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headings list	keywords list	title stringlengths 20 281	id stringlengths 20 20	toc stringlengths 57 522 ⌀	sections list	abstract list	summary list	year stringclasses 13 values
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology/gene expression", "molecular biology/translation mechanisms", "molecular biology/bioinformatics", "biochemistry/transcription and translation", "molecular biology/translational regulation", "computational biology/systems biology" ]	A Comprehensive, Quantitative, and Genome-Wide Model of Translation	journal.pcbi.1000865	null	[ [ "The rate of translation differs for individual proteins , reflecting both the intrinsic capability of an mRNA molecule to be translated and the environmental factors affecting the efficiency of the translation process .", "The first is well characterised in other studies [1]–[3] that discuss mRNA feature...	[ "Translation is still poorly characterised at the level of individual proteins and its role in regulation of gene expression has been constantly underestimated .", "To better understand the process of protein synthesis we developed a comprehensive and quantitative model of translation , characterising protein syn...	[ "Translation is the production of proteins by decoding mRNA produced in transcription , and is a part of the overall process of gene expression .", "Although the general theoretical background of translation is known , the process is still poorly characterised at the level of individual proteins .", "In particu...	2010
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "body weight", "medicine and health sciences", "chemical compounds", "quantitative trait loci", "gene regulation", "population genetics", "carbohydrates", "organic compounds", "glucose", "epistasis", "physiological parameters", "chromosome mapping", "molecular biology techniques", "populat...	Widespread epistasis regulates glucose homeostasis and gene expression	journal.pgen.1007025	null	[ [ "The genetic basis of complex traits and diseases results from the combined action of many genetic variants [1] .", "However , it remains unclear whether these variants act individually in an additive manner or via non-additive epistatic interactions .", "Epistasis has been widely observed in model or...	[ "The relative contributions of additive versus non-additive interactions in the regulation of complex traits remains controversial .", "This may be in part because large-scale epistasis has traditionally been difficult to detect in complex , multi-cellular organisms .", "We hypothesized that it would be easier ...	[ "Most complex traits and diseases are regulated by the combined influence of multiple genetic variants .", "However , it remains controversial whether these genetic variants independently influence complex traits , and therefore the impact of each variant could be simply added together ( additivity ) , or whether...	2017
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "microbiology/plant-biotic interactions", "microbiology/microbial evolution and genomics" ]	Experimental Evolution of a Plant Pathogen into a Legume Symbiont	journal.pbio.1000280	Following acquisition of a rhizobial symbiotic plasmid, adaptive mutations in the virulence pathway allowed pathogenic Ralstonia solanacearum to evolve into a legume symbiont under plant selection.	[ [ "Bacteria known as rhizobia have evolved a mutualistic endosymbiosis of major ecological importance with legumes that contributes ca .", "25% of global nitrogen cycling .", "Rhizobia induce the formation on legumes of root nodules that they colonize intracellularly [1] and in which they fix nitrogen t...	[ "Rhizobia are phylogenetically disparate α- and β-proteobacteria that have achieved the environmentally essential function of fixing atmospheric nitrogen in symbiosis with legumes .", "Ample evidence indicates that horizontal transfer of symbiotic plasmids/islands has played a crucial role in rhizobia evolution ....	[ "Most leguminous plants can form a symbiosis with members of a group of soil bacteria known as rhizobia .", "On the roots of their hosts , some rhizobia elicit the formation of specialized organs , called nodules , that they colonize intracellularly and within which they fix nitrogen to the benefit of the plant ....	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "pediatrics and child health/developmental and pediatric neurology", "infectious diseases/infectious diseases of the nervous system", "infectious diseases/viral infections", "public health and epidemiology/infectious diseases", "public health and epidemiology/immunization" ]	Subacute Sclerosing Panencephalitis in Papua New Guinean Children: The Cost of Continuing Inadequate Measles Vaccine Coverage	journal.pntd.0000932	null	[ [ "Despite a declining incidence in developed countries , acute measles infection is still responsible for an estimated 164 , 000 deaths/year and is therefore a major vaccine-preventable cause of death worldwide [1] , [2] .", "Subacute sclerosing panencephalitis ( SSPE ) is a rare but usually fatal late com...	[ "Subacute sclerosing panencephalitis ( SSPE ) is a late , rare and usually fatal complication of measles infection .", "Although a very high incidence of SSPE in Papua New Guinea ( PNG ) was first recognized 20 years ago , estimated measles vaccine coverage has remained at ≤70% since and a large measles epidemic ...	[ "Subacute sclerosing panencephalitis ( SSPE ) is a disabling and usually fatal brain disorder that typically occurs 3–10 years after acute measles infection .", "Papua New Guinea ( PNG ) has particularly high rates of SSPE .", "We report 22 cases of PNG children presenting to the provincial referral hospital in...	2011
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases/protozoal infections", "infectious diseases/infectious diseases of the nervous system", "microbiology/parasitology", "infectious diseases/neglected tropical diseases" ]	Murine Models for Trypanosoma brucei gambiense Disease Progression—From Silent to Chronic Infections and Early Brain Tropism	journal.pntd.0000509	null	[ [ "Human African Trypanosomiasis ( HAT ) , also called sleeping sickness , is a widespread fatal disease in many rural areas of sub-Saharan Africa caused by protozoan parasites of the genus Trypanosoma transmitted by tsetse flies .", "Trypanosoma brucei rhodesiense is responsible for the acute form in East ...	[ "Human African trypanosomiasis ( HAT ) caused by Trypanosoma brucei gambiense remains highly prevalent in west and central Africa and is lethal if left untreated .", "The major problem is that the disease often evolves toward chronic or asymptomatic forms with low and fluctuating parasitaemia producing apparently...	[ "Trypanosoma brucei gambiense is responsible for more than 90% of reported cases of human African trypanosomosis ( HAT ) .", "Infection can last for months or even years without major signs or symptoms of infection , but if left untreated , sleeping sickness is always fatal .", "In the present study , different...	2009
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "phosphorylation", "medicine and health sciences", "gene regulation", "immunology", "regulator genes", "genome analysis", "gene types", "mapk signaling cascades", "proteins", "gene expression", "biochemistry", "signal transduction", "cell biology", "post-translational modification", "imm...	The Trihelix transcription factor GT2-like 1 (GTL1) promotes salicylic acid metabolism, and regulates bacterial-triggered immunity	journal.pgen.1007708	null	[ [ "Plants are faced with a constant threat of potential infections by a multiplicity of pathogenic microorganisms in their habitat .", "Pathogen-independent preformed physical borders like the cuticle , cell walls and wax coating represents the first line of plant defense to prevent pathogen invasion .", ...	[ "The Trihelix Transcription factor GT2-like 1 ( GTL1 ) was previously shown to be a key regulator of ploidy-dependent trichome growth and drought tolerance .", "Here , we report that GTL1 plays an important role in coordinating plant immunity .", "We show that gtl1 mutants are compromised in the regulation of b...	[ "The trihelix-transcription factor GT-2-like 1 ( GTL1 ) belongs to the seven genes containing GT-2 family of the plant-specific trihelix transcription factors .", "Previously , GTL1 was shown to be a key regulator of ploidy-dependent trichome growth and drought tolerance .", "In this report , we show that GTL1 ...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "medicine and health sciences", "pathology and laboratory medicine", "caenorhabditis", "liquid chromatography", "parasitic diseases", "animals", "toxicology", "nematode infections", "animal models", "toxicity", "caenorhabditis elegans", "model organisms", "metabolites", ...	The novel nematicide wact-86 interacts with aldicarb to kill nematodes	journal.pntd.0005502	null	[ [ "Parasitic nematodes infect more than one billion people worldwide , negatively impacting human health and productivity [1 , 2] .", "Dramatic worldwide economic losses are incurred from nematode infections of commercially vital crops and livestock [3–5] .", "As a result of the growing resistance of ne...	[ "Parasitic nematodes negatively impact human and animal health worldwide .", "The market withdrawal of nematicidal agents due to unfavourable toxicities has limited the available treatment options .", "In principle , co-administering nematicides at lower doses along with molecules that potentiate their activity...	[ "Many nematicides that have been used to kill plant and animal parasitic nematodes are being phased out over concerns of toxicity to humans .", "One potential solution to reduce toxicity is to use the nematicide at a lower concentration in combination with a second compound that together will produce a synergisti...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "immunology", "homo (human)" ]	BDCA2/FcεRIγ Complex Signals through a Novel BCR-Like Pathway in Human Plasmacytoid Dendritic Cells	journal.pbio.0050248	Plasmacytoid dendritic cells (pDCs) are renowned for their production of type 1 interferon in response to viral infection, which is signified by Toll-like receptor (TLR) activation. Here, blood dendritic cell antigen 2(BDCA2), a C-type lectin receptor expressed uniquely on pDCs, is shown to block the ultimate effectors...	[ [ "Dendritic cells ( DCs ) are specialized sentinels in the immune system that detect invading pathogens and pathological damages of the host .", "Upon activation , DCs instruct appropriate and effective immune responses [1–3] .", "Their extraordinary ability to capture antigens ( self or foreign ) is l...	[ "Dendritic cells are equipped with lectin receptors to sense the extracellular environment and modulate cellular responses .", "Human plasmacytoid dendritic cells ( pDCs ) uniquely express blood dendritic cell antigen 2 ( BDCA2 ) protein , a C-type lectin lacking an identifiable signaling motif .", "We demonstr...	[ "Dendritic cells ( DCs ) are specialized sentinels in the immune system that detect invading pathogens and , upon activation , initiate immune responses .", "DCs express C-type lectin receptors on their surface , which facilitate antigen capture .", "A distinct population of DCs , called plasmacytoid DCs ( pDCs...	2007
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "parasite groups", "body fluids", "plasmodium", "tropical diseases", "parasitic diseases", "animals", "parasitic protozoans", "parasitology", "parasitemia", "apicomplexa", "protozoans", "gastroenterology and hepatology", "liver function te...	Safety and Reproducibility of a Clinical Trial System Using Induced Blood Stage Plasmodium vivax Infection and Its Potential as a Model to Evaluate Malaria Transmission	journal.pntd.0005139	null	[ [ "A renewed focus on malaria elimination has increased the priority of research towards development of interventions to block malaria transmission , including transmission blocking vaccines ( TBVs ) .", "By interrupting transmission of malaria parasites to mosquito vectors , a reduction in the number of se...	[ "Interventions to interrupt transmission of malaria from humans to mosquitoes represent an appealing approach to assist malaria elimination .", "A limitation has been the lack of systems to test the efficacy of such interventions before proceeding to efficacy trials in the field .", "We have previously demonstr...	[ "Blocking the transmission of malaria from infected individuals to mosquitoes is an appealing approach to malaria elimination .", "However , at present there is no reliable experimental model to test the efficacy of transmission blocking interventions .", "In this study , we assessed the safety and reproducibil...	2016
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "leptospira", "immune physiology", "pathology and laboratory medicine", "pathogens", "immunology", "tropical diseases", "microbiology", "vertebrates", "animals", "mammals", "vaccines", "bacterial diseases", "neglected tropical diseases", "infectious diseas...	LigB subunit vaccine confers sterile immunity against challenge in the hamster model of leptospirosis	journal.pntd.0005441	null	[ [ "Leptospirosis , a spirochaetal zoonosis , has spread from its traditional rural base to cause epidemics in the urban centres of developing countries .", "Outbreaks occur during seasonal periods of heavy rainfall and affect at-risk groups in poor , urban slum communities .", "However , the global burd...	[ "Neglected tropical diseases , including zoonoses such as leptospirosis , have a major impact on rural and poor urban communities , particularly in developing countries .", "This has led to major investment in antipoverty vaccines that focus on diseases that influence public health and thereby productivity .", ...	[ "Leptospirosis , also known as Weil’s disease , is spread by contact with infected animals or with water and soil containing pathogenic spirochaetes belonging to the Leptospira genus .", "Leptospirosis is a serious public health problem that can cause kidney failure , pulmonary complications and can be fatal .", ...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "auditory system", "visual system", "computational neuroscience", "biology", "sensory systems", "neuroscience", "coding mechanisms" ]	Analysis of Slow (Theta) Oscillations as a Potential Temporal Reference Frame for Information Coding in Sensory Cortices	journal.pcbi.1002717	null	[ [ "Oscillatory activity generated by local cortical networks is considered to be a crucial component of sensory processing [1] , [2] , [3] and has been implicated in processes such as the temporal binding of neural assemblies , the control of information flow between areas [4] , [5] , or the multiplexing of inf...	[ "While sensory neurons carry behaviorally relevant information in responses that often extend over hundreds of milliseconds , the key units of neural information likely consist of much shorter and temporally precise spike patterns .", "The mechanisms and temporal reference frames by which sensory networks partiti...	[ "Neurons in sensory cortices encode objects in our sensory environment by varying the timing and number of action potentials that they emit .", "Brain networks that ‘decode’ this information need to partition those spike trains into their individual informative units .", "Experimenters achieve such partitioning...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments	journal.pcbi.1006982	null	[ [ "While millions of candidate enhancers have been predicted in the human genome , annotation of their target genes remains challenging , because enhancers do not always regulate the closest gene in the linear genome sequence [1] .", "Recognizing that distal enhancers frequently form chromatin loops with th...	[ "Hi-C and chromatin immunoprecipitation ( ChIP ) have been combined to identify long-range chromatin interactions genome-wide at reduced cost and enhanced resolution , but extracting information from the resulting datasets has been challenging .", "Here we describe a computational method , MAPS , Model-based Anal...	[ "Chromatin spatial organization plays an important role in genome function .", "The recently developed PLAC-seq and HiChIP technologies have become powerful tools to study long-range chromatin interactions .", "However , the biases introduced by the ChIP procedure have added substantial difficulty in data analy...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Structural Insights into Separase Architecture and Substrate Recognition through Computational Modelling of Caspase-Like and Death Domains	journal.pcbi.1004548	null	[ [ "Separase overexpression and aberrant nuclear localization are reported in a broad range of human tumours , and its overexpression in mouse models results in tumourigenesis [1 , 2] .", "A strong correlation has been made between overexpression of separase protein in adult glioblastoma and a high incidence...	