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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", "Methods", "Results", "Discussion" ]	[ "physics", "computer science", "chemistry", "biology" ]	Defining the Nature of Thermal Intermediate in 3 State Folding Proteins: Apoflavodoxin, a Study Case	journal.pcbi.1002647	null	[ [ "In addition to the folded and unfolded states , many proteins may adopt stable conformations that display mixed properties of the native and denatured states .", "These conformations , usually known as intermediates , may appear under unusual external conditions ( i . e . non-physiological pH , pressure ...	[ "The early stages of the thermal unfolding of apoflavodoxin have been determined by using atomistic multi microsecond-scale molecular dynamics ( MD ) simulations complemented with a variety of experimental techniques .", "Results strongly suggest that the intermediate is reached very early in the thermal unfoldin...	[ "A simplistic view of protein structure tends to emphasize the opposition between the native state and the denatured ensemble of unfolded conformations .", "In addition to these extreme conformations , proteins subjected to a variety of perturbations often populate alternative partly unfolded conformations , some...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience/behavioral neuroscience", "neuroscience/neurobiology of disease and regeneration", "neuroscience/animal cognition", "neuroscience/experimental psychology" ]	Stress-Induced Out-of-Context Activation of Memory	journal.pbio.1000570	An intensely stressful experience can itself activate memories that are unrelated to the stressful experience. This previously unknown property of stress could help explain how traumatic memories become pathological.	[ [ "Inappropriate negative responses in emotionally neutral circumstances and the development of negative associations to harmless stimuli are core , debilitating features of post-traumatic stress disorder ( PTSD ) , depression , and a host of anxiety and mood disorders .", "The possibility that stress itsel...	[ "Inappropriate recollections and responses in stressful conditions are hallmarks of post-traumatic stress disorder and other anxiety and mood disorders , but how stress contributes to the disorders is unclear .", "Here we show that stress itself reactivates memories even if the memory is unrelated to the stressfu...	[ "This work identifies a powerful effect of stressful experiences on memories .", "We report that a single intensely stressful experience can activate memories in a situation that has essentially no physical or motivational relationship to the stressful experience .", "Using a forced-swim test as a stressor in r...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "biochemistry", "infectious diseases", "microbiology", "molecular biology", "eubacteria" ]	Twin RNA Polymerase–Associated Proteins Control Virulence Gene Expression in Francisella tularensis	journal.ppat.0030084	null	[ [ "Francisella tularensis is a Gram-negative , facultative intracellular pathogen and the aetiological agent of tularemia , a disease that can be fatal in humans .", "Although outbreaks of tularemia are thought to be rare , infections caused by F . tularensis have become a public health issue because of the...	[ "The MglA protein is the only known regulator of virulence gene expression in Francisella tularensis , yet it is unclear how it functions .", "F . tularensis also contains an MglA-like protein called SspA .", "Here , we show that MglA and SspA cooperate with one another to control virulence gene expression in F...	[ "The Gram-negative bacterium Francisella tularensis is an intracellular pathogen and the causative agent of tularemia .", "In F . tularensis , the MglA protein is the only known regulator of virulence genes that are important for intracellular survival , yet it is not known how MglA functions .", "F . tularensi...	2007
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Geometry of the Gene Expression Space of Individual Cells	journal.pcbi.1004224	null	[ [ "Recent advances allow high-throughput measurement of biological information from individual cells [1–12] .", "This is an improvement over standard experiments which mask the range of states in the population because they average over millions of cells .", "Therefore , it is expected that single-cell ...	[ "There is a revolution in the ability to analyze gene expression of single cells in a tissue .", "To understand this data we must comprehend how cells are distributed in a high-dimensional gene expression space .", "One open question is whether cell types form discrete clusters or whether gene expression forms ...	[ "In the past , biological experiments usually pooled together millions of cells , masking the differences between individual cells .", "Current technology takes a big step forward by measuring gene expression from individual cells .", "Interpreting this data is challenging because we need to understand how cell...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "flow cytometry", "medicine and health sciences", "immune cells", "enzyme-linked immunoassays", "immune physiology", "gene regulation", "immunology", "microbiology", "cell differentiation", "developmental biology", "antibodies", "immunologic techniques", "research and analys...	RIG-I-like receptor activation by dengue virus drives follicular T helper cell formation and antibody production	journal.ppat.1006738	null	[ [ "Dengue virus is a global mosquito-transmitted pathogen that infects 400 mln people annually [1] .", "The majority of patients experience only mild fever , but the disease can progress to life-threatening dengue shock syndrome and dengue hemorrhagic fever .", "With no specific antivirals or effective ...	[ "Follicular T helper cells ( TFH ) are fundamental in orchestrating effective antibody-mediated responses critical for immunity against viral infections and effective vaccines .", "However , it is unclear how virus infection leads to TFH induction .", "We here show that dengue virus ( DENV ) infection of human ...	