anti-microbial response to invading microbes .", "The ...	[ "The unfolded protein response ( UPR ) , which is activated by perturbations of the endoplasmic reticulum homeostasis , has been shown to play an important role in innate immunity and inflammation .", "However , little is known about the molecular mechanisms underlying activation of the UPR during immune response...	[ "In the model organism Caenorhabditis elegans , the IRE1–XBP1 pathway , a major branch of the unfolded protein response ( UPR ) , is required for host defense against pathogens .", "However , how innate immune responses activate the UPR is not fully understood .", "In this report , we find that Pseudomonas aeru...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "public health and epidemiology", "epidemiology", "global health", "neglected tropical diseases", "public health" ]	Density-Dependent Mortality of the Human Host in Onchocerciasis: Relationships between Microfilarial Load and Excess Mortality	journal.pntd.0001578	null	[ [ "Human onchocerciasis , also known as ‘river blindness’ , is the parasitic infection caused by the filarial nematode Onchocerca volvulus .", "This neglected tropical disease [1] is the second most common cause of infectious blindness worldwide , after trachoma [2] , [3] .", "The parasite is transmitte...	[ "The parasite Onchocerca volvulus has , until recently , been regarded as the cause of a chronic yet non-fatal condition .", "Recent analyses , however , have indicated that in addition to blindness , the parasite can also be directly associated with human mortality .", "Such analyses also suggested that the re...	[ "Human onchocerciasis ( River Blindness ) is a parasitic disease leading to visual impairment including blindness .", "Blindness may lead to premature death , but infection with the parasite itself ( Onchocerca volvulus ) may also cause excess mortality in sighted individuals .", "The excess risk of mortality m...	2012
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "machine learning algorithms", "medicine and health sciences", "pathology and laboratory medicine", "neural networks", "animal models of disease", "applied mathematics", "neuroscience", "learning and memory", "simulation and modeling", "animal models", "algorithms", "sepsis", "model organism...	Computational translation of genomic responses from experimental model systems to humans	journal.pcbi.1006286	null	[ [ "Generalization of insights from disease model systems to the human in vivo context remains a persistent challenge in biomedical science .", "The association of molecular features with a phenotype in a model system often does not hold true in the corresponding human indication , due to some combination of...	[ "The high failure rate of therapeutics showing promise in mouse models to translate to patients is a pressing challenge in biomedical science .", "Though retrospective studies have examined the fidelity of mouse models to their respective human conditions , approaches for prospective translation of insights from ...	[ "Empirical comparison of genomic responses in mouse models and human disease contexts is not sufficient for addressing the challenge of prospective translation from mouse models to human disease contexts .", "We address this challenge by developing a semi-supervised machine learning approach that combines supervi...	2019
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "urology", "medicine and health sciences", "keratinocytes", "pathology and laboratory medicine", "cell cycle and cell division", "pathogens", "cell processes", "opportunistic infections", "cell differentiation", "epithelial cells", "developmental biology", "sexually transmitted diseases", "b...	Epithelial stratification shapes infection dynamics	journal.pcbi.1006646	null	[ [ "Stratified epithelia cover most of the human body’s exterior and line the inner cavities , such as the mouth and vagina .", "Localized ( non-systemic ) infections of these epithelia can cause a wide range of conditions that collectively represent a major burden on global public health systems .", "Fo...	[ "Infections of stratified epithelia contribute to a large group of common diseases , such as dermatological conditions and sexually transmitted diseases .", "To investigate how epithelial structure affects infection dynamics , we develop a general ecology-inspired model for stratified epithelia .", "Our model a...	[ "Many epithelia are stratified in layers of cells and their infection can result in many pathologies , from rashes to cancer .", "It is important to understand to what extent the epithelial structure determines infection dynamics and outcomes .", "To aid experimental and clinical studies , we develop a mathemat...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "sequencing techniques", "medicine and health sciences", "body fluids", "melioidosis", "geographical locations", "india", "bacterial diseases", "molecular biology techniques", "research and analysis methods", "sequence analysis", "infectious diseases", "bioinformatics", "biological databases...	Multi locus sequence typing of Burkholderia pseudomallei isolates from India unveils molecular diversity and confers regional association in Southeast Asia	journal.pntd.0006558	null	[ [ "Burkholderia pseudomallei , the causative agent of the infectious disease melioidosis , is estimated to cause 165 , 000 cases of human melioidosis per year worldwide [1] .", "B . pseudomallei , an environmental saprophyte is commonly found in wet soil and stagnant water throughout endemic regions .", ...	[ "Burkholderia pseudomallei , the causative agent for melioidosis , has become a public health problem in India and across the world .", "Melioidosis can be difficult to diagnose because of the inconsistent clinical presentations of the disease .", "This study aims to determine the genetic diversity among the cl...	[ "Burkholderia pseudomallei , a gram negative bacteria , is the causative agent for melioidosis .", "Annually , around 165 , 000 people suffer from melioidosis worldwide .", "B . pseudomallei is present in wet soil and stagnant water .", "It enters the human body via percutaneous inoculation , inhalation , asp...	2018
[ "Introduction", "Results", "Discussion", "Models" ]	[ "systems biology", "systems ecology", "ecology", "theoretical ecology", "chemistry", "biology", "computational chemistry", "theoretical chemistry" ]	Gause's Principle and the Effect of Resource Partitioning on the Dynamical Coexistence of Replicating Templates	journal.pcbi.1003193	null	[ [ "Gause ( 1934 ) in the Golden Age of theoretical ecology formulated the principle of competitive exclusion , proposing in effect what usually is being referred to as “complete competitors cannot coexist” [1] .", "Later investigations have confirmed that in stable steady state the number of coexisting spec...	[ "Models of competitive template replication , although basic for replicator dynamics and primordial evolution , have not yet taken different sequences explicitly into account , neither have they analyzed the effect of resource partitioning ( feeding on different resources ) on coexistence .", "Here we show by ana...	[ "The dynamical theory of competing templates has not yet taken the effect of sequences explicitly into account .", "One might think that complementary sequences have very limited competition only .", "We show that , despite interesting sequence effects , competing template replicators yield to Gause's principle...	2013
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "medicine and health sciences", "pathology and laboratory medicine", "helminths", "gene regulation", "tropical diseases", "parasitic diseases", "animals", "physiological processes", "gastropods", "neglected tropical diseases", "snails", "small interfering rn...	Schistosome infectivity in the snail, Biomphalaria glabrata, is partially dependent on the expression of Grctm6, a Guadeloupe Resistance Complex protein.	journal.pntd.0005362	null	[ [ "The World Health Organization ( WHO ) has estimated that schistosomiasis , a detrimental parasitic helminth disease , affects approximately 258 million people , making it one of the most important parasitic diseases in the world [1 , 2] .", "Millions of people are chemotherapeutically treated for schisto...	[ "Schistosomiasis is one of the most important neglected tropical diseases .", "Despite effective chemotherapeutic treatments , this disease continues to afflict hundreds of millions of people .", "Understanding the natural intermediate snail hosts of schistosome parasites is vital to the suppression of this dis...	[ "Schistosomiasis is one of the most prevalent parasitic diseases in the world .", "Though treatments for schistosomiasis infection exist , there is no vaccine , and reinfection is common in areas where the parasite occurs .", "One possible way to mitigate schistosomiasis is by controlling the transmission of th...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Evolution of Bow-Tie Architectures in Biology	journal.pcbi.1004055	null	[ [ "Many natural and engineered systems show a bow-tie architecture [1 , 2] .", "A bow-tie ( also termed hourglass ) architecture is a feature of multi-layered networks in which the intermediate layer has significantly fewer components than the input and output layers .", "The intermediate layer is calle...	[ "Bow-tie or hourglass structure is a common architectural feature found in many biological systems .", "A bow-tie in a multi-layered structure occurs when intermediate layers have much fewer components than the input and output layers .", "Examples include metabolism where a handful of building blocks mediate b...	[ "Many biological systems show bow-tie ( also called hourglass ) architecture .", "A bow-tie means that a large number of inputs are converted to a small number of intermediates , which then fan out to generate a large number of outputs .", "For example , cells use a wide variety of nutrients; process them into ...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "cell motility", "medicine and health sciences", "pathology and laboratory medicine", "insertion mutation", "pathogens", "bacillus", "microbiology", "flagellar motility", "mutation", "prokaryotic models", "experimental organism systems", "nonsense mutation", "sequence motif analysis", "fra...	Suppressor mutations in ribosomal proteins and FliY restore Bacillus subtilis swarming motility in the absence of EF-P	journal.pgen.1008179	null	[ [ "Translation elongation factor P ( EF-P ) has been shown to alleviate ribosome pausing at consecutive proline residues ( XPPX motifs ) in Bacteria and Eukaryotes [1–3] .", "While EF-P is widely distributed and often required for rapid growth , the reason it is highly conserved is unknown [4–6] .", "In...	[ "Translation elongation factor P ( EF-P ) alleviates ribosome pausing at a subset of motifs encoding consecutive proline residues , and is required for growth in many organisms .", "Here we show that Bacillus subtilis EF-P also alleviates ribosome pausing at sequences encoding tandem prolines and ribosomes paused...	[ "Translation elongation factor P ( EF-P ) is a highly conserved protein that alleviates ribosome pausing at consecutive proline residues .", "Unlike most organisms , EF-P in the bacterium Bacillus subtilis is not required for growth but is instead required for a flagellar-mediated form of motility called swarming...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "neuroscience/motor systems", "neuroscience", "neuroscience/neurodevelopment", "neuroscience/neuronal signaling mechanisms" ]	Foxp1 and Lhx1 Coordinate Motor Neuron Migration with Axon Trajectory Choice by Gating Reelin Signalling	journal.pbio.1000446	During embryonic development of the vertebrate motor system, the same transcription factors that regulate axonal trajectories can also regulate cell body migration, thereby controlling topographic map formation.	[ [ "Neural circuits are frequently organised in a topographic manner such that the position of a neuronal cell body is correlated with the location of the post-synaptic target and therefore its axon trajectory .", "Since the inference of such organisational principles [1] , the molecular identity of many neu...	[ "Topographic neuronal maps arise as a consequence of axon trajectory choice correlated with the localisation of neuronal soma , but the identity of the pathways coordinating these processes is unknown .", "We addressed this question in the context of the myotopic map formed by limb muscles innervated by spinal la...	[ "Many areas of our nervous system are organized in a topographic manner , such that the location of a neuron relative to its neighbors is often spatially correlated with its axonal trajectory and therefore target identity .", "In this study , we focus on the spinal myotopic map , which is characterized by the ste...	2010
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "nervous system", "vertebrates", "neuroscience", "animals", "animal models", "osteichthyes", "developmental biology", "model organisms", "experimental organism systems", "nerve fibers", "embryos", "research and analysis methods", "spinal cord", "developmen...	TNFa/TNFR2 signaling is required for glial ensheathment at the dorsal root entry zone	journal.pgen.1006712	null	[ [ "Efficient somatosensory perception requires that neurons propagate sensory stimuli from the periphery to the central nervous system ( CNS ) .", "Cutaneous somatosensory stimuli are first detected by excitable neurites in the skin , transduced past the dorsal root ganglion ( DRG ) cell soma and then conve...	[ "Somatosensory information from the periphery is routed to the spinal cord through centrally-projecting sensory axons that cross into the central nervous system ( CNS ) via the dorsal root entry zone ( DREZ ) .", "The glial cells that ensheath these axons ensure rapid propagation of this information .", "Despit...	[ "To survive , animals must receive sensory information from their environment and relay it to the central nervous system .", "The efficient transfer of this environmental information to the brain and spinal cord requires both neuronal and glial populations found along peripheral sensory nerves .", "In this work...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology", "evolutionary biology" ]	Sex Pheromone Evolution Is Associated with Differential Regulation of the Same Desaturase Gene in Two Genera of Leafroller Moths	journal.pgen.1002489	null	[ [ "Variation is the raw material of evolution; however the nature of this variation remains a topic of much discussion amongst evolutionary biologists [1] , [2] , [3] .", "The potential role in evolution of mutations that impact gene regulation rather than the amino acid sequence of a protein was initially ...	[ "Chemical signals are prevalent in sexual communication systems .", "Mate recognition has been extensively studied within the Lepidoptera , where the production and recognition of species-specific sex pheromone signals are typically the defining character .", "While the specific blend of compounds that makes up...	[ "Chemical signals are prevalent in sexual communication systems , especially within the Lepidoptera where sex pheromones are typically one of the defining characteristics of species .", "We have isolated six desaturases from two groups of sibling species of leafroller moths belonging to the genera Ctenopseustis a...	2012