[ "Separases are large proteins that mediate sister chromatid disjunction in all eukaryotes .", "They belong to clan CD of cysteine peptidases and contain a well-conserved C-terminal catalytic protease domain similar to caspases and gingipains .", "However , unlike other well-characterized groups of clan CD pepti...	[ "The separation of sister chromatids is a crucial step in cell division and is triggered by the activation of separase , a protease that cleaves the proteins that maintain the cohesion between sister chromatids .", "Knowledge of the molecular structure and activation mechanism of separase is limited by the diffic...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "cell death", "medicine and health sciences", "chemical compounds", "cell processes", "microbiology", "protozoan life cycles", "parasitic protozoans", "organic compounds", "developmental biology", "trypomastigotes", "protozoans", "pharmaceutics", "bioassays and physiological analysis", "ep...	Trypanocidal Effect of Isotretinoin through the Inhibition of Polyamine and Amino Acid Transporters in Trypanosoma cruzi	journal.pntd.0005472	null	[ [ "Chagas disease is a major health and economic problem in the Americas and its causative agent is the hemoflagellate Trypanosoma cruzi [1] .", "According to the World Health Organization , about 8 million people worldwide are infected with the parasite , and 10 , 000 people per year die from complications...	[ "Polyamines are essential compounds to all living organisms and in the specific case of Trypanosoma cruzi , the causative agent of Chagas disease , they are exclusively obtained through transport processes since this parasite is auxotrophic for polyamines .", "Previous works reported that retinol acetate inhibits...	[ "Polyamines are polycationic compounds essential for the regulation of cell growth and differentiation .", "In contrast with other protozoa , Trypanosoma cruzi , the etiological agent of Chagas disease , is auxotrophic for polyamines; therefore the intracellular availability of these molecules depends exclusively...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Antenna Mechanism of Length Control of Actin Cables	journal.pcbi.1004160	null	[ [ "Eukaryotic cells have a complex cytoskeleton that includes vast arrays of microtubules and actin filaments , which governs the internal positioning and movement of cellular substructures such as vesicles and organelles , and dynamic changes in cell polarity , shape , and movement .", "Many of these proce...	[ "Actin cables are linear cytoskeletal structures that serve as tracks for myosin-based intracellular transport of vesicles and organelles in both yeast and mammalian cells .", "In a yeast cell undergoing budding , cables are in constant dynamic turnover yet some cables grow from the bud neck toward the back of th...	[ "Based on published cell experiments , we propose a novel mechanism of length control of actin cables in budding yeast cells .", "The key feature of this “antenna mechanism” is negative feedback of the cable length on the activity of formins , which are proteins that attach to the growing ends of actin filaments ...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	A New Glycan-Dependent CD4-Binding Site Neutralizing Antibody Exerts Pressure on HIV-1 In Vivo	journal.ppat.1005238	null	[ [ "Although the envelope glycoproteins ( Env ) of primate immunodeficiency viruses have extremely variable sequences [1] , most of them engage CD4 as the primary cellular receptor to initiate the viral life cycle [2] .", "The consequence is that the CD4 binding site ( CD4bs ) is a comparatively well-conserv...	[ "The CD4 binding site ( CD4bs ) on the envelope glycoprotein is a major site of vulnerability that is conserved among different HIV-1 isolates .", "Many broadly neutralizing antibodies ( bNAbs ) to the CD4bs belong to the VRC01 class , sharing highly restricted origins , recognition mechanisms and viral escape pa...	[ "CD4bs is a central viral vulnerability site and isolation of new anti-HIV-1 CD4bs broadly neutralizing antibodies ( bNAbs ) provides information about viral escape mechanisms .", "Here we describe a new anti-HIV-1 bNAb that was isolated from an HIV-1 infected donor .", "The antibody , 179NC75 , targets the CD4...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "plant biology", "plant cell biology", "microbiology", "signaling in selected disciplines", "plant science", "crops", "plant microbiology", "plant signaling", "crop diseases", "biology", "agriculture", "biochemistry", "plant biochemistry", "signal transduction", "cell biology", "molecu...	The Tomato Prf Complex Is a Molecular Trap for Bacterial Effectors Based on Pto Transphosphorylation	journal.ppat.1003123	null	[ [ "Plant immunity is innate and relies on two levels of pathogen perception , underpinned by different recognition strategies [1] .", "The first level of perception occurs at the cell surface where plasma membrane receptors called pattern recognition receptors ( PRRs ) recognise and respond to conserve path...	[ "The major virulence strategy of phytopathogenic bacteria is to secrete effector proteins into the host cell to target the immune machinery .", "AvrPto and AvrPtoB are two such effectors from Pseudomonas syringae , which disable an overlapping range of kinases in Arabidopsis and Tomato .", "Both effectors targe...	[ "The bacteria Pseudomonas syringae is a pathogen of many crop species and one of the model pathogens for studying plant and bacterial arms race coevolution .", "In the current model , plants perceive bacteria pathogens via plasma membrane receptors , and recognition leads to the activation of general defenses .",...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases/neglected tropical diseases", "infectious diseases/helminth infections" ]	Evaluation of Immunoassays for the Diagnosis of Schistosoma japonicum Infection Using Archived Sera	journal.pntd.0000949	null	[ [ "Schistosomiasis , caused by infection with Schistosoma spp .", ", remains a public health problem in tropical and subtropical areas of the world .", "It is currently estimated that 207 million people harbor the parasites and about 779 million people are at risk of being infected with schistosomes [1]...	[ "With a national program initiated recently to reduce transmission of Schistosoma japonicum in the People's Republic of China ( P . R . China ) , there is an urgent need for accessible , quality-assured diagnostics for case detection , surveillance , and program monitoring of chemotherapy efficacy and other control...	[ "With the advantages of higher sensitivity and simpler ease of use over stool examination , antibody-detection methods have been integrated into programs for schistosomiasis control in the People's Republic of China after the notable decrease of prevalence and intensity of Schistosoma japonicum infection .", "We ...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "neuroscience/behavioral neuroscience", "neuroscience", "computational biology/computational neuroscience" ]	Shaping Embodied Neural Networks for Adaptive Goal-directed Behavior	journal.pcbi.1000042	null	[ [ "One of the most important features of the brain is the ability to adapt or learn to achieve a specific goal , which requires continuous sensory feedback about the success of its motor output in a specific context .", "We developed tools [1]–[3] for closing the sensory-motor loop between a cultured networ...	[ "The acts of learning and memory are thought to emerge from the modifications of synaptic connections between neurons , as guided by sensory feedback during behavior .", "However , much is unknown about how such synaptic processes can sculpt and are sculpted by neuronal population dynamics and an interaction with...	[ "The ability of a brain to learn has been studied at various levels .", "However , a large gap exists between behavioral studies of learning and memory and studies of cellular plasticity .", "In particular , much remains unknown about how cellular plasticity scales to affect network population dynamics .", "I...	2008
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Post-treatment Vascular Leakage and Inflammatory Responses around Brain Cysts in Porcine Neurocysticercosis	journal.pntd.0003577	null	[ [ "Neurocysticercosis ( NCC ) , an infection with the larval stage of the tapeworm , Taenia solium , is the most common cause of adult onset epilepsy worldwide .", "Infection is acquired from adult tapeworm carriers who excrete infectious ova either within proglottids or free in the feces .", "Following...	[ "Cysticidal treatment of neurocysticercosis , an infection of humans and pig brains with Taenia solium , results in an early inflammatory response directed to cysts causing seizures and focal neurological manifestations .", "Treatment-induced pericystic inflammation and its association with blood brain barrier ( ...	[ "Neurocysticercosis is caused by infection of the brain with the larval ( cyst ) stage of the tape worm Taenia solium in humans and pigs .", "Antiparasitic drug treatment is compromised by worsening of neurological symptoms during therapy due to reactive inflammation triggered by the dying parasite .", "The imm...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "genome-wide association studies", "major histocompatibility complex", "heredity", "gene expression", "genetics", "immunology", "biology", "human genetics", "genetics of disease", "genetics and genomics", "immunoglobulins" ]	A Genome-Wide Integrative Genomic Study Localizes Genetic Factors Influencing Antibodies against Epstein-Barr Virus Nuclear Antigen 1 (EBNA-1)	journal.pgen.1003147	null	[ [ "Epstein-Barr virus ( EBV ) belongs to the herpes virus family , which consists of double-stranded DNA viruses , composed of a DNA core surrounded by a nucleocapsid and a tegument , with relatively large genomes ( 100–200 genes ) .", "There are currently eight known human herpesviruses , which include her...	[ "Infection with Epstein-Barr virus ( EBV ) is highly prevalent worldwide , and it has been associated with infectious mononucleosis and severe diseases including Burkitt lymphoma , Hodgkin lymphoma , nasopharyngeal lymphoma , and lymphoproliferative disorders .", "Although EBV has been the focus of extensive rese...	[ "Many factors influence individual differences in susceptibility to infectious disease , including genetic factors of the host .", "Here we use several genome-wide investigative tools ( linkage , association , joint linkage and association , and the analysis of gene expression data ) to search for host genetic fa...	2013
[ "Introduction", "Results", "Discussion and conclusion", "Materials and methods" ]	[ "protons", "ion channel gating", "medicine and health sciences", "crystal structure", "condensed matter physics", "electrophysiology", "neuroscience", "germ cells", "oocytes", "ion channels", "protein structure", "crystallography", "nicotinic acetylcholine receptors", "solid state physics"...	Full mutational mapping of titratable residues helps to identify proton-sensors involved in the control of channel gating in the Gloeobacter violaceus pentameric ligand-gated ion channel	journal.pbio.2004470	null	[ [ "Pentameric ligand-gated ion channels ( pLGICs ) are key players of neuronal communication .", "They promote either cell depolarization or hyperpolarization with the passive permeation of ions through an intrinsic channel , whose opening is stabilized by the binding of specific neurotransmitters .", "...	[ "The Gloeobacter violaceus ligand-gated ion channel ( GLIC ) has been extensively studied by X-ray crystallography and other biophysical techniques .", "This provided key insights into the general gating mechanism of pentameric ligand-gated ion channel ( pLGIC ) signal transduction .", "However , the GLIC is ac...	[ "Pentameric ligand-gated ion channels are an important class of receptors that are involved in many neurological diseases .", "They have been extensively studied but a full understanding of their mechanism of action has yet to be achieved .", "In an effort to bypass obstacles in the research of human receptors ...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "crystal structure", "pathology and laboratory medicine", "pathogens", "condensed matter physics", "microbiology", "viral structure", "orthomyxoviruses", "viruses", "rna viruses", "protein structure", "crystallography", "research and analysis methods", "sequ...	Structural insights into reptarenavirus cap-snatching machinery	journal.ppat.1006400	null	[ [ "The family of arenaviruses is divided in two genera: mammarenaviruses and reptarenaviruses .", "With the notable exception of Tacaribe virus , rodents are described as the natural reservoirs for mammarenaviruses .", "Reptarenaviruses have only been found in captive snakes [1] .", "Some arenavirus...	[ "Cap-snatching was first discovered in influenza virus .", "Structures of the involved domains of the influenza virus polymerase , namely the endonuclease in the PA subunit and the cap-binding domain in the PB2 subunit , have been solved .", "Cap-snatching endonucleases have also been demonstrated at the very N...	[ "Arenaviruses occur worldwide and can cause severe , often fatal hemorrhagic fever in humans .", "Vaccines and effective treatments are not available .", "Arenaviruses replicate in the cytoplasm of infected cells and since they cannot synthesize cap-structures they use a mechanism called cap-snatching to steal ...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "infectious diseases", "immune cells", "cytokines", "immunity", "hiv", "innate immunity", "antigen-presenting cells", "immune defense", "immunology", "immunity to infections", "biology", "lymphoid organs", "viral diseases", "retrovirology and hiv immunopathogenesis", "infec...	Plasmacytoid Dendritic Cell Dynamics Tune Interferon-Alfa Production in SIV-Infected Cynomolgus Macaques	journal.ppat.1003915	null	[ [ "HIV-1 infection is characterized by chronic immune activation , a major cause of CD4 T-cell depletion and HIV/SIV-specific immunity dysfunction , and facilitating viral replication and progression to AIDS [1] .", "Simian immunodeficiency virus ( SIV ) infection in non human primates ( NHP ) leads to chro...	[ "IFN-I production is a characteristic of HIV/SIV primary infections .", "However , acute IFN-I plasma concentrations rapidly decline thereafter .", "Plasmacytoid dendritic cells ( pDC ) are key players in this production but primary infection is associated with decreased responsiveness of pDC to TLR 7 and 9 tri...	[ "Chronic immune activation is a characteristic of HIV infection and a key contributor to CD4 T-cell depletion and progression to AIDS .", "Persistent up-regulation of interferon-induced genes ( ISG ) is associated with chronic immune activation and is a molecular signature of the progression of SIV infection in n...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/comparative genomics", "evolutionary biology/evolutionary and comparative genetics" ]	Uncoupling of Satellite DNA and Centromeric Function in the Genus Equus	journal.pgen.1000845	null	[ [ "Centromeres , cytologically appearing as visible primary constrictions in metaphase chromosomes , are essential for the proper segregation of sister chromatids during cell division .", "They are the sites of kinetochore assembly and spindle fiber attachment and consist of protein-DNA complexes , in which...	[ "In a previous study , we showed that centromere repositioning , that is the shift along the chromosome of the centromeric function without DNA sequence rearrangement , has occurred frequently during the evolution of the genus Equus .", "In this work , the analysis of the chromosomal distribution of satellite tan...	[ "Centromeres are the functional elements controlling chromosome segregation during cell division .", "Vertebrate centromeres , which typically contain large amounts of tandem repeats ( satellite DNA ) , are highly conserved for function but not for DNA sequence , suggesting that centromeric function is mainly det...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/prion diseases", "computational biology/systems biology" ]	Investigating the Conformational Stability of Prion Strains through a Kinetic Replication Model	journal.pcbi.1000420	null	[ [ "Prions are infectious agents composed solely of proteins , whose replication does not rely upon the presence of nucleic acids [1] .", "Although the molecular mechanisms of prion replication are poorly understood , the current working hypothesis is based on the assumption that prions replicate by means of...	