[ "Strong antibody production is critical for effective immune responses against viral infections and is a primary factor in the development of successful vaccines .", "However , it is unclear how virus infection leads to effective antibody responses .", "Dengue virus ( DENV ) is known to induce potent antibody p...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "uterus", "medicine and health sciences", "reproductive system", "vesicles", "pathology and laboratory medicine", "maternal health", "obstetrics and gynecology", "hela cells", "immunology", "biological cultures", "collagens", "preterm birth", "women's health", "signs and symptoms", "micr...	Membrane Vesicles of Group B Streptococcus Disrupt Feto-Maternal Barrier Leading to Preterm Birth	journal.ppat.1005816	null	[ [ "Preterm birth is the leading cause of neonatal mortality worldwide [1] .", "Globally , an estimated 13 million babies are born prematurely each year , out of which more than one million succumb to death [2] .", "In addition , being the leading cause of neonatal death , preterm birth also increases th...	[ "Infection of the genitourinary tract with Group B Streptococcus ( GBS ) , an opportunistic gram positive pathogen , is associated with premature rupture of amniotic membrane and preterm birth .", "In this work , we demonstrate that GBS produces membrane vesicles ( MVs ) in a serotype independent manner .", "Th...	[ "Preterm birth is a major health concern globally as it is not only a leading cause of neonatal death , but also has long term consequences including defective brain development .", "Infection of vagina and cervix of pregnant women with the bacteria , Group B Streptococcus ( GBS ) , causes chorio-amnionitis that ...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "dengue virus", "medicine and health sciences", "pathology and laboratory medicine", "gene regulation", "pathogens", "biological cultures", "microbiology", "wolbachia", "viruses", "micrornas", "rna viruses", "cell cultures", "bacteria", "research and analysis methods", "small interfering...	Wolbachia-mediated virus blocking in mosquito cells is dependent on XRN1-mediated viral RNA degradation and influenced by viral replication rate	journal.ppat.1006879	null	[ [ "Dengue is the most important mosquito-transmitted viral disease of humans in terms of the global burden of disease[1] .", "Current control methods focus almost entirely on vector control through either preventative source reduction or insecticide spraying in response to outbreaks .", "The increasing ...	[ "Wolbachia is currently being developed as a novel tool to block the transmission of dengue viruses ( DENV ) by Aedes aegypti .", "A number of mechanisms have been proposed to explain the DENV-blocking phenotype in mosquitoes , including competition for fatty acids like cholesterol , manipulation of host miRNAs a...	[ "Dengue virus ( DENV ) is a human pathogen transmitted by Aedes mosquitoes .", "Infection with DENV causes dengue fever and may develop into life-threatening dengue hemorrhagic fever .", "Dengue disease is increasing globally and current control methods are proving ineffective in curtailing this growing problem...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunology", "computational biology" ]	Quantifying the Impact of Human Immunodeficiency Virus-1 Escape From Cytotoxic T-Lymphocytes	journal.pcbi.1000981	null	[ [ "The CTL response is thought to play a role in firstly reducing [1] , [2] and then controlling the level of HIV-1 viraemia .", "Evidence for the protective role of CTLs in humans includes HLA class I heterozygous advantage [3] , the evolution of multiple viral mechanisms to evade CTL surveillance [4]–[6] ...	[ "HIV-1 escape from the cytotoxic T-lymphocyte ( CTL ) response leads to a weakening of viral control and is likely to be detrimental to the patient .", "To date , the impact of escape on viral load and CD4+ T cell count has not been quantified , primarily because of sparse longitudinal data and the difficulty of ...	[ "HIV , like many viruses , has evolved multiple strategies to evade immune surveillance .", "One of these strategies is the evolution of escape mutations which reduce the ability of the immune response to kill HIV-infected cells .", "But does HIV escape matter ?", "Some believe that the accumulation of escape...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "sequencing techniques", "medicine and health sciences", "cancer genetics", "breast tumors", "obstetrics and gynecology", "cancer treatment", "cancers and neoplasms", "hematologic cancers and related disorders", "oncology", "genome sequencing", "women's health", "genome analysis", "molecular...	SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution	journal.pcbi.1003665	null	[ [ "Cancer is a disease largely driven by accumulated somatic mutations .", "Many of these are clonal mutations and occur in the founding cell to initiate disease .", "These become uniformly present in the tumor by propagating to that cell's progeny during clonal expansion .", "Others are subclonal e...	[ "The sensitivity of massively-parallel sequencing has confirmed that most cancers are oligoclonal , with subpopulations of neoplastic cells harboring distinct mutations .", "A fine resolution view of this clonal architecture provides insight into tumor heterogeneity , evolution , and treatment response , all of w...	[ "Sequencing the genomic DNA of cancers has revealed that tumors are not homogeneous .", "As a tumor grows , new mutations accumulate in individual cells , and as these cells replicate , the mutations are passed on to their offspring , which comprise only a portion of the tumor when it is sampled .", "We present...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "systems biology", "model organisms", "yeast and fungal models", "biology", "computational biology", "microbiology", "genetics and genomics" ]	System-Level Insights into Yeast Metabolism by Thermodynamic Analysis of Elementary Flux Modes	journal.pcbi.1002415	null	[ [ "Metabolic fluxes give immediate insights into the metabolism of a cell [1] , [2] .", "Metabolic flux analysis has proven to be useful , for example for the determination of enzyme functions [3] , for the identification of regulatory mechanisms in response to environmental perturbations [4] , or as a tool...	