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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" ]	[ "medicine and health sciences", "classical mechanics", "engineering and technology", "limbs (anatomy)", "social sciences", "neuroscience", "mechanical energy", "optimization", "mathematics", "vision", "kinematics", "musculoskeletal system", "hands", "pendulums", "physics", "mechanical ...	Sensory Agreement Guides Kinetic Energy Optimization of Arm Movements during Object Manipulation	journal.pcbi.1004861	null	[ [ "One of the most established findings in planar multi-joint reaching movements is that hand trajectories tend to be executed along straight paths with a bell-shaped velocity profile [1–3] .", "Given that there are theoretically infinite paths that the hand could take for reaching from one point to another...	[ "The laws of physics establish the energetic efficiency of our movements .", "In some cases , like locomotion , the mechanics of the body dominate in determining the energetically optimal course of action .", "In other tasks , such as manipulation , energetic costs depend critically upon the variable properties...	[ "Recent studies have shown that when learning novel dynamics in the context of reaching movements , people often ignore energetic optimality in favor of Euclidean geometric optimality , preferring rectilinear paths over mechanically optimal trajectories .", "Although an explanation could be that sensory-motor coo...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "learning", "medicine and health sciences", "disabilities", "health services research", "tropical diseases", "social sciences", "limbs (anatomy)", "neuroscience", "learning and memory", "health care", "bacterial diseases", "research design", "cognitive psychology", "neglected tropical dise...	The Use of Assistive Technology to Promote Care of the Self and Social Inclusion in Patients with Sequels of Leprosy	journal.pntd.0004644	null	[ [ "The interest on the topic emerged after the implantation of the service of Occupational Therapy in a University Hospital in Rio de Janeiro , among the interdisciplinary team for Prevention , Physical and Surgical Rehabilitation in Leprosy .", "Once we started investigating the functional limitations of p...	[ "This study is about the contribution of occupational therapy inside a rehabilitation group , and we focus on the autonomy of patients with disabilities due to leprosy .", "There are few studies on the use of assistive technology by leprosy patients; to our knowledge , none of them aim to have a subjective approa...	[ "This study is about occupational therapy and we focus on the autonomy of patients with disabilities due to leprosy .", "Our purpose was to analyze the repercussions of assistive technology on the autonomy of care of the self in patients with sequels of leprosy We performed a qualitative , descriptive , explorato...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "physiology/cell signaling", "cell biology", "plant biology/plant growth and development", "plant biology" ]	Arabidopsis CULLIN3 Genes Regulate Primary Root Growth and Patterning by Ethylene-Dependent and -Independent Mechanisms	journal.pgen.1000328	null	[ [ "Regulation of protein stability through the ubiquitin proteasome system ( UPS ) is now considered as a major mechanism underlying many cellular and organismal processes , such as cell division , DNA repair , quality control of newly produced proteins , developmental and immune defense pathways , and in plant...	[ "CULLIN3 ( CUL3 ) together with BTB-domain proteins form a class of Cullin-RING ubiquitin ligases ( called CRL3s ) that control the rapid and selective degradation of important regulatory proteins in all eukaryotes .", "Here , we report that in the model plant Arabidopsis thaliana , CUL3 regulates plant growth an...	[ "Ubiquitin-mediated proteolysis plays a central role in controlling intracellular levels of essential regulatory molecules in all eukaryotic organisms .", "This protein degradation pathway has a large number of components , including hundreds of ubiquitin protein ligases ( E3s ) that are predicted to have regulat...	2009
[ "Introduction", "Materials and Methods", "Results", "Discussion", "Conclusion" ]	[ "blood cells", "children", "innate immune system", "medicine and health sciences", "immune cells", "immune physiology", "cytokines", "body fluids", "cell cycle and cell division", "immunology", "cell processes", "parasitic diseases", "pediatrics", "age groups", "developmental biology", ...	Maternal Filarial Infection Influences the Development of Regulatory T Cells in Children from Infancy to Early Childhood	journal.pntd.0005144	null	[ [ "Lymphatic filariasis ( LF ) is a major cause of chronic morbidity in the tropics and sub tropics .", "According to a recent estimate more than 1 . 4 billion people across the world are at the risk of infection [1] .", "To eliminate LF globally by 2020 , WHO has introduced annual mass drug administrat...	[ "Children born from filarial infected mothers are comparatively more susceptible to filarial infection than the children born to uninfected mothers .", "But the mechanism of such increased susceptibility to infection in early childhood is not exactly known .", "Several studies have shown the association of acti...	[ "Lymphatic filariasis caused by thread like filarial worms involves asymptomatic to acute and/or disfiguring chronic conditions like lymphoedema , elephantiasis and scrotal swelling .", "Infection occurs when filarial parasites are transmitted to humans through mosquitoes .", "Adult worms lodge in the lymphatic...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases/neglected tropical diseases", "pediatrics and child health", "surgery/transplantation", "microbiology/parasitology", "infectious diseases/protozoal infections" ]	Accurate Real-Time PCR Strategy for Monitoring Bloodstream Parasitic Loads in Chagas Disease Patients	journal.pntd.0000419	null	[ [ "Infection with the parasite Trypanosoma cruzi ( T . cruzi ) remains a major concern in 21 endemic countries of America , with an estimated prevalence of almost 8 million infected people [1] .", "The infection may be acquired mainly through the triatomid insect vector , blood transfusion or the trans-plac...	[ "This report describes a real-time PCR ( Q-PCR ) strategy to quantify Trypanosoma cruzi ( T . cruzi ) DNA in peripheral blood samples from Chagas disease patients targeted to conserved motifs within the repetitive satellite sequence .", "The Q-PCR has a detection limit of 0 . 1 and 0 . 01 parasites/mL , with a dy...	[ "Infection with the parasite Trypanosoma cruzi ( T . cruzi ) , causing American trypanosomiasis or Chagas disease , remains a major public health concern in 21 endemic countries of America , with an estimated prevalence of 8 million infected people .", "Chagas disease shows a variable clinical course , ranging fr...	2009
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "immune physiology", "spleen", "immunology", "microbiology", "vertebrates", "animals", "mammals", "protozoan life cycles", "parasitic protozoans", "developmental biology", "protozoans", "pharmaceutics", "leishmania", "promastigotes", "hamsters", "life ...	Combined treatment of miltefosine and paromomycin delays the onset of experimental drug resistance in Leishmania infantum	journal.pntd.0005620	null	[ [ "Depending on the geographical location , visceral leishmaniasis ( VL ) can either be caused by Leishmania donovani ( East Africa and Indian subcontinent ) or L . infantum ( Mediterranean basin , central Asia and Latin America ) [1] .", "Although both species are closely related and belong to the same com...	[ "Since miltefosine monotherapy against visceral leishmaniasis ( VL ) caused by Leishmania donovani has been discontinued in the Indian subcontinent due to an increase in the number of treatment failures , single dose liposomal amphotericin B is now advocated as a treatment option of choice .", "Paromomycin-miltef...	[ "Liposomal amphotericin B is presently being used as first-line treatment option against visceral leishmaniasis in the Indian subcontinent .", "However , the need for temperature-controlled transport and storage limits its widespread use in rural areas .", "Previous studies already suggested that paromomycin-mi...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Single-Cell and Single-Cycle Analysis of HIV-1 Replication	journal.ppat.1004961	null	[ [ "The HIV-1 replication cycle consists of several discrete , sequentially occurring processes , involving numerous viral and host cell components .", "For the early steps in HIV-1 replication , there is a reasonably good appreciation of the kinetics with which individual steps occur .", "Viral entry oc...	[ "The dynamics of the late stages of the HIV-1 life cycle are poorly documented .", "Viral replication dynamics are typically measured in populations of infected cells , but asynchrony that is introduced during the early steps of HIV-1 replication complicates the measurement of the progression of subsequent steps ...	[ "The HIV-1 replication cycle is composed of several sequential steps .", "While the timing of the early steps of HIV-1 replication is quite well understood , measuring the duration of later steps is complicated by the fact that asynchrony is introduced into populations of infected cells during early steps .", "...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "biochemistry", "infectious diseases", "enzyme metabolism", "enzymes", "neglected tropical diseases", "biology", "viral diseases", "parasitic diseases" ]	Arginase Activity in the Blood of Patients with Visceral Leishmaniasis and HIV Infection	journal.pntd.0001977	null	[ [ "Visceral leishmaniasis ( VL ) , a neglected tropical disease caused by the parasite Leishmania ( L . ) donovani , is one of the most significant vector-borne diseases in Ethiopia , with an estimated 4500 to 5000 new cases every year [2] .", "VL is associated with high mortality and morbidity and hinders ...	[ "Visceral leishmaniasis is a parasitic disease associated with high mortality .", "The most important foci of visceral leishmaniasis in Ethiopia are in the Northwest and are predominantly associated with high rates of HIV co-infection .", "Co-infection of visceral leishmaniasis patients with HIV results in high...	[ "Visceral leishmaniasis ( VL ) in Ethiopia is caused by the parasite Leishmania donovani .", "This disease has one of the highest mortality rates: if left untreated , it is almost always fatal .", "VL belongs to the most neglected tropical diseases , affecting the poorest populations , for whom access to diagno...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "oncology", "immunology", "molecular biology", "hematology" ]	In Vivo Reinsertion of Excised Episomes by the V(D)J Recombinase: A Potential Threat to Genomic Stability	journal.pbio.0050043	Episomal DNA circles are the by-products of immunoreceptor gene rearrangements in lymphoid cells. Episomal circles can be reintegrated into the genome by trans-V(D)J recombination and cause oncogene deregulation.	[ [ "V ( D ) J recombination is a unique mechanism of somatic recombination aimed to provide a large", "antigen receptor repertoire in T and B cells ( for review , see [1] and references therein ) .", "During", "this process , the variable ( V ) diversity ( D ) and joining ( J ) gene segments present ...	[ "It has long been thought that signal joints , the byproducts of V ( D ) J recombination , are", "not involved in the dynamics of the rearrangement process .", "Evidence has now started to", "accumulate that this is not the case , and that signal joints play unsuspected roles in", "events that might comprom...	[ "Lymphoid cells recognize billions of pathogens as a result of gene rearrangements that", "generate pathogen-specific B- and T-cell receptors .", "This genetic reshuffling , called", "V ( D ) J recombination , occasionally misfires and damages genomic integrity .", "When such", "aberrations dysregulate pr...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	αvβ6- and αvβ8-Integrins Serve As Interchangeable Receptors for HSV gH/gL to Promote Endocytosis and Activation of Membrane Fusion	journal.ppat.1003806	null	[ [ "The glycoproteins of enveloped virions fulfill three major functions to enable virus entry into target cells; the attachment of virions to cells , a step that partly determines the type of cells that the virus targets , hence the viral tropism; the triggering of fusion , i . e . the activation of the fusion ...	[ "Herpes simplex virus ( HSV ) - and herpesviruses in general - encode for a multipartite entry/fusion apparatus .", "In HSV it consists of the HSV-specific glycoprotein D ( gD ) , and three additional glycoproteins , gH/gL and gB , conserved across the Herpesviridae family and responsible for the execution of fus...	[ "In order to infect their hosts and cause disease , viruses must enter their host cells .", "The human pathogen herpes simplex virus ( HSV ) - and herpesviruses in general - are equipped with a complex , multipartite entry apparatus , made of four glycoproteins – gD , gH/gL , gB .", "These glycoproteins must be...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "carbohydrate metabolism", "medicine and health sciences", "protein metabolism", "respiratory infections", "gene regulation", "pulmonology", "dna transcription", "animal models", "model organisms", "experimental organism systems", "pharmacology", "drug metabolism", "research and analysis met...	Transient In Vivo Resistance Mechanisms of Burkholderia pseudomallei to Ceftazidime and Molecular Markers for Monitoring Treatment Response	journal.pntd.0005209	null	[ [ "Understanding the mode of action and potential resistance mechanisms of frontline chemotherapeutics provides information about how clinically used drugs exert their efficacious effect .", "Typically the lethal effect of a drug is investigated in the laboratory under artificial conditions and is defined a...	[ "Much is known about the mode of action of drugs and resistance mechanisms under laboratory growth conditions , but research on the bacterial transcriptional response to drug pressure in vivo or efficacious mode of action and transient resistance mechanisms of clinically employed drugs is limited .", "Accordingly...	[ "The mode of action and resistance mechanisms for many clinically used drugs are elucidated under defined artificial laboratory growth conditions , and do not necessarily represent the efficacious mode of action or predict the transient resistance mechanisms that are active during infection .", "Here , we report ...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public health and epidemiology", "epidemiology", "public health" ]	Human Echinococcosis Mortality in the United States, 1990–2007	journal.pntd.0001524	null	[ [ "Human echinococcosis , a neglected disease caused by the larval stages of the cestode parasites Echinococcus granulosus ( hydatid cyst disease ) and E . multilocularis ( alveolar hydatid disease ) , affects an estimated 2–3 million people and results in an annual monetary loss of over $750 , 000 , 000 worldw...	[ "Despite the endemic nature of Echinococcus granulosus and Echinococcus multilocularis infection in regions of the United States ( US ) , there is a lack of data on echinococcosis-related mortality .", "To measure echinococcosis-associated mortality in the US and assess possible racial/ethnic disparities , we rev...	[ "Human echinococcosis is a parasitic disease that affects an estimated 2–3 million people and results in an annual monetary loss of over $750 , 000 , 000 worldwide .", "It results in the development of life threatening tissue cysts , primarily in the liver and lung , following accidental ingestion of eggs in infe...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "buruli ulcer", "neglected tropical diseases", "immunology", "biology", "microbiology", "host-pathogen interaction", "immune response" ]	Corticosteroid-Induced Immunosuppression Ultimately Does Not Compromise the Efficacy of Antibiotherapy in Murine Mycobacterium ulcerans Infection	journal.pntd.0001925	null	[ [ "Buruli ulcer ( BU ) is a necrotizing disease of the skin , subcutaneous tissue and bone [1] , [2] .", "The pathogenesis of the disease is associated with local and regional cytotoxic/immunosuppressive activities of the lipidic toxin mycolactone , produced by the environmental pathogen Mycobacterium ulcer...	[ "Buruli ulcer ( BU ) is a necrotizing disease of the skin , subcutaneous tissue and bone caused by Mycobacterium ulcerans .", "It has been suggested that the immune response developed during the recommended rifampicin/streptomycin ( RS ) antibiotherapy is protective , contributing to bacterial clearance .", "On...	[ "Buruli ulcer ( BU ) is an infectious disease caused by the environmental pathogen Mycobacterium ulcerans that affects the skin , subcutaneous tissue and bone , presenting extensive tissue necrosis .", "Standard treatment of BU patients consists of a combination of the antibiotics rifampicin and streptomycin ( RS...	2012