[ "Prion proteins are known to misfold into a range of different aggregated forms , showing different phenotypic and pathological states .", "Understanding strain specificities is an important problem in the field of prion disease .", "Little is known about which PrPSc structural properties and molecular mechanis...	[ "Prion diseases are caused by the accumulation of a cellular prion protein with an altered conformation , which acts as a catalyst for the further recruitment and the modification of the normal form of the protein .", "Protein polymerization appears to have a central role in the progression of the disease , an as...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/bacterial infections", "microbiology/microbial physiology and metabolism", "microbiology/cellular microbiology and pathogenesis" ]	The Mycobacterium tuberculosis Proteasome Active Site Threonine Is Essential for Persistence Yet Dispensable for Replication and Resistance to Nitric Oxide	journal.ppat.1001040	null	[ [ "Most cells continuously synthesize and degrade proteins in a regulated manner .", "Protein degradation is highly selective and this is achieved in part by localization of protease active sites within a barrel-shaped complex .", "This self-compartmentalization was first discovered for the proteasome [...	[ "Previous work revealed that conditional depletion of the core proteasome subunits PrcB and PrcA impaired growth of Mycobacterium tuberculosis in vitro and in mouse lungs , caused hypersusceptibility to nitric oxide ( NO ) and impaired persistence of the bacilli during chronic mouse infections .", "Here , we show...	[ "The eukaryotic proteasome is ubiquitous and essential for many basic cellular processes .", "In contrast to most bacteria , which do not express a proteasome , Mycobacterium tuberculosis encodes a proteasome predicted to be essential or required for optimal growth of the pathogen .", "Genetic silencing of the ...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "neuroscience/behavioral neuroscience", "neuroscience/neural homeostasis", "neuroscience/neurodevelopment", "neuroscience/neuronal and glial cell biology", "computational biology", "neuroscience/theoretical neuroscience" ]	Synaptic Plasticity and Connectivity Requirements to Produce Stimulus-Pair Specific Responses in Recurrent Networks of Spiking Neurons	journal.pcbi.1001091	null	[ [ "Most environmental stimuli , to which an animal must develop an appropriate response , comprise multiple features and sub-features that are common to many other stimuli .", "Since these other stimuli could engender an alternative response by the animal , it is essential that an animal is able to recogniz...	[ "Animals must respond selectively to specific combinations of salient environmental stimuli in order to survive in complex environments .", "A task with these features , biconditional discrimination , requires responses to select pairs of stimuli that are opposite to responses to those stimuli in another combinat...	[ "Learning to associate relevant stimuli in our environment is important for survival .", "For example , identification of an object , such as an edible fruit , may require us to recognize a unique combination of features – color , shape , size – each of which is present in other , perhaps inedible , objects .", ...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "herpes simplex", "virology", "biology", "microbiology", "viral diseases", "viral replication" ]	Host Factor SAMHD1 Restricts DNA Viruses in Non-Dividing Myeloid Cells	journal.ppat.1003481	null	[ [ "It is becoming increasingly evident that host cells employ metabolic regulatory mechanisms in order to restrict the life cycle of pathogens [1] , [2] , [3] , [4] .", "The recent discovery of sterile alpha motif ( SAM ) domain and histidine-aspartic ( HD ) domain-containing protein 1 ( SAMHD1 ) has contri...	[ "SAMHD1 is a newly identified anti-HIV host factor that has a dNTP triphosphohydrolase activity and depletes intracellular dNTP pools in non-dividing myeloid cells .", "Since DNA viruses utilize cellular dNTPs , we investigated whether SAMHD1 limits the replication of DNA viruses in non-dividing myeloid target ce...	[ "Various viral pathogens such as HIV-1 , herpes simplex virus ( HSV ) and vaccinia virus infect terminally-differentiated/non-dividing macrophages during the course of viral pathogenesis .", "Unlike dividing cells , non-dividing cells lack chromosomal DNA replication , do not enter the cell cycle , and harbor ver...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell processes", "microbiology", "light microscopy", "viral structure", "nucleocapsids", "microscopy", "densitometry", "cellular structures and organelles", "research and analysis methods", "contractile proteins", "actins", "actin polymerization", "proteins", "fluorescence microscopy", ...	Autographa californica Multiple Nucleopolyhedrovirus Ac34 Protein Retains Cellular Actin-Related Protein 2/3 Complex in the Nucleus by Subversion of CRM1-Dependent Nuclear Export	journal.ppat.1005994	null	[ [ "Actin polymerization is an evolutionarily conserved biological process in eukaryotic cells .", "The key elements of cellular actin polymerization machinery include , but are not limited to , actin , nucleation promoting factors ( NPFs ) , and the actin-related protein 2/3 complex ( Arp2/3 ) .", "Arp2...	[ "Actin , nucleation-promoting factors ( NPFs ) , and the actin-related protein 2/3 complex ( Arp2/3 ) are key elements of the cellular actin polymerization machinery .", "With nuclear actin polymerization implicated in ever-expanding biological processes and the discovery of the nuclear import mechanisms of actin...	[ "Actin is one of the most abundant molecules in eukaryotic cells .", "Actin polymerization is a process that nucleates actin monomers into filamentous structures , and this cellular process is frequently used by viruses to facilitate virus multiplication in host cells .", "Arp2/3 , the central regulator of acti...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetic mutation", "gene expression", "genetics", "molecular genetics", "biology", "human genetics", "genetics and genomics", "autosomal dominant" ]	Exome Sequencing Identifies ZNF644 Mutations in High Myopia	journal.pgen.1002084	null	[ [ "Myopia is the most common ocular disorder worldwide , with a prevalence of 20–30% in North American , European and Australian populations [1] , [2] and as high as 40–70% in the Asian population [3]–[5] .", "One type of myopia is high myopia , and it is prevalent in 1–2% in the general population [1]–[6] ...	[ "Myopia is the most common ocular disorder worldwide , and high myopia in particular is one of the leading causes of blindness .", "Genetic factors play a critical role in the development of myopia , especially high myopia .", "Recently , the exome sequencing approach has been successfully used for the disease ...	[ "People with myopia see near objects more clearly than objects far away .", "Myopia is the most common ocular disorder worldwide , with a high prevalence in Asian ( 40%–70% ) and Caucasian ( 20%–30% ) populations .", "Although the etiologies of myopia have not yet been established , previous studies have indica...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "plant biology", "genetics and genomics", "computational biology" ]	Computational Complementation: A Modelling Approach to Study Signalling Mechanisms during Legume Autoregulation of Nodulation	journal.pcbi.1000685	null	[ [ "Legumes are one of the largest families of flowering plants that occupy about 15% of Earth's arable surface; yet they provide 27% of the world's primary crop production and more than 35% of the world's processed vegetable oil [1] , signifying their cropping potential .", "Legumes are also the major natur...	[ "Autoregulation of nodulation ( AON ) is a long-distance signalling regulatory system maintaining the balance of symbiotic nodulation in legume plants .", "However , the intricacy of internal signalling and absence of flux and biochemical data , are a bottleneck for investigation of AON .", "To address this , a...	[ "Endogenous signals , such as phytohormones , play a vital role in plant development and function , controlling processes such as flowering , branching , disease response , and nodulation .", "However , the signalling mechanisms are so subtle and so complex that details about them remain largely unknown .", "In...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "oncology", "microbiology", "virology" ]	Upregulation of xCT by KSHV-Encoded microRNAs Facilitates KSHV Dissemination and Persistence in an Environment of Oxidative Stress	journal.ppat.1000742	null	[ [ "Patients with immune deficiencies are at risk for life-threatening illnesses caused by herpesviruses , including the Kaposi's sarcoma-associated herpesvirus ( KSHV ) .", "Bone marrow failure [1] , lymphoproliferative syndromes [2] , [3] , and sarcoma [4] have all been etiologically linked to KSHV infecti...	[ "Upregulation of xCT , the inducible subunit of a membrane-bound amino acid transporter , replenishes intracellular glutathione stores to maintain cell viability in an environment of oxidative stress .", "xCT also serves as a fusion-entry receptor for the Kaposi's sarcoma-associated herpesvirus ( KSHV ) , the cau...	[ "Herpesviruses are the most common etiologic agents of cancer in patients with suppressed immune function , and the Kaposi's sarcoma-associated herpesvirus ( KSHV ) is one of the most common causes of cancer in this setting .", "KSHV infection of new cell targets is critical for tumor progression , and a better u...	2010
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "chemical compounds", "carbohydrates", "organic compounds", "glucose", "fungi", "model organisms", "protein structure prediction", "experimental organism systems", "protein structure", "evolutionary adaptation", "saccharomyces", "research and analysis methods", "sequence analysis", "sequen...	Evolution of a novel chimeric maltotriose transporter in Saccharomyces eubayanus from parent proteins unable to perform this function	journal.pgen.1007786	null	[ [ "Proteins with novel functions can arise through a variety of mechanisms [1] .", "One of the best studied mechanisms is gene duplication , followed by divergence through sequential point mutations [1 , 2] .", "While this method of new protein evolution is thought to be common , evolution through stepw...	[ "At the molecular level , the evolution of new traits can be broadly divided between changes in gene expression and changes in protein-coding sequence .", "For proteins , the evolution of novel functions is generally thought to proceed through sequential point mutations or recombination of whole functional units ...	[ "Hybrids of the yeasts Saccharomyces cerevisiae and Saccharomyces eubayanus ( lager-brewing yeasts ) dominate the modern brewing industry .", "S . cerevisiae , also known as baker’s yeast , is well-known for its role in industry and scientific research .", "Less well recognized is S . eubayanus , which was only...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "signal transduction", "inflammation", "immunity", "innate immunity", "immunology", "biology", "molecular cell biology" ]	Negative Regulation of TLR Inflammatory Signaling by the SUMO-deconjugating Enzyme SENP6	journal.ppat.1003480	null	[ [ "Toll like receptors ( TLRs ) are a family of membrane receptors that sense a wide range of invading pathogens , including bacteria , fungi and viruses .", "Upon activation , TLRs trigger innate immune responses and prime the adaptive immune system to eliminate the pathogens [1] , [2] .", "However , t...	[ "The signaling of Toll-like receptors ( TLRs ) induces host defense against microbial invasion .", "Protein posttranslational modifications dynamically shape the strength and duration of the signaling pathways .", "It is intriguing to explore whether de-SUMOylation could modulate the TLR signaling .", "Here w...	[ "Given the double-edged nature of the TLR functions , the strength and duration of the TLR signaling are dynamically modulated via protein posttranslational modifications , which ensure that the invading microbes are quickly eliminated and the damages to the host are reduced to the minimum .", "Besides the ubiqui...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/viral infections", "microbiology/innate immunity", "microbiology/immunity to infections", "immunology/innate immunity" ]	Induction of IFN-β and the Innate Antiviral Response in Myeloid Cells Occurs through an IPS-1-Dependent Signal That Does Not Require IRF-3 and IRF-7	journal.ppat.1000607	null	[ [ "The rapid production of type I interferon ( IFN-α/β ) and the IFN-induced antiviral response serve as primary host defense mechanisms against infection by many viruses ( reviewed in [1]–[3] ) .", "IFN-α/β gene transcription is induced after host pattern recognition receptors ( PRR ) bind pathogen-associa...	[ "Interferon regulatory factors ( IRF ) -3 and IRF-7 are master transcriptional factors that regulate type I IFN gene ( IFN-α/β ) induction and innate immune defenses after virus infection .", "Prior studies in mice with single deletions of the IRF-3 or IRF-7 genes showed increased vulnerability to West Nile virus...	[ "West Nile virus ( WNV ) is a mosquito-transmitted virus that infects birds , horses , and humans and has become an emerging infectious disease threat in the Western Hemisphere .", "In humans , WNV can invade into the brain and spinal cord and destroy neurons , causing severe neurological disease , particularly i...	2009
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "meiosis", "homologous chromosomes", "cell cycle and cell division", "cell processes", "chromosome mapping", "dna", "molecular biology techniques", "homologous recombination", "research and analysis methods", "gene mapping", "chromosome biology", "genetic interference", "chromosome pairs", ...	Amplifying recombination genome-wide and reshaping crossover landscapes in Brassicas	journal.pgen.1006794	null	[ [ "Meiotic recombination through crossovers ( COs ) is the key mechanism ensuring both the proper segregation of homologous chromosomes during meiosis and the generation of diversity in all sexual organisms .", "Indeed , following the formation of DNA Double Strand Breaks ( DSBs ) , during the Prophase I of...	[ "Meiotic recombination by crossovers ( COs ) is tightly regulated , limiting its key role in producing genetic diversity .", "However , while COs are usually restricted in number and not homogenously distributed along chromosomes , we show here how to disrupt these rules in Brassica species by using allotriploid ...	[ "In organisms with sexual reproduction , meiosis generates gametes containing half of the genetic material of parents .", "During this process , the reciprocal exchanges between the homologous chromosomes due to crossovers ( COs ) ensure their proper segregation as well as the generation of diversity .", "Howev...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Beyond GLMs: A Generative Mixture Modeling Approach to Neural System Identification	journal.pcbi.1003356	null	[ [ "To account for the stochasticity inherent to neural responses , single cells as well as populations of cells are often characterized in terms of a probabilistic model .", "A popular choice for this task are generalized linear models ( GLMs ) and related approaches [1]–[6] .", "These models can often ...	[ "Generalized linear models ( GLMs ) represent a popular choice for the probabilistic characterization of neural spike responses .", "While GLMs are attractive for their computational tractability , they also impose strong assumptions and thus only allow for a limited range of stimulus-response relationships to be...	[ "An essential goal of sensory systems neuroscience is to characterize the functional relationship between neural responses and external stimuli .", "Of particular interest are the nonlinear response properties of single cells .", "Inherently linear approaches such as generalized linear modeling can nevertheless...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics", "biology", "neuroscience", "genetics and genomics" ]	CULLIN-3 Controls TIMELESS Oscillations in the Drosophila Circadian Clock	journal.pbio.1001367	The ubiquitin ligases CUL-3 and SLMB collaborate to regulate the Drosophila circadian clock by controlling TIMELESS oscillations.	[ [ "Circadian clocks are present in most living organisms and control a variety of physiological and behavioral functions .", "Eukaryotic clocks stem from a transcriptional negative feedback loop where activators induce the expression of repressors , which then inhibit the activators [1] .", "The accumul...	[ "Eukaryotic circadian clocks rely on transcriptional feedback loops .", "In Drosophila , the PERIOD ( PER ) and TIMELESS ( TIM ) proteins accumulate during the night , inhibit the activity of the CLOCK ( CLK ) /CYCLE ( CYC ) transcriptional complex , and are degraded in the early morning .", "The control of PER...	[ "Circadian clocks adjust the physiology and behavior of organisms to the day/night cycle and rely on molecular feedback loops that generate daily oscillations of transcription .", "In the Drosophila fruit fly , the PERIOD ( PER ) and TIMELESS ( TIM ) proteins coordinate the clock–they accumulate during the night ...	2012