[ "One of the most obvious phenotypes of a cell is its metabolic activity , which is defined by the fluxes in the metabolic network .", "Although experimental methods to determine intracellular fluxes are well established , only a limited number of fluxes can be resolved .", "Especially in eukaryotes such as yeas...	[ "Fluxes in metabolic pathways are a highly informative aspect of an organism's phenotype .", "The experimental determination of such fluxes is well established and has proven very useful .", "To address some of the limitations of experimental flux analysis , such as when the cell is divided in multiple compartm...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "viruses", "herpes simplex virus", "gene expression and vector techniques", "medical microbiology", "virology", "viral pathogens", "molecular biology", "microbial pathogens", "biology and life sciences", "molecular biology techniques", "microbiology", "herpesviruses", "herpes simplex virus-1...	IFI16 Restricts HSV-1 Replication by Accumulating on the HSV-1 Genome, Repressing HSV-1 Gene Expression, and Directly or Indirectly Modulating Histone Modifications	journal.ppat.1004503	null	[ [ "Herpes simplex virus type I ( HSV-1 ) is a ubiquitous and highly contagious virus that establishes a life-long infection in host organisms .", "It typically enters the host through mucosal epithelia and causes a lytic , productive infection in many cell types , including fibroblast , epithelial , and end...	[ "Interferon-γ inducible factor 16 ( IFI16 ) is a multifunctional nuclear protein involved in transcriptional regulation , induction of interferon-β ( IFN-β ) , and activation of the inflammasome response .", "It interacts with the sugar-phosphate backbone of dsDNA and modulates viral and cellular transcription th...	[ "HSV-1 , a ubiquitous human pathogen that establishes a life-long infection , has evolved several mechanisms to evade host immune detection and responses .", "However , it is still subject to regulation by cellular factors .", "Recently , a host nuclear protein , IFI16 , was shown to be involved in the innate d...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "body fluids", "pathology and laboratory medicine", "dysentery", "pathogens", "tropical diseases", "microbiology", "shigella", "pediatrics", "diarrhea", "bacterial diseases", "signs and symptoms", "gastroenterology and hepatology", "neglected tropical diseas...	The other Campylobacters: Not innocent bystanders in endemic diarrhea and dysentery in children in low-income settings	journal.pntd.0006200	null	[ [ "Campylobacter are curved gram-negative bacteria and a common cause of enteritis worldwide .", "The Campylobacter genus is composed of 26 species [1] , some of which are thermo-tolerant such as C . jejuni and C . coli , the most commonly reported Campylobacter species affecting humans ( 82 . 7% and 17 . 3...	[ "Campylobacter is one of the main causes of gastroenteritis worldwide .", "Most of the current knowledge about the epidemiology of this food-borne infection concerns two species , C . coli and C . jejuni .", "Recent studies conducted in developing countries and using novel diagnostic techniques have generated e...	[ "Campylobacter is a major public health concern in developed and developing countries .", "C . coli and C . jejuni have long been considered to be the major disease-causing species , and clinical microbiologic approaches target these two species .", "However , less selective diagnostic approaches have shown the...	2018
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "reverse transcriptase-polymerase chain reaction", "taxonomy", "dengue virus", "medicine and health sciences", "lao people", "pathology and laboratory medicine", "pathogens", "tropical diseases", "microbiology", "rna extraction", "ethnicities", "viruses", "phylogenetics", "data management"...	Molecular epidemiology of dengue viruses in three provinces of Lao PDR, 2006-2010	journal.pntd.0006203	null	[ [ "Dengue is an arboviral disease transmitted to humans by Aedes mosquitoes .", "Infections are caused by single-stranded positive-sense RNA Dengue virus ( DENV ) from the Flavivirus genus , Flaviviridae family .", "Any of the four virus serotypes ( DENV-1 to DENV-4 ) can cause dengue fever , dengue hem...	[ "Few data on dengue epidemiology are available for Lao PDR .", "Here , we provide information on the complexity of dengue epidemiology in the country , demonstrating dynamic circulation that varies over space and time , according to serotype .", "We recruited 1 , 912 consenting patients presenting with WHO deng...	[ "Dengue is a mosquito-borne disease that can be caused by 4 viruses .", "It is a flu-like disease but can sometime be more severe and cause hemorrhage or death .", "An estimated 390 million people are infected every year , mainly in the Western Pacific and in South-East Asia .", "In Laos , where our study was...	2018
[ "Introduction", "Results/Discussion", "Methods" ]	[ "mutagenesis", "mutation", "model organisms", "genetic mutation", "gene expression", "genetics", "population genetics", "yeast and fungal models", "biology", "saccharomyces cerevisiae" ]	Latent Effects of Hsp90 Mutants Revealed at Reduced Expression Levels	journal.pgen.1003600	null	[ [ "Genetic changes that alter protein sequence or expression level can lead to adaptation , suggesting these protein properties are central to evolutionary processes .", "Many studies have individually investigated the effects of changes to either protein sequence or expression level .", "For example , ...	[ "In natural systems , selection acts on both protein sequence and expression level , but it is unclear how selection integrates over these two dimensions .", "We recently developed the EMPIRIC approach to systematically determine the fitness effects of all possible point mutants for important regions of essential...	[ "Changes in protein sequence or expression strength can both lead to adaptation in natural systems .", "While many studies have focused individually on either expression strength or protein sequence , in principle the fitness effects of these two protein properties are interdependent .", "We systematically inve...	2013