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "neurochemistry", "action potentials", "nervous system", "membrane potential", "electrophysiology", "neuroscience", "surgical and invasive medical procedures", "functional electrical stimulation", "neurotransmitters", "calcium signaling", "cholinergics", "shor...	Recurrent excitation between motoneurones propagates across segments and is purely glutamatergic	journal.pbio.2003586	null	[ [ "Motoneurones ( Mns ) are the ultimate neural targets of effector commands issued from the central nervous system .", "Their activity is modulated by an intricate network of interneurones [1] that affect the spatial and temporal distribution of excitation to different motor pools [2] .", "Mns also rec...	[ "Spinal motoneurones ( Mns ) constitute the final output for the execution of motor tasks .", "In addition to innervating muscles , Mns project excitatory collateral connections to Renshaw cells ( RCs ) and other Mns , but the latter have received little attention .", "We show that Mns receive strong synaptic i...	[ "Motoneurones ( Mns ) are the last elements of the networks that command , coordinate , and actuate the most essential of behaviours: movement .", "Their activation triggers muscle contractions , and the many diseases affecting Mns cause progressive and fatal paralysis .", "We show here that Mns themselves form...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "parasite groups", "medicine and health sciences", "body fluids", "maternal health", "plasmodium", "obstetrics and gynecology", "tropical diseases", "parasitic diseases", "parasitic protozoans", "anemia", "parasitology", "apicomplexa", "women's health", "protozoans", "pregnancy", "mala...	Burden and impact of Plasmodium vivax in pregnancy: A multi-centre prospective observational study	journal.pntd.0005606	null	[ [ "More than a third of the world′s population is at risk of Plasmodium vivax infection , 90% of whom live in the Asia and the Pacific regions , while the rest live in the American ( 6% ) and African ( 3% ) regions .", "[1–3] In comparison with P . falciparum , P . vivax infection has received little attent...	[ "Despite that over 90 million pregnancies are at risk of Plasmodium vivax infection annually , little is known about the epidemiology and impact of the infection in pregnancy .", "We undertook a health facility-based prospective observational study in pregnant women from Guatemala ( GT ) , Colombia ( CO ) , Brazi...	[ "More than 90 million pregnancies are exposed to P . vivax infection every year .", "While it is well known that pregnant women have an increased risk of P . falciparum infection and disease , much less is known on the epidemiology and the impact of P . vivax in pregnancy .", "A health-facility based observatio...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "systems biology", "stochastic processes", "mathematics", "theoretical biology", "regulatory networks", "synthetic biology", "biology", "computational biology", "signaling networks", "molecular biology", "genetics and genomics", "probability theory" ]	Stochastic Delay Accelerates Signaling in Gene Networks	journal.pcbi.1002264	null	[ [ "Gene regulation forms a basis for cellular decision-making processes and transcriptional signaling is one way in which cells can modulate gene expression patterns [1] .", "The intricate networks of transcription factors and their targets are of intense interest to theorists because it is hoped that topol...	[ "The creation of protein from DNA is a dynamic process consisting of numerous reactions , such as transcription , translation and protein folding .", "Each of these reactions is further comprised of hundreds or thousands of sub-steps that must be completed before a protein is fully mature .", "Consequently , th...	[ "Delay in gene regulatory networks often arises from the numerous sequential reactions necessary to create fully functional protein from DNA .", "While the molecular mechanisms behind protein production and maturation are known , it is still unknown to what extent the resulting delay affects signaling in transcri...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "plant cell biology", "messenger rna", "chloroplasts", "plant science", "model organisms", "experimental organism systems", "molecular biology techniques", "seedlings", "plants", "cellular structures and organelles", "genetic footprinting", "research and analysis methods", "grasses", "gene...	Multilevel effects of light on ribosome dynamics in chloroplasts program genome-wide and psbA-specific changes in translation	journal.pgen.1007555	null	[ [ "Energy from sunlight fuels life on earth through the process of photosynthesis .", "Light is both an essential resource and a source of stress for photosynthetic organisms , as it damages cellular structures through photo-oxidative processes and the production of reactive oxygen species .", "Photosyn...	[ "Plants and algae adapt to fluctuating light conditions to optimize photosynthesis , minimize photodamage , and prioritize energy investments .", "Changes in the translation of chloroplast mRNAs are known to contribute to these adaptations , but the scope and magnitude of these responses are unclear .", "To cla...	[ "Our experiments address the effects of light on protein synthesis within chloroplasts , whose ~80 genes are essential for photosynthesis and account for a large fraction of the protein synthesis in leaf tissue .", "Light is necessary for photosynthesis but it also triggers photo-oxidative damage .", "It is kno...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing techniques", "transfer rna", "molecular probe techniques", "natural antisense transcripts", "gene regulation", "enzymes", "geographical locations", "enzymology", "phosphatases", "northern blot", "micrornas", "methylation", "molecular biology techniques", "rna sequencing", "ge...	BCDIN3D regulates tRNAHis 3’ fragment processing	journal.pgen.1008273	null	[ [ "The 5’ ends of eukaryotic RNAs are vital for determining their processing and function [1] .", "The most well-known 5’ end RNA modification is the m7G cap , which has multiple functions , including of protecting messenger RNAs from exonucleolytic degradation , and of marking them for nucleo-cytoplasmic e...	[ "5’ ends are important for determining the fate of RNA molecules .", "BCDIN3D is an RNA phospho-methyltransferase that methylates the 5’ monophosphate of specific RNAs .", "In order to gain new insights into the molecular function of BCDIN3D , we performed an unbiased analysis of its interacting RNAs by Thermos...	[ "We previously identified an important modification of human microRNAs , written by BCDIN3D , an RNA phospho-methyltransferase linked to triple negative breast cancer , obesity and type II diabetes .", "Here , we employed a powerful sequencing method that overcomes RNA secondary structure and RNA modifications , ...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics", "immunology", "biology", "microbiology", "molecular cell biology", "genetics and genomics" ]	The Rhoptry Proteins ROP18 and ROP5 Mediate Toxoplasma gondii Evasion of the Murine, But Not the Human, Interferon-Gamma Response	journal.ppat.1002784	null	[ [ "Toxoplasma gondii is a widespread intracellular parasite capable of infecting most warm-blooded animals and is an important opportunistic pathogen for immunocompromised individuals and unborn fetuses .", "Toxoplasma resides within a non-fusogenic parasitophorous vacuole and has three apical secretory org...	[ "The obligate intracellular parasite Toxoplasma gondii secretes effector proteins into the host cell that manipulate the immune response allowing it to establish a chronic infection .", "Crosses between the types I , II and III strains , which are prevalent in North America and Europe , have identified several se...	[ "Toxoplasma gondii can infect any warm-blooded animal and is transmitted orally by consumption of tissue cysts .", "To facilitate transmission , the parasite must balance induction and evasion of host immune responses to allow parasite growth and persistence , while avoiding excessive parasite burden , which can ...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "plant anatomy", "gene regulation", "cell cycle and cell division", "cell processes", "brassica", "plant science", "model organisms", "experimental organism systems", "plants", "flower anatomy", "arabidopsis thaliana", "research and analysis methods", "cell proliferation", "gene expression...	STERILE APETALA modulates the stability of a repressor protein complex to control organ size in Arabidopsis thaliana	journal.pgen.1007218	null	[ [ "How plants control final organ size is an intriguing question in developmental biology .", "Organ size is also important for plant yield and biomass .", "Previous studies suggest that the developing organs possess intrinsic signals to control their final size , although plant growth is affected by va...	[ "Organ size control is of particular importance for developmental biology and agriculture , but the mechanisms underlying organ size regulation remain elusive in plants .", "Meristemoids , which possess stem cell-like properties , have been recognized to play important roles in leaf growth .", "We have recently...	[ "Organ size is coordinately regulated by cell proliferation and cell expansion; however , the mechanisms of organ size control are still poorly understood .", "We have previously demonstrated that the Arabidopsis F-box protein STERILE APETALA ( SAP ) /SUPPRESSOR OF DA1 ( SOD3 ) controls organ size by promoting me...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "systems biology", "biochemical simulations", "signaling networks", "biology", "computational biology" ]	STL-based Analysis of TRAIL-induced Apoptosis Challenges the Notion of Type I/Type II Cell Line Classification	journal.pcbi.1003056	null	[ [ "Apoptosis , a major form of programmed cell death , plays a crucial role in shaping organs during development and controls homeostasis and tissue integrity throughout life [1] , [2] .", "Moreover defective apoptosis is often involved in cancer development and progression [3] .", "Apoptosis can be tri...	[ "Extrinsic apoptosis is a programmed cell death triggered by external ligands , such as the TNF-related apoptosis inducing ligand ( TRAIL ) .", "Depending on the cell line , the specific molecular mechanisms leading to cell death may significantly differ .", "Precise characterization of these differences is cru...	[ "Apoptosis , a major form of programmed cell death , plays a crucial role in shaping organs during development and controls homeostasis and tissue integrity throughout life .", "Defective apoptosis is often involved in cancer development and progression .", "Current understanding of externally triggered apoptos...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology", "arthropods", "vertebrates", "mus (mouse)", "neuroscience", "mammals" ]	Cdk5 Is Involved in BDNF-Stimulated Dendritic Growth in Hippocampal Neurons	journal.pbio.0050063	Dendritic growth stimulated by brain-derived neurotrophic factor (BDNF) requires phosphorylation of the BDNF receptor, TrkB, by a kinase known as cyclin-dependent kinase 5 (Cdk5). This study identifies a novel interplay between Cdk5 and TrkB.	[ [ "Neurotrophins are indispensable for multiple aspects of neuronal development , such as the maintenance of neuronal survival , regulation of neuronal architecture , and synaptic plasticity .", "Members of the neurotrophins include the prototypic member nerve growth factor ( NGF ) , brain-derived neurotrop...	[ "Neurotrophins are key regulators of neuronal survival and differentiation during development .", "Activation of their cognate receptors , Trk receptors , a family of receptor tyrosine kinases ( RTKs ) , is pivotal for mediating the downstream functions of neurotrophins .", "Recent studies reveal that cyclin-de...	[ "Accurate transmission of information in the nervous system requires the precise formation of contact points between neurons .", "Regulation of these contact sites involves fine tuning the number and branching of dendritic processes on neurons .", "Throughout development , several secreted factors act to regula...	2007