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "phosphorylation", "cell death", "medicine and health sciences", "breast tumors", "cell processes", "cancers and neoplasms", "basic cancer research", "oncology", "immunologic techniques", "research and analysis methods", "specimen preparation and treatment", "staining", "proteins", "breast...	TRIM59 promotes breast cancer motility by suppressing p62-selective autophagic degradation of PDCD10	journal.pbio.3000051	Bioinformatic analysis and experiments on clinical samples and mouse models of breast cancer unveil a new signaling protein degradation pathway involving TRIM59 and PDCD10 that modulates breast cancer cell growth, survival, and metastasis.	[ [ "The tripartite motif ( TRIM ) protein family of E3 ubiquitin ligases is intimately implicated in tumorigenesis by enhancing gene translocation and fusion [1 , 2] , promoting cell cycle arrest through deregulation of tumor protein 53 ( p53 ) and cyclin-dependent kinase ( CDK ) inhibitors degradation [3 , 4] ,...	[ "Cancer cells adopt various modes of migration during metastasis .", "How the ubiquitination machinery contributes to cancer cell motility remains underexplored .", "Here , we report that tripartite motif ( TRIM ) 59 is frequently up-regulated in metastatic breast cancer , which is correlated with advanced clin...	[ "Cancer cell metastasis is the primary cause of mortality in cancer patients .", "Changes in cell morphology are critical for cancer cell motility and metastasis , and this process requires spatiotemporal control of the turnover or stabilization of signaling components that regulate cell polarity .", "Autophagy...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "chemical compounds", "nucleases", "enzymes", "messenger rna", "dna-binding proteins", "enzymology", "organic compounds", "rna stem-loop structure", "basic amino acids", "amino acids", "translation termination", "cellular structures and organelles", "rna structure", "proteins", "gene exp...	mRNA dynamics and alternative conformations adopted under low and high arginine concentrations control polyamine biosynthesis in Salmonella	journal.pgen.1007646	null	[ [ "Regulatory RNAs are now recognized as important players in many adaptive and physiological responses in bacteria .", "RNA regulators allow bacterial cells to fine-tune their metabolism during growth [1] , sense population density [2] , modulate and modify cell-surface properties [3] , and regulate virule...	[ "Putrescine belongs to the large group of polyamines , an essential class of metabolites that exists throughout all kingdoms of life .", "The Salmonella speF gene encodes an inducible ornithine decarboxylase that produces putrescine from ornithine .", "Putrescine can be also synthesized from arginine in a paral...	[ "Polyamines are widely distributed in nature , they bind nucleic acids and proteins and although their exact mechanism of action is not clear , their effect on fundamental cellular functions is well documented .", "The canonical biosynthesis pathway of polyamines is conserved and begins with speF encoding ornithi...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "speciation", "genetics", "introgression", "population genetics", "hybridization", "biology", "evolutionary biology", "genomic evolution", "evolutionary processes", "evolutionary genetics" ]	Evidence for Mito-Nuclear and Sex-Linked Reproductive Barriers between the Hybrid Italian Sparrow and Its Parent Species	journal.pgen.1004075	null	[ [ "Hybridization between divergent populations has diverse impacts on evolution [1]–[3] , including the rapid formation of hybrid species [1]–[6] .", "Homoploid hybrid speciation ( HHS ) is the process through which hybridization between two taxa results in a third , novel taxon that remains distinct by mea...	[ "Studies of reproductive isolation between homoploid hybrid species and their parent species have rarely been carried out .", "Here we investigate reproductive barriers between a recently recognized hybrid bird species , the Italian sparrow Passer italiae and its parent species , the house sparrow P . domesticus ...	[ "Hybridization between two species has the potential to create a third , hybrid species .", "However this process , known as hybrid speciation , is thought to be unlikely because it requires reproductive barriers against both parent species to develop despite the barriers between parents being weak enough to allo...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "ecology and environmental sciences", "pathology and laboratory medicine", "togaviruses", "chikungunya infection", "pathogens", "tropical diseases", "microbiology", "geographical locations", "animals", "alphaviruses", "viruses", "north ameri...	Autocidal gravid ovitraps protect humans from chikungunya virus infection by reducing Aedes aegypti mosquito populations	journal.pntd.0007538	null	[ [ "Lack of sustainable and effective tools to control Aedes aegypti mosquito populations has resulted in the continued expansion of dengue virus ( DENV ) transmission worldwide and the recent emergence of chikungunya ( CHIKV ) and Zika ( ZIKV ) viruses in the western hemisphere [1 , 2] .", "Despite the rece...	[ "Public health responses to outbreaks of dengue , chikungunya , and Zika virus have been stymied by the inability to control the primary vector , Aedes aegypti mosquitos .", "Consequently , the need for novel approaches to Aedes vector control is urgent .", "Placement of three autocidal gravid ovitraps ( AGO tr...	[ "Aedes species mosquitos transmit pathogens of public health importance , including dengue , Zika , and chikungunya viruses .", "No tools exist to control these mosquitos that sustainably and effectively prevent human infections .", "Autocidal gravid ovitraps ( AGO traps ) have been shown to sustainably reduce ...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Transgenic Expression of the Dicotyledonous Pattern Recognition Receptor EFR in Rice Leads to Ligand-Dependent Activation of Defense Responses	journal.ppat.1004809	null	[ [ "Plants possess multi-layered immune systems enabling them to fend off most pathogens .", "Plasma membrane localized pattern recognition receptors ( PRRs ) sense danger-associated molecules , including pathogen/microbe-associated molecular patterns ( P/MAMPs ) and endogenous elicitors released during the ...	[ "Plant plasma membrane localized pattern recognition receptors ( PRRs ) detect extracellular pathogen-associated molecules .", "PRRs such as Arabidopsis EFR and rice XA21 are taxonomically restricted and are absent from most plant genomes .", "Here we show that rice plants expressing EFR or the chimeric recepto...	[ "Plants possess multi-layered immune recognition systems .", "Early in the infection process , plants use receptor proteins to recognize pathogen molecules .", "Some of these receptors are present in only in a subset of plant species .", "Transfer of these taxonomically restricted immune receptors between pla...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "transfection", "luciferase", "hela cells", "enzymes", "gene regulation", "messenger rna", "biological cultures", "enzymology", "microbiology", "cell cultures", "molecular biology techniques", "research and analysis methods", "small interfering rnas", "proteins", "gene expression", "ox...	The 5'-poly(A) leader of poxvirus mRNA confers a translational advantage that can be achieved in cells with impaired cap-dependent translation	journal.ppat.1006602	null	[ [ "All viruses rely entirely on their infected host cells for protein synthesis .", "Not surprisingly , to boost production of viral proteins , many viral evolutionary strategies usurp the host translation machinery .", "In doing so they target every step of protein synthesis , from mRNA production and ...	[ "The poly ( A ) leader at the 5’-untranslated region ( 5’-UTR ) is an unusually striking feature of all poxvirus mRNAs transcribed after viral DNA replication ( post-replicative mRNAs ) .", "These poly ( A ) leaders are non-templated and of heterogeneous lengths; and their function during poxvirus infection remai...	[ "Poxviruses continue to impact public health significantly , despite the eradication of smallpox , the deadliest disease in human history .", "As a tool , poxviruses are being engineered to treat various infectious diseases and multiple cancers .", "All poxvirus mRNAs transcribed after viral DNA replication hav...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "plant anatomy", "medicine and health sciences", "action potentials", "neurochemistry", "vesicles", "chemical compounds", "nervous system", "nucleus accumbens", "membrane potential", "brain", "electrophysiology", "neuroscience", "organic compounds", "hormones", "plant science", "amines...	Short-term synaptic depression can increase the rate of information transfer at a release site	journal.pcbi.1006666	null	[ [ "Chemical synapses are the main conduits of information in the nervous system [1] .", "At such synapses , a presynaptic action potential induces docked vesicles , packed with neurotransmitters , to release with a certain probability .", "A vesicle release leads to a local postsynaptic dendritic voltag...	[ "The release of neurotransmitters from synapses obeys complex and stochastic dynamics .", "Depending on the recent history of synaptic activation , many synapses depress the probability of releasing more neurotransmitter , which is known as synaptic depression .", "Our understanding of how synaptic depression a...	[ "Fatigue is an intrinsic property of living systems and synapses are no exception .", "Synaptic depression reduces the ability of synapses to release vesicles in response to an incoming action potential .", "Whether synaptic depression simply reflects the exhaustion of neuronal resources or whether it serves so...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences" ]	Challenges in Dengue Fever in the Elderly: Atypical Presentation and Risk of Severe Dengue and Hospita-Acquired Infection	journal.pntd.0002777	null	[ [ "Dengue is the most significant mosquito-borne virus in humans [1] and is endemic to Singapore .", "In Asia dengue classically affects children with the majority of cases of dengue hemorrhagic fever ( DHF ) , dengue shock syndrome ( DSS ) , and dengue related mortality observed in this group [2] .", "...	[ "To better understand dengue fever in the elderly , we compared clinical features , World Health Organization ( WHO ) dengue classification and outcomes between adult ( <60 ) and elderly ( ≥60 ) dengue patients .", "We explored the impact of co-morbidity and hospital-acquired infection ( HAI ) on clinical outcome...	[ "Dengue is a neglected tropical disease that is increasingly affecting elderly patients; however , there is a paucity of data on clinical presentation and outcomes in this group .", "The limited data suggests that elderly dengue patients have the highest case-fatality rate but the pathogenesis of mortality in eld...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "chemical bonding", "chromosome structure and function", "applied mathematics", "simulation and modeling", "algorithms", "chromosome mapping", "mathematics", "materials science", "network analysis", "genome analysis", "molecular biology techniques", "cell nucleus", "macromolecules", "cellu...	Transient crosslinking kinetics optimize gene cluster interactions	journal.pcbi.1007124	null	[ [ "The 4D Nucleome Project [1] proposes the integration of diverse approaches: increasingly powerful chromosome conformation capture techniques including high-throughput chromosome conformation capture ( Hi-C ) ; statistical and topological analyses of these massive Hi-C datasets; 3-dimensional ( 3D ) and 4D su...	[ "Our understanding of how chromosomes structurally organize and dynamically interact has been revolutionized through the lens of long-chain polymer physics .", "Major protein contributors to chromosome structure and dynamics are condensin and cohesin that stochastically generate loops within and between chains , ...	[ "The spatiotemporal organization of the genome plays an important role in cellular processes involving DNA , but remains poorly understood , especially in the nucleolus , which does not facilitate conventional techniques .", "Polymer chain models have shown ability in recent years to make accurate predictions of ...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	PAF Complex Plays Novel Subunit-Specific Roles in Alternative Cleavage and Polyadenylation	journal.pgen.1005794	null	[ [ "Paf1C has been intensively explored in yeast , flies , and mammalian cells , which has led to diverse , and sometimes differing , conclusions .", "The complex was first characterized in yeast as a PolII-associated factor , and extensive use of mutants revealed that it plays a role in transcriptional elon...	[ "The PAF complex ( Paf1C ) has been shown to regulate chromatin modifications , gene transcription , and RNA polymerase II ( PolII ) elongation .", "Here , we provide the first genome-wide profiles for the distribution of the entire complex in mammalian cells using chromatin immunoprecipitation and high throughpu...	[ "Gene transcription can be regulated through multiple mechanisms , such as histone modifications that create structural changes of the chromatin leading to gene activation or suppression , or regulation of the 3’ cleavage site of the mRNA , known as alternative cleavage and polyadenylation ( APA ) , resulting in th...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma mansoni", "medicine and health sciences", "immune physiology", "enzyme-linked immunoassays", "helminths", "immunology", "tropical diseases", "parasitic diseases", "animals", "liver diseases", "vaccines", "preventive medicine", "infectious hepa...	Schistosoma mansoni Infection Can Jeopardize the Duration of Protective Levels of Antibody Responses to Immunizations against Hepatitis B and Tetanus Toxoid	journal.pntd.0005180	null	[ [ "It is estimated that globally over 240 million people have schistosomiasis , with the bulk of cases occurring in sub-Saharan Africa [1 , 2] .", "A vast majority of those infected in the region harbor either Schistosoma mansoni , S . haematobium or both [3] , with an estimated 122 million cases occurring ...	[ "Schistosomiasis is a disease of major public health importance in sub-Saharan Africa .", "Immunoregulation begins early in schistosome infection and is characterized by hyporesponsiveness to parasite and bystander antigens , suggesting that a schistosome infection at the time of immunization could negatively imp...	[ "Vaccines are a mainstay for the prevention of morbidity and mortality to numerous infectious diseases .", "Concurrent schistosomiasis infection at the time of immunizations has been implicated in the impairment of protective immune responses to vaccines .", "We asked if schistosomiasis at the initiation of the...	2016