[ "Introduction", "Methods", "Results", "Discussion", "Conclusions" ]	[ "medicine and health sciences", "lens disorders", "tropical diseases", "geographical locations", "ocular anatomy", "parasitic diseases", "surgical and invasive medical procedures", "bacterial diseases", "eye diseases", "neglected tropical diseases", "ethiopia", "eyes", "africa", "infectiou...	Podoconiosis, trachomatous trichiasis and cataract in northern Ethiopia: A comparative cross sectional study	journal.pntd.0005388	null	[ [ "Neglected tropical diseases ( NTDs ) do not occur in isolation but have substantial geographical overlap .", "This results in an increased burden of co-morbidity within a population , commonly leading to individuals suffering from one or more NTDs[1] .", "These conditions share common risk factors in...	[ "Rural populations in low-income countries commonly suffer from the co-morbidity of neglected tropical diseases ( NTDs ) .", "Podoconiosis , trachomatous trichiasis ( both NTDs ) and cataract are common causes of morbidity among subsistence farmers in the highlands of northern Ethiopia .", "We explored whether ...	[ "Podoconiosis is an NTD causing chronic leg swelling in subsistence farming communities in the tropics .", "There is no research on the association between podoconiosis and two common causes of blindness and visual impairment; trachomatous trichiasis ( TT ) and cataract .", "TT is the blinding consequence of co...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "dengue virus", "medicine and health sciences", "immune physiology", "enzyme-linked immunoassays", "pathology and laboratory medicine", "togaviruses", "chikungunya infection", "federated states of micronesia", "pathogens", "immunology", "tropical diseases", "microbiology", "geographical loca...	Chikungunya virus disease outbreak in Yap State, Federated States of Micronesia	journal.pntd.0005410	null	[ [ "Chikungunya virus is a mosquito-borne alphavirus capable of causing large outbreaks of acute febrile illness with severe polyarthralgia [1 , 2] .", "First identified in East Africa in 1952 , as of mid-2013 chikungunya virus had caused outbreaks in Africa , Europe , Asia , and islands in the Indian and We...	[ "Chikungunya virus is a mosquito-borne alphavirus which causes an acute febrile illness associated with polyarthralgia .", "Beginning in August 2013 , clinicians from the Yap State Department of Health in the Federated States of Micronesia ( FSM ) identified an unusual cluster of illness which was subsequently co...	[ "Chikungunya virus can cause large outbreaks with substantial morbidity , especially in places with certain Aedes species of mosquitos and immunologically-naïve populations .", "In August 2013 , chikungunya virus disease was identified for the first time in the Federated States of Micronesia .", "The explosive ...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "medicine and health sciences", "oxygen", "neuroscience", "biological locomotion", "pulmonology", "animals", "animal models", "organisms", "developmental biology", "drosophila melanogaster", "model organisms", "hypoxia", "experimental organism systems", "drosophila", "...	Glial response to hypoxia in mutants of NPAS1/3 homolog Trachealess through Wg signaling to modulate synaptic bouton organization	journal.pgen.1007980	null	[ [ "Animals need oxygen and food , not only to sustain life , but also for motility .", "In vertebrates , oxygen and nutrients are delivered through the vascular systems to organs and tissues throughout the body .", "To maintain proper nutrient and oxygen supply , and thus physiological functions , the v...	[ "Synaptic structure and activity are sensitive to environmental alterations .", "Modulation of synaptic morphology and function is often induced by signals from glia .", "However , the process by which glia mediate synaptic responses to environmental perturbations such as hypoxia remains unknown .", "Here , w...	[ "Oxygen is essential for animals to maintain their life such as growth , metabolism , responsiveness , and movement .", "It is therefore important to understand how animal cells trigger hypoxia response and adapt to hypoxia thereafter .", "Both mammalian vascular and insect tracheal branches are induced to enha...	2019
[ "Introduction", "Results and Discussion", "Materials and Methods" ]	[]	Genomic Selection and Association Mapping in Rice (Oryza sativa): Effect of Trait Genetic Architecture, Training Population Composition, Marker Number and Statistical Model on Accuracy of Rice Genomic Selection in Elite, Tropical Rice Breeding Lines	journal.pgen.1004982	null	[ [ "Over the next 30 years , the production of staple cereal grains including wheat , maize , and rice must to be doubled to keep pace with global population and income growth .", "At the same time , agriculture , in general , is imperiled by human-induced climate change , and plant breeders and farmers toge...	[ "Genomic Selection ( GS ) is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population .", "GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species , and here we evaluate for the first time its efficacy...	[ "Genomic selection is a promising breeding technique that aims to improve the efficiency and speed of the breeding process .", "While it has been shown to be effective in crops such as wheat and corn , it has not yet been applied to rice breeding .", "Genome-wide association studies ( GWAS ) , by contrast , are...	2015