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "genetics", "biology", "microbiology", "genetics and genomics" ]	The Splicing Factor Proline-Glutamine Rich (SFPQ/PSF) Is Involved in Influenza Virus Transcription	journal.ppat.1002397	null	[ [ "The influenza A viruses belong to the family Orthomyxoviridae and contain a segmented , single-stranded RNA genome of negative polarity ( for a review see [1] .", "Each of the genomic RNA segments is encapsidated in a ribonucleoprotein particle ( RNP ) containing the polymerase complex and a number of nu...	[ "The influenza A virus RNA polymerase is a heterotrimeric complex responsible for viral genome transcription and replication in the nucleus of infected cells .", "We recently carried out a proteomic analysis of purified polymerase expressed in human cells and identified a number of polymerase-associated cellular ...	[ "The influenza A viruses cause annual epidemics and occasional pandemics of respiratory infections that may be life threatening .", "The viral genome contains 8 RNA molecules forming ribonucleoproteins that replicate and transcribe in the nucleus of infected cells .", "Influenza viruses are intracellular parasi...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "plant anatomy", "brassica", "endosperm", "developmental biology", "plant science", "model organisms", "experimental organism systems", "epigenetics", "dna", "plants", "dna methylation", "chromatin", "research and analysis methods", "arabidopsis thaliana", "chromosome biology", "animal...	A variably imprinted epiallele impacts seed development	journal.pgen.1007469	null	[ [ "DNA methylation is a heritable epigenetic mark that can , on occasion , effect gene transcription and influence development .", "DNA methylation is a particularly influential regulator of gene expression in endosperm , a triploid extraembryonic seed tissue that supports embryo development .", "In end...	[ "The contribution of epigenetic variation to phenotypic variation is unclear .", "Imprinted genes , because of their strong association with epigenetic modifications , represent an opportunity for the discovery of such phenomena .", "In mammals and flowering plants , a subset of genes are expressed from only on...	[ "The contribution of genetic variation to phenotypic variation is well-established .", "By contrast , it is unknown how frequently epigenetic variation causes differences in organismal phenotypes .", "Epigenetic information is closely associated with but not encoded in the DNA sequence .", "In practice , it i...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "plant biology/plant genomes and evolution", "developmental biology/plant growth and development", "genetics and genomics/gene function", "plant biology/plant growth and development", "plant biology/plant genetics and gene expression" ]	FON2 SPARE1 Redundantly Regulates Floral Meristem Maintenance with FLORAL ORGAN NUMBER2 in Rice	journal.pgen.1000693	null	[ [ "Intercellular communication plays a crucial role in the determination of cell fate in plant development .", "Cell fate is determined by positional information emanating from neighboring or distant cells .", "Recent molecular genetic studies have revealed that peptide signaling molecules are involved ...	[ "CLAVATA signaling restricts stem cell identity in the shoot apical meristem ( SAM ) in Arabidopsis thaliana .", "In rice ( Oryza sativa ) , FLORAL ORGAN NUMBER2 ( FON2 ) , closely related to CLV3 , is involved as a signaling molecule in a similar pathway to negatively regulate stem cell proliferation in the flor...	[ "The body plan of plants is regulated by the function of apical meristems that are generated in the embryo .", "Leaves and floral organs are derived from cells supplied by stem cells in the vegetative shoot apical meristem ( SAM ) and the floral meristem ( FM ) , respectively .", "Thus , genetic regulation of s...	2009
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "biochemistry", "veterinary diseases", "veterinary parasitology", "proteins", "biology and life sciences", "proteomics", "microbiology", "veterinary science", "parasitology" ]	Proteomic Selection of Immunodiagnostic Antigens for Trypanosoma congolense	journal.pntd.0002936	null	[ [ "Animal African Trypanosomosis ( AAT ) presents a severe problem for agricultural development in sub-Saharan Africa .", "The economic loss in cattle production is estimated to be between US$ 1 billion per annum [1]–[3] , increasing to US$ 5 billion when secondary costs are taken into consideration [1] , [...	[ "Animal African Trypanosomosis ( AAT ) presents a severe problem for agricultural development in sub-Saharan Africa .", "It is caused by several trypanosome species and current means of diagnosis are expensive and impractical for field use .", "Our aim was to discover antigens for the detection of antibodies to...	[ "Animal African Trypanosomosis ( AAT ) is a set of diseases whereby animals are infected with single-cell parasites that replicate in their bloodstream .", "The disease in cattle results in weight-loss and death , and AAT is a significant veterinary problem for sub-Saharan Africa .", "One of the principal trypa...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "pathology and laboratory medicine", "gene regulation", "immunology", "parasitic diseases", "animals", "nematode infections", "animal models", "ascaris", "model organisms", "research and analysis methods", "immune system proteins", "proteins...	A Proteomic Investigation of Hepatic Resistance to Ascaris in a Murine Model	journal.pntd.0004837	null	[ [ "Ascariasis is an important , widespread geohelminth disease of humans and pigs [1] .", "Over 800 million people are estimated to be infected with the causative agent , the human roundworm , Ascaris lumbricoides [2] and the equivalent in pigs , Ascaris suum , is equally ubiquitious [3] .", "The impact...	[ "The helminth Ascaris causes ascariasis in both humans and pigs .", "Humans , especially children , experience significant morbidity including respiratory complications , growth deficits and intestinal obstruction .", "Given that 800 million people worldwide are infected by Ascaris , this represents a significa...	[ "Ascaris infection is a significant burden on the people who live in developing countries with infection being linked to poor hygiene and low socio-economic status .", "The parasite causes a range of symptoms , especially in children , which include both chronic morbidity , such as growth retardation , and acute ...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "reverse transcriptase-polymerase chain reaction", "medicine and health sciences", "chemical compounds", "gene regulation", "messenger rna", "genetic diseases", "fibrosis", "pulmonology", "epithelial cells", "developmental biology", "cystic fibrosis", "bioassays and physiological analysis", ...	Capitalizing on the heterogeneous effects of CFTR nonsense and frameshift variants to inform therapeutic strategy for cystic fibrosis	journal.pgen.1007723	null	[ [ "The development of variant-specific modulators that correct dysfunctional cystic fibrosis transmembrane conductance regulator ( CFTR ) protein is an excellent model for precision medicine [1–4] .", "Cystic fibrosis ( CF ) is a progressive , multi-organ , life-threating , autosomal recessive disease cause...	[ "CFTR modulators have revolutionized the treatment of individuals with cystic fibrosis ( CF ) by improving the function of existing protein .", "Unfortunately , almost half of the disease-causing variants in CFTR are predicted to introduce premature termination codons ( PTC ) thereby causing absence of full-lengt...	[ "The development of variant specific modulators that correct dysfunctional cystic fibrosis transmembrane conductance regulator ( CFTR ) protein is an excellent example of precision medicine .", "Currently there is no molecular treatment available for individuals with cystic fibrosis ( CF ) carrying nonsense or fr...	2018
[ "Introduction", "Results", "Discussion", "Material and Methods", "Supporting Information" ]	[ "oryza", "developmental biology", "arabidopsis (thale cress)", "plant biology", "computational biology", "evolutionary biology", "molecular biology" ]	Network Discovery Pipeline Elucidates Conserved Time-of-Day–Specific cis-Regulatory Modules	journal.pgen.0040014	null	[ [ "The circadian clock functions to optimize physiology and metabolism to the correct time of the day and is crucial for fitness .", "Organisms experience the external environment as a dynamic relationship between daily changes in temperature ( thermocycles ) and light ( photocycles ) that vary by season an...	[ "Correct daily phasing of transcription confers an adaptive advantage to almost all organisms , including higher plants .", "In this study , we describe a hypothesis-driven network discovery pipeline that identifies biologically relevant patterns in genome-scale data .", "To demonstrate its utility , we analyze...	[ "As the earth rotates , environmental conditions oscillate between illuminated warm days and dark cool nights .", "Plants have adapted to these changes by timing physiological processes to specific times of the day or night .", "Light and temperature signaling and the circadian clock regulate this adaptive resp...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The Differential Mobilization of Histones H3.1 and H3.3 by Herpes Simplex Virus 1 Relates Histone Dynamics to the Assembly of Viral Chromatin	journal.ppat.1003695	null	[ [ "Cellular DNA is wrapped around protein octamers containing two molecules each of histones H2A , H2B , H3 , and H4 , forming the nucleosome [1] .", "Linker histone H1 binds to DNA at the entry and exit sites of the core nucleosome to promote the formation of higher-order chromatin structures [2] .", "...	[ "During lytic infections , HSV-1 genomes are assembled into unstable nucleosomes .", "The histones required for HSV-1 chromatin assembly , however , are in the cellular chromatin .", "We have shown that linker ( H1 ) and core ( H2B and H4 ) histones are mobilized during HSV-1 infection , and proposed that the m...	[ "H3 . 1 is typically assembled into chromatin during DNA replication-dependent chromatin assembly .", "However , histones undergo exchange with those not bound in chromatin .", "During such exchanges , DNA replication-independent chromatin assembly incorporates histone variants , such as H3 . 3 .", "The HSV-1...	2013
[ "Introduction", "Models", "Results", "Discussion" ]	[ "medicine and health sciences", "g1 phase", "cell cycle and cell division", "cell processes", "messenger rna", "dna transcription", "physiological processes", "homeostasis", "stem cells", "synthesis phase", "animal cells", "embryonic stem cells", "gene expression", "molecular evolution", ...	The nonlinear dynamics and fluctuations of mRNA levels in cell cycle coupled transcription	journal.pcbi.1007017	null	[ [ "Single cell studies over last decades have shown that gene transcription is inherently a stochastic process in a bursting fashion [1–5] .", "The transcriptional bursting , whereby a gene promoter transits randomly between short periods of mRNA production and long periods of no productions , has been wide...	[ "Gene transcription is a noisy process , and cell division cycle is an important source of gene transcription noise .", "In this work , we develop a mathematical approach by coupling transcription kinetics with cell division cycles to delineate how they are combined to regulate transcription output and noise .", ...	[ "Gene transcription in single cells is inherently a stochastic process , resulting in a large variability in the number of transcripts and constituting the phenotypic heterogeneity in cell population .", "Cell division cycle has global effects on transcriptional outputs , and is thought to be an additional source...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "transfection", "medicine and health sciences", "pathology and laboratory medicine", "viral transmission and infection", "gene regulation", "pathogens", "microbiology", "cytomegalovirus infection", "dna transcription", "viruses", "micrornas", "dna viruses", "molecular biology techniques", ...	Human Cytomegalovirus miR-UL148D Facilitates Latent Viral Infection by Targeting Host Cell Immediate Early Response Gene 5	journal.ppat.1006007	null	[ [ "Human cytomegalovirus ( HCMV ) , a member of the β-herpesvirus subfamily , is a ubiquitous human virus that has infected up to 90% of the adult population worldwide [1] .", "Although HCMV infection rarely causes clinically symptomatic disease in immunocompetent healthy hosts , HCMV can establish a latent...	[ "The mechanisms underlying human cytomegalovirus ( HCMV ) latency remain incompletely understood .", "Here , we showed that a HCMV-encoded miRNA , miR-UL148D , robustly accumulates during late stages of experimental latent HCMV infection in host cells and promotes HCMV latency by modulating the immediate early re...	[ "Human cytomegalovirus ( HCMV ) is a herpesvirus that is prevalent around the world .", "Following primary infection , HCMV can persist for the lifetime of a host by establishing a latent infection .", "While HCMV infection normally causes no clinical symptoms , reactivation of HCMV from latency can cause deadl...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "ecology and environmental sciences", "pathology and laboratory medicine", "tropical diseases", "social sciences", "parasitic diseases", "parasitic protozoans", "human mobility", "protozoans", "signs and symptoms", "aquatic environments", "bodies of water", "i...	Malaria Elimination Campaigns in the Lake Kariba Region of Zambia: A Spatial Dynamical Model	journal.pcbi.1005192	null	[ [ "Malaria is a vector-borne parasitic disease affecting millions of people worldwide , with Plasmodium falciparum still causing over 400 , 000 deaths per year [1] .", "Recent escalation in vector control has greatly reduced global burden and brought many regions close to elimination [2] .", "In some se...	[ "As more regions approach malaria elimination , understanding how different interventions interact to reduce transmission becomes critical .", "The Lake Kariba area of Southern Province , Zambia , is part of a multi-country elimination effort and presents a particular challenge as it is an interconnected region o...	[ "What would it take to eliminate malaria in southern Africa ?", "While the past century has seen many countries eliminate malaria , and many regions have dramatically reduced malaria burden in the last fifteen years , no sub-Saharan African country has yet eliminated malaria .", "In the Lake Kariba region of So...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "blood cells", "medicine and health sciences", "clinical laboratory sciences", "body fluids", "immune cells", "pathology and laboratory medicine", "statistics", "blood counts", "immunology", "tropical diseases", "mathematics", "signs and symptoms", "forecasting", "platelets", "neglected ...	Use of structural equation models to predict dengue illness phenotype	journal.pntd.0006799	null	[ [ "Dengue virus ( DENV ) infection is a major public health issue worldwide particularly in tropical and subtropical regions .", "An estimated 390 million new DENV infections and 90 million cases of dengue illnesses are estimated to occur in more than 100 endemic countries , resulting in 20 , 000 deaths ann...	[ "Early recognition of dengue , particularly patients at risk for plasma leakage , is important to clinical management .", "The objective of this study was to build predictive models for dengue , dengue hemorrhagic fever ( DHF ) , and dengue shock syndrome ( DSS ) using structural equation modelling ( SEM ) , a st...	[ "Dengue virus infection is one of the most critical public health issues , particularly in tropical and subtropical regions .", "This study developed statistical predictive models using the data obtained from 257 Thai children for dengue , dengue hemorrhagic fever , and dengue shock syndrome using structural equa...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Mre11 and Blm-Dependent Formation of ALT-Like Telomeres in Ku-Deficient Ustilago maydis	journal.pgen.1005570	null	[ [ "Eukaryotic chromosome ends , or telomeres , consist of repetitive DNA sequences and a plethora of protective proteins that are crucial for chromosome stability [1 , 2] .", "Aberrations in the DNA repeat tracts or the protective telomere proteins have been shown to induce chromosome re-arrangements .", ...	[ "A subset of human cancer cells uses a specialized , aberrant recombination pathway known as ALT to maintain telomeres , which in these cells are characterized by complex aberrations including length heterogeneity , high levels of unpaired C-strand , and accumulation of extra-chromosomal telomere repeats ( ECTR ) ....	[ "The majority of cancer cells use a special enzyme called telomerase to maintain telomeres .", "However , some cancer cells do not possess telomerase and use instead the so-called ALT mechanism to maintain telomeres .", "ALT is a complex pathway that entails the action of many factors , and the telomere DNAs of...	2015