[ "Introduction", "Material and Methods", "Results", "Discussion" ]	[ "dengue virus", "invertebrates", "medicine and health sciences", "pathology and laboratory medicine", "togaviruses", "viral transmission and infection", "pathogens", "microbiology", "vertebrates", "animals", "alphaviruses", "mammals", "viruses", "chikungunya virus", "rna viruses", "bio...	DNA Microarray Platform for Detection and Surveillance of Viruses Transmitted by Small Mammals and Arthropods	journal.pntd.0005017	null	[ [ "Human activity is responsible for global environmental and climate changes , which can negatively impact human health .", "Uncontrolled urbanization , deforestation , large-scale agriculture , road construction , dam building , and rapid expansion of global trade and air travel are important factors that...	[ "Viruses transmitted by small mammals and arthropods serve as global threats to humans .", "Most emergent and re-emergent viral agents are transmitted by these groups; therefore , the development of high-throughput screening methods for the detection and surveillance of such viruses is of great interest .", "In...	[ "Viruses transmitted by small mammals and blood-feeding insects represent global threats to humans .", "Most emergent viral agents are transmitted by these groups; therefore , the development of methods for the detection and surveillance of such viruses is of great interest .", "Here , we describe a DNA microch...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "infectious diseases/hiv infection and aids", "virology/animal models of infection", "immunology/immunity to infections", "evolutionary biology/bioinformatics" ]	Generation of Neutralizing Antibodies and Divergence of SIVmac239 in Cynomolgus Macaques Following Short-Term Early Antiretroviral Therapy	journal.ppat.1001084	null	[ [ "The design of an HIV-1 envelope ( Env ) immunogen capable of inducing broadly reactive neutralizing antibodies ( NAb ) has so far proven extremely difficult .", "Although NAb directed against Env can be detected early in infection in a majority of patients , this antibody response is generally not able t...	[ "Neutralizing antibodies ( NAb ) able to react to heterologous viruses are generated during natural HIV-1 infection in some individuals .", "Further knowledge is required in order to understand the factors contributing to induction of cross-reactive NAb responses .", "Here a well-established model of experiment...	[ "In a longitudinal study of clinical and evolutionary responses to transient treatment in 12 experimentally-infected macaques , subjects show clear stratification into two groups based on viral load , immunological response , and evolutionary factors .", "Subjects that controlled viremia following withdrawal of t...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology/persistence and latency", "virology/virulence factors and mechanisms", "cell biology/cell growth and division", "virology/viruses and cancer", "oncology/hematological malignancies" ]	Micro RNAs of Epstein-Barr Virus Promote Cell Cycle Progression and Prevent Apoptosis of Primary Human B Cells	journal.ppat.1001063	null	[ [ "Thousands of microRNAs ( miRNAs ) have been identified so far ( miRBase , release 14 , Sept . 2009; http://www . mirbase . org ) , which are small noncoding single-stranded RNAs of about 21 to 25 nucleotides in length .", "They are found transcribed in all multicellular organisms and certain viruses and ...	[ "Cellular and viral microRNAs ( miRNAs ) are involved in many different processes of key importance and more than 10 , 000 miRNAs have been identified so far .", "In general , relatively little is known about their biological functions in mammalian cells because their phenotypic effects are often mild and many of...	[ "Micro RNAs ( miRNAs ) are small , non-coding RNAs that bind to mRNA transcripts and abrogate their protein coding functions .", "Only a few of their mRNA targets are known , although miRNAs are found in all multicellular organisms and certain viruses .", "In particular , members of the herpesvirus family encod...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "sequencing techniques", "ion channel gating", "medicine and health sciences", "depolarization", "membrane potential", "electrophysiology", "neuroscience", "mutation", "ion channels", "physiological parameters", "body temperature", "molecular biology techniques", "research and analysis metho...	The Biophysical Basis Underlying Gating Changes in the p.V1316A Mutant Nav1.7 Channel and the Molecular Pathogenesis of Inherited Erythromelalgia	journal.pbio.1002561	Mutations in the Nav1.7 sodium channel cause idiopathic erythromelalgia. This study shows that the pathogenic resurgent sodium currents arise via modification of gating behavior rather than via competing pore block by the Navβ4 peptide.	[ [ "Voltage-gated sodium channels , such as the Nav1 . 7 channel ( ~1 , 980 amino acids; ~225 kDa ) , are heteromeric protein complexes composed chiefly of a pore loop-forming alpha subunit , which is a large transmembrane protein containing four similar domains , and an auxiliary beta subunit [1–3] .", "The...	[ "The Nav1 . 7 channel critically contributes to the excitability of sensory neurons , and gain-of-function mutations of this channel have been shown to cause inherited erythromelalgia ( IEM ) with neuropathic pain .", "In this study , we report a case of a severe phenotype of IEM caused by p . V1316A mutation in ...	[ "The gain-of-function mutation ( p . V1316A ) of the Nav1 . 7 channel causes inherited erythromelalgia ( IEM ) , a disease characterized by extremely enhanced activity in relevant neural tissues that results in neuropathic pain .", "We found that the p . V1316A mutation alters the basic gating properties of the c...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "innate immune system", "medicine and health sciences", "pathology and laboratory medicine", "immunity", "host-pathogen interactions", "biology and life sciences", "immunology", "immunoregulation", "microbiology", "pathogenesis", "parasitology", "immune system" ]	Ly6Chigh Monocytes Become Alternatively Activated Macrophages in Schistosome Granulomas with Help from CD4+ Cells	journal.ppat.1004080	null	[ [ "Alternatively activated macrophages ( AAM ) are a key feature of the immune response elicited by helminth infections [1] .", "AAM are activated and maintained by the TH2 cytokines IL-4 and IL-13 to adopt a phenotype characterized by the expression of signature genes such as arginase-1 , Ym1/Chi3l3 , Fizz...	[ "Alternatively activated macrophages ( AAM ) that accumulate during chronic T helper 2 inflammatory conditions may arise through proliferation of resident macrophages or recruitment of monocyte-derived cells .", "Liver granulomas that form around eggs of the helminth parasite Schistosoma mansoni require AAM to li...	[ "Macrophages will adopt different characteristics based on different types of inflammatory responses .", "During infection by parasitic helminths such as Schistosoma mansoni , macrophages adopt an “alternatively activated” or M2 phenotype ( AAM ) .", "These AAM are important for protecting liver hepatocytes fro...	2014
[ "Introduction", "Results", "Discussion", "Materials And Methods" ]	[ "medicine and health sciences", "cardiovascular anatomy", "cardiac ventricles", "alleles", "ventricular septal defects", "animal models", "developmental biology", "model organisms", "embryos", "morphogenesis", "research and analysis methods", "cardiology", "embryology", "birth defects", ...	Conditional Creation and Rescue of Nipbl-Deficiency in Mice Reveals Multiple Determinants of Risk for Congenital Heart Defects	journal.pbio.2000197	null	[ [ "Congenital heart defects ( CHDs ) are the most common of human birth defects , and a leading cause of perinatal morbidity and mortality [1] .", "The genetics of CHDs are complex , with only a fraction being associated with chromosomal abnormalities or Mendelian developmental syndromes [2–4] .", "As w...	[ "Elucidating the causes of congenital heart defects is made difficult by the complex morphogenesis of the mammalian heart , which takes place early in development , involves contributions from multiple germ layers , and is controlled by many genes .", "Here , we use a conditional/invertible genetic strategy to id...	[ "Congenital heart defects , the most common birth defect , are thought mainly to arise through interactions among multiple genes .", "We studied atrial septal defects ( a common type of heart defect ) in a mouse model of Cornelia de Lange Syndrome , in which loss of one copy of the Nipbl gene produces frequent de...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "antimicrobials", "bacteriology", "medicine and health sciences", "lysosomes", "immune cells", "pathology and laboratory medicine", "pathogens", "drugs", "immunology", "microbiology", "antibacterials", "pharmacology", "cellular structures and organelles", "bacteria", "ne...	Neutrophil and Alveolar Macrophage-Mediated Innate Immune Control of Legionella pneumophila Lung Infection via TNF and ROS	journal.ppat.1005591	null	[ [ "L . pneumophila is a Gram-negative bacterium with global distribution in freshwater environments , where it replicates intracellularly mainly in amoebae [1–3] .", "L . pneumophila commonly causes community acquired and nosocomial pneumonia .", "Although it is normally controlled by the innate immune ...	[ "Legionella pneumophila is a facultative intracellular bacterium that lives in aquatic environments where it parasitizes amoeba .", "However , upon inhalation of contaminated aerosols it can infect and replicate in human alveolar macrophages , which can result in Legionnaires’ disease , a severe form of pneumonia...	[ "Legionella pneumophila is a motile gram-negative bacterium found mainly in fresh water environments where it replicates in amoeba .", "It uses a molecular syringe to inject effector molecules into these predatory host cells , reprograming them to support L . pneumophila growth .", "Upon inhalation of contamina...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "vaccination", "clinical immunology", "immunity", "virology", "vaccine development", "biology", "microbiology", "immunology" ]	Loss of Anti-Viral Immunity by Infection with a Virus Encoding a Cross-Reactive Pathogenic Epitope	journal.ppat.1002633	null	[ [ "The desired consequence of vaccination or viral infection is long lasting immunity that protects the host from re-infection or else quickly restricts viral replication to prevent disease and immune pathology .", "In many cases neutralizing antibody produced by stable plasma cell populations restricts re-...	[ "T cell cross-reactivity between different strains of the same virus , between different members of the same virus group , and even between unrelated viruses is a common occurrence .", "We questioned here how an intervening infection with a virus containing a sub-dominant cross-reactive T cell epitope would affec...	[ "The purpose of vaccination against viruses is to induce strong neutralizing antibody responses that inactivate viruses on contact and strong T cell responses that attack and kill virus-infected cells .", "Some viruses , however , like HIV and hepatitis C virus , are only weakly controlled by neutralizing antibod...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Development of Resistance to Pyrethroid in Culex pipiens pallens Population under Different Insecticide Selection Pressures	journal.pntd.0003928	null	[ [ "Culex mosquitoes are important vectors responsible for transmission of lymphatic filariasis ( LF ) and several viral pathogens to millions of people worldwide , including St . Louis encephalitis , West Nile encephalitis , eastern equine encephalitis , Venezuelan equine encephalitis and Japanese encephalitis ...	[ "Current vector control programs are largely dependent on pyrethroids , which are the most commonly used and only insecticides recommended by the World Health Organization for insecticide-treated nets ( ITNs ) .", "However , the rapid spread of pyrethroid resistance worldwide compromises the effectiveness of cont...	[ "Successful population control of mosquitoes is key to preventing transmission and epidemics of mosquito-borne diseases .", "This strategy relies heavily on insecticides , particularly pyrethroids .", "However , widespread pyrethroid resistance has hindered vector control implementation and sustainability .", ...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "public and occupational health", "medicine and health sciences", "epidemiology" ]	Spatiotemporal Transmission Dynamics of Hemorrhagic Fever with Renal Syndrome in China, 2005–2012	journal.pntd.0003344	null	[ [ "Hemorrhagic fever with renal syndrome ( HFRS ) is a viral zoonosis caused by different species of hantaviruses .", "The disease is characterized by fever , hemorrhage , headache , back pain , abdominal pain , acute renal dysfunction and hypotension [1] .", "In China , HFRS is mainly caused by two typ...	[ "Hemorrhagic fever with renal syndrome ( HFRS ) is a rodent-borne disease caused by many serotypes of hantaviruses .", "In China , HFRS has been recognized as a severe public health problem with 90% of the total reported cases in the world .", "This study describes the spatiotemporal dynamics of HFRS cases in C...	[ "Hemorrhagic fever with renal syndrome ( HFRS ) is a rodent-borne viral disease caused by many serotypes of hantaviruses .", "In China , HFRS has been recognized as a severe public health problem and accounts for 90% of the reported cases in the world .", "We examined the spatiotemporal dynamics of HFRS cases i...	2014
[ "Introduction", "Models", "Results", "Discussion" ]	[ "medicine and health sciences", "myofibrils", "muscle tissue", "muscle contraction", "simulation and modeling", "probability distribution", "mathematics", "statistics (mathematics)", "research and analysis methods", "muscle physiology", "animal cells", "proteins", "mathematical and statistic...	Computing Average Passive Forces in Sarcomeres in Length-Ramp Simulations	journal.pcbi.1004904	null	[ [ "Passive forces in sarcomeres or myofibrils are almost exclusively governed by the giant protein titin [1] .", "A titin strand spans the half sarcomere from Z-disk to M-band .", "While its section located in the thick filament is nearly inextensible , its I-band region functions as a molecular spring ...	[ "Passive forces in sarcomeres are mainly related to the giant protein titin .", "Titin’s extensible region consists of spring-like elements acting in series .", "In skeletal muscles these elements are the PEVK segment , two distinct immunoglobulin ( Ig ) domain regions ( proximal and distal ) , and a N2A portio...	[ "We provide a simple and stable algorithm to determine the exact solution of passive forces in a half sarcomere in length-ramp simulations .", "The approach is applicable to a wide range of stochastic models of protein unfolding ." ]	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "plant biology/plant-biotic interactions", "biochemistry/biomacromolecule-ligand interactions", "microbiology/innate immunity" ]	RIN4 Functions with Plasma Membrane H+-ATPases to Regulate Stomatal Apertures during Pathogen Attack	journal.pbio.1000139	In plants, the protein Rin4 acts with the plasma membrane H+-ATPase to regulate pathogen entry and the innate immune response, in part, through the regulation of stomatal closure.	[ [ "Plants are continuously exposed to a variety of microorganisms .", "In order to successfully avoid infection , they have evolved a series of defense mechanisms that work in concert to limit pathogen invasion and multiplication [1] .", "Unlike vertebrates , plants lack an adaptive immune system and re...	[ "Pathogen perception by the plant innate immune system is of central importance to plant survival and productivity .", "The Arabidopsis protein RIN4 is a negative regulator of plant immunity .", "In order to identify additional proteins involved in RIN4-mediated immune signal transduction , we purified componen...	[ "Plants are continuously exposed to microorganisms .", "In order to resist infection , plants rely on their innate immune system to inhibit both pathogen entry and multiplication .", "We investigated the function of the Arabidopsis protein RIN4 , which acts as a negative regulator of plant innate immunity .", ...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Natural Variation in Preparation for Nutrient Depletion Reveals a Cost–Benefit Tradeoff	journal.pbio.1002041	Yeast can anticipate the depletion of a preferred nutrient by preemptively activating genes for alternative nutrients; the degree of this preparation varies across natural strains and is subject to a fitness tradeoff.	[ [ "Natural environments contain complex , time-varying mixtures of nutrients and stresses .", "Understanding how cells use external cues to maximize growth and survival is key to understanding the evolution and function of regulatory circuits .", "Gene regulation allows cells to express pathways for spe...	[ "Maximizing growth and survival in the face of a complex , time-varying environment is a common problem for single-celled organisms in the wild .", "When offered two different sugars as carbon sources , microorganisms first consume the preferred sugar , then undergo a transient growth delay , the “diauxic lag , ”...	[ "When microorganisms encounter multiple sugars , they often consume a preferred sugar ( such as glucose ) before consuming alternative sugars ( such as galactose ) .", "In experiments on laboratory strains of yeast , cells typically stop growing when the preferred sugar runs out , and start growing again only aft...