[ "Introduction", "Model and numerical methods", "Results and discussion" ]	[ "medicine and health sciences", "fish", "eels", "swimming", "classical mechanics", "fluid mechanics", "vertebrates", "animals", "biological locomotion", "osteichthyes", "bioassays and physiological analysis", "muscle electrophysiology", "kinematics", "research and analysis methods", "con...	3D computational models explain muscle activation patterns and energetic functions of internal structures in fish swimming	journal.pcbi.1006883	null	[ [ "During the undulatory swimming of fish , a backward-traveling wave of body bending is formed to push against the water and generate propulsion .", "Muscle is the executor of the neural control and the source of mechanical power in fish swimming .", "Therefore , how muscles are used is a key question ...	[ "How muscles are used is a key to understanding the internal driving of fish swimming .", "However , the underlying mechanisms of some features of the muscle activation patterns and their differential appearance in different species are still obscure .", "In this study , we explain the muscle activation pattern...	[ "For undulatory swimming , fish form posteriorly traveling waves of body bending by activating their muscles sequentially along the body .", "However , experimental observations have shown that the muscle activation wave does not simply match the bending wave .", "Researchers have previously computed the torque...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "blood cells", "genome-wide association studies", "medicine and health sciences", "chronic kidney disease", "anemia", "ethnicities", "red blood cells", "genome analysis", "african american people", "hemoglobin", "genomics", "globins", "animal cells", "proteins", "hematology", "people a...	Common α-globin variants modify hematologic and other clinical phenotypes in sickle cell trait and disease	journal.pgen.1007293	null	[ [ "Hemoglobin , the primary component of the red blood cell that carries oxygen to tissues in the body , is comprised of two β-globin chains , two α-globin chains , and a heme molecule bound to each subunit .", "In African Americans , β-globin protein structural variants , including hemoglobin S ( HbS ) and...	[ "Co-inheritance of α-thalassemia has a significant protective effect on the severity of complications of sickle cell disease ( SCD ) , including stroke .", "However , little information exists on the association and interactions for the common African ancestral α-thalassemia mutation ( −α3 . 7 deletion ) and β-gl...	[ "Recent work has shown that inheriting a single copy of the β-globin gene variant which causes sickle cell disease can be associated with medical risks , such as worsening kidney function .", "In individuals with sickle cell disease , co-inheritance of other globin gene variants , notably α-thalassemia , can modi...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "meiosis", "invertebrates", "animal genetics", "cell cycle and cell division", "cell processes", "animals", "animal models", "mitosis", "developmental biology", "drosophila melanogaster", "model organisms", "organism development", "chromatin", "drosophila", "research and analysis methods...	The Cohesin Subunit Rad21 Is Required for Synaptonemal Complex Maintenance, but Not Sister Chromatid Cohesion, during Drosophila Female Meiosis	journal.pgen.1004540	null	[ [ "During meiosis , haploid germ cells are generated from diploid parental cells by two consecutive cell divisions without intervening DNA replication .", "Before the first meiotic division , homologous chromosomes are paired into bivalents and the two sister centromeres in each homolog are constrained to b...	[ "Replicated sister chromatids are held in close association from the time of their synthesis until their separation during the next mitosis .", "This association is mediated by the ring-shaped cohesin complex that appears to embrace the sister chromatids .", "Upon proteolytic cleavage of the α-kleisin cohesin s...	[ "Meiosis is a specialized form of cell division that ensures production of germ cells with the right number of chromosomes , so that at fertilization the embryo receives complete sets of paternal and maternal chromosomes .", "The accurate distribution of chromosomes during cell divisions is dependent on a ring-sh...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "immunology/immune response", "infectious diseases/viral infections", "immunology/immunity to infections" ]	Human Fatal Zaire Ebola Virus Infection Is Associated with an Aberrant Innate Immunity and with Massive Lymphocyte Apoptosis	journal.pntd.0000837	null	[ [ "Ebolavirus ( EBOV ) and Marburgvirus ( MARV ) are among the most deadly human pathogens , causing a severe hemorrhagic fever syndrome in both humans and non human primates [1]–[2] .", "EBOV is subdivided into five species with different pathogenicities [3] .", "Zaire ebolavirus ( ZEBOV ) , the most l...	[ "Ebolavirus species Zaire ( ZEBOV ) causes highly lethal hemorrhagic fever , resulting in the death of 90% of patients within days .", "Most information on immune responses to ZEBOV comes from in vitro studies and animal models .", "The paucity of data on human immune responses to this virus is mainly due to th...	[ "Ebolavirus , especially the species Zaïre ( ZEBOV ) , causes a fulminating hemorrhagic fever syndrome resulting in the death of most patients within a few days .", "In vitro studies and animal models have brought some insight as to the immune responses to ZEBOV infection .", "However , human immune responses h...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "mechanisms of resistance and susceptibility", "immunity", "virology", "innate immunity", "host-pathogen interaction", "biology", "microbiology", "viral replication" ]	Implication of PMLIV in Both Intrinsic and Innate Immunity	journal.ppat.1003975	null	[ [ "The establishment of an antiviral state in cells is the defining property of interferons ( IFNs ) , as well as the activity that led to their discovery .", "IFNs are the first line of defense against viral infections .", "IFN-regulatory factor 3 ( IRF3 ) , a ubiquitously expressed transcription facto...	[ "PML/TRIM19 , the organizer of nuclear bodies ( NBs ) , has been implicated in the antiviral response to diverse RNA and DNA viruses .", "Several PML isoforms generated from a single PML gene by alternative splicing , share the same N-terminal region containing the RBCC/tripartite motif but differ in their C-term...	[ "PML is expressed as seven isoforms , designated PMLI to PMLVIIb , each with specific functions conferred by their C-terminal regions .", "PML isoforms are implicated in several cell processes , including antiviral defense .", "Very few studies have been performed with all PML isoforms to investigate their indi...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunodeficiency viruses", "medicine and health sciences", "pathology and laboratory medicine", "viral persistence and latency", "host-pathogen interactions", "medical microbiology", "hiv", "viral pathogens", "virology", "microbial pathogens", "biology and life sciences", "microbiology", "p...	Dynamics of HIV Latency and Reactivation in a Primary CD4+ T Cell Model	journal.ppat.1004156	null	[ [ "Successful antiretroviral therapy reduces HIV plasma viremia to undetectable levels; however , the virus is not eradicated [1] .", "Current and non-mutually exclusive hypotheses to explain this phenomenon include", "( i ) the presence of anatomic viral reservoirs that are inaccessible to drugs ,", ...	[ "HIV latency is a major obstacle to curing infection .", "Current strategies to eradicate HIV aim at increasing transcription of the latent provirus .", "In the present study we observed that latently infected CD4+ T cells from HIV-infected individuals failed to produce viral particles upon ex vivo exposure to ...	[ "HIV-infected individuals must receive lifelong antiviral therapy because treatment discontinuation generally results in rapid viral rebound .", "The field has identified a state of latency at the level of transcription of the integrated provirus as the major mechanism of persistence .", "A number of drugs are ...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Utilizing Chemical Genomics to Identify Cytochrome b as a Novel Drug Target for Chagas Disease	journal.ppat.1005058	null	[ [ "Chagas disease , or American trypanosomiasis , is a neglected disease caused by the kinetoplastid protozoan Trypanosoma cruzi ( T . cruzi ) .", "Endemic to Latin America , Chagas disease is increasingly globalized due to population migration from endemic regions into developed countries , and the U . S ....	[ "Unbiased phenotypic screens enable identification of small molecules that inhibit pathogen growth by unanticipated mechanisms .", "These small molecules can be used as starting points for drug discovery programs that target such mechanisms .", "A major challenge of the approach is the identification of the cel...	[ "Chagas Disease , or American trypanosomiasis , is caused by the kinetoplastid protozoan Trypanosoma cruzi and is primarily transmitted to a mammalian host via a triatomine insect vector ( the “kissing bug” ) infected with T . cruzi parasites .", "Although discovered in 1909 by the physician Dr . Carlos Chagas , ...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Knowledge, Attitudes and Practices of Animal Bite Victims Attending an Anti-rabies Health Center in Jimma Town, Ethiopia	journal.pntd.0003867	null	[ [ "As a disease that mostly impacts poor communities , rabies is a classic example of a neglected tropical disease [1] .", "A vaccine-preventable disease , most deaths from rabies arise due to lack of awareness and poor access to proper health services [2] .", "It is estimated that around half of the gl...	[ "Rabies is an important but preventable cause of death in Ethiopia .", "We assessed the knowledge , attitudes and practices of animal bite victims attending an anti-rabies health center in Jimma Town , Ethiopia .", "Between July 2012 and March 2013 a cross-sectional questionnaire was administered to 384 bite vi...	[ "Rabies is an important but preventable cause of death in Ethiopia .", "We assessed the knowledge , attitudes and practices of animal bite victims attending an anti-rabies health center in Jimma Town , Ethiopia .", "We found generally high levels of knowledge about rabies .", "Participants recognized domestic...	2015
[ "Introduction", "Materials And Methods", "Results", "Discussion" ]	[ "infectious diseases", "microbiology/immunity to infections", "infectious diseases/neglected tropical diseases", "cell biology", "molecular biology", "microbiology/parasitology", "infectious diseases/protozoal infections", "infectious diseases/tropical and travel-associated diseases", "infectious di...	An ex-vivo Human Intestinal Model to Study Entamoeba histolytica Pathogenesis	journal.pntd.0000551	null	[ [ "The protozoan intestinal parasite Entamoeba histolytica is the causative agent of human amoebiasis .", "This disease is primarily a problem in the developing world , where it leads to 50 million clinical cases and 100 , 000 deaths per year [1] .", "One of the most puzzling clinical aspects of E . his...	[ "Amoebiasis ( a human intestinal infection affecting 50 million people every year ) is caused by the protozoan parasite Entamoeba histolytica .", "To study the molecular mechanisms underlying human colon invasion by E . histolytica , we have set up an ex vivo human colon model to study the early steps in amoebias...	[ "Entamoeba histolytica is the causative agent of amoebiasis , a human disease .", "Like other enteric infections , the lack of animal models enhances the difficulty of studying the development of amoebiasis .", "To date , no experimental model has been developed that reproduces the invasive intestinal amoebic l...	2009
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "coronaviruses", "pathology and laboratory medicine", "viral transmission and infection", "enzymes", "pathogens", "sars coronavirus", "microbiology", "enzymology", "viral structure", "electron cryo-microscopy", "viruses", "serine proteases", "rna viruses", ...	Cryo-EM structure of the SARS coronavirus spike glycoprotein in complex with its host cell receptor ACE2	journal.ppat.1007236	null	[ [ "Coronaviruses are a family of large , enveloped , positive-stranded RNA viruses that cause upper respiratory , gastrointestinal and central nervous system diseases in humans and other animals [1] .", "Human coronaviruses HCoV-OC43 , HCoV-229E , HCoV-NL63 and HCoV-HKU1 circulate in humans and cause mild r...	[ "The trimeric SARS coronavirus ( SARS-CoV ) surface spike ( S ) glycoprotein consisting of three S1-S2 heterodimers binds the cellular receptor angiotensin-converting enzyme 2 ( ACE2 ) and mediates fusion of the viral and cellular membranes through a pre- to postfusion conformation transition .", "Here , we repor...	[ "The global outbreak of SARS in 2002–2003 was caused by infection by a human coronavirus , SARS-CoV .", "Although the virus has been extensively studied with regard to epidemiology , virology , clinical features and other aspects , there are still no approved antiviral drugs and vaccines to treat and prevent infe...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "genetic networks", "gene regulation", "cell cycle and cell division", "cell processes", "optimization", "regulator genes", "mathematics", "network analysis", "gene types", "thermodynamics", "computer and information sciences", "entropy", "gene expression", "centrality", "physics", "bi...	Solving the influence maximization problem reveals regulatory organization of the yeast cell cycle	journal.pcbi.1005591	null	[ [ "In order to respond to messages and environmental changes , cells dynamically process information arriving from cell surface receptors [1 , 2] .", "Information is transferred , stored , and processed in the cell via molecular mechanisms , often triggering a response in the regulatory program .", "The...	[ "The Influence Maximization Problem ( IMP ) aims to discover the set of nodes with the greatest influence on network dynamics .", "The problem has previously been applied in epidemiology and social network analysis .", "Here , we demonstrate the application to cell cycle regulatory network analysis for Saccharo...	[ "The Influence Maximization Problem ( IMP ) has been applied in fields such as epidemiology and social network analysis .", "Here , we apply the method to biological networks , aiming to discover the set of regulatory genes with the greatest influence on network dynamics .", "Fundamentally , since gene regulati...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology" ]	The Plant Actin Cytoskeleton Responds to Signals from Microbe-Associated Molecular Patterns	journal.ppat.1003290	null	[ [ "Actin filament arrays in plant cells undergo constant remodeling and can respond rapidly to a diverse array of extracellular stimuli .", "Even in unstimulated epidermal cells , architectural rearrangements occur within seconds due to myosin-dependent translocation , remarkably fast filament assembly , an...	