[ "Introduction", "Materials and methods", "Results and discussion" ]	[ "chemical characterization", "medicine and health sciences", "molecular dynamics", "protein interactions", "electrophysiology", "neuroscience", "ion channels", "molecular motors", "actin motors", "protein structure", "thermodynamics", "motor proteins", "research and analysis methods", "con...	Effect of Ca2+ on the promiscuous target-protein binding of calmodulin	journal.pcbi.1006072	null	[ [ "Calmodulin ( CaM ) , Fig 1a and 1b , is a promiscuous Ca2+-sensing protein that plays part in many physiologically important cellular processes [1] .", "Its two lobes , connected by a flexible linker , have one beta sheet and two EF-hand motifs each , Fig 1a–1c .", "The EF-hand binds a Ca2+ ion which...	[ "Calmodulin ( CaM ) is a calcium sensing protein that regulates the function of a large number of proteins , thus playing a crucial part in many cell signaling pathways .", "CaM has the ability to bind more than 300 different target peptides in a Ca2+-dependent manner , mainly through the exposure of hydrophobic ...	[ "Calmodulin is a protein involved in the regulation of a variety of cell signaling pathways .", "It acts by making usually calcium-insensitive proteins sensitive to changes in the calcium concentration inside the cell .", "Its two lobes bind calcium and allow the energetically unfavorable exposure of hydrophobi...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "test evaluation", "survey methods", "diagnostic medicine", "emerging infectious diseases", "infectious disease epidemiology", "virology", "epidemiology", "emerging viral diseases", "neglected tropical diseases", "arboviral infections", "biology", "microb...	Dried-Blood Spots: A Cost-Effective Field Method for the Detection of Chikungunya Virus Circulation in Remote Areas	journal.pntd.0002339	null	[ [ "Chikungunya virus ( CHIKV ) is an arthropod-borne alphavirus transmitted by mosquitoes of the Aedes genus .", "Chikungunya has spread widely through Africa [1] , [2] , [3] , South-East Asia , the Indian subcontinent [4] , [5] , [6] , and most recently Southern Europe [7] , [8] .", "There was a large ...	[ "In 2005 , there were outbreaks of febrile polyarthritis due to Chikungunya virus ( CHIKV ) in the Comoros Islands .", "CHIKV then spread to other islands in the Indian Ocean: La Réunion , Mauritius , Seychelles and Madagascar .", "These outbreaks revealed the lack of surveillance and preparedness of Madagascar...	[ "Chikungunya is a mosquito-transmitted viral disease .", "No treatment is currently available .", "The only way to prevent infection is to avoid mosquito bites .", "Surveillance of circulation by early diagnosis is useful to prevent or limit outbreak .", "CHIKV , like all RNA viruses , is heat-labile .", ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/infectious diseases of the nervous system", "infectious diseases/prion diseases", "pathology/histopathology", "genetics and genomics/genetics of disease", "neuroscience/neurobiology of disease and regeneration" ]	Prion Protein Amino Acid Determinants of Differential Susceptibility and Molecular Feature of Prion Strains in Mice and Voles	journal.ppat.1000113	null	[ [ "The conversion of the cellular prion protein ( PrPC ) into an abnormally-folded isoform ( PrPSc ) that accumulates in the brain of affected individuals represents the key feature of transmissible spongiform encephalopathies ( TSEs ) , or prion diseases [1] .", "They include bovine spongiform encephalopat...	[ "The bank vole is a rodent susceptible to different prion strains from humans and various animal species .", "We analyzed the transmission features of different prions in a panel of seven rodent species which showed various degrees of phylogenetic affinity and specific prion protein ( PrP ) sequence divergences i...	[ "Prions are unconventional infectious agents that cause fatal neurodegenerative diseases in animals and humans .", "A pathological form of the cellular prion protein ( PrPC ) , named PrPSc , appears to be the major or the sole component of prions .", "These agents are transmitted by inducing the conversion of h...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "organismal evolution", "infectious diseases", "forms of evolution", "microevolution", "microbial evolution", "virology", "biology", "evolutionary biology", "microbiology", "evolutionary genetics", "viral evolution" ]	Sequential Adaptive Mutations Enhance Efficient Vector Switching by Chikungunya Virus and Its Epidemic Emergence	journal.ppat.1002412	null	[ [ "The potential of RNA viruses to emerge into new environments often depends on their ability to efficiently adapt to new hosts .", "These adaptations sometimes comprise a stepwise process that includes", "1 ) initial viral introduction/establishment in the recipient species , followed by", "2 ) fi...	[ "The adaptation of Chikungunya virus ( CHIKV ) to a new vector , the Aedes albopictus mosquito , is a major factor contributing to its ongoing re-emergence in a series of large-scale epidemics of arthritic disease in many parts of the world since 2004 .", "Although the initial step of CHIKV adaptation to A . albo...	[ "Since 2004 , chikungunya virus ( CHIKV ) has caused a series of devastating outbreaks in Asia , Africa and Europe that resulted in up to 6 . 5 million cases of arthritic disease and have been associated with several thousand human deaths .", "Although the initial step of CHIKV adaptation to A . albopictus mosqui...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "infographics", "medicine and health sciences", "non-coding rna sequences", "pathology and laboratory medicine", "pathogens", "messenger rna", "microbiology", "nucleotides", "charts", "viruses", "dna viruses", "rna isolation", "epigenetics", "molecular biology techniques", "chromatin", ...	Two herpesviral noncoding PAN RNAs are functionally homologous but do not associate with common chromatin loci	journal.ppat.1007389	null	[ [ "Kaposi’s sarcoma-associated herpesvirus ( KSHV ) is an opportunistic pathogen of human immunodeficiency virus ( HIV ) patients and the etiological agent of several human cancers , including Kaposi sarcoma and primary effusion lymphoma [1] .", "The KSHV life cycle includes a latent phase , when viral gene...	[ "During lytic replication of Kaposi’s sarcoma-associated herpesvirus ( KSHV ) , a nuclear viral long noncoding RNA known as PAN RNA becomes the most abundant polyadenylated transcript in the cell .", "Knockout or knockdown of KSHV PAN RNA results in loss of late lytic viral gene expression and , consequently , re...	[ "Herpesviruses produce noncoding RNAs , some of which are essential to the viral life cycle .", "One such noncoding RNA from Kaposi’s sarcoma-associated herpesvirus is the polyadenylated , nuclear ( PAN ) RNA , which is required for production and release of progeny virions from infected cells .", "In this stud...