[ "Introduction", "Results and Discussion", "Methods" ]	[]	The Internal Dynamics of Fibrinogen and Its Implications for Coagulation and Adsorption	journal.pcbi.1004346	null	[ [ "Fibrinogen ( Fg ) is a 340kD multi-chain glyco-protein which can polymerize into fibrin , one of the main components of blood clots .", "Fibrin formation and lysis ( fibrinolysis ) are tightly controlled processes along the pathway leading to coagulation [1] .", "Fg , once activated by thrombin , whi...	[ "Fibrinogen is a serum multi-chain protein which , when activated , aggregates to form fibrin , one of the main components of a blood clot .", "Fibrinolysis controls blood clot dissolution through the action of the enzyme plasmin , which cleaves fibrin at specific locations .", "Although the main biochemical fa...	[ "Fibrinogen , a protein found in the blood of vertebrates , when activated , aggregates and forms fibrin fibers , the basis of a blood clot .", "Clots are broken down by the enzyme plasmin , which cuts fibrin fibers at specific places , thus helping the regulation of clot persistence .", "A mechanistic understa...	2015
[ "Introduction", "Results", "Discussion" ]	[ "medicine", "public health and epidemiology", "infectious disease epidemiology", "spatial epidemiology", "biodiversity", "parasitic diseases", "neglected tropical diseases", "echinococcosis", "disease mapping", "infectious diseases", "environmental epidemiology", "epidemiology", "biology", ...	Drivers of Echinococcus multilocularis Transmission in China: Small Mammal Diversity, Landscape or Climate?	journal.pntd.0002045	null	[ [ "Ecologic systems are nested within one another .", "This well-known fundamental hierarchical organization [1] is easy to detect in nature but has been generally undervalued as a source of influence on the structure and development of pathogen transmission patterns , and also as a means of understanding t...	[ "Human alveolar echinococcocosis ( AE ) is a highly pathogenic zoonotic disease caused by the larval stage of the cestode E . multilocularis .", "Its life-cycle includes more than 40 species of small mammal intermediate hosts .", "Therefore , host biodiversity losses could be expected to alter transmission .", ...	[ "The loss or gain of certain host species may either dilute or amplify the risk of pathogen and parasite infection through direct or indirect effects .", "The relative contribution of host communities combined with climate and landscape characteristics on non-vector-borne parasite transmission to humans has been ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/respiratory infections" ]	Human-Like Receptor Specificity Does Not Affect the Neuraminidase-Inhibitor Susceptibility of H5N1 Influenza Viruses	journal.ppat.1000043	null	[ [ "The spread of highly pathogenic avian influenza A ( H5N1 ) viruses from Asia to the Middle East , Europe , and Africa raises serious concern about a potential human pandemic [1] , [2] .", "H5N1 avian influenza virus has been reported in poultry in 63 countries; 359 human cases have been confirmed in 14 c...	[ "If highly pathogenic H5N1 influenza viruses acquire affinity for human rather than avian respiratory epithelium , will their susceptibility to neuraminidase ( NA ) inhibitors ( the likely first line of defense against an influenza pandemic ) change as well ?", "Adequate pandemic preparedness requires that this q...	[ "If the avian influenza H5N1 viruses adapt to human hosts , the first step is likely to be a switch in the preference of their viral hemagglutinin ( HA ) glycoprotein to bind to human rather than avian cell receptors .", "Such a switch may also alter virus susceptibility to neuraminidase ( NA ) inhibitors , which...	2008
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "phosphorylation", "chemical compounds", "vacuoles", "aliphatic amino acids", "molecular probe techniques", "immunoblotting", "organic compounds", "leucine", "fungi", "immunoprecipitation", "acidic amino acids", "amino acids", "molecular biology techniques", "cellular structures and organe...	Gtr/Ego-independent TORC1 activation is achieved through a glutamine-sensitive interaction with Pib2 on the vacuolar membrane	journal.pgen.1007334	null	[ [ "Cell growth is primarily governed by environmental nutritional conditions [1] .", "TORC1 , a protein complex that is universally conserved among eukaryotes , plays a pivotal role in the cell’s coordinated response to amino acids [2 , 3] .", "In the budding yeast , Saccharomyces cerevisiae , TORC1 con...	[ "TORC1 is a central regulator of cell growth in response to amino acids .", "The role of the evolutionarily conserved Gtr/Rag pathway in the regulation of TORC1 is well-established .", "Recent genetic studies suggest that an additional regulatory pathway , depending on the activity of Pib2 , plays a role in TOR...	[ "TORC1 is a central regulator of cell growth in response to amino acids .", "The evolutionarily conserved Gtr/Rag pathway is a well-established TORC1 regulatory pathway .", "In this study , we show that two molecular machineries , Pib2 and Gtr/Ego , form distinct complexes with TORC1 in a mutually exclusive man...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "learning", "psychometrics", "psychology", "medicine and health sciences", "cognitive psychology", "emotions", "mental health and psychiatry", "decision making", "human learning", "cognition", "behavior", "biology and life sciences", "social sciences", "cognitive science", "neuroscience"...	Change, stability, and instability in the Pavlovian guidance of behaviour from adolescence to young adulthood	journal.pcbi.1006679	null	[ [ "A leitmotif in the nascent field of computational psychiatry [1–4] is that carefully curated cognitive tasks can be used to identify latent dimensions of decision-making .", "These parametrize process accounting for how the tasks are solved , and are identified according to the models that best fit behav...	[ "Pavlovian influences are important in guiding decision-making across health and psychopathology .", "There is an increasing interest in using concise computational tasks to parametrise such influences in large populations , and especially to track their evolution during development and changes in mental health ....	[ "Choice behaviour is guided by Pavlovian influences , so that particular features of a situation , e . g . if one seeks to gain rewards to avoid losses , privilege certain decisions over others–here , to be active versus vs . inactive respectively .", "Such privileging may be useful but may also impair optimal in...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Within-host Competition Does Not Select for Virulence in Malaria Parasites; Studies with Plasmodium yoelii	journal.ppat.1004628	null	[ [ "Malaria is caused by a diverse group of parasites composed of at least six species of the genus Plasmodium .", "Genetic diversity within these species is high , with multiple strains often co-infecting the same host , and is driven and maintained by mutation and through recombination between strains .", ...	[ "In endemic areas with high transmission intensities , malaria infections are very often composed of multiple genetically distinct strains of malaria parasites .", "It has been hypothesised that this leads to intra-host competition , in which parasite strains compete for resources such as space and nutrients .", ...	[ "Malaria infections are very often composed of multiple strains of malaria parasites .", "It is thought that these strains may compete for resources such as space and nutrients within the host .", "Here we show that such “within-host competition” has repercussions for the virulence of the malaria infection , so...	2015
[ "Introduction", "Results and Discussion", "Conclusions", "Materials and Methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "immune physiology", "spleen", "immunology", "tropical diseases", "vertebrates", "parasitic diseases", "animals", "mammals", "parasitic protozoans", "protozoans", "leishmania", "neglected tropical diseases", "hamsters", "...	Transcriptional Profiling in Experimental Visceral Leishmaniasis Reveals a Broad Splenic Inflammatory Environment that Conditions Macrophages toward a Disease-Promoting Phenotype	journal.ppat.1006165	null	[ [ "Visceral leishmaniasis ( VL ) , caused by the intracellular protozoa Leishmania donovani and L . infantum ( syn L . chagasi ) , affects nearly a half-million people each year [1] .", "It occurs in tropical and subtropical regions of the world and is commonly associated with poverty .", "Infection is ...	[ "Visceral Leishmaniasis ( VL ) , caused by the intracellular protozoan Leishmania donovani , is characterized by relentlessly increasing visceral parasite replication , cachexia , massive splenomegaly , pancytopenia and ultimately death .", "Progressive disease is considered to be due to impaired effector T cell ...	[ "Visceral leishmaniasis ( VL ) is a neglected parasitic disease that is caused by the intracellular protozoan Leishmania donovani .", "Patients with this disease suffer from muscle wasting , enlargement of the spleen , reduced blood counts and ultimately will die without treatment .", "Progressive disease is co...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "ecology", "global health", "epidemiology", "biology", "public health" ]	Mapping the Geographical Distribution of Lymphatic Filariasis in Zambia	journal.pntd.0002714	null	[ [ "Little has been reported about lymphatic filariasis ( LF ) in Zambia in the past .", "According to Buckley [1] , local medical reports from the 1930's and 1940's mentioned the recovery of microfilariae ( mf ) of Wuchereria bancrofti from patients in Zambia , but the history and movements of the infected ...	[ "Past case reports have indicated that lymphatic filariasis ( LF ) occurs in Zambia , but knowledge about its geographical distribution and prevalence pattern , and the underlying potential environmental drivers , has been limited .", "As a background for planning and implementation of control , a country-wide ma...	[ "Lymphatic filariasis ( LF ) is a debilitating mosquito borne parasitic infection which worldwide affects more than 120 million people .", "It is also widespread in Sub-Saharan Africa .", "A World Health Organization coordinated Global Programme to Eliminate LF has targeted LF for elimination as a public health...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "calcium-activated potassium channels", "medicine and health sciences", "drugs", "tropical diseases", "antihelmintics", "parasitic diseases", "neuroscience", "parasitology", "parasite physiology", "nematode infections", "ion channels", "drug information", "intestinal parasites", "filariasi...	Characterization of the Ca2+-Gated and Voltage-Dependent K+-Channel Slo-1 of Nematodes and Its Interaction with Emodepside	journal.pntd.0003401	null	[ [ "In Ecdysozoa , large conductance potassium channels ( also BK or Maxi-K channels ) are encoded by slo-1 genes [1] .", "Due to their large conductance in the open state , typically exceeding 200 pS , Slo-1 channels are of major importance for repolarization of excitable cells .", "These channels are t...	[ "The cyclooctadepsipeptide emodepside and its parent compound PF1022A are broad-spectrum nematicidal drugs which are able to eliminate nematodes resistant to other anthelmintics .", "The mode of action of cyclooctadepsipeptides is only partially understood , but involves the latrophilin Lat-1 receptor and the vol...	[ "Emodepside is an anthelmintic introduced into the market as an ingredient of different dewormers for cats and dogs , and is the only member of the cyclooctadepsipeptide class which has been commercialized .", "The voltage-gated and calcium-activated potassium channel Slo-1 has been implicated in the mode of acti...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "microbiome", "microbiology", "parasitic diseases", "parasitic protozoans", "animals", "protozoans", "mathematics", "insect vectors", "triatoma", "bacteria", "discrete mathematics", "microbial genomics", "combinatorics", "infectious dise...	Hindgut microbiota in laboratory-reared and wild Triatoma infestans	journal.pntd.0007383	null	[ [ "Chagas disease , caused by the protozoan parasite Trypanosoma cruzi , infects an estimated six million people residing in 21 endemic countries in the Americas , with 30 , 000 new infections yearly [1] .", "The most important method of T . cruzi transmission to humans is vector-borne: T . cruzi undergoes ...	[ "Triatomine vectors transmit Trypanosoma cruzi , the etiological agent of Chagas disease in humans .", "Transmission to humans typically occurs when contaminated triatomine feces come in contact with the bite site or mucosal membranes .", "In the Southern Cone of South America , where the highest burden of dise...	[ "Chagas disease in humans is caused by the parasite Trypanosoma cruzi and it is endemic to the Americas .", "Poor populations are most at risk .", "The parasite infects an estimated six million people of 21 endemic countries in the Americas , with 30 , 000 new infections yearly .", "The main mode of transmiss...