[ "Plants are constantly exposed to a large and diverse array of microbes; however , most plants are immune to the majority of potential invaders and susceptible to only a small subset of pathogens .", "The cytoskeleton comprises a dynamic intracellular framework that responds rapidly to biotic stresses and support...	[ "The cytoskeleton is a dynamic platform for sensing and responding to a diverse array of biotic and abiotic stresses .", "The nature and timing of the changes in actin organization range from excessive bundling , to massive depolymerization , to new filament assembly , depending on the particular signal and the r...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "biology" ]	Loss of ATRX, Genome Instability, and an Altered DNA Damage Response Are Hallmarks of the Alternative Lengthening of Telomeres Pathway	journal.pgen.1002772	null	[ [ "In the absence of telomerase activity , telomeres shorten with cell division , ultimately leading to senescence .", "Hence , the development of human cancer is associated with an active telomere maintenance system that provides an infinite source of telomeric DNA to potentiate immortality .", "Althou...	[ "The Alternative Lengthening of Telomeres ( ALT ) pathway is a telomerase-independent pathway for telomere maintenance that is active in a significant subset of human cancers and in vitro immortalized cell lines .", "ALT is thought to involve templated extension of telomeres through homologous recombination , but...	[ "Telomeres , the protective elements at the ends of chromosomes , need to be maintained for cells to proliferate indefinitely .", "In many human cancers , the telomeric DNA is replenished by telomerase .", "However , a second pathway for telomere maintenance , referred to as the ALT pathway , has increasingly b...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "meiosis", "protein interactions", "cell cycle and cell division", "split-decomposition method", "cell processes", "dna-binding proteins", "multiple alignment calculation", "fungi", "model organisms", "experimental organism systems", "dna", "epigenetics", "chromatin", "dna methylation", ...	The PHD finger protein Spp1 has distinct functions in the Set1 and the meiotic DSB formation complexes	journal.pgen.1007223	null	[ [ "In sexually reproducing organisms , recombination between homologous chromosomes at meiosis plays an important role to form gametes with a normal chromosome content .", "Meiotic recombination is initiated by the programmed formation of DNA double-strand breaks ( DSBs ) catalyzed by the conserved Spo11 pr...	[ "Histone H3K4 methylation is a feature of meiotic recombination hotspots shared by many organisms including plants and mammals .", "Meiotic recombination is initiated by programmed double-strand break ( DSB ) formation that in budding yeast takes place in gene promoters and is promoted by histone H3K4 di/trimethy...	[ "Meiotic recombination is a conserved pathway of sexual reproduction that is required to faithfully segregate homologous chromosomes and produce viable gametes .", "Recombination events between homologous chromosomes are triggered by the programmed formation of DNA breaks , which occur preferentially at places ca...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "bacterial diseases", "infectious diseases", "buruli ulcer", "animal types", "wildlife", "emerging infectious diseases", "veterinary microbiology", "neglected tropical diseases", "biology", "microbiology", "veterinary science" ]	Clinical, Microbiological and Pathological Findings of Mycobacterium ulcerans Infection in Three Australian Possum Species	journal.pntd.0002666	null	[ [ "Mycobacterium ulcerans is an environmental organism that causes distinctive dermal lesions in people and animals , via the elaboration of the cytotoxic and immunosuppressive polyketide toxin , mycolactone [1] .", "The disease is known internationally as Buruli Ulcer ( BU ) .", "It has a worldwide but...	[ "Buruli ulcer ( BU ) is a skin disease caused by Mycobacterium ulcerans , with endemicity predominantly in sub-Saharan Africa and south-eastern Australia .", "The mode of transmission and the environmental reservoir ( s ) of the bacterium and remain elusive .", "Real-time PCR investigations have detected M . ul...	[ "Mycobacterium ulcerans causes skin disease predominantly in sub-Saharan Africa and southeastern Australia .", "The mode of transmission and the environmental reservoir ( s ) of the bacterium are unknown .", "Investigations have detected M . ulcerans DNA in a variety of Australian environmental samples , includ...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology and life sciences", "microbiology" ]	IscR Is Essential for Yersinia pseudotuberculosis Type III Secretion and Virulence	journal.ppat.1004194	null	[ [ "Type III secretion systems ( T3SS ) are important components in the progression of disease for a number of clinically relevant human pathogens , including those in the genera Shigella , Salmonella , Escherichia , Chlamydia , Vibrio , Pseudomonas , and Yersinia [1] , [2] .", "The T3SS functions as an inje...	[ "Type III secretion systems ( T3SS ) are essential for virulence in dozens of pathogens , but are not required for growth outside the host .", "Therefore , the T3SS of many bacterial species are under tight regulatory control .", "To increase our understanding of the molecular mechanisms behind T3SS regulation ...	[ "Bacterial pathogens use regulators that sense environmental cues to enhance their fitness .", "Here , we identify a transcriptional regulator in the human gut pathogen , Yersinia pseudotuberculosis , which controls a specialized secretion system essential for bacterial growth in mammalian tissues .", "This reg...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "public and occupational health", "medicine and health sciences", "infectious disease epidemiology", "epidemiology", "biology and life sciences", "population biology", "disease informatics" ]	Wikipedia Usage Estimates Prevalence of Influenza-Like Illness in the United States in Near Real-Time	journal.pcbi.1003581	null	[ [ "Each year , there are an estimated 250 , 000–500 , 000 deaths worldwide that are attributed to seasonal influenza [1] , with anywhere between 3 , 000–50 , 000 deaths occurring in the United States of America ( US ) [2] .", "In the US , the Centers for Disease Control and Prevention ( CDC ) continuously m...	[ "Circulating levels of both seasonal and pandemic influenza require constant surveillance to ensure the health and safety of the population .", "While up-to-date information is critical , traditional surveillance systems can have data availability lags of up to two weeks .", "We introduce a novel method of esti...	[ "Although influenza is largely avoidable through vaccination , between 3 , 000–50 , 000 deaths occur in the United States each year that are attributed to this disease .", "The Centers for Disease Control and Prevention continuously monitor the amount of influenza that is present in the American population and co...	2014
[ "Introduction", "Materials and Methods", "Results/Discussion" ]	[ "evolutionary biology", "genetics", "population genetics", "biology" ]	GAGA: A New Algorithm for Genomic Inference of Geographic Ancestry Reveals Fine Level Population Substructure in Europeans	journal.pcbi.1003480	null	[ [ "At what degree genetically homogeneous groups of human individuals exist is a long-standing and yet unsolved debate in the scientific community [1] .", "Answering this question is important for better understanding recent human evolutionary history [1] , for reducing the amount of false positives in gene...	[ "Attempts to detect genetic population substructure in humans are troubled by the fact that the vast majority of the total amount of observed genetic variation is present within populations rather than between populations .", "Here we introduce a new algorithm for transforming a genetic distance matrix that reduc...	[ "Understanding genetic population substructure is important in evolutionary biology , behavioral ecology , medical genetics and forensic genetics , among others .", "Several algorithms have recently been developed for investigating genetic population substructure .", "However , detecting genetic population subs...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/bacterial infections", "microbiology/microbial growth and development", "genetics and genomics", "microbiology" ]	Genetic Dissection of an Exogenously Induced Biofilm in Laboratory and Clinical Isolates of E. coli	journal.ppat.1000432	null	[ [ "Biofilms are an integral component in the life-cycle of many microorganisms .", "Compared to their planktonic complement , however , bacterial biofilms have remained poorly understood , mostly due to the inherent complexities associated with biofilm studies , including spatial heterogeneity of the biofil...	[ "Microbial biofilms are a dominant feature of many human infections .", "However , developing effective strategies for controlling biofilms requires an understanding of the underlying biology well beyond what currently exists .", "Using a novel strategy , we have induced formation of a robust biofilm in Escheri...	[ "Both in the wild and in the clinical setting many bacterial species live within surface-attached communities called biofilms .", "It is still unclear the extent to which the biofilm lifestyle and its associated phenotypes , such as hyper-tolerance to antimicrobial agents , can be attributed to structural charact...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	A Household Serosurvey to Estimate the Magnitude of a Dengue Outbreak in Mombasa, Kenya, 2013	journal.pntd.0003733	null	[ [ "Dengue is a mosquito-borne acute febrile illness caused by one of four dengue viruses ( DENV-1-4 ) .", "It is endemic throughout the tropics and sub-tropics [1 , 2] where more than 40% of the world’s population is at risk and approximately 400 million DENV infections are estimated to have occurred in 201...	[ "Dengue appears to be endemic in Africa with a number of reported outbreaks .", "In February 2013 , several individuals with dengue-like illnesses and negative malaria blood smears were identified in Mombasa , Kenya .", "Dengue was laboratory confirmed and an investigation was conducted to estimate the magnitud...	[ "Dengue appears to be endemic in Africa with a number of reported outbreaks .", "In February 2013 , several individuals with dengue-like illnesses and negative malaria blood smears were identified in Mombasa , Kenya .", "Dengue was laboratory confirmed and an investigation was conducted to estimate the magnitud...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "invertebrates", "plant anatomy", "machine learning algorithms", "medicine and health sciences", "pathology and laboratory medicine", "markov models", "pathogens", "applied mathematics", "vascular bundles", "phloem", "plant physiology", "neuroscience", "animals", "simulation and modeling",...	Machine Learning for Characterization of Insect Vector Feeding	journal.pcbi.1005158	null	[ [ "The invention of an electronic method for monitoring the feeding behavior of sucking insects [1–4] provided a potentially powerful tool to describe the cryptic behavior of the mouthparts of fluid-feeding phytophagous insects inside a host plant ( Fig 1 ) .", "Coupled with histological studies to correlat...	[ "Insects that feed by ingesting plant and animal fluids cause devastating damage to humans , livestock , and agriculture worldwide , primarily by transmitting pathogens of plants and animals .", "The feeding processes required for successful pathogen transmission by sucking insects can be recorded by monitoring v...	[ "Insect vectors acquire and transmit pathogens causing infectious diseases through probing on host tissues and ingesting host fluids .", "By connecting insects and their food source via an electrical circuit , computers , using machine learning algorithms , can learn to recognize insect feeding patterns involved ...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "plant biology", "computational biology" ]	Root System Architecture from Coupling Cell Shape to Auxin Transport	journal.pbio.0060307	Experimental data and computer modeling show that lateral root positioning can be controlled by the physical stimulus of root curvature, which triggers self-organizing alterations in auxin transport.	[ [ "Developmental biologists often conceptualize patterning mechanisms in uniform fields of cells , but in reality , positional information may be generated and translated in dynamic circumstances in which cells divide , grow , and change shape .", "These circumstances allow for unexpected feedbacks , making...	[ "Lateral organ position along roots and shoots largely determines plant architecture , and depends on auxin distribution patterns .", "Determination of the underlying patterning mechanisms has hitherto been complicated because they operate during growth and division .", "Here , we show by experiments and comput...	[ "Plant architecture is determined by where shoots or roots form along the main axis , but the mechanism responsible for lateral root initiation has long puzzled biologists .", "Here , we show that stretching root cells initiates changes in hormone transport , leading to lateral root initiation in plants , thereby...	2008
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "chromosome structure and function", "messenger rna", "telomeres", "mutation", "fungi", "dna replication", "dna", "molecular biology techniques", "research and analysis methods", "telomere length", "chromosome biology", "hyperexpression techniques", "gene expression", "molecular biology", ...	Overlapping open reading frames strongly reduce human and yeast STN1 gene expression and affect telomere function	journal.pgen.1007523	null	[ [ "The bulk of the genome is duplicated precisely once each cell cycle but telomeres are replicated differently .", "DNA polymerases cannot replicate the ends of linear molecules and therefore different strategies are needed to replicate telomeric DNA .", "The majority of eukaryotes use a reverse transc...	[ "The levels of telomeric proteins , such as telomerase , can have profound effects on telomere function , cell division and human disease .", "Here we demonstrate how levels of Stn1 , a component of the conserved telomere capping CST ( Cdc13 , Stn1 , Ten1 ) complex , are tightly regulated by an upstream overlappi...	[ "Telomeres are special structures at the ends of linear chromosomes that help protect the genetic information that chromosomes carry .", "The levels of telomere proteins are important and can affect diseases such as cancer and ageing .", "The CST complex is comprised of three proteins and binds human and yeast ...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "japanese encephalitis virus", "medicine and health sciences", "body fluids", "enzyme-linked immunoassays", "pathology and laboratory medicine", "laboratory equipment", "engineering and technology", "nervous system", "pathogens", "geographical locations", "microbiology", "viruses", "rna viru...	Pre-cut Filter Paper for Detecting Anti-Japanese Encephalitis Virus IgM from Dried Cerebrospinal Fluid Spots	journal.pntd.0004516	null	[ [ "The last few decades have seen a substantial growth of novel and complex diagnostic tests [1] .", "This has not been accompanied by the same development in global laboratory infrastructure , a fundamental component of any effective healthcare system [2]–[4] .", "In settings with poor access to labora...	[ "The use of filter paper as a simple , inexpensive tool for storage and transportation of blood , ‘Dried Blood Spots’ or Guthrie cards , for diagnostic assays is well-established .", "In contrast , there are a paucity of diagnostic evaluations of dried cerebrospinal fluid ( CSF ) spots .", "These have potential...	[ "Japanese encephalitis virus infection is widespread in Asia , and primarily affects children in poor , rural areas .", "The virus spreads to the brain and spinal cord resulting in significant death and disability .", "Diagnosis requires testing for the immune response ‘antibody’ specific to Japanese encephalit...