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	CTXφ Replication Depends on the Histone-Like HU Protein and the UvrD Helicase	journal.pgen.1005256	null	[ [ "Cholera remains a major health problem in many part of the developing world , with an estimation of 2 . 8 million cases and 100 000 to 200 000 deaths each year [1] .", "The agent of the cholera , the Vibrio cholerae bacterium , is found in briny waters all over the world [2] .", "However , most V . c...	[ "The Vibrio cholerae bacterium is the agent of cholera .", "The capacity to produce the cholera toxin , which is responsible for the deadly diarrhea associated with cholera epidemics , is encoded in the genome of a filamentous phage , CTXφ .", "Rolling-circle replication ( RCR ) is central to the life cycle of ...	[ "One of the major strategies to prevent Cholera epidemics is the development of oral vaccines based on live attenuated Vibrio cholerae strains .", "The most promising vaccine strains have been obtained by deletion of the cholera toxin genes , which are harboured in the genome of an integrated phage , CTXϕ .", "...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology and life sciences", "computer and information sciences" ]	Controlling Meiotic Recombinational Repair – Specifying the Roles of ZMMs, Sgs1 and Mus81/Mms4 in Crossover Formation	journal.pgen.1004690	null	[ [ "Homologous recombination during meiosis plays an integral role in ensuring that each gamete receives exactly one copy of each chromosome from its diploid parent .", "COs , representing reciprocal repair between homologs , become chiasmata – physical bridges between homologous chromosomes that are require...	[ "Crossovers ( COs ) play a critical role in ensuring proper alignment and segregation of homologous chromosomes during meiosis .", "How the cell balances recombination between CO vs . noncrossover ( NCO ) outcomes is not completely understood .", "Further lacking is what constrains the extent of DNA repair such...	[ "A critical component of successful reproduction is ensuring that the correct number of chromosomes is distributed to the gametes ( i . e . sperm , eggs ) .", "Incorrect numbers of chromosomes in our gametes can directly result in infertility , miscarriages and developmental disabilities such as Down syndrome .",...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "bacteriophages", "pathogens", "microbiology", "pseudomonas aeruginosa", "viruses", "virus effects on host gene expression", "bacterial diseases", "pseudomonas infections", "bacteria", "bacterial pathogens", "pseudomonas", ...	Next-Generation “-omics” Approaches Reveal a Massive Alteration of Host RNA Metabolism during Bacteriophage Infection of Pseudomonas aeruginosa	journal.pgen.1006134	null	[ [ "The threat of antibiotic resistance has renewed attention to phage therapy leading to isolation of many bacteriophages ( phages ) targeting human pathogens such as Pseudomonas aeruginosa and , consequently , an increasing number of phage genome sequences are available [1] .", "Comparative genomics has al...	[ "As interest in the therapeutic and biotechnological potentials of bacteriophages has grown , so has value in understanding their basic biology .", "However , detailed knowledge of infection cycles has been limited to a small number of model bacteriophages , mostly infecting Escherichia coli .", "We present her...	[ "The increase of the proportion of multidrug resistant bacterial strains is alarming and alternative ways to treat infections are necessary such as the use of the natural enemies of bacteria , also known as phage therapy .", "However , explorations of the molecular mechanisms underlying the viral cycle of bacteri...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "mathematics", "computer science/applications", "computational biology/computational neuroscience" ]	Stochastic Differential Equation Model for Cerebellar Granule Cell Excitability	journal.pcbi.1000004	null	[ [ "Neurons express intrinsic bioelectrical activity which is known to be stochastic in nature .", "In order to understand this complex dynamic behavior , computational modeling is inevitable .", "But , how to develop models that are capable of mimicking the intrinsic dynamic behavior of the biological c...	[ "Neurons in the brain express intrinsic dynamic behavior which is known to be stochastic in nature .", "A crucial question in building models of neuronal excitability is how to be able to mimic the dynamic behavior of the biological counterpart accurately and how to perform simulations in the fastest possible way...	[ "Computational modeling is of importance in striving to understand the complex dynamic behavior of a neuron .", "In neuronal modeling , the function of the neuron's components , including the cell membrane and voltage-dependent ion channels , is typically described using deterministic ordinary differential equati...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "chemical compounds", "viral transmission and infection", "pathogens", "microbiology", "organic compounds", "epithelial cells", "pseudomonas aeruginosa", "membrane proteins", "physiological processes", "yersinia", "amino ac...	The Type III Secretion Translocation Pore Senses Host Cell Contact	journal.ppat.1005530	null	[ [ "Type III secretion systems ( T3SSs ) are molecular syringes employed by a wide range of Gram-negative pathogens to directly inject effector proteins into targeted host cells , and thereby promote disease [1 , 2] .", "A hallmark of these virulence-associated T3SSs is that effector secretion is triggered b...	[ "Type III secretion systems ( T3SS ) are nano-syringes used by a wide range of Gram-negative pathogens to promote infection by directly injecting effector proteins into targeted host cells .", "Translocation of effectors is triggered by host-cell contact and requires assembly of a pore in the host-cell plasma mem...	[ "Type III secretion systems ( T3SSs ) are molecular syringes used by a wide variety of Gram-negative pathogens to directly deliver proteins ( effectors ) into host cells , allowing the bacteria to cause disease .", "Injection of proteins is triggered by host-cell contact , but how the machinery to deliver effecto...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "onchocerca volvulus", "clinical research design", "tropical diseases", "parasitic diseases", "animals", "onchocerca", "research design", "filariasis", "pharmaceutics", "neglected tropical diseases", "pharmacology", "onchocerciasis", "lymp...	Effect of Two or Six Doses 800 mg of Albendazole Every Two Months on Loa loa Microfilaraemia: A Double Blind, Randomized, Placebo-Controlled Trial	journal.pntd.0004492	null	[ [ "Loiasis is a parasitic infection endemic in the African equatorial rain forest areas , caused by the filarial nematode Loa loa .", "It is estimated that at least 14 . 4 million people live in loiasis endemic areas [1] .", "Clinical manifestations include chronic intense itching and transient localize...	[ "Loiasis is a parasitic infection endemic in the African rain forest caused by the filarial nematode Loa loa .", "Loiasis can be co-endemic with onchocerciasis and/or lymphatic filariasis .", "Ivermectin , the drug used in the control of these diseases , can induce serious adverse reactions in patients with hig...	[ "Loiasis is a big obstacle for the elimination of onchocerciasis and lymphatic filariasis in Central Africa in areas where loiasis is endemic .", "In these areas , some subjects who are heavily infected ( microfilaraemia > 30 000 microfilariae/ml blood ) can develop severe and serious adverse reactions to ivermec...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "sequencing techniques", "invertebrates", "medicine and health sciences", "rna interference", "caenorhabditis", "gene regulation", "messenger rna", "operons", "animals", "animal models", "caenorhabditis elegans", "model organisms", "dna", "epigenetics", "molecular biology techniques", ...	XRN2 Autoregulation and Control of Polycistronic Gene Expresssion in Caenorhabditis elegans	journal.pgen.1006313	null	[ [ "Polycistronic gene expression is common in prokaryotes: multiple genes are arranged tandemly and transcribed from a single promoter , as one RNA precursor .", "This organization of genes into an operon permits regulation of functionally related genes in one unit .", "By contrast , protein-coding gene...	[ "XRN2 is a conserved 5’→3’ exoribonuclease that complexes with proteins that contain XRN2-binding domains ( XTBDs ) .", "In Caenorhabditis elegans ( C . elegans ) , the XTBD-protein PAXT-1 stabilizes XRN2 to retain its activity .", "XRN2 activity is also promoted by 3' ( 2' ) , 5'-bisphosphate nucleotidase 1 ( ...	[ "XRN2 is a conserved eukaryotic protein that controls gene expression by degrading or processing various types of RNA .", "Here we find that XRN2 negatively regulates its own levels in the nematode C . elegans .", "In response to reduction of XRN2 activity , this self-repression is alleviated , increasing xrn-2...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "dengue virus", "medicine and health sciences", "body fluids", "pathology and laboratory medicine", "cell cycle and cell division", "pathogens", "cell processes", "microbiology", "animals", "viruses", "mitosis", "rna viruses", "insect vectors", "digestive system", "inf...	Regulation of midgut cell proliferation impacts Aedes aegypti susceptibility to dengue virus	journal.pntd.0006498	null	[ [ "The mosquito Aedes aegypti is a vector of several human pathogens , such as flaviviruses , including yellow fever ( YFV ) , dengue ( DENV ) and zika ( ZIKV ) , and thus this mosquito exerts an enormous public health burden worldwide [1 , 2] .", "During the transmission cycle , these insects feed on volum...	[ "Aedes aegypti is the vector of some of the most important vector-borne diseases like dengue , chikungunya , zika and yellow fever , affecting millions of people worldwide .", "The cellular processes that follow a blood meal in the mosquito midgut are directly associated with pathogen transmission .", "We studi...	[ "Aedes mosquitoes are important vectors of arboviruses , representing a major threat to public health .", "While feeding on blood , mosquitoes address the challenges of digestion and preservation of midgut homeostasis .", "Damaged or senescent cells must be constantly replaced by new cells to maintain midgut ep...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genome analysis tools", "genomics", "genetic networks", "biophysic al simulations", "regulatory networks", "biology", "computational biology", "genetics and genomics", "transcriptomes" ]	Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density	journal.pcbi.1002830	null	[ [ "MicroRNAs ( miRNAs ) belong to a class of short ( 18–25 nucleotide ) non-coding RNAs that regulate gene expression post-transcriptionally .", "Their regulatory activity depends heavily on the recognition of target sites located primarily on the 3′-untranslated regions ( 3′UTRs ) of messenger RNAs [1] but...	[ "MicroRNAs ( miRNAs ) are post-transcriptional regulators that bind to their target mRNAs through base complementarity .", "Predicting miRNA targets is a challenging task and various studies showed that existing algorithms suffer from high number of false predictions and low to moderate overlap in their predictio...	[ "MicroRNA genes ( miRNAs ) are small non-coding RNAs that regulate the expression levels of mRNAs post-transcriptionally .", "miRNAs are critical in many important biological processes , like development , and are important markers for many diseases .", "Identifying the targets of miRNAs is not an easy task .",...	2012
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "medicine and health sciences", "enzyme-linked immunoassays", "helminths", "tropical diseases", "geographical locations", "parasitic diseases", "animals", "schistosomiasis japonica", "age groups", "neglected tropical diseases", "immunologic techniques", "res...	Comparison of Kato Katz, antibody-based ELISA and droplet digital PCR diagnosis of schistosomiasis japonica: Lessons learnt from a setting of low infection intensity	journal.pntd.0007228	null	[ [ "Schistosomiasis japonica , a disease of poverty , remains a public health concern in China and the Philippines .", "A significant reduction in the prevalence of schistosomiasis has been achieved in China due to extensive integrated control efforts underpinned by mass drug administration ( MDA ) with the ...	[ "Zoonotic schistosomiasis in Asia , caused by Schistosoma japonicum , remains a major public health concern in China and the Philippines .", "The developing epidemiological and socio-economic picture of the disease in endemic areas necessitates the development of affordable and highly accurate field diagnostics a...	[ "Schistosomiasis japonica remains prevalent in China and in the Philippines .", "The current changes in the epidemiological and socio-economic picture in the endemic areas makes it imperative that affordable and more sensitive field diagnostics are developed as an important component to evaluate ongoing integrate...	2019
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "cancer detection and diagnosis", "medicine and health sciences", "clinical research design", "statistics", "cancer risk factors", "geographical locations", "oncology", "dna damage", "research design", "multivariate analysis", "mathematics", "drug design", "case series", "medical risk fact...	A region-based gene association study combined with a leave-one-out sensitivity analysis identifies SMG1 as a pancreatic cancer susceptibility gene	journal.pgen.1008344	null	[ [ "Pancreatic adenocarcinoma ( PC ) remains one of the most lethal malignancies , with a 5-year survival rate of only 9%[1 , 2] .", "Since 10% of PC cases are familial ( FPC ) or can be accounted for by genes implicated in hereditary cancer syndromes[3 , 4] , gene-based surveillance strategies may enable ea...	[ "Pancreatic adenocarcinoma ( PC ) is a lethal malignancy that is familial or associated with genetic syndromes in 10% of cases .", "Gene-based surveillance strategies for at-risk individuals may improve clinical outcomes .", "However , familial PC ( FPC ) is plagued by genetic heterogeneity and the genetic basi...	[ "Pancreatic cancer ( PC ) remains one of the most lethal malignancies , with a 5-year survival rate of only 9% .", "Approximately 10% of PC occurs in families or in patients with hereditary mutations that are known to cause PC .", "The genetic causes of familial PC remain largely unknown .", "Using a new stat...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "infectious diseases", "hiv", "viral diseases" ]	Activation of HIV Transcription by the Viral Tat Protein Requires a Demethylation Step Mediated by Lysine-specific Demethylase 1 (LSD1/KDM1)	journal.ppat.1002184	null	[ [ "Epigenetic processes are critical in the regulation of gene expression from the integrated HIV provirus and have become a focal point of research in therapeutics for HIV latency .", "Latently infected T cells persist in HIV-infected individuals despite highly active antiretroviral therapy ( HAART ) and r...	[ "The essential transactivator function of the HIV Tat protein is regulated by multiple posttranslational modifications .", "Although individual modifications are well characterized , their crosstalk and dynamics of occurrence during the HIV transcription cycle remain unclear .", "We examine interactions between...	[ "One of the remaining questions in HIV research is how the virus establishes a dormant ( latent ) stage and thereby escapes eradication by current antiretroviral therapy .", "Latently infected T cells do not produce significant amounts of viral genomes or viral proteins due to the silencing of a specific step in ...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "tropical diseases", "geographical locations", "social sciences", "health care", "vaccines", "inpatients", "neglected tropical diseases", "infectious disease control", "patients", "africa", "infectious diseases", "health economics", "dengue fever", "econom...	A multi-country study of the economic burden of dengue fever based on patient-specific field surveys in Burkina Faso, Kenya, and Cambodia	journal.pntd.0007164	null	[ [ "Dengue fever is a vector-borne disease and transmitted by Aedes mosquitoes [1–3] .", "Dengue immunity and population biology are complex [4 , 5] .", "There are four serotypes , which are antigenically distinct viruses but interact with each other .", "It is known that infection with one serotype ...	[ "Dengue fever is a rapidly growing public health problem in many parts of the tropics and sub-tropics in the world .", "While there are existing studies on the economic burden of dengue fever in some of dengue-endemic countries , cost components are often not standardized , making cross-country comparisons challe...	[ "Dengue fever is a major public health concern in many parts of South-East Asia and South America .", "In addition to countries where dengue has been highly prevalent for many years , there is a growing concern on the undocumented burden of dengue in Africa .", "Following the successful execution of the first-r...	2019