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "immune cells", "filariasis", "t cells", "immunology", "biology", "parasitic diseases", "immune response", "helminth infection" ]	Parasite-Antigen Driven Expansion of IL-5− and IL-5+ Th2 Human Subpopulations in Lymphatic Filariasis and Their Differential Dependence on IL-10 and TGFβ	journal.pntd.0002658	null	[ [ "Th2 cells were initially characterized as expressing the cytokines – IL-4 , IL-5 and IL-13 [1] .", "Although Th2 cells can express a variety of other cytokines , these three cytokines remain the hallmark Th2 cytokines .", "Each Th2 cytokine has a well-defined and relatively specific function .", ...	[ "Two different Th2 subsets have been defined recently on the basis of IL-5 expression – an IL-5+Th2 subset and an IL-5−Th2 subset in the setting of allergy .", "However , the role of these newly described CD4+ T cells subpopulations has not been explored in other contexts .", "To study the role of the Th2 subpo...	[ "Th2 cells are CD4+ T cells that produce a unique set of cytokines - IL-4 , IL-5 and IL-13 .", "Th2 cells are commonly associated with allergies , asthma and helminth infections .", "A common helminth infection that infects over 120 million people worldwide is lymphatic filarial infection caused by filarial par...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "biology" ]	Treatment with IL-7 Prevents the Decline of Circulating CD4+ T Cells during the Acute Phase of SIV Infection in Rhesus Macaques	journal.ppat.1002636	null	[ [ "Although HIV-1 establishes a chronic active infection that evolves toward clinical immunodeficiency over a span of several years , accumulating evidence indicates that critical pathogenic events take place during the acute phase of infection , leading to a massive and seemingly irreversible depletion of CD4+...	[ "Although treatment with interleukin-7 ( IL-7 ) was shown to transiently expand the naïve and memory T-cell pools in patients with chronic HIV-1 infection receiving antiretroviral therapy ( ART ) , it is uncertain whether a full immunologic reconstitution can be achieved .", "Moreover , the effects of IL-7 have n...	[ "The development of highly effective cocktails of antiretroviral drugs has had a major impact on the survival and quality of life of individuals with HIV-1 infection .", "Yet , current protocols often fail to fully restore the immunologic function , a limitation that has prompted the clinical evaluation of immune...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Myeloid Cell Arg1 Inhibits Control of Arthritogenic Alphavirus Infection by Suppressing Antiviral T Cells	journal.ppat.1005191	null	[ [ "Arthritogenic alphaviruses , including chikungunya virus ( CHIKV ) and Ross River virus ( RRV ) , are re-emerging , mosquito-transmitted alphaviruses that cause both endemic and explosive epidemics of debilitating musculoskeletal inflammatory disease [1] .", "CHIKV has caused outbreaks of unprecedented s...	[ "Arthritogenic alphaviruses , including Ross River virus ( RRV ) and chikungunya virus ( CHIKV ) , are responsible for explosive epidemics involving millions of cases .", "These mosquito-transmitted viruses cause inflammation and injury in skeletal muscle and joint tissues that results in debilitating pain .", ...	[ "Mosquito-transmitted chikungunya virus ( CHIKV ) , Ross River virus ( RRV ) , and related alphaviruses cause epidemics involving millions of persons , such as on-going CHIKV outbreaks in the Caribbean and Central and South America .", "Infection with these viruses results in severe pain due to inflammation of mu...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biophysics", "biology and life sciences", "computational biology" ]	Membrane Interaction of Bound Ligands Contributes to the Negative Binding Cooperativity of the EGF Receptor	journal.pcbi.1003742	null	[ [ "The epidermal growth factor receptor ( EGFR ) , a member of the Her ( ErbB ) family of cell-surface receptors , is critical to a variety of cellular processes and is implicated in the development of several forms of cancer and other diseases [1]–[3] .", "In normal cells , EGFR activation is initiated by ...	[ "The epidermal growth factor receptor ( EGFR ) plays a key role in regulating cell proliferation , migration , and differentiation , and aberrant EGFR signaling is implicated in a variety of cancers .", "EGFR signaling is triggered by extracellular ligand binding , which promotes EGFR dimerization and activation ...	[ "Epidermal growth factor receptor ( EGFR ) molecules are of central importance in cellular communication .", "Embedded in the cell membrane , these receptors bind epidermal growth factor ( EGF ) molecules outside the cell and translate this binding into specific biochemical signals inside the cell , which in turn...	2014
[ "Introduction", "Methods", "Results and Discussion" ]	[ "mycobacterium leprae", "medicine and health sciences", "pathology and laboratory medicine", "intracellular pathogens", "pathogens", "tropical diseases", "animal models", "bacterial diseases", "model organisms", "metabolites", "neglected tropical diseases", "bacteria", "nucleic acid metaboli...	Profiling of Intracellular Metabolites: An Approach to Understanding the Characteristic Physiology of Mycobacterium leprae	journal.pntd.0004881	null	[ [ "Mycobacterium leprae , the causative agent of leprosy , is an obligate intracellular pathogen having unique features .", "The doubling time of M . leprae is about 14 days as compared to approximately 24 hours of M . tuberculosis or the vaccine strain M . bovis BCG .", "The inability to cultivate M . ...	[ "Mycobacterium leprae is the causative agent of leprosy and also known to possess unique features such as inability to proliferate in vitro .", "Among the cellular components of M . leprae , various glycolipids present on the cell envelope are well characterized and some of them are identified to be pathogenic fa...	[ "Mycobacterium leprae , the causative agent of leprosy , has unique physiological features including being uncultivable in artificial media .", "This fact raises the possibility that M . leprae possesses specific metabolism that are different from other cultivable mycobacteria .", "Among the components of M . l...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "animal genetics", "molecular development", "gene expression", "genetics", "gene regulation", "biology and life sciences", "molecular genetics", "morphogenesis", "pattern formation", "cell differentiation", "gene function" ]	Spermatid Cyst Polarization in Drosophila Depends upon apkc and the CPEB Family Translational Regulator orb2	journal.pgen.1004380	null	[ [ "Polarity plays a central role in a diverse array of biological contexts in organisms ranging from single cell bacteria to complex multicellular eukaryotes .", "In multicellular eukaryotes , the steps involved in establishing , maintaining , and transmitting polarity are typically controlled by an interac...	[ "Mature Drosophila sperm are highly polarized cells—on one side is a nearly 2 mm long flagellar tail that comprises most of the cell , while on the other is the sperm head , which carries the gamete's genetic information .", "The polarization of the sperm cells commences after meiosis is complete and the 64-cell ...	[ "After completion of meiosis , the 64 cells in the spermatid cyst begin differentiating into sperm .", "Sperm are highly polarized cells and a critical step in their differentiation is spermatid cyst polarization .", "Spermatids are also polarized within the testis , with the heads of the elongating spermatids ...	2014
[ "Introduction", "Results", "Discussion" ]	[ "chemical biology/small molecule chemistry", "infectious diseases", "genetics and genomics/comparative genomics", "pharmacology/drug development", "computational biology/metabolic networks", "pharmacology", "computational biology/metagenomics", "genetics and genomics", "computational biology/systems...	A Mapping of Drug Space from the Viewpoint of Small Molecule Metabolism	journal.pcbi.1000474	null	[ [ "Drug developers have long mined small molecule metabolism for new drug targets and chemical strategies for inhibition .", "The approach leverages the “chemical similarity principle” [1] which states that similar molecules likely have similar properties .", "Applied to small molecule metabolism , this...	[ "Small molecule drugs target many core metabolic enzymes in humans and pathogens , often mimicking endogenous ligands .", "The effects may be therapeutic or toxic , but are frequently unexpected .", "A large-scale mapping of the intersection between drugs and metabolism is needed to better guide drug discovery ...	[ "All humans , plants , and animals use enzymes to metabolize food for energy , build and maintain the body , and get rid of toxins .", "Drugs used to clear infections or cure cancer often target enzymes in bacteria or cancer cells , but the drugs can interfere with the proper function of human enzymes as well .",...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "body fluids", "legs", "pathology and laboratory medicine", "pathogens", "geographical locations", "microbiology", "limbs (anatomy)", "saliva", "animals", "ethnicities", "viruses", "rna viruses", "insect vectors", "infectious diseases", ...	Vector Competence of French Polynesian Aedes aegypti and Aedes polynesiensis for Zika Virus	journal.pntd.0005024	null	[ [ "Zika virus ( ZIKV; Flaviviridae: Flavivirus ) infection usually produces fever , skin rashes , conjunctivitis , muscle and joint pain , malaise and headache with potential neurological and auto-immune complications [1] .", "Isolated first in 1947 from a febrile monkey in the Zika forest in Uganda [2] , o...	[ "In 2013–2014 , French Polynesia experienced for the first time a Zika outbreak .", "Two Aedes mosquitoes may have contributed to Zika virus ( ZIKV ) transmission in French Polynesia: the worldwide distributed Ae .", "aegypti and the Polynesian islands-endemic Ae .", "polynesiensis mosquito .", "To evaluate...	[ "From 2007 , Zika virus has caused several outbreaks in the Pacific including French Polynesia .", "Aedes aegypti mosquito which is present in almost all Pacific Island Countries is reasonably expected to have been involved in the Zika outbreaks .", "In addition endemic Aedes mosquito species may have sustained...	2016
[ "Introduction", "Results", "Discussion", "Materials & methods" ]	[ "medicine and health sciences", "chemical compounds", "pathology and laboratory medicine", "pathogens", "microbiology", "cloning", "organic compounds", "organisms", "fungi", "deletion mutagenesis", "experimental organism systems", "molecular biology techniques", "pharmacology", "mutagenesi...	Global analysis of genetic circuitry and adaptive mechanisms enabling resistance to the azole antifungal drugs	journal.pgen.1007319	null	[ [ "The evolution of drug resistance in fungal pathogens poses grave concern given the limited number of antifungal drugs currently available to treat systemic infections .", "These infections have increased in prevalence in recent years and are now a major cause of human mortality worldwide [1] , with the m...	[ "Invasive fungal infections caused by the pathogen Candida albicans have transitioned from a rare curiosity to a major cause of human mortality .", "This is in part due to the emergence of resistance to the limited number of antifungals available to treat fungal infections .", "Azoles function by targeting the ...	[ "Fungal infections caused by the pathogen Candida albicans pose a serious threat to human health .", "Treating these infections relies heavily on the azole antifungals , however , resistance to these drugs develops readily demanding novel therapeutic strategies .", "We performed large-scale systematic screens i...	2018
[ "Introduction", "Results", "Discussion", "Material and Methods" ]	[ "genetics and genomics/gene expression", "genetics and genomics/functional genomics", "developmental biology/plant growth and development", "plant biology/plant growth and development", "plant biology/plant genetics and gene expression", "genetics and genomics/plant genetics and gene expression" ]	Repression of Flowering by the miR172 Target SMZ	journal.pbio.1000148	The flowering repressors SMZ and FLM, members of the AP-2 and MADS domain transcription factor families, unexpectedly work together to regulate flowering time via their effects on expression of the FT gene.	[ [ "Throughout their lives , plants progress through distinct developmental phases , from germination and vegetative growth to flowering and , finally , senescence .", "The transition from vegetative growth to flowering is of particular importance because the correct timing of this switch is mandatory to ens...	[ "A small mobile protein , encoded by the FLOWERING LOCUS T ( FT ) locus , plays a central role in the control of flowering .", "FT is regulated positively by CONSTANS ( CO ) , the output of the photoperiod pathway , and negatively by FLC , which integrates the effects of prolonged cold exposure .", "Here , we r...	[ "Flowering is a pivotal event in the life cycle of many plants and is therefore under tight control .", "The ability to detect the daily photoperiod is of particular importance in many plant species , as it enables them to enter the reproductive phase in response to seasonal changes in day length .", "When the ...	2009
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "nucleic acid synthesis", "pathology and laboratory medicine", "togaviruses", "chikungunya infection", "gene regulation", "pathogens", "tropical diseases", "microbiology", "alphaviruses", "viruses", "chikungunya virus", "rna viruses", "neglected tropical dis...	Chikungunya virus requires cellular chloride channels for efficient genome replication	journal.pntd.0007703	null	[ [ "Chikungunya virus ( CHIKV ) is a mosquito-borne virus of the Alphavirus genus in the Togaviridae family .", "It was first isolated during an outbreak in Tanzania in 1952 [1] , since which its geographic range has expanded globally to include almost 40 countries [2] .", "Following transmission , CHIKV...	[ "Chikungunya virus ( CHIKV ) is a re-emerging , pathogenic alphavirus that is transmitted to humans by Aedes spp .", "mosquitoes—causing fever and debilitating joint pain , with frequent long-term health implications and high morbidity .", "The CHIKV lifecycle is poorly understood and specific antiviral therape...	[ "Chikungunya virus ( CHIKV ) is a mosquito-borne virus that infects humans and causes chikungunya fever—characterized by fever , rash and chronic arthralgia .", "Treatment of chikungunya fever is limited to the alleviation of the symptoms and no vaccine is available to prevent infection .", "Consequently , new ...	2019