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "horizontal gene transfer", "genetics", "microbial genetics", "biology and life sciences", "dna repair", "dna", "dna recombination", "evolutionary biology", "molecular genetics", "evolutionary processes", "gene transfer" ]	RecFOR Is Not Required for Pneumococcal Transformation but Together with XerS for Resolution of Chromosome Dimers Frequently Formed in the Process	journal.pgen.1004934	null	[ [ "Homologous recombination ( HR ) is crucial for both maintenance of genome integrity and generation of diversity across all kingdoms of life .", "HR initiates universally from single-stranded ( ss ) DNA and involves strand exchange between homologous DNA sequences , catalyzed by homologous recombinases ."...	[ "Homologous recombination ( HR ) is required for both genome maintenance and generation of diversity in eukaryotes and prokaryotes .", "This process initiates from single-stranded ( ss ) DNA and is driven by a universal recombinase , which promotes strand exchange between homologous sequences .", "The bacterial...	[ "Homologous recombination ( HR ) is a widespread process which maintains genome integrity and promotes diversity .", "In bacteria , HR mends damaged DNA to ensure genome integrity and is also involved in transformation , a mechanism of horizontal gene transfer allowing acquisition of new genetic traits .", "HR ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	MYB97, MYB101 and MYB120 Function as Male Factors That Control Pollen Tube-Synergid Interaction in Arabidopsis thaliana Fertilization	journal.pgen.1003933	null	[ [ "In flowering plants , the proper development of male gametophytes is essential for successful fertilization during reproduction [1] , [2] .", "The male gametophyte life cycle can be divided into two distinct phases: ( 1 ) a developmental phase , also known as the early developmental phase , which takes p...	[ "Pollen tube reception involves a pollen tube-synergid interaction that controls the discharge of sperm cells into the embryo sac during plant fertilization .", "Despite its importance in the sexual reproduction of plants , little is known about the role of gene regulation in this process .", "We report here th...	[ "Pollen tube reception is an important step of fertilization and is controlled by interactions between the pollen tube and synergid .", "Components of both the pollen tube and synergid are believed to be involved in the process .", "Several proteins associated with this process have been identified in synergid ...	2013
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "blood cells", "medicine and health sciences", "leptospira", "immune cells", "pathology and laboratory medicine", "immune physiology", "spleen", "pathogens", "immunology", "microbiology", "animal models", "model organisms", "experimental organism systems", "cytotoxic t cells", "kidneys",...	Pre-treatment with Lactobacillus plantarum prevents severe pathogenesis in mice infected with Leptospira interrogans and may be associated with recruitment of myeloid cells	journal.pntd.0005870	null	[ [ "A recent review on global morbidity and mortality caused by Leptospirosis estimates about 1 . 03 million cases and 58 , 900 deaths a year worldwide [1] , mostly in resource-poor countries [2][3] .", "Human leptospirosis is an acute febrile illness with a broad clinical spectrum ranging from mild influenz...	[ "Recent estimates on global morbidity and mortality caused by Leptospirosis point to one million cases and almost 60 , 000 deaths a year worldwide , especially in resource poor countries .", "We analyzed how a commensal probiotic immunomodulator , Lactobacillus plantarum , affects Leptospira interrogans pathogene...	[ "Leptospirosis is an emerging neglected zoonotic disease with worldwide distribution that affects nearly all vertebrates and causes infection in ~1 million people on a yearly basis .", "Effective cross-protective vaccines are not available and antibiotic treatment is only effective if used early in the course of ...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion", "Conclusions" ]	[]	Economic and Disease Burden of Dengue in Mexico	journal.pntd.0003547	null	[ [ "Dengue fever is the most important arthropod-borne viral disease affecting humans , with about half the world’s population estimated to be at risk of infection , and epidemics increasing in frequency , magnitude , and geographical reach [1–4] .", "Dengue imposes a substantial economic and disease burden ...	[ "Dengue imposes a substantial economic and disease burden in most tropical and subtropical countries .", "Dengue incidence and severity have dramatically increased in Mexico during the past decades .", "Having objective and comparable estimates of the economic burden of dengue is essential to inform health poli...	[ "During the past decades , dengue fever has become the most common arthropod-borne viral disease , imposing a substantial economic and disease burden in most tropical and subtropical countries , including Mexico .", "Dengue incidence and severity have dramatically increased in Mexico , with transmission regularly...	2015
[ "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", "microbiology", "pathogenesis", "immune system" ]	In Vivo Ligands of MDA5 and RIG-I in Measles Virus-Infected Cells	journal.ppat.1004081	null	[ [ "The retinoic acid inducible gene I ( RIG-I ) -like receptor ( RLR ) proteins are key players in innate immunity and act by recognizing viral RNA ( vRNA ) in the cytosol .", "The RLR family consists of the members retinoic acid inducible gene I ( RIG-I ) , melanoma differentiation associated protein 5 ( M...	[ "RIG-I-like receptors ( RLRs: RIG-I , MDA5 and LGP2 ) play a major role in the innate immune response against viral infections and detect patterns on viral RNA molecules that are typically absent from host RNA .", "Upon RNA binding , RLRs trigger a complex downstream signaling cascade resulting in the expression ...	[ "RIG-I-like receptors ( RLRs ) are helicase-like molecules that detect cytosolic RNAs that are absent in the non-infected host .", "Upon binding to specific RNA patterns , RLRs elicit a signaling cascade that leads to host defense via the production of antiviral molecules .", "To understand how RLRs sense RNA ,...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Varicella Viruses Inhibit Interferon-Stimulated JAK-STAT Signaling through Multiple Mechanisms	journal.ppat.1004901	null	[ [ "The alphaherpesvirus varicella zoster virus ( VZV ) is the causative agent of chickenpox .", "After primary infection , VZV establishes latency in sensory ganglia .", "Reactivation from latency , which typically occurs in elderly individuals , can cause shingles or herpes zoster that is associated wi...	[ "Varicella zoster virus ( VZV ) causes chickenpox in humans and , subsequently , establishes latency in the sensory ganglia from where it reactivates to cause herpes zoster .", "Infection of rhesus macaques with simian varicella virus ( SVV ) recapitulates VZV pathogenesis in humans thus representing a suitable a...	[ "In this manuscript we demonstrate that the immediate early protein ORF63 encoded by varicella zoster virus ( VZV ) and simian varicella virus ( SVV ) interferes with interferon type I-mediated activation of JAK-STAT signaling and thereby inhibits the expression of interferon stimulated genes .", "ORF63 blocks th...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular cell biology", "rna processing", "virology", "gene expression", "viral enzymes", "biology", "microbiology", "viral replication", "viral replication complex", "molecular biology" ]	A Freeze Frame View of Vesicular Stomatitis Virus Transcription Defines a Minimal Length of RNA for 5′ Processing	journal.ppat.1002073	null	[ [ "The RNA synthesis machinery of the non-segmented negative-strand ( NNS ) RNA viruses contains at its core a large polymerase protein ( L ) that possesses all the enzymatic activities for genome transcription and replication .", "During transcription , L catalyzes nucleotide polymerization [1]–[3] as well...	[ "The RNA synthesis machinery of vesicular stomatitis virus ( VSV ) comprises the genomic RNA encapsidated by the viral nucleocapsid protein ( N ) and associated with the RNA dependent RNA polymerase , the viral components of which are a large protein ( L ) and an accessory phosphoprotein ( P ) .", "The 241 kDa L ...	[ "Using a prototype of the nonsegmented negative strand RNA viruses , vesicular stomatitis virus , we probed the spatial relationship between the RNA dependent RNA polymerase and 5′ mRNA capping and methylation activities of the large polymerase protein .", "Because the 5′ mRNA processing reactions dramatically im...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "plant biology/plant growth and development", "plant biology/plant genetics and gene expression", "plant biology" ]	Microdissection of Shoot Meristem Functional Domains	journal.pgen.1000476	null	[ [ "The maize shoot apical meristem ( SAM ) is a complex signaling network of distinct structural and functional domains that performs two essential developmental functions during plant shoot development: ( 1 ) self-maintenance and ( 2 ) organogenesis .", "Responsible for the development of all above ground ...	[ "The shoot apical meristem ( SAM ) maintains a pool of indeterminate cells within the SAM proper , while lateral organs are initiated from the SAM periphery .", "Laser microdissection–microarray technology was used to compare transcriptional profiles within these SAM domains to identify novel maize genes that fun...	[ "All the organs of plant shoots are derived from the shoot apical meristem ( SAM ) , a pool of plant stem cells that are both organogenic and self-sustaining .", "These dual SAM functions take place in distinct yet adjacent meristematic domains; leaves are derived from the peripheral zone ( PZ ) of the SAM wherea...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "public health and epidemiology", "epidemiology", "global health", "neurology", "neurological disorders", "public health", "veterinary science" ]	Toxocariasis and Epilepsy: Systematic Review and Meta-Analysis	journal.pntd.0001775	null	[ [ "Human toxocariasis is a parasitic zoonosis caused by the larval stages of the ascarids Toxocara canis ( T . canis ) , the common roundworm of dogs , and by the roundworm of cats , Toxocara cati ( T . cati ) [1] .", "The reported prevalence of soil contamination with Toxocara spp .", "eggs is variable...	[ "Human toxocariasis is a zoonotic infection caused by the larval stages of Toxocara canis ( T . canis ) and less frequently Toxocara cati ( T . cati ) .", "A relationship between toxocariasis and epilepsy has been hypothesized .", "We conducted a systematic review and a meta-analysis of available data to evalua...	[ "Human toxocariasis is an infection caused by the larval stage of the worms Toxocara canis and less frequently Toxocara cati , common parasites of domestic and peridomestic dogs and cats .", "It is a cosmopolitan infection , occurring whenever the man-soil-dog relationship is particularly close , especially in tr...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Bidirectional Regulation of Innate and Learned Behaviors That Rely on Frequency Discrimination by Cortical Inhibitory Neurons	journal.pbio.1002308	Modulating the activity of a specific type of cortical neuron can either improve or impair the ability to discriminate between tones of different frequencies and to associate danger with specific sounds.	[ [ "Frequency discrimination is a fundamental task in everyday hearing and can be vitally important , as spectral differences can be used to distinguish dangerous and safe sounds [1–3] .", "However , our knowledge of the neuronal mechanisms that support frequency discrimination remains incomplete .", "Th...	[ "The ability to discriminate tones of different frequencies is fundamentally important for everyday hearing .", "While neurons in the primary auditory cortex ( AC ) respond differentially to tones of different frequencies , whether and how AC regulates auditory behaviors that rely on frequency discrimination rema...	[ "Hearing perception relies on our ability to tell apart the spectral content of different sounds , and to learn to use this difference to distinguish behaviorally relevant ( such as dangerous and safe ) sounds .", "Recently , we demonstrated that the auditory cortex regulates frequency discrimination acuity follo...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "viruses", "infectious diseases", "virology", "in vitro", "immunology", "microbiology", "eukaryotes", "mus (mouse)", "homo (human)" ]	Secreted NS1 of Dengue Virus Attaches to the Surface of Cells via Interactions with Heparan Sulfate and Chondroitin Sulfate E	journal.ppat.0030183	null	[ [ "Dengue hemorrhagic fever and dengue shock syndrome ( DHF/DSS ) are severe and potentially fatal complications of infection by dengue virus ( DENV ) , a mosquito-borne RNA virus of the Flaviviridae family .", "Globally , DENV infects 25 to 100 million people per year , but the life-threatening complicatio...	[ "Dengue virus ( DENV ) nonstructural protein-1 ( NS1 ) is a secreted glycoprotein that is absent from viral particles but accumulates in the supernatant and on the plasma membrane of cells during infection .", "Immune recognition of cell surface NS1 on endothelial cells has been hypothesized as a mechanism for th...	[ "Dengue virus ( DENV ) is a mosquito-transmitted virus that infects humans and has become a global emerging infectious disease threat .", "Four serotypes of DENV exist , and the most severe cases are associated with secondary infection with a different virus serotype .", "Clinical deterioration is characterized...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "animal models", "drosophila melanogaster", "model organisms", "molecular cell biology", "cell biology", "chromosome biology", "genetics", "molecular genetics", "biology", "genomics", "chromatin", "genetics and genomics", "gene function" ]	Tissue-Specific Regulation of Chromatin Insulator Function	journal.pgen.1003069	null	[ [ "Chromatin insulators are DNA-protein complexes that influence eukaryotic gene expression by organizing the genome into distinct transcriptional domains .", "Functionally conserved from Drosophila to humans , insulators regulate interactions between regulatory elements such as enhancers and promoters and ...	[ "Chromatin insulators organize the genome into distinct transcriptional domains and contribute to cell type–specific chromatin organization .", "However , factors regulating tissue-specific insulator function have not yet been discovered .", "Here we identify the RNA recognition motif-containing protein Shep as...	[ "Mounting evidence in human , mouse , and Drosophila demonstrates a role for the DNA–protein complexes known as chromatin insulators in orchestrating three-dimensional genome organization .", "Several genes that are only expressed in specific cell types display distinct chromatin configurations correlated with ex...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Development of a screening eye clinic for Ebola virus disease survivors: Lessons learned and rapid implementation at ELWA Hospital in Monrovia, Liberia 2015	journal.pntd.0007209	null	[ [ "The West African Ebola virus disease ( EVD ) outbreak from 2014–2016 was of historic magnitude with over 28 , 600 cases and 11 , 300 deaths predominantly within the highest transmission countries of Liberia , Sierra Leone and Guinea . [1]", "This has resulted in the largest cohort of EVD survivors in his...	[ "In the wake of the West African Ebola virus disease ( EVD ) outbreak of 2014–2016 , thousands of EVD survivors began to manifest a constellation of systemic and ophthalmic sequelae .", "Besides systemic arthralgias , myalgias , and abdominal pain , patients were developing uveitis , a spectrum of inflammatory ey...	[ "The West African Ebola virus disease ( EVD ) outbreak from 2014–2016 resulted in thousands of EVD survivors at-risk for uveitis , an inflammatory eye condition with the potential for vision impairment or blindness if not promptly diagnosed and treated .", "Given the equipment and resource limitations within West...