[ "Introduction", "Results and discussion", "Materials and methods" ]	[ "medicine and health sciences", "fish", "classical mechanics", "engineering and technology", "social sciences", "vertebrates", "neuroscience", "animals", "throat", "animal behavior", "cognition", "reflection", "optical equipment", "zoology", "animal cognition", "behavior", "short rep...	If a fish can pass the mark test, what are the implications for consciousness and self-awareness testing in animals?	journal.pbio.3000021	A marine fish, the cleaner wrasse, appears to perform all the appropriate behavioural responses during the mirror, or mark test. Does this mean that cleaner wrasse are self-conscious? Or that our interpretation of what the mark test means needs to be updated?	[ [ "The mark test , in which a coloured mark is placed on a test subject in a location that can only be viewed in a mirror reflection , is held as the benchmark behavioural assay for assessing whether an individual has the capacity for self-recognition [1 , 2] .", "In human infants , approximately 65% of ind...	[ "This Short Report received both positive and negative reviews by experts .", "The Academic Editor has written an accompanying Primer that we are publishing alongside this article ( https://doi . org/10 . 1371/journal . pbio . 3000112 ) .", "The linked Primer presents a complementary expert perspective; it disc...	[ "The ability to perceive and recognise a reflected mirror image as self is considered a hallmark of cognition across species .", "Here , we show that a fish , the cleaner wrasse , shows behavioural responses that can be interpreted as passing the mark ( or mirror ) test , a classic test for self-awareness in anim...	2019
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "public health and epidemiology", "emerging viral diseases", "immunology", "microbiology", "rift valley fever", "neglected tropical diseases", "infectious disease control", "veterinary science", "veterinary medicine", "immunizations", "infectious diseases", "veterinary diseases",...	Characterization of Rift Valley Fever Virus MP-12 Strain Encoding NSs of Punta Toro Virus or Sandfly Fever Sicilian Virus	journal.pntd.0002181	null	[ [ "Rift Valley fever virus ( RVFV ) , which belongs to the family Bunyaviridae , genus Phlebovirus , is a zoonotic pathogen transmitted by mosquitoes , and the causative agent for Rift Valley fever ( RVF ) .", "RVF is characterized by a high rate of abortion and fetal malformation in pregnant ruminants , fe...	[ "Rift Valley fever virus ( RVFV; genus Phlebovirus , family Bunyaviridae ) is a mosquito-borne zoonotic pathogen which can cause hemorrhagic fever , neurological disorders or blindness in humans , and a high rate of abortion in ruminants .", "MP-12 strain , a live-attenuated candidate vaccine , is attenuated in t...	[ "Upon outbreak of zoonotic viral diseases in herds of animals , early detection of naturally infected animals and prevention of further viral spread are important for minimizing the impact of outbreak in the society .", "Vaccination may compromise the identification of infected animals since both natural infectio...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/protozoal infections", "microbiology/cellular microbiology and pathogenesis", "microbiology/medical microbiology", "microbiology/parasitology" ]	A Cysteine Protease Is Critical for Babesia spp. Transmission in Haemaphysalis Ticks	journal.ppat.1000062	null	[ [ "The ixodid ticks are obligate hematophagous organisms that belong to the phylum Arthropda , and are classified with spiders and scorpions in the class Arachnida [1] .", "Ticks are long-term blood-pool feeders , while mosquitoes are short-term vessel-feeders , and the process of blood digestion in ticks d...	[ "Vector ticks possess a unique system that enables them to digest large amounts of host blood and to transmit various animal and human pathogens , suggesting the existence of evolutionally acquired proteolytic mechanisms .", "We report here the molecular and reverse genetic characterization of a multifunctional c...	[ "Ticks are important ectoparasites among the blood-feeding arthropods and serve as vectors of many deadly diseases of humans and animals .", "Of tick-transmitted pathogens , Babesia , an intracellular haemoprotozoan parasite causing a malaria-like disease , called babesiosis , gain increasing interest due to its ...	2008
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "public health and epidemiology/infectious diseases", "microbiology", "evolutionary biology/evolutionary and comparative genetics" ]	Phylogeography of Recently Emerged DENV-2 in Southern Viet Nam	journal.pntd.0000766	null	[ [ "Dengue viruses ( DENV ) are mosquito-borne RNA viruses ( family Flaviviridae ) that exist as four antigenically distinct viruses or serotypes ( DENV-1 through DENV-4 ) and show complex immunological interactions within a human host and at the epidemiological scale [1] .", "Current estimates suggest that ...	[ "Revealing the dispersal of dengue viruses ( DENV ) in time and space is central to understanding their epidemiology .", "However , the processes that shape DENV transmission patterns at the scale of local populations are not well understood , particularly the impact of such factors as human population movement a...	[ "Dengue virus ( DENV ) is the cause of the most common vector-borne viral disease of humans , and is at particularly high prevalence in parts of Southeast Asia .", "Most studies of DENV transmission have focused on very local or international movement patterns , and have not explored how DENV moves through an end...	2010
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "zoology", "immunology", "biology", "lymphoid organs", "microbiology", "host-pathogen interaction", "parasitology", "helminthology", "immune system" ]	Blood Flukes Exploit Peyer's Patch Lymphoid Tissue to Facilitate Transmission from the Mammalian Host	journal.ppat.1003063	null	[ [ "Schistosomes are large metazoan pathogens of humans that parasitise the blood of >200 million people worldwide [1] .", "Unlike the majority of infections caused by viruses , bacteria and protozoa , schistosome infections are chronic , with a fecund worm life span of more than 10 years , and re-infections...	[ "Schistosomes are blood-dwelling parasitic helminths which produce eggs in order to facilitate transmission .", "Intestinal schistosomes lay eggs in the mesenteries , however , it is unclear how their eggs escape the vasculature to exit the host .", "Using a murine model of infection , we reveal that Schistosom...	[ "Schistosomes are parasitic helminths that parasitise >200 million people worldwide .", "Adult worm pairs of intestinal schistosomes lay their eggs in the mesenteric veins from which the eggs need to pass into the lumen prior to excretion and completion of their life cycle .", "However , it is not known how egg...	2012
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "medicine and health sciences", "rna interference", "caenorhabditis", "oxidative stress", "animals", "animal models", "physiological processes", "developmental biology", "caenorhabditis elegans", "model organisms", "organism development", "experimental organism systems", "...	Transaldolase inhibition impairs mitochondrial respiration and induces a starvation-like longevity response in Caenorhabditis elegans	journal.pgen.1006695	null	[ [ "Mitochondria are the primary sites of aerobic metabolism and energy production in the cell .", "The mitochondrial free radical theory of aging posits that reactive oxygen species ( ROS ) produced by mitochondria during oxidative metabolism cause damage to macromolecules which , over time , leads to the a...	[ "Mitochondrial dysfunction can increase oxidative stress and extend lifespan in Caenorhabditis elegans .", "Homeostatic mechanisms exist to cope with disruptions to mitochondrial function that promote cellular health and organismal longevity .", "Previously , we determined that decreased expression of the cytos...	[ "There are a growing number of studies linking mitochondrial dysfunction to enhanced longevity , especially in the nematode C . elegans .", "The reasons for these pro-longevity effects have been elusive , but one current model is that adaptive responses to mitochondrial inhibition promote organismal health and st...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "action potentials", "pathology and laboratory medicine", "membrane potential", "brain electrophysiology", "brain", "electrophysiology", "neuroscience", "signs and symptoms", "brain mapping", "bioassays and physiological analysis", "electroencephalography", "n...	The Impact of Cortical Lesions on Thalamo-Cortical Network Dynamics after Acute Ischaemic Stroke: A Combined Experimental and Theoretical Study	journal.pcbi.1005048	null	[ [ "The brain is a complex network of segregated , functionally specialised , yet densely interconnected regions that exchange and integrate signals with high spatio-temporal precision [1 , 2] .", "Pathological perturbations of a focal area within this network can spread to distant regions , and affect their...	[ "The neocortex and thalamus provide a core substrate for perception , cognition , and action , and are interconnected through different direct and indirect pathways that maintain specific dynamics associated with functional states including wakefulness and sleep .", "It has been shown that a lack of excitation , ...	[ "The thalamus is involved in the relay and processing of most sensory information , and provides an interface between subcortical structures and the neocortex .", "However , disruptions in the subcortical communication with the thalamus are known to lead to thalamo-cortical dysrhythmia ( TCD ) , which is linked t...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "veterinary diseases", "biology and life sciences", "veterinary pharmacology", "veterinary science", "veterinary medicine" ]	Trichuris suis and Oesophagostomum dentatum Show Different Sensitivity and Accumulation of Fenbendazole, Albendazole and Levamisole In Vitro	journal.pntd.0002752	null	[ [ "The whipworm Trichuris trichiura has been estimated to infect 600 million people worldwide resulting in an estimated 1 . 6–6 . 4 million disability adjusted life-years lost globally [1] .", "The current control strategy against T . trichiura and other soil-transmitted helminths ( STHs ) is administration...	[ "The single-dose benzimidazoles used against Trichuris trichiura infections in humans are not satisfactory .", "Likewise , the benzimidazole , fenbendazole , has varied efficacy against Trichuris suis whereas Oesophagostomum dentatum is highly sensitive to the drug .", "The reasons for low treatment efficacy of...	[ "The human whipworm Trichuris trichiura is together with the roundworm Ascaris lumbricoides and the hookworms Ancylostoma duodenale and Necator Americanus the most common intestinal worms worldwide .", "Together they place more than 5 billion people at risk of infection .", "The current global control strategy ...	2014
[ "Introduction", "Results", "Discussion", "Conclusion", "Materials & Methods" ]	[ "flow cytometry", "nuclear staining", "radii", "geometry", "probability distribution", "mathematics", "cytometry", "skewness", "research and analysis methods", "staining", "specimen preparation and treatment", "probability density", "probability theory", "spectrophotometry", "cytophotome...	Kinetic Modeling of ABCG2 Transporter Heterogeneity: A Quantitative, Single-Cell Analysis of the Side Population Assay	journal.pcbi.1005188	null	[ [ "The side population ( SP ) assay is used to identify stem cells by flow cytometry through the characteristic of enhanced dye efflux mediated via ATP-binding cassette ( ABC ) transporters [1] .", "The SP was first identified by Goodell et al . as hematopoietic stem cells in samples of murine bone marrow a...	[ "The side population ( SP ) assay , a technique used in cancer and stem cell research , assesses the activity of ABC transporters on Hoechst staining in the presence and absence of transporter inhibition , identifying SP and non-SP cell ( NSP ) subpopulations by differential staining intensity .", "The interpreta...	[ "A common method of evaluating stemness among pluripotent cells or cancer cells is the side population assay , a flow cytometry technique which identifies a subgroup of cells that exhibit differences in dye fluorescence upon blocking of a membrane transporter .", "A technical limitation of this assay is that it r...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunopathology", "adaptive immunity", "animal genetics", "inflammation", "immune cells", "cytokines", "antigen processing and recognition", "immunity", "immune activation", "genetics", "t cells", "immunology", "allergy and hypersensitivity", "biology", "autoimmunity", "immune system"...	NKT Cell-TCR Expression Activates Conventional T Cells in Vivo, but Is Largely Dispensable for Mature NKT Cell Biology	journal.pbio.1001589	null	[ [ "Natural Killer T ( NKT ) cells represent a subset of T cells in mice and humans that express NK cell markers and recognize a small class of glycolipid ( auto- ) antigens [1] , [2] .", "Most mouse NKT cells express an invariant Vα14-Jα18 ( Vα14i ) TCRα rearrangement ( Vα24-Jα18 in humans ) .", "In pri...	[ "Natural killer T ( NKT ) cell development depends on recognition of self-glycolipids via their semi-invariant Vα14i-TCR .", "However , to what extent TCR-mediated signals determine identity and function of mature NKT cells remains incompletely understood .", "To address this issue , we developed a mouse strain...	[ "Immune system natural killer T ( NKT ) cells help to protect against certain strains of bacteria and viruses , and suppress the development of autoimmune diseases and cancer .", "However , NKT cells are also central mediators of allergic responses .", "The recognition of one's own glycolipid antigens ( self-gl...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "bacteriology", "organismal evolution", "microbial metabolism", "cellular stress responses", "gene regulation", "cell processes", "bacillus", "microbiology", "bacterial biochemistry", "prokaryotic models", "model organisms", "molecular cell biology", "microbial evolution", "bioinorganic ch...	Transport of Magnesium by a Bacterial Nramp-Related Gene	journal.pgen.1004429	null	[ [ "Metal ions are essential and serve many cellular purposes , including functioning as cofactors for numerous metalloenzymes .", "The latter are responsible for a diverse array of biochemical reactions and , together , comprise one third of all cellular proteins [1]–[3] .", "Conversely , all metals eli...	[ "Magnesium is an essential divalent metal that serves many cellular functions .", "While most divalent cations are maintained at relatively low intracellular concentrations , magnesium is maintained at a higher level ( ∼0 . 5–2 . 0 mM ) .", "Three families of transport proteins were previously identified for ma...	[ "Magnesium ions are essential for life , and , correspondingly , all organisms must encode for proteins to transport them .", "Three classes of bacterial proteins ( CorA , MgtE and MgtA/B ) have previously been identified for transport of the ion .", "This current study introduces a new route of magnesium impor...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell death", "gene networks", "cellular stress responses", "mechanisms of signal transduction", "gene function", "c-jun n-terminal kinase signaling cascade", "crosstalk", "apoptotic signaling", "mapk signaling cascades", "signaling in cellular processes", "stress signaling cascade", "biology"...	MK2-Dependent p38b Signalling Protects Drosophila Hindgut Enterocytes against JNK-Induced Apoptosis under Chronic Stress	journal.pgen.1002168	null	[ [ "In its function as a protective barrier , the intestinal epithelium is constantly exposed to stressors from the outside [1] .", "It acts as a mediator between the bacterial flora and the host's immune system , and the intestinal epithelial cells have to respond to extrinsic and intrinsic factors to ensur...	[ "The integrity of the intestinal epithelium is crucial for the barrier function of the gut .", "Replenishment of the gut epithelium by intestinal stem cells contributes to gut homeostasis , but how the differentiated enterocytes are protected against stressors is less well understood .", "Here we use the Drosop...	