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "cell cycle and cell division", "cell processes", "bacillus", "microbiology", "light microscopy", "staphylococcus aureus", "prokaryotic models", "dna replication", "microscopy", "experimental organism systems",...	The nucleoid occlusion factor Noc controls DNA replication initiation in Staphylococcus aureus	journal.pgen.1006908	null	[ [ "Binary fission in bacteria is carried out by a multiprotein complex called the divisome [1] .", "Assembly of this complex initiates with the formation of a ring-like structure at mid-cell called the Z-ring composed of the tubulin homolog FtsZ [2] .", "The Z-ring functions as a dynamic scaffold for th...	[ "Successive division events in the spherically shaped bacterium Staphylococcus aureus are oriented in three alternating perpendicular planes .", "The mechanisms that underlie this relatively unique pattern of division and coordinate it with chromosome segregation remain largely unknown .", "Thus far , the only ...	[ "The mechanisms by which bacteria coordinate cell division with chromosome replication and segregation remain poorly understood .", "This coordination is particularly challenging in the spherical bacterium Staphylococcus aureus , which unlike rod-shaped bacteria , divides in three consecutive perpendicular divisi...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "developmental biology", "computational biology/systems biology" ]	Systematic Analysis of Pleiotropy in C. elegans Early Embryogenesis	journal.pcbi.1000003	null	[ [ "The phenomenon of pleiotropy highlights the fact that some genes in the genome perform multiple biological functions .", "Although individual examples of pleiotropic genes have been discovered [1]–[4] , pleiotropy remains a poorly understood genetic phenomenon and there have been very few systematic stud...	[ "Pleiotropy refers to the phenomenon in which a single gene controls several distinct , and seemingly unrelated , phenotypic effects .", "We use C . elegans early embryogenesis as a model to conduct systematic studies of pleiotropy .", "We analyze high-throughput RNA interference ( RNAi ) data from C . elegans ...	[ "In a biological system , some genes play single roles while others perform multiple functions .", "How can we determine which genes are multi-functional ?", "An informative way for probing gene functions is to eliminate the expression of a given gene and observe the phenotypic consequences .", "RNAi techniqu...	2008
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "blood cells", "medicine and health sciences", "immune cells", "immune physiology", "pathology and laboratory medicine", "spleen", "melioidosis", "immunology", "bacterial diseases", "signs and symptoms", "abscesses", "infectious diseases", "white blood cells", "animal cells", "t cells", ...	Persistent infection due to a small-colony variant of Burkholderia pseudomallei leads to PD-1 upregulation on circulating immune cells and mononuclear infiltration in viscera of experimental BALB/c mice	journal.pntd.0005702	null	[ [ "Burkholderia pseudomallei ( B . pseudomallei ) is the causative agent of melioidosis , an infectious disease , endemic across parts of South East Asia and Northern Australia [1] .", "Despite causing an estimated 89 , 000 deaths worldwide annually , melioidosis still remains a neglected tropical disease [...	[ "Melioidosis is a neglected tropical disease endemic across South East Asia and Northern Australia .", "The etiological agent , Burkholderia pseudomallei ( B . pseudomallei ) , is a Gram-negative , rod-shaped , motile bacterium residing in the soil and muddy water across endemic regions of the tropical world .", ...	[ "B . pseudomallei is a bacterium that causes melioidosis , a disease endemic in Southeastern Asia and Northern Australia .", "It is estimated that melioidosis leads to 89 , 000 deaths worldwide each year .", "Nevertheless , melioidosis continues to remain a neglected tropical disease that is not even on the lis...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Maternal Depletion of Piwi, a Component of the RNAi System, Impacts Heterochromatin Formation in Drosophila	journal.pgen.1003780	null	[ [ "Eukaryotic genomes are packaged into chromatin , which can broadly be characterized as having two alternative forms , euchromatin and heterochromatin .", "Heterochromatin was first distinguished as dense ( darkly staining ) chromosomal material , seen by microscopy [1] .", "Since that time , heteroch...	[ "A persistent question in epigenetics is how heterochromatin is targeted for assembly at specific domains , and how that chromatin state is faithfully transmitted .", "Stable heterochromatin is necessary to silence transposable elements ( TEs ) and maintain genome integrity .", "Both the RNAi system and heteroc...	[ "Most eukaryotes harbor a high proportion of transposable elements ( TEs ) in their genomes .", "Heterochromatin , a condensed chromatin state found at domains enriched for TEs and other repetitious elements , is important for silencing TEs and maintaining the integrity of the genome .", "The RNAi system has be...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "geomorphology", "schistosoma", "invertebrates", "medicine and health sciences", "ecology and environmental sciences", "surface water", "water resources", "landforms", "helminths", "topography", "tropical diseases", "parasitic diseases", "animals", "health care", "vaccines", "aquatic e...	Perceptions about interventions to control schistosomiasis among the Lake Victoria island communities of Koome, Uganda	journal.pntd.0005982	null	[ [ "Schistosomiasis affects an estimated 240 million people worldwide and over 90% of all Schistosoma infections are found in sub-Saharan Africa [1] .", "In Uganda , an estimated four million people are infected with Schistosoma and about 55% of the population is at risk of infection [2] .", "The Lake Vi...	[ "Praziquantel-based mass treatment is the main approach to controlling schistosomiasis mansoni in endemic areas .", "Interventions such as provision and use of safe water , minimising contact with infested water , disposal of stool in latrines and snail control provide key avenues to break the transmission cycle ...	