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/microbial evolution and genomics", "microbiology/cellular microbiology and pathogenesis", "infectious diseases/gastrointestinal infections" ]	A Global Overview of the Genetic and Functional Diversity in the Helicobacter pylori cag Pathogenicity Island	journal.pgen.1001069	null	[ [ "Helicobacter pylori persistently infects more than one half of all humans , and can cause ulcer disease , gastric cancer , and MALT lymphoma [1] .", "The H . pylori cag pathogenicity island ( cagPAI ) is an intriguing virulence module of this obligate host-associated bacterium [2]–[4] .", "H . pylori...	[ "The Helicobacter pylori cag pathogenicity island ( cagPAI ) encodes a type IV secretion system .", "Humans infected with cagPAI–carrying H . pylori are at increased risk for sequelae such as gastric cancer .", "Housekeeping genes in H . pylori show considerable genetic diversity; but the diversity of virulence...	[ "Most humans are infected with Helicobacter pylori .", "The H . pylori cag pathogenicity island ( cagPAI ) encodes a secretion apparatus that can translocate the CagA protein into host cells .", "Humans infected with cagPAI–carrying H . pylori are at increased risk of severe disease , including gastric cancer ....	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/epigenetics", "molecular biology/dna methylation", "nutrition" ]	Season of Conception in Rural Gambia Affects DNA Methylation at Putative Human Metastable Epialleles	journal.pgen.1001252	null	[ [ "Epigenetic mechanisms maintain mitotically heritable differences in gene expression potential without alterations in DNA sequence [1] , enabling the diverse cell types of multicellular organisms to stably regulate appropriate patterns of gene expression .", "The established role of epigenetic mechanisms ...	[ "Throughout most of the mammalian genome , genetically regulated developmental programming establishes diverse yet predictable epigenetic states across differentiated cells and tissues .", "At metastable epialleles ( MEs ) , conversely , epigenotype is established stochastically in the early embryo then maintaine...	[ "There is growing interest in the possibility that interindividual epigenetic variation plays an important role in a broad range of human diseases .", "The tissue-specificity of epigenetic regulation , however , will in many cases make it difficult to obtain the appropriate tissues in which to perform large-scale...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "flow cytometry", "medicine and health sciences", "immune cells", "respiratory infections", "pathology and laboratory medicine", "pathogens", "antigen-presenting cells", "immunology", "microbiology", "orthomyxoviruses", "pulmonology", "viruses", "dendritic cells", "rna vir...	PI3Kγ Is Critical for Dendritic Cell-Mediated CD8+ T Cell Priming and Viral Clearance during Influenza Virus Infection	journal.ppat.1005508	null	[ [ "Phosphoinositide 3-kinases ( PI3K ) are classified into three main groups ( class I , class II and class III ) according to sequence homology of the catalytic subunit and their substrate specificity [1] .", "Class I PI3K are further divided into class IA and class IB .", "Class IA PI3K form dimers co...	[ "Phosphoinositide-3-kinases have been shown to be involved in influenza virus pathogenesis .", "They are targeted directly by virus proteins and are essential for efficient viral replication in infected lung epithelial cells .", "However , to date the role of PI3K signaling in influenza infection in vivo has no...	[ "Acute respiratory viral infections like influenza virus can cause life-threatening disease in infected individuals .", "Phosphoinositide-3-kinases have been suggested to be important factors used by the virus to infect and replicate in host cells , and thereby cause viral pneumonia .", "However , to date the r...	2016
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "distance measurement", "medicine and health sciences", "pathology and laboratory medicine", "engineering and technology", "pathogens", "geographical locations", "microbiology", "health care", "simulation and modeling", "network analysis", "pharmacology", "infectious disease control", "unite...	Measuring distance through dense weighted networks: The case of hospital-associated pathogens	journal.pcbi.1005622	null	[ [ "A growing body of literature shows the influence of contact networks on the spread of infectious diseases .", "This extends from individual hosts [1–5] to entire countries [6–10] or organisations , such a healthcare institutions for pathogens that are predominantly transmitted through hospital contacts [...	[ "Hospital networks , formed by patients visiting multiple hospitals , affect the spread of hospital-associated infections , resulting in differences in risks for hospitals depending on their network position .", "These networks are increasingly used to inform strategies to prevent and control the spread of hospit...	[ "Shared patients can spread hospital-associated pathogens between hospitals , together forming a large network in which all hospitals are connected .", "We set out to measure the distance between hospitals in such a network , best reflecting the risk of a hospital-associated pathogen spreading from one to the oth...	2017
[ "Introduction", "Materials and methods", "Results", "Discussion", "Conclusion" ]	[ "invertebrates", "medicine and health sciences", "body fluids", "pathology and laboratory medicine", "togaviruses", "chikungunya infection", "pathogens", "tropical diseases", "microbiology", "geographical locations", "vector-borne diseases", "animals", "alphaviruses", "viruses", "develop...	Vector competence of Aedes bromeliae and Aedes vitattus mosquito populations from Kenya for chikungunya virus	journal.pntd.0006746	null	[ [ "Chikungunya virus ( CHIKV ) is vector-borne virus of genus Alphavirus and family Togaviridae that is principally transmitted from human to humans by Ae .", "aegypti and Ae .", "albopictus .", "The first CHIKV outbreak was documented in Makonde village in Tanzania in 1956 [1 , 2] and since then , ...	[ "Kenya has experienced outbreaks of chikungunya in the past years with the most recent outbreak occurring in Mandera in the northern region in May 2016 and in Mombasa in the coastal region from November 2017 to February 2018 .", "Despite the outbreaks in Kenya , studies on vector competence have only been conduct...	[ "Kenya experienced its first chikungunya outbreak in 2004/2005 along the coastal area , followed by sporadic outbreaks in Mandera in 2016 , and subsequently in Mombasa city in late 2017 and early 2018 .", "Despite the rising risk of transmission of the virus in the country based on evidence of outbreaks in Kenya ...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology", "biology and life sciences", "immunology", "microbiology", "molecular cell biology", "biophysics" ]	IFITM3 Restricts Influenza A Virus Entry by Blocking the Formation of Fusion Pores following Virus-Endosome Hemifusion	journal.ppat.1004048	null	[ [ "The recently identified interferon-induced transmembrane proteins ( IFITMs ) inhibit infection of diverse enveloped viruses [1]–[3] .", "Ectopic expression of IFITM1 , -2 and -3 restricts a growing number of unrelated viruses , including IAV [1] , [2] , [4]–[7] .", "IFITM3 has been shown to potently ...	[ "Interferon-induced transmembrane proteins ( IFITMs ) inhibit infection of diverse enveloped viruses , including the influenza A virus ( IAV ) which is thought to enter from late endosomes .", "Recent evidence suggests that IFITMs block virus hemifusion ( lipid mixing in the absence of viral content release ) by ...	[ "Interferon-induced transmembrane proteins ( IFITMs ) block infection of many enveloped viruses , including the influenza A virus ( IAV ) that enters from late endosomes .", "IFITMs are thought to prevent virus hemifusion ( merger of contacting leaflets without formation of a fusion pore ) by altering the propert...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "action potentials", "medicine and health sciences", "neural networks", "membrane potential", "brain", "electrophysiology", "neuroscience", "simulation and modeling", "network analysis", "research and analysis methods", "computer and information sciences", "network motifs", "animal cells", ...	Higher-Order Synaptic Interactions Coordinate Dynamics in Recurrent Networks	journal.pcbi.1005078	null	[ [ "Understanding any complex system requires a mechanistic account of how dynamics arise from underlying architecture .", "Patterns of connections shape dynamics in diverse settings ranging from electric power grids to gene transcription networks[1–5] .", "It is critical to establish how synaptic connec...	[ "Linking synaptic connectivity to dynamics is key to understanding information processing in neocortex .", "Circuit dynamics emerge from complex interactions of interconnected neurons , necessitating that links between connectivity and dynamics be evaluated at the network level .", "Here we map propagating acti...	[ "Active networks of neurons exhibit beyond-pairwise dynamical features .", "In this work , we identify a canonical higher-order correlation in network dynamics and trace its emergence to synaptic integration .", "We find that temporally coordinated firing preferentially occurs at sites of fan-in triangles—a syn...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Responses of Murine and Human Macrophages to Leptospiral Infection: A Study Using Comparative Array Analysis	journal.pntd.0002477	null	[ [ "Leptospirosis is an important tropical infectious disease around the world , particularly in humid tropical and subtropical countries [1] , [2] .", "The causal agents include several pathogenic Leptospira spp .", ", of which the highly virulent strains ( e . g . Leptospira interrogans ) chronically i...	[ "Leptospirosis is a re-emerging tropical infectious disease caused by pathogenic Leptospira spp .", "The different host innate immune responses are partially related to the different severities of leptospirosis .", "In this study , we employed transcriptomics and cytokine arrays to comparatively calculate the r...	[ "Although pathogenic Leptospira is not an obligate intracellular pathogen , recent studies have shown that phagocytosis and innate immunity play important roles in leptospirosis .", "The Leptospira-macrophage interaction is a common model used to elucidate the initial response in leptospiral infection .", "Our ...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "flow cytometry", "mycobacterium leprae", "medicine and health sciences", "chemical compounds", "gene regulation", "tropical diseases", "light microscopy", "carbohydrates", "organic compounds", "macroglial cells", "organisms", "bacterial diseases", "microscopy", "schwann cells", "neglect...	PGL I expression in live bacteria allows activation of a CD206/PPARγ cross-talk that may contribute to successful Mycobacterium leprae colonization of peripheral nerves	journal.ppat.1007151	null	[ [ "The most serious consequence of leprosy is the peripheral nerve damage that occurs in all clinical forms of the disease .", "Nerve damage results from the capacity of M . leprae , an obligate intracellular bacillus , to infect SCs , the glial cells of the peripheral nervous system ( PNS ) .", "SCs sh...	[ "Mycobacterium leprae , an obligate intracellular bacillus , infects Schwann cells ( SCs ) , leading to peripheral nerve damage , the most severe leprosy symptom .", "In the present study , we revisited the involvement of phenolic glycolipid I ( PGL I ) , an abundant , private , surface M . leprae molecule , in M...	[ "Nerve damage is the most severe symptom of leprosy , an ancient disease that continues to be a major health problem in several countries .", "Nerve damage is due to the ability of Mycobacterium leprae , the etiologic agent , to invade SCs , the glial cells of the peripheral nervous system .", "Understanding th...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology", "computational biology", "neuroscience" ]	Colocalization of Protein Kinase A with Adenylyl Cyclase Enhances Protein Kinase A Activity during Induction of Long-Lasting Long-Term-Potentiation	journal.pcbi.1002084	null	[ [ "Synaptic plasticity , the activity-dependent change in the strength of neuronal connections , is a cellular mechanism proposed to underlie memory storage .", "One type of synaptic plasticity is long term potentiation ( LTP ) , which displays physiological properties that are highly suggestive of informat...	[ "The ability of neurons to differentially respond to specific temporal and spatial input patterns underlies information storage in neural circuits .", "One means of achieving spatial specificity is to restrict signaling molecules to particular subcellular compartments using anchoring molecules such as A-Kinase An...	[ "The hippocampus is a part of the cerebral cortex involved in formation of certain types of long term memories .", "Activity-dependent change in the strength of neuronal connections in the hippocampus , known as synaptic plasticity , is one mechanism used to store memories .", "The ability to form crisp and dis...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "pathogens", "immunology", "microbiology", "cloning", "cell differentiation", "retroviruses", "viruses", "bone marrow cells", "developmental biology", "rna viruses", "cytotoxic t cells", ...	Human T-cell leukemia virus type 1 infects multiple lineage hematopoietic cells in vivo	journal.ppat.1006722	null	[ [ "Human T-cell leukemia virus type 1 ( HTLV-1 ) is the causal agent of adult T-cell leukemia-lymphoma ( ATL ) and inflammatory diseases including HTLV-1 associated myelopathy/tropical spastic paraparesis ( HAM/TSP ) [1–4] .", "HTLV-1 is a unique retrovirus since this virus transmits only by cell-to-cell in...	[ "Human T-cell leukemia virus type 1 ( HTLV-1 ) infects mainly CD4+CCR4+ effector/memory T cells in vivo .", "However , it remains unknown whether HTLV-1 preferentially infects these T cells or this virus converts infected precursor cells to specialized T cells .", "Expression of viral genes in vivo is critical ...	[ "HTLV-1 primarily infects peripheral CD4+CCR4+CADM1+ T cells in vivo .", "In this study , we show that HTLV-1 infects HSCs , which differentiate into multiple lineages of hematopoietic cells , and likely act as viral reservoir , giving rise to infected neutrophils , monocytes and B cells .", "Infected monocytes...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology and life sciences" ]	Nicotiana Small RNA Sequences Support a Host Genome Origin of Cucumber Mosaic Virus Satellite RNA	journal.pgen.1004906	null	[ [ "Satellite RNAs ( satRNAs ) are among the smallest RNA pathogens in plants and depend on associated viruses ( helper viruses ) for replication , encapsidation and movement inside the host plant [1] , [2] .", "Their RNA genomes range from 220 to 1500 nucleotides ( nt ) in size and can form compact secondar...	[ "Satellite RNAs ( satRNAs ) are small noncoding subviral RNA pathogens in plants that depend on helper viruses for replication and spread .", "Despite many decades of research , the origin of satRNAs remains unknown .", "In this study we show that a β-glucuronidase ( GUS ) transgene fused with a Cucumber mosaic...	[ "Satellite RNAs ( satRNAs ) are small RNA pathogens in plants that depend on associated viruses for replication and spread .", "While much is known about the replication and pathogenicity of satRNAs , their origin remains a mystery .", "We report evidence for a host genome origin of the Cucumber mosaic virus ( ...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "dimers (chemical physics)", "medicine and health sciences", "crystal structure", "pathology and laboratory medicine", "molecular probe techniques", "enzymes", "pathogens", "condensed matter physics", "microbiology", "immunoblotting", "enzymology", "phosphatases", "membrane proteins", "neg...	Assembly and stoichiometry of the core structure of the bacterial flagellar type III export gate complex	journal.pbio.2002281	null	[ [ "The bacterial flagellum is supramolecular motility machinery consisting of basal body rings and an axial structure consisting of the rod , the hook , the hook-filament junction , the filament , and the filament cap .", "Flagellar axial proteins are translocated across the cytoplasmic membrane by a type I...	[ "The bacterial flagellar type III export apparatus , which is required for flagellar assembly beyond the cell membranes , consists of a transmembrane export gate complex and a cytoplasmic ATPase complex .", "FlhA , FlhB , FliP , FliQ , and FliR form the gate complex inside the basal body MS ring , although FliO i...	[ "The bacterial flagellar type III export gate complex is a membrane-embedded nanomachine responsible for flagellar protein export and exits in a patch of membrane within the central pore of the basal body MS ring .", "In this work , we investigate how formation of the export gate complex is initiated .", "The e...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/viral infections", "biochemistry/biomacromolecule-ligand interactions", "infectious diseases/respiratory infections" ]	Structures of Receptor Complexes of a North American H7N2 Influenza Hemagglutinin with a Loop Deletion in the Receptor Binding Site	journal.ppat.1001081	null	[ [ "Influenza is an acute respiratory virus that infects up to 20% of the population in the United States , resulting in ∼36 , 000 deaths annually [1] , [2] .", "The two membrane glycoproteins on the surface of influenza A virus , hemagglutinin ( HA ) , which functions as the receptor binding and membrane fu...	[ "Human infections with subtype H7 avian influenza viruses have been reported as early as 1979 .", "In 1996 , a genetically stable 24-nucleotide deletion emerged in North American H7 influenza virus hemagglutinins , resulting in an eight amino acid deletion in the receptor-binding site .", "The continuous circul...	[ "Influenza virus adaptation to different hosts usually results in a switch in receptor specificity of the viral surface coat protein , hemagglutinin .", "Indeed , the hemagglutinin subtypes from the last two human influenza pandemics of the 20th Century ( H2 in 1957 and H3 1968 ) both adapted successfully to huma...	2010