[ "The gut epithelium forms the first barrier against pathogens and stressors in the gut lumen , and a loss of this defence function can result in intestinal diseases .", "Damage in the gut epithelium triggers the proliferation of intestinal stem cells to replenish the epithelium .", "However , little is known ab...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/microbial evolution and genomics", "genetics and genomics/gene expression", "genetics and genomics/functional genomics", "microbiology/microbial evolution and genomics", "evolutionary biology/genomics", "evolutionary biology", "microbiology/microbial physiology and metabolism", ...	E Unibus Plurum: Genomic Analysis of an Experimentally Evolved Polymorphism in Escherichia coli	journal.pgen.1000713	null	[ [ "Evolutionary biologists have long sought to understand mechanistically how adaptive genetic variation arises and persists .", "Experimental studies using model organisms such as Drosophila [1]–[3] and C . elegans [4]–[6] transformed the search for such mechanisms from a retrospective to a prospective end...	[ "Microbial populations founded by a single clone and propagated under resource limitation can become polymorphic .", "We sought to elucidate genetic mechanisms whereby a polymorphism evolved in Escherichia coli under glucose limitation and persisted because of cross-feeding among multiple adaptive clones .", "A...	[ "Experimental evolution of asexual species has shown that multiple genotypes can arise from a single ancestor and stably coexist ( e unibus plurum ) .", "Although facilitated by environmental heterogeneity , this phenomenon also occurs in simple , homogeneous environments provisioned with a single limiting nutrie...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "animal models", "aging", "caenorhabditis elegans", "animal genetics", "model organisms", "rna interference", "genetic screens", "gene expression", "genetics", "population biology", "biology", "gene function" ]	Dietary Restriction Induced Longevity Is Mediated by Nuclear Receptor NHR-62 in Caenorhabditis elegans	journal.pgen.1003651	null	[ [ "Genetic and environmental factors can cause profound changes in organism lifespan .", "Genetic alterations that stimulate robust longevity across taxa include reduced insulin/IGF and TOR signaling , reduced mitochondrial function , and reduced signaling from germline stem cells [1] .", "One of the mo...	[ "Dietary restriction ( DR ) extends lifespan in a wide variety of species , yet the underlying mechanisms are not well understood .", "Here we show that the Caenorhabditis elegans HNF4α-related nuclear hormone receptor NHR-62 is required for metabolic and physiologic responses associated with DR-induced longevity...	[ "Dietary restriction extends the life span of diverse species across taxa , yet the underlying mechanisms are poorly understood .", "In humans there are clear health benefits associated with DR such as improved serum cholesterol and lipid levels .", "In Caenorhabditis elegans , genes implicated in the TOR pathw...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Molecular Characterization of Host-Specific Biofilm Formation in a Vertebrate Gut Symbiont	journal.pgen.1004057	null	[ [ "Most members of the animal kingdom form associations with symbiotic microorganisms that are often of fundamental importance for their biology [1] .", "These symbioses vary in terms of their effects on the host and the evolutionary and ecological processes that maintain the partnership .", "To date , ...	[ "Although vertebrates harbor bacterial communities in their gastrointestinal tract whose composition is host-specific , little is known about the mechanisms by which bacterial lineages become selected .", "The goal of this study was to characterize the ecological processes that mediate host-specificity of the ver...	[ "The bacterial communities found in the vertebrate gastrointestinal tract are remarkably stable and host-specific .", "However , the ecological and molecular processes that facilitate the selection of microbial symbionts and the exclusion of detrimental bacteria are not well understood .", "Here , we explore th...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "flow cytometry", "medicine and health sciences", "vesicles", "diagnostic radiology", "hela cells", "biological cultures", "cell processes", "light microscopy", "membrane proteins", "microscopy", "cell cultures", "confocal microscopy", "cellular structures and organelles", "endosomes", "...	Enteropathogenic Escherichia coli remodels host endosomes to promote endocytic turnover and breakdown of surface polarity	journal.ppat.1007851	null	[ [ "Enteropathogenic Escherichia coli ( EPEC ) and enterohemorrhagic Escherichia coli ( EHEC ) are diarrheagenic extracellular pathogens affecting humans worldwide [1] .", "EPEC utilizes a molecular syringe termed type III secretion system ( T3SS ) to deliver a set of effector proteins from the bacterial cyt...	[ "Enteropathogenic E . coli ( EPEC ) is an extracellular diarrheagenic human pathogen which infects the apical plasma membrane of the small intestinal enterocytes .", "EPEC utilizes a type III secretion system to translocate bacterial effector proteins into its epithelial hosts .", "This activity , which subvert...	[ "Enteropathogenic Escherichia coli ( EPEC ) are pathogenic bacteria that cause infantile diarrhea .", "Upon ingestion , EPEC reaches the small intestine , where an injection device termed the type III secretion system is utilized to inject a set of effector proteins from the bacteria into the host cell .", "The...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell physiology", "keratinocytes", "medicine and health sciences", "gene regulation", "cell processes", "junctional complexes", "epithelial cells", "membrane proteins", "immunologic techniques", "cellular structures and organelles", "research and analysis methods", "small interfering rnas", ...	RPGRIP1L is required for stabilizing epidermal keratinocyte adhesion through regulating desmoglein endocytosis	journal.pgen.1007914	null	[ [ "Retinitis pigmentosa GTPase regulator interacting protein 1-like ( RPGRIP1L , also known as NPHP8 , MKS5 , KIAA1005 , or Ftm in mouse ) is a transition zone protein that has important roles in regulating cilia formation and function [1–5] .", "Mutations in the RPGRIP1L gene cause Joubert syndrome ( JBTS ...	[ "Cilia-related proteins are believed to be involved in a broad range of cellular processes .", "Retinitis pigmentosa GTPase regulator interacting protein 1-like ( RPGRIP1L ) is a ciliary protein required for ciliogenesis in many cell types , including epidermal keratinocytes .", "Here we report that RPGRIP1L is...	[ "The desmosome is a type of intercellular junction , essential for cells to adhere to one another .", "Abnormalities in desmosomes can cause disorders in the hair , skin , and heart , some of which are severe or even fatal .", "Here , we discovered that RPGRIP1L , a protein known to regulate cilia formation and...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "public health", "medicine", "infectious diseases", "schistosomiasis", "public health and epidemiology", "drug policy", "neglected tropical diseases", "parasitic diseases" ]	Performance and Safety of Praziquantel for Treatment of Intestinal Schistosomiasis in Infants and Preschool Children	journal.pntd.0001864	null	[ [ "Schistosomiasis is one of the major neglected tropical diseases ( NTDs ) affecting over 207 million people worldwide .", "Since the agreement of the eight Millennium Goals in 2000 , control of the infection has gained much international interest and political commitment , leading to the World Health Asse...	[ "In 2012 the WHO formally recognised that infants and preschool children are at significant risk of schistosomiasis and qualify for treatment with praziquantel ( PZQ ) .", "Targeted surveys determining both the performance and safety of this drug are now needed in endemic areas .", "We have formally assessed pa...	[ "Although there is now extensive evidence for infection in preschool-aged children , and even a change in WHO guidelines endorsing treatment of this young age class in endemic areas , very little work has been published on the performance of praziquantel in children below the age of six .", "Previous work on praz...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "death rates", "hiv infections", "medicine and health sciences", "pathology and laboratory medicine", "demography", "pathogens", "microbiology", "retroviruses", "viruses", "immunodeficiency viruses", "probability distribution", "mathematics", "rna viruses", "distribution curves", "popula...	Impact of Heterogeneity in Sexual Behavior on Effectiveness in Reducing HIV Transmission with Test-and-Treat Strategy	journal.pcbi.1005012	null	[ [ "Recently , a large trial conducted at various sites in 34 countries provided evidence that starting ART as soon as possible regardless of CD4 count is advantageous for health prospects of HIV infected persons [1] .", "The WHO’s early-release guideline for ART initiation now reflects these findings recomm...	[ "The WHO’s early-release guideline for antiretroviral treatment ( ART ) of HIV infection based on a recent trial conducted in 34 countries recommends starting treatment immediately upon an HIV diagnosis .", "Therefore , the test-and-treat strategy may become more widely used in an effort to scale up HIV treatment...	[ "HIV is endemic in populations of MSM in Western countries .", "As ART reduces transmission risk , increased testing and treatment rates are expected to lower HIV incidence .", "However , concerns are that in MSM populations changing risk behavior may counteract the impact of ART on transmission .", "Using a ...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "molecular biology/histone modification", "biochemistry", "genetics and genomics/gene discovery", "genetics and genomics/nuclear structure and function", "genetics and genomics/chromosome biology", "genetics and genomics/gene function", "molecular biology/dna methylation", "genetics and genomics/epige...	DNA Methylation and Normal Chromosome Behavior in Neurospora Depend on Five Components of a Histone Methyltransferase Complex, DCDC	journal.pgen.1001196	null	[ [ "Methylation of selected cytosines in DNA is a prototypical epigenetic process found in many eukaryotes .", "DNA methylation has been implicated in embryonic development , genome imprinting , X chromosome inactivation , transposon silencing and gene regulation [1]–[5] .", "Conversely , abnormal DNA me...	[ "Methylation of DNA and of Lysine 9 on histone H3 ( H3K9 ) is associated with gene silencing in many animals , plants , and fungi .", "In Neurospora crassa , methylation of H3K9 by DIM-5 directs cytosine methylation by recruiting a complex containing Heterochromatin Protein-1 ( HP1 ) and the DIM-2 DNA methyltrans...	[ "Eukaryotic genomes are composed of distinct structural and functional domains marked by various covalent modifications of histone proteins and , in some organisms , by methylation of cytosine bases in DNA .", "Gene-rich euchromatin exists in a relatively open conformation , facilitating DNA transactions such as ...	2010
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell death", "fluorescence imaging", "medicine and health sciences", "lysosomes", "toxins", "pathology and laboratory medicine", "molecular probe techniques", "pathogens", "endoplasmic reticulum", "cell processes", "immunoblotting", "light microscopy", "toxicology", "toxic agents", "con...	Host cell interactions of outer membrane vesicle-associated virulence factors of enterohemorrhagic Escherichia coli O157: Intracellular delivery, trafficking and mechanisms of cell injury	journal.ppat.1006159	null	[ [ "Enterohemorrhagic Escherichia coli ( EHEC ) O157 , the leading EHEC serogroup causing human diseases including life-threatening hemolytic uremic syndrome ( HUS ) [1] , consist of classical non-sorbitol-fermenting ( NSF ) O157:H7 and sorbitol-fermenting ( SF ) O157:H- ( non-motile ) strains [2] .", "Sever...	[ "Outer membrane vesicles ( OMVs ) are important tools in bacterial virulence but their role in the pathogenesis of infections caused by enterohemorrhagic Escherichia coli ( EHEC ) O157 , the leading cause of life-threatening hemolytic uremic syndrome , is poorly understood .", "Using proteomics , electron and con...	[ "Enterohemorrhagic Escherichia coli ( EHEC ) O157 , the leading EHEC group causing diarrhea and the life-threatening hemolytic uremic syndrome in humans , produce several virulence factors which play distinct roles in the pathogenesis of these diseases .", "However , the mechanisms of their secretion and host cel...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology" ]	The NDR/LATS Kinase Cbk1 Controls the Activity of the Transcriptional Regulator Bcr1 during Biofilm Formation in Candida albicans	journal.ppat.1002683	null	[ [ "Biofilms are surface-attached microbial communities embedded in an extracellular matrix .", "Cells in a biofilm exhibit phenotypic properties different from those of their planktonic counterparts , including an increased resistance to the host immune system and to antimicrobial agents [1]–[3] .", "Se...	[ "In nature , many microorganisms form specialized complex , multicellular , surface-attached communities called biofilms .", "These communities play critical roles in microbial pathogenesis .", "The fungal pathogen Candida albicans is associated with catheter-based infections due to its ability to establish bio...	[ "C . albicans infections frequently involve the formation of biofilms on implanted devices such as indwelling catheters .", "These complex communities of surface-associated fungal cells embedded in a matrix of extracellular polysaccharides protect C . albicans from host defences and antifungal agents .", "In re...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology", "molecular biology/dna repair", "molecular biology/transcription initiation and activation" ]	Differentiation Driven Changes in the Dynamic Organization of Basal Transcription Initiation	journal.pbio.1000220	A novel mouse model reveals that the dynamic behavior of transcription factors can vary considerably between different cells of an organism.	[ [ "Basal transcription/repair factor IIH ( TFIIH ) is a ten-subunit complex [1] , essential for both RNA polymerase I and II ( RNAP1 and", "2 ) transcription initiation and nucleotide excision repair ( NER ) [2] .", "NER is an important DNA repair process , which is able to remove a broad spectrum of di...	[ "Studies based on cell-free systems and on in vitro–cultured living cells support the concept that many cellular processes , such as transcription initiation , are highly dynamic: individual proteins stochastically bind to their substrates and disassemble after reaction completion .", "This dynamic nature allows ...	[ "The accepted model of eukaryotic mRNA production is that transcription factors spend most of their time diffusing throughout the cell nucleus , encountering gene promoters ( their substrate ) in a random fashion and binding to them for a very short time .", "A similar modus operandi has been accepted as a paradi...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "crystal structure", "built structures", "pathology and laboratory medicine", "engineering and technology", "pathogens", "condensed matter physics", "microbiology", "viral structure", "viruses", "membrane fusion", "rna viruses", "membrane structures", "glyco...	Acidic pH-Induced Conformations and LAMP1 Binding of the Lassa Virus Glycoprotein Spike	journal.ppat.1005418	null	[ [ "Lassa virus ( LASV ) is an enveloped , ambi-sense , bi-segmented RNA virus endemic throughout Western Africa and is the most lethal of all known Old World arenaviruses .", "Due to the high mortality rates amongst hospitalized patients ( ~15% ) , ability of the virus to be spread by aerosol , and absence ...	[ "Lassa virus is an enveloped , bi-segmented RNA virus and the most prevalent and fatal of all Old World arenaviruses .", "Virus entry into the host cell is mediated by a tripartite surface spike complex , which is composed of two viral glycoprotein subunits , GP1 and GP2 , and the stable signal peptide .", "Of ...	[ "Lassa virus is a zoonotic , hemorrhagic fever-causing pathogen .", "Because the virus can spread as an aerosol and there are no approved vaccines or specific antiviral drugs currently available , it poses a major impact on human health , affecting annually up to half a million people in West-African countries ."...	2016

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