[ "Schistosomiasis , a neglected tropical disease caused by the blood fluke Schistosoma , is still a huge burden in sub-Saharan Africa .", "The modalities for its control are mass treatment of the population with praziquantel , minimising contact with infested water , provision and use of safe water , intermediate ...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "phosphorylation", "learning", "medicine and health sciences", "breast tumors", "ontologies", "protein interaction networks", "signaling networks", "social sciences", "cancers and neoplasms", "neuroscience", "learning and memory", "oncology", "data management", "cognitive psychology", "n...	Computational discovery of dynamic cell line specific Boolean networks from multiplex time-course data	journal.pcbi.1006538	null	[ [ "Regarding the training of BNs with respect to multiple perturbation datasets , CellNOpT ( CNO ) [16] assembles BNs from a Prior Knowledge Network ( PKN ) and phosphoproteomic datasets .", "Their tool has been implemented using stochastic search algorithms ( more precisely , a genetic algorithm ) , to sug...	[ "Protein signaling networks are static views of dynamic processes where proteins go through many biochemical modifications such as ubiquitination and phosphorylation to propagate signals that regulate cells and can act as feed-back systems .", "Understanding the precise mechanisms underlying protein interactions ...	[ "Traditional canonical signaling pathways help to understand overall signaling processes inside the cell .", "Large scale phosphoproteomic data provide insight into alterations among different proteins under different experimental settings .", "Our goal is to combine the traditional signaling networks with comp...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "cell physiology", "carbohydrate metabolism", "innate immune system", "medicine and health sciences", "immune cells", "immune physiology", "pathology and laboratory medicine", "cytokines", "yeast infections", "pathogens", "metabolic processes", "immunology", "microbiology", ...	Rewiring monocyte glucose metabolism via C-type lectin signaling protects against disseminated candidiasis	journal.ppat.1006632	null	[ [ "The immune system is constantly challenged by pathogens , and this requires immune cells to optimize the management of metabolic resources in order to exert their crucial role in host defense .", "A number of studies have shown how different stimuli induce metabolic reprogramming in immune cells , requir...	[ "Monocytes are innate immune cells that play a pivotal role in antifungal immunity , but little is known regarding the cellular metabolic events that regulate their function during infection .", "Using complementary transcriptomic and immunological studies in human primary monocytes , we show that activation of m...	[ "Fungal infections are a major health concern for immunocompromised individuals due to the lack of success of the currently available antifungal therapies .", "Unveiling the metabolic processes involved in the immune function offers a promising opportunity for the development of new therapeutic approaches against...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "immune cells", "clinical research design", "jungle yellow fever", "flavivirus", "immunity to infections", "dengue", "immunology", "vaccines", "adaptive immunity", "cohort studies", "neglected tropical diseases", "immunizations", "vaccination", "viral hemorrhagic fevers", "...	T-Cell Memory Responses Elicited by Yellow Fever Vaccine are Targeted to Overlapping Epitopes Containing Multiple HLA-I and -II Binding Motifs	journal.pntd.0001938	null	[ [ "The yellow fever ( YF ) vaccines ( YF-17D-204 and 17DD ) are considered to be among the most effective vaccines [1] , [2] .", "Antibody and T-cell responses are believed to mediate protection [3] , [4] , [5] , and recent studies have also implicated the innate immune responses as one of the critical elem...	[ "The yellow fever vaccines ( YF-17D-204 and 17DD ) are considered to be among the safest vaccines and the presence of neutralizing antibodies is correlated with protection , although other immune effector mechanisms are known to be involved .", "T-cell responses are known to play an important role modulating anti...	[ "T-cell responses are considered to be very important; however , the role of T-cell responses in vaccine mediated immunity is still controversial .", "One reason may be that most studies of human T-cell responses are focused on a few epitopes .", "We still lack a systematic view of the repertoire of peptides pr...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "physics", "medicine", "condensed-matter physics", "mathematics", "neuroanatomy", "computational neuroscience", "neurology", "interdisciplinary physics", "neurological disorders", "biology", "neuroscience", "nonlinear dynamics" ]	Dynamic Effective Connectivity of Inter-Areal Brain Circuits	journal.pcbi.1002438	null	[ [ "In Arcimboldo's ( 1527–1593 ) paintings , whimsical portraits emerge out of arrangements of flowers and vegetables .", "Only directing attention to details , the illusion of seeing a face is suppressed ( Figure 1A–B ) .", "Our brain is indeed hardwired to detect facial features and a complex network ...	[ "Anatomic connections between brain areas affect information flow between neuronal circuits and the synchronization of neuronal activity .", "However , such structural connectivity does not coincide with effective connectivity ( or , more precisely , causal connectivity ) , related to the elusive question “Which ...	[ "The circuits of the brain must perform a daunting amount of functions .", "But how can “brain states” be flexibly controlled , given that anatomic inter-areal connections can be considered as fixed , on timescales relevant for behavior ?", "We hypothesize that , thanks to the nonlinear interaction between brai...