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Knockdown of Asparagine Synthetase A Renders Trypanosoma brucei Auxotrophic to Asparagine	journal.pntd.0002578	null	[ [ "Asparagine is a naturally occurring non-essential amino acid found in many proteins .", "Due to its high nitrogen/carbon ratio , asparagine is likely to be linked to nitrogen homeostasis and protein biosynthesis [1] .", "AS is the protein involved in asparagine biosynthesis .", "There are two dis...	[ "Asparagine synthetase ( AS ) catalyzes the ATP-dependent conversion of aspartate into asparagine using ammonia or glutamine as nitrogen source .", "There are two distinct types of AS , asparagine synthetase A ( AS-A ) , known as strictly ammonia-dependent , and asparagine synthetase B ( AS-B ) , which can use ei...	[ "The amino acid asparagine is important not only for protein biosynthesis , but also for nitrogen homeostasis .", "Asparagine synthetase catalyzes the synthesis of this amino acid .", "There are two forms of asparagine synthetase , A and B . The presence of type A in trypanosomes , and its absence in humans , m...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "hepatitis b", "hepatitis", "viral diseases", "gastrointestinal infections" ]	Hepatitis B Virus Induces IL-23 Production in Antigen Presenting Cells and Causes Liver Damage via the IL-23/IL-17 Axis	journal.ppat.1003410	null	[ [ "Hepatitis B virus ( HBV ) is a noncytopathic , hepatotropic and stealth DNA virus that has been implicated in the etiology of chronic hepatitis B ( CHB ) and HBV-associated acute-on-chronic liver failure ( ACLF ) .", "HBV-induced hepatic injury is known to be mediated by a variety of immunocytes that pla...	[ "IL-23 regulates myriad processes in the innate and adaptive immune systems , and is a critical mediator of the proinflammatory effects exerted by Th17 cells in many diseases .", "In this study , we investigated whether and how hepatitis B virus ( HBV ) causes liver damage directly through the IL-23 signaling pat...	[ "While it is known that IL-23 plays a pivotal role in maintenance of the Th17 phenotype and their production of the IL-17 cytokine , the mechanisms by which HBV induces particular immune cell types to produce IL-23 remain unknown .", "In the study of human hepatitis B described herein , we demonstrated that IL-23...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Trial-Type Dependent Frames of Reference for Value Comparison	journal.pcbi.1003225	null	[ [ "Accounts of how the brain supports value-guided decision-making have been characterised as lying along a continuous spectrum [1] .", "At one end of the spectrum , it is argued that decisions are a serial process , in which stimuli are first perceived , then assigned values and fed to a subsequent decisio...	[ "A central question in cognitive neuroscience regards the means by which options are compared and decisions are resolved during value-guided choice .", "It is clear that several component processes are needed; these include identifying options , a value-based comparison , and implementation of actions to execute ...	[ "There are several competing theories of how the primate brain supports the ability to choose between different opportunities to obtain rewards – such as food , shelter , or more abstract goods ( e . g . money ) .", "These theories suggest that the comparison of different options is either fundamentally dependent...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "disease mapping", "socioeconomic aspects of health", "environmental health", "disease ecology", "public health and epidemiology", "epidemiology", "global health", "public health" ]	Regional, Household and Individual Factors that Influence Soil Transmitted Helminth Reinfection Dynamics in Preschool Children from Rural Indigenous Panamá	journal.pntd.0002070	null	[ [ "The soil transmitted helminth ( STH ) infections , Ascaris lumbricoides , Trichuris trichiura and the hookworms Ancylostoma duodenale and Necator americanus are estimated to result in the loss of 39 million disability adjusted life years ( DALYs ) annually [1] and to have long-lasting implications for child ...	[ "Few studies have investigated the relative influence of individual susceptibility versus household exposure factors versus regional clustering of infection on soil transmitted helminth ( STH ) transmission .", "The present study examined reinfection dynamics and spatial clustering of Ascaris lumbricoides , Trich...	[ "Control of soil transmitted helminth ( STH ) infections is of central importance to improving preschool child health because these infections can have long lasting consequences on growth and development .", "Our study in indigenous Ngäbe preschool children in western Panama was conducted over a period of 16 mont...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "vesicles", "pathology and laboratory medicine", "molecular probe techniques", "gene regulation", "pathogens", "cell processes", "immunology", "microbiology", "immunoblotting", "staphylococcus aureus", "immune receptor signalin...	The TLR4 adaptor TRAM controls the phagocytosis of Gram-negative bacteria by interacting with the Rab11-family interacting protein 2	journal.ppat.1007684	null	[ [ "Phagocytosis is a complex and versatile process that eliminates pathogens and is performed by specialized cells such as macrophages [1] .", "Phagocytosis requires cell surface receptors recognizing the pathogen [2] and Rho GTPases controlling local actin dynamics that drive engulfment [2–5] .", "Toll...	[ "Phagocytosis is a complex process that eliminates microbes and is performed by specialised cells such as macrophages .", "Toll-like receptor 4 ( TLR4 ) is expressed on the surface of macrophages and recognizes Gram-negative bacteria .", "Moreover , TLR4 has been suggested to play a role in the phagocytosis of ...	[ "The Gram-negative bacteria E . coli is the most common cause of severe human pathological conditions like sepsis .", "Sepsis is a clinical syndrome defined by pathological changes due to systemic inflammation , resulting in paralysis of adaptive T-cell immunity with IFN-β as a critical factor .", "TLR4 is a ke...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Antigenic Properties of the Human Immunodeficiency Virus Envelope Glycoprotein Gp120 on Virions Bound to Target Cells	journal.ppat.1004772	null	[ [ "The attachment and entry steps in the Human immunodeficiency virus 1 ( HIV-1 ) replication process involve sequential interactions between viral envelope glycoprotein trimers and cell surface receptors [1] .", "Each interaction causes conformational alterations in the envelope structure that in turn enab...	[ "The HIV-1 envelope glycoprotein , gp120 , undergoes multiple molecular interactions and structural rearrangements during the course of host cell attachment and viral entry , which are being increasingly defined at the atomic level using isolated proteins .", "In comparison , antigenic markers of these dynamic ch...	[ "A major strategy for blocking HIV-1 infection is to target antiviral antibodies or drugs to sites of vulnerability on the surface proteins of the virus .", "It is a relatively straightforward matter to explore these sites on the surfaces of free HIV-1 particles or on isolated viral envelope antigens .", "Howev...	2015
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "learning", "markov models", "decision making", "statistics", "experimental design", "social sciences", "neuroscience", "learning and memory", "research design", "cognitive psychology", "mathematics", "forecasting", "cognition", "thermodynamics", "research and analysis methods", "behav...	Predicting change: Approximate inference under explicit representation of temporal structure in changing environments	journal.pcbi.1006707	null	[ [ "Our ability to represent time and to generate complex actions and plans based on this representation are central to all aspects of our behavior .", "Knowing when to act , precisely , is clearly crucial for our survival [1 , 2] .", "Thus , it is not surprising that the question of how we perceive and ...	[ "In our daily lives timing of our actions plays an essential role when we navigate the complex everyday environment .", "It is an open question though how the representations of the temporal structure of the world influence our behavior .", "Here we propose a probabilistic model with an explicit representation ...	[ "Although time perception and timed behavior are essential for our everyday experience , it is still unclear how the human brain represents the underlying temporal regularities of our dynamic environment .", "These regularities and their representations in the brain are important to generate well-timed behavior ....	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology" ]	The Bicoid Stability Factor Controls Polyadenylation and Expression of Specific Mitochondrial mRNAs in Drosophila melanogaster	journal.pgen.1002324	null	[ [ "The maternal to zygotic transition , during which control of development shifts from maternally contributed mRNAs to genes expressed in the zygote , is of considerable interest .", "The maternally contributed bicoid mRNA , encoding a protein important for formation of anterior body patterning , is depend...	[ "The bicoid stability factor ( BSF ) of Drosophila melanogaster has been reported to be present in the cytoplasm , where it stabilizes the maternally contributed bicoid mRNA and binds mRNAs expressed from early zygotic genes .", "BSF may also have other roles , as it is ubiquitously expressed and essential for su...	[ "The majority of the cellular energy currency ATP is formed in a tubular network , termed mitochondria , present within virtually all eukaryotic cells .", "The mitochondria are unique among cellular organelles in that they contain their own genome , which encodes critical proteins necessary for cellular energy pr...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "fusarium", "chemical compounds", "pathology and laboratory medicine", "phosphates", "fungal genetics", "pathogens", "microbiology", "fusarium graminearum", "cereal crops", "model organisms", "crops", "fungal diseases", "plants", "fungal pathogens", "res...	Cellular Tracking and Gene Profiling of Fusarium graminearum during Maize Stalk Rot Disease Development Elucidates Its Strategies in Confronting Phosphorus Limitation in the Host Apoplast	journal.ppat.1005485	null	[ [ "The main stem ( i . e . stalk ) of maize ( Zea mays ) represents about 50% of the total plant dry biomass at the grain maturity stage [1] .", "Stalk rot is a major disease of maize worldwide [2] , and tends to be more common in higher yielding hybrids that produce larger ears [3] .", "The ascomycete ...	[ "The ascomycete fungus Fusarium graminearum causes stalk rot in maize .", "We tracked this pathogen’s growth in wound-inoculated maize stalks using a fluorescence-labeled fungal isolate and observed that invasive hyphae grew intercellularly up to 24 h post inoculation , grew intra- and inter-cellularly between 36...	[ "Gibberella stalk rot of maize is an economically important crop disease caused by the filamentous fungus Fusarium graminearum ( previously also called Gibberella zeae ) .", "Stalk rots develop in the main stem of mature maize plants .", "Detailed anatomical studies of the complete infection process in maize st...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology/microbial physiology and metabolism", "genetics and genomics/microbial evolution and genomics", "genetics and genomics/gene expression", "microbiology/microbial evolution and genomics", "genetics and genomics/chromosome biology", "cell biology/microbial growth and development", "biochemist...	Conjugative DNA Transfer Induces the Bacterial SOS Response and Promotes Antibiotic Resistance Development through Integron Activation	journal.pgen.1001165	null	[ [ "Free-living bacteria commonly face changing environments and must cope with varying conditions .", "These adaptive strategies involve temporary physiological responses through various groups of genes gathered in regulons that are induced or repressed according to the surrounding conditions .", "This ...	[ "Conjugation is one mechanism for intra- and inter-species horizontal gene transfer among bacteria .", "Conjugative elements have been instrumental in many bacterial species to face the threat of antibiotics , by allowing them to evolve and adapt to these hostile conditions .", "Conjugative plasmids are transfe...	[ "Bacteria exchange DNA in their natural environments .", "The process called conjugation consists of DNA transfer by cell contact from one bacterium to another .", "Conjugative circular plasmids have been identified as shuttles and reservoirs for adaptive genes .", "It is now established that such lateral gen...	2010