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "biology" ]	MAPK/ERK Signaling Regulates Insulin Sensitivity to Control Glucose Metabolism in Drosophila	journal.pgen.1002429	null	[ [ "The insulin signaling pathway is a highly conserved regulatory network coordinating animal metabolism and growth with nutritional status .", "In mammals , energy metabolism is regulated by insulin , and tissue growth by insulin-like growth factors ( IGFs ) , through their respective receptors ( for revie...	[ "The insulin/IGF-activated AKT signaling pathway plays a crucial role in regulating tissue growth and metabolism in multicellular animals .", "Although core components of the pathway are well defined , less is known about mechanisms that adjust the sensitivity of the pathway to extracellular stimuli .", "In hum...	[ "Insulin signaling is an important and conserved physiological regulator of growth , metabolism , and longevity in multicellular animals .", "Disturbance in insulin signaling is common in human metabolic disorders .", "For example insulin resistance is a hallmark of diabetes and metabolic syndrome .", "While ...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "growth restriction", "brown adipose tissue", "pediatrics", "animal models", "age groups", "developmental biology", "adults", "model organisms", "child growth", "mitochondria", "epigenetics", "bioenergetics", "cellular structures and organelles", "research...	Cdkn1c Boosts the Development of Brown Adipose Tissue in a Murine Model of Silver Russell Syndrome	journal.pgen.1005916	null	[ [ "Silver-Russell syndrome ( SRS; MIM 180860 ) , Beckwith Weidemann Syndrome ( BWS; MIM 130650 ) and IMAGe syndrome ( MIM 614732 ) are all rare imprinted developmental disorders that occur as a result of genetic or epigenetic alterations primarily at human chromosome 11p15 [1 , 2] .", "Recent studies highli...	[ "The accurate diagnosis and clinical management of the growth restriction disorder Silver Russell Syndrome ( SRS ) has confounded researchers and clinicians for many years due to the myriad of genetic and epigenetic alterations reported in these patients and the lack of suitable animal models to test the contributi...	[ "Silver Russell syndrome is a severe developmental disorder characterised by low birth weight , sparing of the head and neonatal hypoglycemia .", "SRS adults are small and can be extremely thin , lacking body fat .", "Numerous genetic and epigenetic mutations have been linked to SRS primarily involving imprinte...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell cycle and cell division", "cell processes", "dna-binding proteins", "dna damage", "fungi", "model organisms", "polymerases", "dna replication", "immunoprecipitation", "experimental organism systems", "dna", "epigenetics", "synthesis phase", "co-immunoprecipitation", "chromatin", ...	PCNA ubiquitylation ensures timely completion of unperturbed DNA replication in fission yeast	journal.pgen.1006789	null	[ [ "It is well established that the replication machinery encounters a variety of obstacles and is thus designed with a degree of flexibility .", "This plasticity of DNA replication depends on both alternative components and regulation by post-translational modification .", "For example , while genetic a...	[ "PCNA ubiquitylation on lysine 164 is required for DNA damage tolerance .", "In many organisms PCNA is also ubiquitylated in unchallenged S phase but the significance of this has not been established .", "Using Schizosaccharomyces pombe , we demonstrate that lysine 164 ubiquitylation of PCNA contributes to effi...	[ "PCNA is a homotrimeric complex that clamps around the DNA to provide a sliding platform for DNA polymerases and other replication and repair enzymes .", "The covalent modification of PCNA by ubiquitin on lysine reside 164 has been extensively studied in the context of DNA repair: it is required to mediate the by...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "mammals", "physiology", "eukaryotes", "vertebrates", "mus (mouse)", "animals", "genetics and genomics" ]	COUP-TFII Mediates Progesterone Regulation of Uterine Implantation by Controlling ER Activity	journal.pgen.0030102	null	[ [ "Establishment of uterine receptivity is mandatory for successful embryo apposition , attachment , and implantation; failure to manifest this uterine state is an underlying cause of most pregnancy failures in women .", "A multitude of signaling molecules have been shown to play key roles in the elaboratio...	[ "Progesterone and estrogen are critical regulators of uterine receptivity .", "To facilitate uterine remodeling for embryo attachment , estrogen activity in the uterine epithelia is attenuated by progesterone; however , the molecular mechanism by which this occurs is poorly defined .", "COUP-TFII ( chicken oval...	[ "Pregnancy is established and maintained through a series of precisely choreographed cellular and molecular events that are controlled by two sex hormones , estrogen and progesterone .", "Both hormones exert their actions through their distinct nuclear receptors .", "During the peri-implantation period , estrog...	2007
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics and genomics", "virology" ]	Unexpected Inheritance: Multiple Integrations of Ancient Bornavirus and Ebolavirus/Marburgvirus Sequences in Vertebrate Genomes	journal.ppat.1001030	null	[ [ "The integration of a DNA copy of the retroviral RNA genome into the DNA of infected cells is an essential step in the replication of these viruses .", "Portions of DNA tumor virus genomes can also become integrated into cellular DNA , but this is a relatively rare event , detected by selection of a clone...	[ "Vertebrate genomes contain numerous copies of retroviral sequences , acquired over the course of evolution .", "Until recently they were thought to be the only type of RNA viruses to be so represented , because integration of a DNA copy of their genome is required for their replication .", "In this study , an ...	[ "Vertebrate genomes contain numerous copies of retroviral sequences , acquired over the course of evolution .", "Until recently they were thought to be the only type of RNA viruses to be so represented .", "In this comprehensive study , we compared sequences representing all known non-retroviruses containing si...	2010
[ "Introduction", "Model", "Results", "Discussion" ]	[ "physics", "mathematics", "biology", "computational biology", "nonlinear dynamics", "biophysics", "neuroscience" ]	Embedding Responses in Spontaneous Neural Activity Shaped through Sequential Learning	journal.pcbi.1002943	null	[ [ "The way in which neural processing of sensory inputs leads to cognitive functions is one of the most important issues in neuroscience .", "Neural activity in the presence of sensory stimuli [1]–[4] and during the execution of cognitive tasks in response to sensory inputs have been measured experimentally...	[ "Recent experimental measurements have demonstrated that spontaneous neural activity in the absence of explicit external stimuli has remarkable spatiotemporal structure .", "This spontaneous activity has also been shown to play a key role in the response to external stimuli .", "To better understand this role ,...	[ "The neural activity without explicit stimuli shows highly structured patterns in space and time , known as spontaneous activity .", "This spontaneous activity plays a key role in the behavior of the response to external stimuli generated by the interplay between the spontaneous activity and external input .", ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biophysics/cell signaling and trafficking structures", "neuroscience/theoretical neuroscience" ]	Quantifying the Effects of Elastic Collisions and Non-Covalent Binding on Glutamate Receptor Trafficking in the Post-Synaptic Density	journal.pcbi.1000780	null	[ [ "Ligand-gated neurotransmitter receptors in the post-synaptic membrane respond to neurotransmitter release and thereby mediate rapid signaling at neuronal synapses .", "Efficient synaptic signaling demands that these receptors be concentrated at high densities in order to optimally respond to rapidly diff...	[ "One mechanism of information storage in neurons is believed to be determined by the strength of synaptic contacts .", "The strength of an excitatory synapse is partially due to the concentration of a particular type of ionotropic glutamate receptor ( AMPAR ) in the post-synaptic density ( PSD ) .", "AMPAR conc...	[ "One of the most accepted theories of information storage in neurons is that it is partially localized in the strength of synaptic contacts .", "Evidence suggests that at the cellular level , in combination with other cellular mechanisms , this is implemented by increasing or decreasing the concentration of a par...	2010
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "chromosome structure and function", "gene therapy", "cancer treatment", "cancers and neoplasms", "oncology", "animal models", "telomeres", "dna damage", "model organisms", "experimental organism systems", "molecular biology techniques", "secondary lung tumors...	AAV9-mediated telomerase activation does not accelerate tumorigenesis in the context of oncogenic K-Ras-induced lung cancer	journal.pgen.1007562	null	[ [ "Telomeres are nucleoprotein structures localized at the ends of eukaryotic chromosomes , which are essential to protect them from degradation and end-to-end chromosome fusions .", "In mammals , telomeric DNA consists of TTAGGG tandem repeats bound by a 6-protein complex known as shelterin [1 , 2] .", ...	[ "Short and dysfunctional telomeres are sufficient to induce a persistent DNA damage response at chromosome ends , which leads to the induction of senescence and/or apoptosis and to various age-related conditions , including a group of diseases known as “telomere syndromes” , which are provoked by extremely short te...	[ "The ends of our chromosomes , or telomeres , shorten with age .", "When telomeres become critically short cells stop dividing and die .", "Shortened telomeres are associated with onset of age-associated diseases .", "Telomerase is a retrotranscriptase enzyme that is able to elongate telomeres by coping an as...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "major histocompatibility complex", "pathology and laboratory medicine", "clinical immunology", "host-pathogen interactions", "immunity", "antigen processing and recognition", "virology", "viral immune evasion", "viral persistence and latency", "viruses and cancer...	Cooperation between Epstein-Barr Virus Immune Evasion Proteins Spreads Protection from CD8+ T Cell Recognition across All Three Phases of the Lytic Cycle	journal.ppat.1004322	null	[ [ "Members of the human herpes family of viruses have co-evolved with their hosts to persist as largely asymptomatic , latent infections .", "However , under conditions of immune T cell impairment as seen for example in immunosuppressed transplant recipients , herpesviruses may reactivate , often with clini...	[ "CD8+ T cell responses to Epstein-Barr virus ( EBV ) lytic cycle expressed antigens display a hierarchy of immunodominance , in which responses to epitopes of immediate-early ( IE ) and some early ( E ) antigens are more frequently observed than responses to epitopes of late ( L ) expressed antigens .", "It has b...	[ "Epstein Barr Virus ( EBV ) , an oncogenic herpesvirus , infects and persists asymptomatically in the majority of humans .", "In immunocompetent individuals , EBV co-exists with its host as a lifelong infection in the face of strong anti-viral CD8+ T-cell responses .", "Evasion of this immune-response is presum...	2014
[ "Introduction", "Results", "Discussion", "Conclusion", "Methods" ]	[ "sequencing techniques", "biogeography", "taxonomy", "organismal evolution", "ecology and environmental sciences", "mitochondrial dna", "population genetics", "microbiology", "vertebrates", "animals", "mammals", "sequence assembly tools", "phylogenetics", "data management", "microbial ev...	Secondary contact between diverged host lineages entails ecological speciation in a European hantavirus	journal.pbio.3000142	Like host, like virus; analysis of a natural hybrid zone in the European common vole reveals speciation processes in Tula hantaviruses triggered by evolutionary divergence in the rodent host lineages.	[ [ "Evolutionary diversification has resulted in a myriad of virus species [1 , 2] , but—despite their great importance as agents of diseases of humans , crops , and livestock—our understanding of their functional partitioning and distribution across hosts is strongly limited .", "The evolution of novel vira...	[ "The diversity of viruses probably exceeds biodiversity of eukaryotes , but little is known about the origin and emergence of novel virus species .", "Experimentation and disease outbreak investigations have allowed the characterization of rapid molecular virus adaptation .", "However , the processes leading to...	[ "Natural biodiversity is driven by stochastic processes and evolutionary adaptation to ecological niches .", "In viruses , adaptation to specific hosts may cause diversification and eventually lead to the emergence of novel viruses .", "Here , we studied diversity in Tula orthohantavirus ( TULV ) in relation to...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "homo (human)", "mammals", "computational biology" ]	Analysis of Sequence Conservation at Nucleotide Resolution	journal.pcbi.0030254	null	[ [ "Comparative sequence analysis has had a major impact on molecular biology and genetics .", "Comparison of the sequences of protein-coding genes between multiple species has enabled prediction of gene function [1] , identification of protein domains [2] , prediction of functional amino acid residues [3 , ...	[ "One of the major goals of comparative genomics is to understand the evolutionary history of each nucleotide in the human genome sequence , and the degree to which it is under selective pressure .", "Ascertainment of selective constraint at nucleotide resolution is particularly important for predicting the functi...	[ "The structure of the human genome remains largely unknown , including which parts of the genome are functionally relevant and which parts are “junk . ”", "The availability of genomic sequence from a large number of mammals allows a more detailed exploration of this structure , using comparison of related sequenc...	2007