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "deletion mutation", "medicine and health sciences", "immune physiology", "enzymes", "immunology", "enzymology", "mutation", "fungi", "antibodies", "immunologic techniques", "research and analysis methods", "immune system proteins", "antibody production", "proteins", "antigens", "yeast...	Optimizing antibody affinity and stability by the automated design of the variable light-heavy chain interfaces	journal.pcbi.1007207	null	[ [ "High-affinity natural antibodies are generated through an iterative process of mutation and selection for antigen binding known as affinity maturation .", "Affinity maturation also selects antibodies that exhibit higher stability and expressibility [1] , both of which are essential parameters in the deve...	[ "Antibodies developed for research and clinical applications may exhibit suboptimal stability , expressibility , or affinity .", "Existing optimization strategies focus on surface mutations , whereas natural affinity maturation also introduces mutations in the antibody core , simultaneously improving stability an...	[ "Antibodies are highly important in research , biotechnology , and medical applications .", "Despite their great utility , however , many antibodies exhibit suboptimal stability and affinity , raising production costs and limiting their practical usefulness .", "To tackle this general limitation , we used deep ...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "invertebrates", "medicine and health sciences", "luciferase", "vacuoles", "gene regulation", "enzymes", "rna extraction", "enzymology", "neuroscience", "biological locomotion", "biomechanics", "animals", "animal models", "age groups", "micrornas", "adults", "model organisms", "dro...	A let-7-to-miR-125 MicroRNA Switch Regulates Neuronal Integrity and Lifespan in Drosophila	journal.pgen.1006247	null	[ [ "RNA-mediated post-transcriptional mechanisms regulate the accumulation and homeostasis of proteins not only during animal development but also during adulthood [1–3] .", "These mechanisms include regulation by microRNAs ( miRNAs ) , a class of small non-coding RNAs that usually silence messenger RNAs ( m...	[ "Messenger RNAs ( mRNAs ) often contain binding sites for multiple , different microRNAs ( miRNAs ) .", "However , the biological significance of this feature is unclear , since such co-targeting miRNAs could function coordinately , independently , or redundantly with one another .", "Here , we show that two co...	[ "Deregulation of mRNAs that are targeted by multiple miRNAs is a common feature of a number of diseased states including neurodegenerative disorders .", "The currently accepted model is that the combined action of all binding miRNAs ensures target repression .", "Here , we show that two co-expressed miRNAs exer...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "genetics", "epigenetics", "biology", "genomics", "molecular cell biology" ]	Integrated Transcriptomic and Epigenomic Analysis of Primary Human Lung Epithelial Cell Differentiation	journal.pgen.1003513	null	[ [ "Over the past two decades the relationship between gene expression and chromatin structure has been increasingly recognized [1]–[4] .", "Elucidation of the histone code and subsequent insights into the functional implications of post-translational modifications of histone tails have begun to provide a me...	[ "Elucidation of the epigenetic basis for cell-type specific gene regulation is key to gaining a full understanding of how the distinct phenotypes of differentiated cells are achieved and maintained .", "Here we examined how epigenetic changes are integrated with transcriptional activation to determine cell phenot...	[ "Understanding the role of epigenetic control of gene expression is critical to the full description of biological processes , such as development and regeneration .", "Herein we utilize the differentiation of cells from the distal lung to gain insight into the correlation between the epigenetic landscape , molec...	2013
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "genetics and genomics/epigenetics", "developmental biology/plant growth and development", "genetics and genomics/plant genetics and gene expression", "evolutionary biology/plant genetics and gene expression" ]	Dosage-Sensitive Function of RETINOBLASTOMA RELATED and Convergent Epigenetic Control Are Required during the Arabidopsis Life Cycle	journal.pgen.1000988	null	[ [ "Independent evolution of multicellularity and thus the cell types has implications for adaptation of distinct developmental strategies in plants and animals [1] .", "Adaptive mechanisms unique to higher plants include alternation between the reduced gametophytic and dominant sporophytic generations , abs...	[ "The plant life cycle alternates between two distinct multi-cellular generations , the reduced gametophytes and the dominant sporophyte .", "Little is known about how generation-specific cell fate , differentiation , and development are controlled by the core regulators of the cell cycle .", "In Arabidopsis , R...	[ "Understanding the convergent developmental mechanisms of core cell cycle genes is highly instructive in biology .", "When these genes are essential in development , lethality precludes mutation analysis throughout the life cycle of an organism .", "We subjected a homozygous lethal mutation in RETINOBLASTOMA RE...	2010
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "cardiovascular anatomy", "gene regulation", "cardiac ventricles", "developmental biology", "mitochondria", "epigenetics", "bioenergetics", "embryos", "mammalian genomics", "cellular structures and organelles", "chromatin", "embryology", "genomics", "chrom...	CTCF counter-regulates cardiomyocyte development and maturation programs in the embryonic heart	journal.pgen.1006985	null	[ [ "The coordinated deployment of genetic programs during lineage commitment and differentiation is a hallmark of developmental processes .", "Cell specification and maturation are coordinated by controlled activation and repression of specific gene expression programs .", "In the heart , the first funct...	[ "Cardiac progenitors are specified early in development and progressively differentiate and mature into fully functional cardiomyocytes .", "This process is controlled by an extensively studied transcriptional program .", "However , the regulatory events coordinating the progression of such program from develop...	[ "Properly regulated gene expression in time and space during development and differentiation requires not only transcriptional inputs , but also specific structuring of the chromatin .", "CTCF is a DNA binding factor that is believed to be critical for this process through binding to tens of thousands of sites ac...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics and genomics/gene expression", "genetics and genomics/comparative genomics", "evolutionary biology/genomics" ]	Evolutionary Mirages: Selection on Binding Site Composition Creates the Illusion of Conserved Grammars in Drosophila Enhancers	journal.pgen.1000829	null	[ [ "The transcriptional output of developmental enhancers is affected by the spatial organization of the transcription factor binding sites they contain .", "The relative positioning of sites is known from individual cases to modulate direct competition between factors for the same site [1] , [2] , cooperati...	[ "The clustering of transcription factor binding sites in developmental enhancers and the apparent preferential conservation of clustered sites have been widely interpreted as proof that spatially constrained physical interactions between transcription factors are required for regulatory function .", "However , we...	[ "Because mutation is a random process , most biologists assume that apparently non-random features of genome sequences must be the result of natural selection acting to create and preserve them .", "Where this is true , genome sequences provide a powerful means to infer aspects of molecular , cellular , and organ...	2010
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "neurobiology of disease and regeneration", "neurodegenerative diseases", "neuroscience", "animal models", "model organisms", "infectious diseases", "biology", "mouse", "neurological disorders", "neurology", "genetics", "human genetics", "genetics and genomics", "prion diseas...	Strain Specific Resistance to Murine Scrapie Associated with a Naturally Occurring Human Prion Protein Polymorphism at Residue 171	journal.ppat.1002275	null	[ [ "TSE or prion diseases are transmissible neurodegenerative diseases occurring in a variety of mammalian species including domestic and wild animals as well as humans [1] .", "Examples include scrapie in sheep , chronic wasting disease ( CWD ) in cervids and bovine spongiform encephalopathy ( BSE ) in catt...	[ "Transmissible spongiform encephalopathies ( TSE ) or prion diseases are neurodegenerative disorders associated with conversion of normal host prion protein ( PrP ) to a misfolded , protease-resistant form ( PrPres ) .", "Genetic variations of prion protein in humans and animals can alter susceptibility to both f...	[ "Transmissible spongiform encephalopathies ( TSE ) or prion diseases are infectious fatal neurological diseases that affect many mammals , including humans .", "In these diseases a misfolded form of host prion protein ( PrP ) leads to brain degeneration and death .", "The genetic code of PrP in individual anima...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "breast tumors", "immunofluorescence staining", "chemical compounds", "cancers and neoplasms", "basic cancer research", "oncology", "animal models", "luminescent proteins", "model organisms", "yellow fluorescent protein", "experimental organism systems", "seco...	Podoplanin+ tumor lymphatics are rate limiting for breast cancer metastasis	journal.pbio.2005907	null	[ [ "Metastasis is responsible for 90% of deaths of breast cancer patients [1 , 2] .", "The contribution of both cancer cells and stromal cells ( such as fibroblasts , endothelial cells , pericytes , and immune cells ) is important for cancer development and metastasis , including in breast cancer [2–5] .", ...	[ "Metastatic dissemination employs both the blood and lymphatic vascular systems .", "Solid tumors dynamically remodel and generate both vessel types during cancer progression .", "Lymphatic vessel invasion and cancer cells in the tumor-draining lymph nodes ( LNs ) are prognostic markers for breast cancer metast...	[ "Cancer progression and metastasis of solid tumors can occur in association with the generation of new lymphatic vessels ( lymphangiogenesis ) .", "Lymphatic vessel invasion and cancer cells in the tumor-draining lymph nodes are used as prognostic markers for breast cancer metastasis and patient outcome .", "Ho...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "circuit models", "mathematics", "computational neuroscience", "statistics", "statistical methods", "biology", "computational biology", "nonlinear dynamics", "neuroscience", "learning and memory" ]	Forward and Backward Inference in Spatial Cognition	journal.pcbi.1003383	null	[ [ "This paper describes a dynamic Bayesian model of spatial cognition .", "Here we define spatial cognition as including the tasks of localisation ( estimating where you are in a known environment ) , sensory imagery ( constructing a virtual scene ) , decision making ( deciding which way to turn to reach a ...	[ "This paper shows that the various computations underlying spatial cognition can be implemented using statistical inference in a single probabilistic model .", "Inference is implemented using a common set of ‘lower-level’ computations involving forward and backward inference over time .", "For example , to esti...	[ "The ability of mammals to navigate is well studied , both behaviourally and in terms on the underlying neurophysiology .", "Navigation is a well studied topic in computational fields such as machine learning and signal processing .", "However , studies in computational neuroscience , which draw together these ...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "vaccines", "medicine", "vaccination", "clinical immunology", "immunity", "parasitology", "immunology", "biology", "microbiology", "vaccine development", "immune response" ]	Safety and Immunogenicity of rSh28GST Antigen in Humans: Phase 1 Randomized Clinical Study of a Vaccine Candidate against Urinary Schistosomiasis	journal.pntd.0001704	null	[ [ "Schistosomiasis , the second major human parasitic infection after malaria , remains a major health problem in many developing countries , mainly among children and it is estimated that this chronic disease is responsible for 300 000 deaths per year .", "During Schistosoma haematobium infection , morbidi...	[ "Treatment of urinary schistosomiasis by chemotherapy remains challenging due to rapid re-infection and possibly to limited susceptibility to praziquantel treatment .", "Therefore , therapeutic vaccines represent an attractive alternative control strategy .", "The objectives of this study were to assess the saf...	[ "Therapeutic vaccines represent an attractive tool in the fight against schistosomiasis .", "Pre-clinical immunization studies with the schistosome enzyme 28 kDa glutathione S-transferase ( 28GST ) has been shown to significantly reduce schistosome egg production and subsequent pathology .", "The objective of t...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Prevention and Immunotherapy of Secondary Murine Alveolar Echinococcosis Employing Recombinant EmP29 Antigen	journal.pntd.0003795	null	[ [ "Alveolar echincoccosis ( AE ) , caused by the metacestode larval stage of the fox tapeworm Echinococcus multilocularis , is one of the most severe helminthic diseases worldwide .", "Human AE affects the liver in more than 98% of the cases [1 , 2] , and metacestodes grow and proliferate continuously and i...	[ "Alveolar echinococcosis ( AE ) is caused by infection with the larval stage of the tapeworm Echinococcus multilocularis .", "An increasing understanding of immunological events that account for the metacestode survival in human and murine AE infection prompted us to undertake explorative experiments tackling the...	[ "Current medical management of AE that relies on surgery and continuous benzimidazole administration is of limited effectiveness .", "Therefore , alternative preventive and therapeutic tools need to be explored .", "Here , we demonstrate that vaccination with recombinant antigen EmP29 ( rEmP29 ) , prior or afte...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "computational biology/macromolecular structure analysis", "biophysics/theory and simulation", "computational biology/macromolecular sequence analysis", "computational biology", "computational biology/molecular dynamics" ]	A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family	journal.pcbi.1000393	null	[ [ "It has long been known that a protein's native state is best represented as an ensemble of conformations rather than as a single structure [1] .", "Conformational ensembles provide a detailed structural picture of protein dynamics .", "As motions are crucial for many aspects of protein function , suc...	[ "Conformational ensembles are increasingly recognized as a useful representation to describe fundamental relationships between protein structure , dynamics and function .", "Here we present an ensemble of ubiquitin in solution that is created by sampling conformational space without experimental information using...	[ "Knowledge of protein properties is essential for enhancing the understanding and engineering of biological functions .", "One key property of proteins is their flexibility—their intrinsic ability to adopt different conformations .", "This flexibility can be measured experimentally but the measurements are indi...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunology/leukocyte signaling and gene expression", "genetics and genomics/gene expression" ]	Identification of CIITA Regulated Genetic Module Dedicated for Antigen Presentation	journal.pgen.1000058	null	[ [ "Most mammalian transcription factors are believed to activate numerous genes having diverse functions .", "Direct support for this pleiotropic nature of transcription factor function has been provided by techniques permitting the unbiased mapping of transcription factor binding sites in substantial segme...	[ "The class II trans-activator CIITA is a transcriptional co-activator required for the expression of Major Histocompatibility Complex ( MHC ) genes .", "Although the latter function is well established , the global target-gene specificity of CIITA had not been defined .", "We therefore generated a comprehensive...	[ "Most mammalian transcription factors and transcriptional co-activators are believed to regulate the activities of numerous genes fulfilling multiple functions .", "This pleiotropic role has recently been confirmed directly for several individual factors by large-scale mapping studies aimed at generating comprehe...	2008
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Epidemiological and Molecular Characterization of Dengue Virus Circulating in Bhutan, 2013-2014	journal.pntd.0004010	null	[ [ "Dengue is one of the most common infectious diseases in tropical and sub-tropical regions of the world [1 , 2] .", "The World Health Organization ( WHO ) estimates 50–100 million infections per year globally; however , other studies have suggested a much higher figure [2] .", "Southeast Asia and West...	[ "Dengue is one of the most significant public health problems in tropical and subtropical countries , and is increasingly being detected in traditionally non-endemic areas .", "In Bhutan , dengue virus ( DENV ) has only recently been detected and limited information is available .", "In this study , we analyzed...	[ "We describe the epidemiological and molecular features of DENV currently circulating in the two southwestern districts of Bhutan , demonstrating a shift in serotype dominance from previous DENV-3 ( 2004–2006 ) to current DENV-1 ( 2013–2014 ) .", "The presence of the dengue virus in Bhutan is a relatively recent ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The GTP- and Phospholipid-Binding Protein TTD14 Regulates Trafficking of the TRPL Ion Channel in Drosophila Photoreceptor Cells	journal.pgen.1005578	null	[ [ "Photoreceptor membrane proteins undergo a carefully regulated turnover that helps to adjust the sensitivity of the receptors and to renew old and possibly worn out proteins .", "Throughout the lifetime of a photoreceptor cell , new proteins are synthesized and transported to the photoreceptive membrane w...	[ "Recycling of signaling proteins is a common phenomenon in diverse signaling pathways .", "In photoreceptors of Drosophila , light absorption by rhodopsin triggers a phospholipase Cβ-mediated opening of the ion channels transient receptor potential ( TRP ) and TRP-like ( TRPL ) and generates the visual response ....	[ "Protein trafficking in neurons occurs throughout the lifetime of a cell and includes the internalization and redistribution of plasma membrane proteins .", "Regulated protein trafficking controls the equipment of the plasma membrane with receptors and ion channels and thereby attenuates or enhances neuronal func...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "parasite groups", "ecology and environmental sciences", "plasmodium", "population genetics", "tropical diseases", "geographical locations", "parasitic diseases", "parasitic protozoans", "parasitology", "genetic mapping", "apicomplexa", "protozoans", "popula...	Substantial population structure of Plasmodium vivax in Thailand facilitates identification of the sources of residual transmission	journal.pntd.0005930	null	[ [ "Although the global incidence of malaria has been greatly reduced in recent years , Plasmodium vivax remains the most geographically widespread human malaria parasite [1] .", "In Thailand , intensified malaria control has resulted in ~50% reduction of clinical cases over the past 10 years .", "In par...	[ "Plasmodium vivax transmission in Thailand has been substantially reduced over the past 10 years , yet it remains highly endemic along international borders .", "Understanding the genetic relationship of residual parasite populations can help track the origins of the parasites that are reintroduced into malaria-f...	[ "This study presents an updated view of the P . vivax populations along the Thai-Myanmar and the Thai-Cambodian borders .", "Genotyping of parasite samples collected after intensified malaria control demonstrated that despite the decline in overall transmission intensity , the genetic diversity of the P . vivax p...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "model organisms", "genomics", "genetics", "microbiology", "biology", "molecular cell biology" ]	Temperate Phages Acquire DNA from Defective Prophages by Relaxed Homologous Recombination: The Role of Rad52-Like Recombinases	journal.pgen.1004181	null	[ [ "Bacteriophages , or phages , the viruses that attack bacteria , have gained a renewed interest in the last decade with the emergence of antibiotic resistant bacteria .", "Despite their early discovery [1] , [2] and the in-depth molecular and genetic characterization of few model phages , overall phage bi...	[ "Bacteriophages ( or phages ) dominate the biosphere both numerically and in terms of genetic diversity .", "In particular , genomic comparisons suggest a remarkable level of horizontal gene transfer among temperate phages , favoring a high evolution rate .", "Molecular mechanisms of this pervasive mosaicism ar...	[ "Temperate bacteriophages ( or phages ) are bacterial viruses that , unlike virulent phages , have the ability to enter a prophage dormant state upon infection , in which they stably replicate with the bacterial genome .", "A majority of bacterial genomes contain multiple active or defective prophages , and numer...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "microbiology/microbial physiology and metabolism", "microbiology/cellular microbiology and pathogenesis" ]	The Pleiotropic CymR Regulator of Staphylococcus aureus Plays an Important Role in Virulence and Stress Response	journal.ppat.1000894	null	[ [ "Cysteine , an important sulfur-containing amino acid , plays a major role in cellular physiology .", "Cysteine residues are required for the biogenesis of [Fe-S] clusters , are found in the catalytic sites of several enzymes and assist in protein folding and assembly through disulfide bond formation [1] ...	[ "We have characterized a novel pleiotropic role for CymR , the master regulator of cysteine metabolism .", "We show here that CymR plays an important role both in stress response and virulence of Staphylococcus aureus .", "Genes involved in detoxification processes , including oxidative stress response and meta...	[ "Staphylococcus aureus is a very harmful human pathogen that is a major cause of nosocomial infections .", "Humans have developed sophisticated defense strategies against invading bacteria , including the innate immune response , with the generation of an oxidative burst inside phagocytic cells .", "Staphylococ...	2010
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "veterinary diseases", "pest control", "biology", "zoology", "veterinary science", "agriculture" ]	Standardizing Visual Control Devices for Tsetse Flies: East African Species Glossina swynnertoni	journal.pntd.0002063	null	[ [ "Glossina swynnertoni Austen ( Diptera , Glossinidae ) is restricted to open savannah in north-western Tanzania and south-western Kenya , extending from Tarangire in the south through Manyara to the Serengeti plains , and into the Maasai Mara in the north [1] .", "Swynnerton [2] found it at 900–1800 m abo...	[ "Here we set out to standardize long-lasting , visually-attractive devices for Glossina swynnertoni , a vector of both human and animal trypanosomiasis in open savannah in Tanzania and Kenya , and in neighbouring conservation areas used by pastoralists .", "The goal was to determine the most practical device/mate...	[ "Glossina swynnertoni is restricted to open savannah in north-western Tanzania and south-western Kenya , where it is a vector of both human and animal trypanosomiasis in wildlife reserves and in neighbouring conservation areas used by pastoralists .", "Despite the challenge to minimize disease transmission throug...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "cytoskeletal proteins", "protein chemistry", "cell motility", "actin filaments", "protein interactions", "cell biology", "molecular complexes", "proteins", "protein structure", "biology and life sciences", "molecular cell biology", "biophysics", "molecular biology" ]	Structural Differences Explain Diverse Functions of Plasmodium Actins	journal.ppat.1004091	null	[ [ "Actins are the most abundant and among the most conserved proteins in eukaryotic cells and play indispensable roles in a plethora of key cellular events , including muscle contraction , cell division , shape determination , transport , and cell motility [1] , [2] .", "Actins are highly conserved in opist...	[ "Actins are highly conserved proteins and key players in central processes in all eukaryotic cells .", "The two actins of the malaria parasite are among the most divergent eukaryotic actins and also differ from each other more than isoforms in any other species .", "Microfilaments have not been directly observe...	[ "Malaria parasites have two actin isoforms , which are among the most divergent within the actin family that comprises highly conserved proteins , essential in all eukaryotic cells .", "In Plasmodium , actin is indispensable for motility and , thus , the infectivity of the deadly parasite .", "Yet , actin filam...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "infectious diseases", "medicine and health sciences", "population modeling", "epidemiology", "biology and life sciences", "spatial epidemiology", "infectious disease modeling", "computational biology", "infectious disease control" ]	The Spatial Resolution of Epidemic Peaks	journal.pcbi.1003561	null	[ [ "Novel respiratory pathogens continue to pose substantial public health challenges , not least because of the risk that large epidemics may overwhelm key health care resources such as vaccination stockpiles and intensive care facilities .", "Recent epidemics of concern include: SARS [1] , influenza [2]–[4...	[ "The emergence of novel respiratory pathogens can challenge the capacity of key health care resources , such as intensive care units , that are constrained to serve only specific geographical populations .", "An ability to predict the magnitude and timing of peak incidence at the scale of a single large populatio...	[ "Fundamental spatial processes such as individuals' interactions and movement are not sufficiently well understood and yet they define the transmission of infectious diseases through populations .", "Spatial models of epidemics represent the region of interest ( such as a city or country ) as a collection of spat...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "engineering and technology", "manufacturing processes", "database searching", "animals", "developmental biology", "infectious disease control", "insect vectors", "research and analysis methods", "infectious diseases", "agrochemicals", "aedes ...	Community effectiveness of pyriproxyfen as a dengue vector control method: A systematic review	journal.pntd.0005651	null	[ [ "Over the past five decades , the global burden of dengue is estimated to have increased massively: Bhatt et al . [1] postulated that in 2010 there were 96 million apparent , and 294 million unapparent infections worldwide , with 22 , 000 registered dengue-related deaths reported in 2014 [2] .", "Transmis...	[ "Vector control is the only widely utilised method for primary prevention and control of dengue .", "The use of pyriproxyfen may be promising , and autodissemination approach may reach hard to reach breeding places .", "It offers a unique mode of action ( juvenile hormone mimic ) and as an additional tool for t...	[ "There is evidence that pyriproxyfen may effectively reduce the density of immature mosquito stages when applied to identified breeding sites .", "Various formulations are commercially available , and easy to use without a health threat to the user .", "However , questions remain regarding its use as a single a...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "public health and epidemiology", "virology", "public health and epidemiology/epidemiology", "virology/emerging viral diseases", "public health and epidemiology/global health", "public health and epidemiology/infectious diseases" ]	Venezuelan Equine Encephalitis Virus in Iquitos, Peru: Urban Transmission of a Sylvatic Strain	journal.pntd.0000349	null	[ [ "Members of the Venezuelan equine encephalitis virus ( VEEV ) complex are arboviruses belonging to the Alphavirus genus of the Togaviridae family .", "First identified among equines in the 1930s [1] , VEEV-associated human disease was not recognized until 1943 [2] , [3] , although epidemiological data sug...	[ "Enzootic strains of Venezuelan equine encephalitis virus ( VEEV ) have been isolated from febrile patients in the Peruvian Amazon Basin at low but consistent levels since the early 1990s .", "Through a clinic-based febrile surveillance program , we detected an outbreak of VEEV infections in Iquitos , Peru , in t...	[ "Venezuelan equine encephalitis ( VEE ) is a mosquito-borne viral disease often causing grave illness and large outbreaks of disease in South America .", "In Iquitos , Peru , a city of 350 , 000 situated in the Amazon forest , we normally observe 10–14 VEE cases per year associated with people traveling to rural ...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Region-Specific Activation of oskar mRNA Translation by Inhibition of Bruno-Mediated Repression	journal.pgen.1004992	null	[ [ "Localized mRNAs function in many biological settings to facilitate region-specific protein synthesis [1–3] .", "Translational repression of these mRNAs helps restrict distribution of the encoded proteins , an essential property if the protein has adverse effects at inappropriate locations .", "In add...	[ "A complex program of translational repression , mRNA localization , and translational activation ensures that Oskar ( Osk ) protein accumulates only at the posterior pole of the Drosophila oocyte .", "Inappropriate expression of Osk disrupts embryonic axial patterning , and is lethal .", "A key factor in trans...	[ "Proteins are often enriched to specific regions within cells via localization of mRNAs .", "This phenomenon serves a variety of roles , both bringing together factors involved in particular cellular processes to enhance their efficiency , and in restricting proteins that could do harm if deployed at inappropriat...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "biology", "genomics", "genetics and genomics" ]	Genetic Variants in REC8, RNF212, and PRDM9 Influence Male Recombination in Cattle	journal.pgen.1002854	null	[ [ "Reciprocal recombination between homologues fulfills an essential mechanistic role during meiosis in most organisms [1] , [2] .", "It is required for proper bivalent alignment on the metaphase I plate preceding disjunction and segregation at anaphase I . Correct segregation of the full chromosome complem...	[ "We use >250 , 000 cross-over events identified in >10 , 000 bovine sperm cells to perform an extensive characterization of meiotic recombination in male cattle .", "We map Quantitative Trait Loci ( QTL ) influencing genome-wide recombination rate , genome-wide hotspot usage , and locus-specific recombination rat...	[ "Homologous recombination is an essential cellular process that determines proper chromosome segregation during meiosis , affects fertility , and influences evolvability .", "Nevertheless , the components of the recombination apparatus remain incompletely characterized in mammals .", "One approach to identify s...	2012
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "reverse transcriptase-polymerase chain reaction", "gene regulation", "brassica", "organisms", "plant science", "model organisms", "experimental organism systems", "sequence motif analysis", "molecular biology techniques", "plants", "research and analysis methods", "arabidopsis thaliana", "s...	Depletion of Arabidopsis SC35 and SC35-like serine/arginine-rich proteins affects the transcription and splicing of a subset of genes	journal.pgen.1006663	null	[ [ "Alternative splicing ( AS ) is an important mechanism in the regulation of gene expression by excising introns and ligating different exons to produce multiple mRNA isoforms from a single gene .", "This post-transcriptional process greatly enhances transcriptome and proteome complexity [1 , 2] .", "I...	[ "Serine/arginine-rich ( SR ) proteins are important splicing factors which play significant roles in spliceosome assembly and splicing regulation .", "However , little is known regarding their biological functions in plants .", "Here , we analyzed the phenotypes of mutants upon depleting different subfamilies o...	[ "SR proteins were identified to be important splicing factors .", "This work generated mutants of different subfamilies of the classic Arabidopsis SR proteins .", "Genetic analysis revealed that loss of the function of SC35/SCL proteins influences the plant development .", "This study revealed SC35/SCL protei...	2017

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