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Trends of Mycobacterium bovis Isolation and First-Line Anti-tuberculosis Drug Susceptibility Profile: A Fifteen-Year Laboratory-Based Surveillance	journal.pntd.0004124	null	[ [ "Tuberculosis ( TB ) remains an important health problem in several regions of the world , especially in countries with a high prevalence of HIV infection .", "Mycobacterium tuberculosis complex ( MTBC ) includes closely related species among which M . tuberculosis , M . bovis , and M . africanum are the ...	[ "Mycobacterium tuberculosis causes the majority of tuberculosis ( TB ) cases in humans; however , in developing countries , human TB caused by M . bovis may be frequent but undetected .", "Human TB caused by M . bovis is considered a zoonosis; transmission is mainly through consumption of unpasteurized dairy prod...	[ "Human tuberculosis caused by Mycobacterium bovis ( HTBMb ) is a lesser-known form of the disease .", "The main route of transmission of HTBMb is the consumption of unpasteurized dairy products , causing mostly extrapulmonary disease .", "M . bovis is naturally resistant to pyrazinamide , a drug that allows for...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "gene regulation", "regulatory proteins", "dna-binding proteins", "dna transcription", "transcription factors", "dna", "epigenetics", "chromatin", "genomic signal processing", "transcriptional control", "chromosome biology", "proteins", "gene expression", "nucleosomes", "biochemistry", ...	Regulation of circadian clock transcriptional output by CLOCK:BMAL1	journal.pgen.1007156	null	[ [ "Virtually every mammalian cell harbors a circadian clock that regulates rhythmic gene expression to enable biological functions to occur at the most appropriate time of day .", "Circadian clocks rely on transcriptional feedback loops which are initiated in mammals by the heterodimeric transcription facto...	[ "The mammalian circadian clock relies on the transcription factor CLOCK:BMAL1 to coordinate the rhythmic expression of 15% of the transcriptome and control the daily regulation of biological functions .", "The recent characterization of CLOCK:BMAL1 cistrome revealed that although CLOCK:BMAL1 binds synchronously t...	[ "Circadian clocks in mammals rely on the heterodimeric transcription factor CLOCK:BMAL1 to drive rhythmic gene expression and allow biological functions to perform best at the most appropriate time of the day .", "Investigation of the mechanisms by which CLOCK:BMAL1 regulates its target genes transcription has le...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "biology" ]	Lu/BCAM Adhesion Glycoprotein Is a Receptor for Escherichia coli Cytotoxic Necrotizing Factor 1 (CNF1)	journal.ppat.1003884	null	[ [ "Urinary tract infections ( UTIs ) are among the most common bacterial infections of humans .", "More than 80% of UTIs are caused by Uropathogenic Escherichia coli ( UPEC ) strains [1] .", "Many pathogenic Escherichia coli strains including UPEC and strains inducing meningitis or soft tissue infection...	[ "The Cytotoxic Necrotizing Factor 1 ( CNF1 ) is a protein toxin which is a major virulence factor of pathogenic Escherichia coli strains .", "Here , we identified the Lutheran ( Lu ) adhesion glycoprotein/basal cell adhesion molecule ( BCAM ) as cellular receptor for CNF1 by co-precipitation of cell surface molec...	[ "We study a crucial virulence factor produced by pathogenic Escherichia coli strains , the Cytotoxic Necrotizing Factor 1 ( CNF1 ) .", "More than 80% of urinary tract infections ( UTIs ) , which are counted among the most common bacterial infections of humans , are caused by Uropathogenic Escherichia coli ( UPEC ...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Visual Nonclassical Receptive Field Effects Emerge from Sparse Coding in a Dynamical System	journal.pcbi.1003191	null	[ [ "As we seek to understand how sensory nervous systems process information about their environment , one of the most common quantitative descriptors of neural coding has been the notion of a classical receptive field ( CRF ) [1] .", "In general , the CRF is a measurement of the portion of the stimulus spac...	[ "Extensive electrophysiology studies have shown that many V1 simple cells have nonlinear response properties to stimuli within their classical receptive field ( CRF ) and receive contextual influence from stimuli outside the CRF modulating the cell's response .", "Models seeking to explain these non-classical rec...	[ "Simple cells in the primary visual cortex ( V1 ) demonstrate many response properties that are either nonlinear or involve response modulations ( i . e . , stimuli that do not cause a response in isolation alter the cell's response to other stimuli ) .", "These non-classical receptive field ( nCRF ) effects are ...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "action potentials", "medicine and health sciences", "neural networks", "applied mathematics", "membrane potential", "electrophysiology", "neuroscience", "simulation and modeling", "algorithms", "mathematics", "network analysis", "membrane electrophysiology", "distribution curves", "bioass...	Identification of excitatory-inhibitory links and network topology in large-scale neuronal assemblies from multi-electrode recordings	journal.pcbi.1006381	null	[ [ "Understanding the relationships between structure and function , dynamics and connectivity of neuronal circuits are a challenge of the modern neurosciences , especially as the characterization of neuronal interaction in terms of functional and effective connectivity [1–3] is concerned .", "Functional con...	[ "Functional-effective connectivity and network topology are nowadays key issues for studying brain physiological functions and pathologies .", "Inferring neuronal connectivity from electrophysiological recordings presents open challenges and unsolved problems .", "In this work , we present a cross-correlation b...	[ "The balance between excitation and inhibition is fundamental for proper brain functions and for this reason is precisely regulated in adult cortices .", "Impaired excitation/inhibition balance is often associated with several neurological disorders , such as epilepsy , autism and schizophrenia .", "However , e...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biofilms", "blood cells", "biotechnology", "fluorescence imaging", "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "pathogens", "immunology", "catheters", "microbiology", "fungi", "model organisms", "microscopy", "cellular structures and organelles",...	The Extracellular Matrix of Candida albicans Biofilms Impairs Formation of Neutrophil Extracellular Traps	journal.ppat.1005884	null	[ [ "Candida albicans is a widespread nosocomial fungal pathogen and frequent cause of bloodstream infection [1] .", "One of the most common risk factors of invasive candidiasis is medical device placement , with nearly 80% of patients having vascular catheters [2] .", "On these and other medical devices ...	[ "Neutrophils release extracellular traps ( NETs ) in response to planktonic C . albicans .", "These complexes composed of DNA , histones , and proteins inhibit Candida growth and dissemination .", "Considering the resilience of Candida biofilms to host defenses , we examined the neutrophil response to C . albic...	[ "Candida spp .", "avidly adhere to medical device surfaces , forming resilient , drug-tolerant biofilms which are encased in a protective extracellular matrix .", "These infections are notoriously difficult to eradicate and little is known about how they evade host defenses .", "Here we show a mechanism by wh...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "veterinary diseases", "genomics", "molecular cell biology", "zoology", "evolutionary biology", "biology", "computational biology", "proteomics", "genetics and genomics", "veterinary science" ]	Comparative Genomics of the Apicomplexan Parasites Toxoplasma gondii and Neospora caninum: Coccidia Differing in Host Range and Transmission Strategy	journal.ppat.1002567	null	[ [ "Toxoplasma gondii and Neospora caninum are closely related tissue-dwelling Coccidia – intracellular protozoan parasites of the phylum Apicomplexa .", "T . gondii can infect essentially any warm-blooded vertebrate and is found in nearly one third of humans , arguably being the world's most successful zoon...	[ "Toxoplasma gondii is a zoonotic protozoan parasite which infects nearly one third of the human population and is found in an extraordinary range of vertebrate hosts .", "Its epidemiology depends heavily on horizontal transmission , especially between rodents and its definitive host , the cat .", "Neospora cani...	[ "Coccidian parasites have a major impact on human and animal health world-wide and are among the most successful and widespread parasitic protozoa .", "They include Neospora caninum which is a leading cause of abortion in cattle and one of its nearest relatives , Toxoplasma gondii .", "Despite its close phyloge...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "microbial mutation", "immune physiology", "pathology and laboratory medicine", "pathogens", "immunology", "microbiology", "viruses", "vaccines", "preventive medicine", "rna viruses", "vaccination and immunization", "public and occupational health", "immune ...	Cold-Adapted Viral Attenuation (CAVA): Highly Temperature Sensitive Polioviruses as Novel Vaccine Strains for a Next Generation Inactivated Poliovirus Vaccine	journal.ppat.1005483	null	[ [ "There are two vaccines that can effectively protect against poliomyelitis which have been available for more than 60 years and are still used today .", "The Inactivated Poliovirus Vaccine ( IPV ) , today referred to as conventional ( c ) IPV , was developed in 1955 by Jonas Salk and contains three formal...	[ "The poliovirus vaccine field is moving towards novel vaccination strategies .", "Withdrawal of the Oral Poliovirus Vaccine and implementation of the conventional Inactivated Poliovirus Vaccine ( cIPV ) is imminent .", "Moreover , replacement of the virulent poliovirus strains currently used for cIPV with atten...	[ "The vaccines that are used to protect against poliovirus infection have been available since the 1950s and have brought the eradication of poliomyelitis to our doorstep .", "For the post-eradication era , an Inactivated Poliovirus Vaccine ( IPV ) based on attenuated Sabin strains is recommended , as these strain...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "oncology", "developmental biology", "oncology/myeloproliferative disorders, including chronic myeloid leukemia", "cell biology", "hematology" ]	Oncogenic Kras Initiates Leukemia in Hematopoietic Stem Cells	journal.pbio.1000059	TheKrasG12D oncogene causes excessive proliferation of stem cells, promoting their preferential expansion and initiating myeloproliferative disease.KrasG12D does not alter self-renewal, but secondary mutations in lymphoid progenitors allow progression to acute leukemia.	[ [ "Self-renewal is integral to the malignant phenotype [1] .", "In principle , the ability of cancer cells to self-renew may be intrinsic to the compartment in which the tumor-initiating mutation occurs , or may be acquired as a consequence of mutations in more differentiated cells .", "The hematopoieti...	[ "How oncogenes modulate the self-renewal properties of cancer-initiating cells is incompletely understood .", "Activating KRAS and NRAS mutations are among the most common oncogenic lesions detected in human cancer , and occur in myeloproliferative disorders ( MPDs ) and leukemias .", "We investigated the effec...	[ "Ras proteins act as molecular switches that relay growth signals from outside the cell .", "This mechanism is often subverted in cancer , and Ras proteins are activated directly by RAS gene mutations in approximately one-third of human malignancies .", "We have modeled this in mice engineered to have a Ras mut...	2009
[ "Introduction", "Results and Discussion", "Materials and Methods" ]	[]	The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds	journal.pbio.1002224	A study of ancient genetic variation reveals genomic evidence for near-simultaneous speciation at the base of Neoaves (a group containing most modern birds), which temporally coincides with the mass extinction of nonavian dinosaurs and archaic birds.	[ [ "The rich biodiversity of many organismal groups is the result of bursts of rapid species diversifications , with extreme examples in angiosperms [1] and vertebrates [2] .", "Among the latter , birds are one of the most speciose groups with a total of >10 , 500 recognized species that are proposed to be t...	[ "The diversification of neoavian birds is one of the most rapid adaptive radiations of extant organisms .", "Recent whole-genome sequence analyses have much improved the resolution of the neoavian radiation and suggest concurrence with the Cretaceous-Paleogene ( K-Pg ) boundary , yet the causes of the remaining g...	[ "The rise of modern birds began after the mass extinction of nonavian dinosaurs and archaic birds at the Cretaceous-Paleogene ( K-Pg ) boundary , about 66 million years ago .", "This coincides with the super-rapid adaptive radiation of Neoaves ( a group that contains most modern birds ) , which has been difficult...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "microbiology/cellular microbiology and pathogenesis" ]	Sphingomyelin Functions as a Novel Receptor for Helicobacter pylori VacA	journal.ppat.1000073	null	[ [ "The vacuolating cytotoxin ( VacA ) is an intracellular-acting toxin generated by the pathogen , Helicobacter pylori , which infects the gastric epithelium of humans and is a significant risk factor for the development of peptic ulcer disease , distal gastric adenocarcinoma , and gastric lymphoma in humans [1...	[ "The vacuolating cytotoxin ( VacA ) of the gastric pathogen Helicobacter pylori binds and enters epithelial cells , ultimately resulting in cellular vacuolation .", "Several host factors have been reported to be important for VacA function , but none of these have been demonstrated to be essential for toxin bindi...	[ "Sensitivity to toxins produced by pathogenic bacteria is largely dictated by the presence or absence of toxin receptors on the plasma membrane of host cells .", "VacA is an important toxin produced by the pathogenic bacterium Helicobacter pylori , which infects the human stomach and causes gastric ulcer disease ...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "cell fate determination", "gene regulation", "genetics", "molecular genetics", "biology", "genetics and genomics", "cell differentiation", "gene function" ]	Nkx6.1 Controls a Gene Regulatory Network Required for Establishing and Maintaining Pancreatic Beta Cell Identity	journal.pgen.1003274	null	[ [ "Innovative strategies for diabetes therapy aim to replace lost insulin-producing beta cells by reprogramming other cell types or by deriving beta cells from pluripotent cells .", "Ectopic expression of the transcription factors Pdx1 , Neurogenin 3 ( encoded by the Neurog3 gene; Ngn3 ) , and MafA has been...	[ "All pancreatic endocrine cell types arise from a common endocrine precursor cell population , yet the molecular mechanisms that establish and maintain the unique gene expression programs of each endocrine cell lineage have remained largely elusive .", "Such knowledge would improve our ability to correctly progra...	[ "Diabetes is a disease caused by the loss or dysfunction of insulin-producing beta cells in the pancreas .", "Recent studies suggest that modification of the beta cells' differentiation state is among the earliest events marking the progressive failure of beta cells in diabetes .", "Currently , very little is k...	2013
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "flow cytometry", "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "biological cultures", "geographical locations", "microbiology", "dna-binding proteins", "hepatoma cells", "vaccines", "animal models", "organisms", "viruses", "model organisms", "polymera...	Yellow fever virus is susceptible to sofosbuvir both in vitro and in vivo	journal.pntd.0007072	null	[ [ "Yellow fever virus ( YFV ) is a single-strand positive-sense RNA virus which belongs to the Flaviviridae family .", "Yellow fever ( YF ) outbreaks were very common throughout the tropical world until the beginning of the 20th century , when vaccination and vector control limited the urban virus circulati...	[ "Yellow fever virus ( YFV ) is a member of the Flaviviridae family .", "In Brazil , yellow fever ( YF ) cases have increased dramatically in sylvatic areas neighboring urban zones in the last few years .", "Because of the high lethality rates associated with infection and absence of any antiviral treatments , i...	[ "Yellow fever virus is transmitted by mosquitoes and its infection may be asymptomatic or lead to a wide clinical spectrum ranging from a mild febrile illness to a potentially lethal viral hemorrhagic fever characterized by liver damage .", "Although a yellow fever vaccine is available , low coverage allows 80 , ...	2019
[ "Introduction", "Results and discussion", "Conclusions", "Materials and methods" ]	[ "methods and resources", "vertebrates", "chickens", "animals", "dna transcription", "developmental biology", "sequence motif analysis", "molecular biology techniques", "embryos", "research and analysis methods", "sequence analysis", "embryology", "birds", "bioinformatics", "gene mapping"...	Systematic analysis of transcription start sites in avian development	journal.pbio.2002887	null	[ [ "Single-molecule sequencing technology in combination with Cap Analysis of Gene Expression ( CAGE ) allows mapping and quantification of transcription start sites ( TSSs ) at single base pair resolution [1 , 2] .", "Application of this technology to a large collection of human and mouse samples , covering...	[ "Cap Analysis of Gene Expression ( CAGE ) in combination with single-molecule sequencing technology allows precision mapping of transcription start sites ( TSSs ) and genome-wide capture of promoter activities in differentiated and steady state cell populations .", "Much less is known about whether TSS profiling ...	[ "Early development cannot be studied in humans .", "Analysis of embryogenesis using avian models , which are phylogenetically closely related to mammals , can help us understand the complex regulatory mechanism of cell lineage specification during human development .", "We monitored the 3 weeks of chicken embry...	2017
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "dengue virus", "medicine and health sciences", "immune physiology", "enzyme-linked immunoassays", "pathology and laboratory medicine", "pathogens", "immunology", "geographical locations", "microbiology", "tropical diseases", "indonesia", "viruses", "age groups", "rna viruses", "neglecte...	Dengue virus serotype distribution based on serological evidence in pediatric urban population in Indonesia	journal.pntd.0006616	null	[ [ "Dengue is a febrile illness caused by dengue virus ( DENV ) infection .", "The clinical manifestations of dengue occur on a spectrum , ranging from asymptomatic or a mild flu-like syndrome known as classic dengue fever ( DF ) , to a more severe form known as dengue hemorrhagic fever ( DHF ) and the poten...	[ "Dengue is a febrile illness transmitted by mosquitoes , causing disease across the tropical and sub-tropical world .", "Antibody prevalence data and serotype distributions describe population-level risk and inform public health decision-making .", "In this cross-sectional study we used data from a pediatric de...	[ "Dengue is a febrile illness transmitted by mosquitoes , causing disease across the tropical and sub-tropical world .", "Antibody prevalence data and serotype distribution describe population-level risk and inform public health decision-making .", "We present data from a dengue seroprevalence study in children ...	2018
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "burkholderia pseudomallei", "melioidosis", "pathogens", "geographical locations", "microbiology", "animal models", "bacterial diseases", "rice", "physicochemical properties", "model organisms", "experimental organism syste...	Presence of B. thailandensis and B. thailandensis expressing B. pseudomallei-like capsular polysaccharide in Thailand, and their associations with serological response to B. pseudomallei	journal.pntd.0006193	null	[ [ "Burkholderia pseudomallei is a soil-dwelling Gram-negative bacterium and the cause of melioidosis , a frequently fatal infectious disease of humans and animals .", "Humans acquire the disease following skin inoculation , inhalation or ingestion of the bacterium from the environment .", "The disease i...	[ "Burkholderia pseudomallei is an environmental Gram-negative bacillus and the cause of melioidosis .", "B . thailandensis , some strains of which express a B . pseudomallei-like capsular polysaccharide ( BTCV ) , is also commonly found in the environment in Southeast Asia but is considered non-pathogenic .", "T...	[ "Burkholderia thailandensis is a non-pathogenic soil-dwelling bacterium and is genetically closely related to Burkholderia pseudomallei , the cause of melioidosis .", "In mouse models , inoculation of a variant of B . thailandensis which express a B . pseudomallei-like capsular polysaccharide ( BTCV ) induces ant...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "animal models", "medicine", "infectious diseases", "model organisms", "parasitic diseases", "chagas disease", "biology", "microbiology", "host-pathogen interaction", "mouse", "infectious disease control", "quantitative parasitology", "parasitology" ]	Parasitic Loads in Tissues of Mice Infected with Trypanosoma cruzi and Treated with AmBisome	journal.pntd.0001216	null	[ [ "Chagas disease is a leading cause of cardiac failure and the most important parasitic disease in terms of morbidity and mortality in Latin America .", "Its causal agent , the protozoan parasite Trypanosoma cruzi , belonging to the family of Trypanosomatidae , currently infects 8 to 10 million persons .",...	[ "Chagas disease is one of the most important public health problems and a leading cause of cardiac failure in Latin America .", "The currently available drugs to treat T . cruzi infection ( benznidazole and nifurtimox ) are effective in humans when administered during months .", "AmBisome ( liposomal amphoteric...	[ "Chagas disease is a leading cause of cardiac failure and the most important parasitic disease in terms of morbidity and mortality in Latin America .", "After an acute parasitaemic phase , infection naturally evolves to a long chronic phase .", "If the currently available trypanocidal drugs , benznidazole and n...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Minipool Caprylic Acid Fractionation of Plasma Using Disposable Equipment: A Practical Method to Enhance Immunoglobulin Supply in Developing Countries	journal.pntd.0003501	null	[ [ "Plasma products to treat congenital bleeding and immunological diseases are made in industrialized countries using complex technologies unavailable in the developing world [1] .", "Low- to medium-income countries may have little or no access to these life-saving products; these nations urgently need prac...	[ "Immunoglobulin G ( IgG ) is an essential plasma-derived medicine that is lacking in developing countries .", "IgG shortages leave immunodeficient patients without treatment , exposing them to devastating recurrent infections from local pathogens .", "A simple and practical method for producing IgG from normal ...	[ "Plasma-derived immunoglobulin G ( IgG ) is on WHO’s Essential Medicines List , yet developing countries face severe shortages of this critical treatment .", "Infusion of IgG prepared from locally-collected plasma provides an advantageous mix of antibodies to viral and bacterial pathogens found in the living envi...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "visual system", "fmri", "computational neuroscience", "sensory systems", "biology", "computational biology", "neuroscience", "neuroimaging", "coding mechanisms" ]	A Two-Stage Cascade Model of BOLD Responses in Human Visual Cortex	journal.pcbi.1003079	null	[ [ "Studies of visual cortex typically measure responses to a narrow set of stimuli designed to investigate a particular phenomenon .", "For example , a study might use sinusoidal gratings varying in contrast to study contrast response functions [1] , [2] , another study might use silhouettes to study shape ...	[ "Visual neuroscientists have discovered fundamental properties of neural representation through careful analysis of responses to controlled stimuli .", "Typically , different properties are studied and modeled separately .", "To integrate our knowledge , it is necessary to build general models that begin with a...	[ "Much has been learned about how stimuli are represented in the visual system from measuring responses to carefully designed stimuli .", "Typically , different studies focus on different types of stimuli .", "Making sense of the large array of findings requires integrated models that explain responses to a wide...	2013
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "lysosomes", "membrane potential", "sorption", "electrophysiology", "cellular structures and organelles", "thermodynamics", "physical chemistry", "lipids", "membrane composition", "chemistry", "cell membranes", "free energy", "cholesterol", "physics", "b...	Concerted regulation of npc2 binding to endosomal/lysosomal membranes by bis(monoacylglycero)phosphate and sphingomyelin	journal.pcbi.1005831	null	[ [ "Cholesterol , ubiquitously present in all vertebrate cells , regulates the structure and permeability of cellular membranes [1 , 2] .", "It comprises typically 20–25 mol % of all lipids in the plasma membrane [1] and acts as a precursor for many bioactive molecules such as steroid hormones , bile acids ,...	[ "Niemann-Pick Protein C2 ( npc2 ) is a small soluble protein critical for cholesterol transport within and from the lysosome and the late endosome .", "Intriguingly , npc2-mediated cholesterol transport has been shown to be modulated by lipids , yet the molecular mechanism of npc2-membrane interactions has remain...	[ "Cholesterol plays essential structural and functional roles in all vertebrate cells .", "Abnormalities in cholesterol metabolism are associated with severe and wide-spread diseases .", "Cholesterol efflux is one of the essential steps in its metabolism and is mediated by Niemann-Pick Protein C2 ( npc2 ) in end...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "population dynamics", "applied mathematics", "pathogens", "microbiology", "mathematical models", "bacterial diseases", "mathematics", "algebra", "enterobacteriaceae", "population biology", "bacteria", "bacterial pathogen...	Coevolutionary dynamics of phenotypic diversity and contingent cooperation	journal.pcbi.1005363	null	[ [ "How to understand the emergence and persistence of cooperation is a key problem in evolutionary biology [1–12] , since individuals sticking to cooperation produce benefits to others at a cost to themselves .", "The Prisoner’s Dilemma game , as an effective paradigm , has been widely employed to character...	[ "Phenotypic diversity is considered beneficial to the evolution of contingent cooperation , in which cooperators channel their help preferentially towards others of similar phenotypes .", "However , it remains largely unclear how phenotypic variation arises in the first place and thus leads to the construction of...	[ "Phenotypic variation is commonly observed from human cells to the intestinal pathogen Salmonella enterica serovar Typhimurium to the wrinkly-spreader morphs .", "Such phenotypic diversity proves effective in promoting cooperation , or confers survival advantage against unfavorable environmental changes .", "Pr...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "biology" ]	Mutated and Bacteriophage T4 Nanoparticle Arrayed F1-V Immunogens from Yersinia pestis as Next Generation Plague Vaccines	journal.ppat.1003495	null	[ [ "Plague , also known as Black Death , is one of the deadliest infectious diseases known to mankind .", "Yersinia pestis , the etiologic agent of plague , is a Gram-negative bacterium transmitted from rodents to humans via fleas [1] .", "The bite of an infected flea results in bubonic plague which can ...	[ "Pneumonic plague is a highly virulent infectious disease with 100% mortality rate , and its causative organism Yersinia pestis poses a serious threat for deliberate use as a bioterror agent .", "Currently , there is no FDA approved vaccine against plague .", "The polymeric bacterial capsular protein F1 , a key...	[ "Plague caused by Yersinia pestis is a deadly disease that wiped out one-third of Europe's population in the 14th century .", "The organism is listed by the CDC as Tier-1 biothreat agent , and currently , there is no FDA-approved vaccine against this pathogen .", "Stockpiling of an efficacious plague vaccine th...	2013

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