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "plant biology/plant-biotic interactions", "plant biology" ]	Enhanced Disease Susceptibility 1 and Salicylic Acid Act Redundantly to Regulate Resistance Gene-Mediated Signaling	journal.pgen.1000545	null	[ [ "Plants have evolved highly specific mechanisms to resist pathogens .", "One of the common ways to counter pathogen growth involves the deployment of resistant ( R ) proteins , which confer protection against specific races of pathogens carrying corresponding avirulence ( Avr ) genes [1] .", "Followin...	[ "Resistance ( R ) protein–associated pathways are well known to participate in defense against a variety of microbial pathogens .", "Salicylic acid ( SA ) and its associated proteinaceous signaling components , including enhanced disease susceptibility 1 ( EDS1 ) , non–race-specific disease resistance 1 ( NDR1 ) ...	[ "Salicylic acid and enhanced disease susceptibility 1 are important components of resistance gene-mediated defense signaling against diverse pathogens in a variety of plants .", "Present understanding of plant defense signaling pathways places salicylic acid and enhanced disease susceptibility 1 downstream of res...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "bacteriology", "genetic mutation", "enzymes", "microbiology", "escherichia coli", "prokaryotic models", "model organisms", "dna replication", "microbial evolution", "cell growth", "dna", "molecular genetics", "dna synthesis", "microbial physiology", "gene expression", "dna amplificati...	A New Role for Translation Initiation Factor 2 in Maintaining Genome Integrity	journal.pgen.1002648	null	[ [ "Translation Initiation Factor 2 ( IF2; for a review , see [1] ) is an essential cellular protein that brings mRNA , the 30S ribosome , and the initiator fMet-tRNA together into the 30S initiation complex and then promotes association with the 50S ribosomal unit to form the 70S initiation complex [2]–[4] .", ...	[ "Escherichia coli translation initiation factor 2 ( IF2 ) performs the unexpected function of promoting transition from recombination to replication during bacteriophage Mu transposition in vitro , leading to initiation by replication restart proteins .", "This function has suggested a role of IF2 in engaging cel...	[ "Translation Initiation Factor 2 ( IF2 ) is a bacterial protein that plays an essential role in the initiation of protein synthesis .", "As such , it not only has an important influence on cellular growth but also is subject to regulation in response to physiological conditions such as nutritional deprivation .",...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Detection of Serotype-Specific Antibodies to the Four Dengue Viruses Using an Immune Complex Binding (ICB) ELISA	journal.pntd.0002580	null	[ [ "Dengue fever is a highly prevalent arthropod-borne viral disease with 2 . 5 billion people in tropical or subtropical areas at risk for infection .", "The clinical picture of dengue may vary considerably from mere fever to severe shock syndrome .", "The annual number of infections is estimated to sev...	[ "Dengue virus ( DENV ) infections are preferentially diagnosed by detection of specific IgM antibodies , DENV NS1 antigen assays or by amplification of viral RNA in serum samples of the patients .", "The type-specific immunity to the four worldwide circulating DENV serotypes can be determined by neutralization as...	[ "Infections with four different dengue viruses are threatening 2 . 5 billion people in tropical countries .", "Since most antibodies to these four viruses are cross-reacting , a type-specific ELISA would be valuable to study the immune response to the circulating viruses in patients but also in healthy subjects i...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry", "rna", "structure prediction", "rna structure", "genomics", "computational chemistry", "molecular dynamics", "nucleic acids", "protein folding", "gene expression", "molecular genetics", "rna synthesis", "biology", "computational biology", "chemistry", "biophysics simula...	The Impact of a Ligand Binding on Strand Migration in the SAM-I Riboswitch	journal.pcbi.1003069	null	[ [ "Riboswitches reveal the versatility of Ribonucleic Acid ( RNA ) folding , and its remarkable biological impact .", "They are folded mRNAs that sense cellular metabolite levels and control expression of downstream genes [1]–[4] .", "Design of altered or novel riboswitches has been suggested for bioeng...	[ "Riboswitches sense cellular concentrations of small molecules and use this information to adjust synthesis rates of related metabolites .", "Riboswitches include an aptamer domain to detect the ligand and an expression platform to control gene expression .", "Previous structural studies of riboswitches largely...	[ "Folding dynamics is crucial for RNA function .", "Riboswitches are a classic example .", "A typical riboswitch senses the cellular concentration of a small molecule .", "By refolding itself into a new structure , the riboswitch converts that information into changes in rates for synthesis of related metaboli...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "mycology", "molecular cell biology", "cell biology", "chromosome biology", "immunity", "biology", "microbiology" ]	Fungal-Induced Cell Cycle Impairment, Chromosome Instability and Apoptosis via Differential Activation of NF-κB	journal.ppat.1002555	null	[ [ "Cryptococcus neoformans is a facultative intracellular pathogen that is the most common cause of systemic fungal infections leading to meningoencephalitis in immunocompromised patients , and notably in people infected with HIV [1] , [2] .", "This saprophytic basidiomycete fungus is characterized by the p...	[ "Microbial pathogens have developed efficient strategies to compromise host immune responses .", "Cryptococcus neoformans is a facultative intracellular pathogen , recognised as the most common cause of systemic fungal infections leading to severe meningoencephalitis , mainly in immunocompromised patients .", "...	[ "Cryptococcus neoformans , the only encapsulated pathogenic yeast , is responsible for severe opportunistic meningoencephalitis mostly in immunocompromised patients .", "It is a facultative intracellular pathogen and , as such , has the ability to survive intra- and extracellularly .", "Whereas interactions of ...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "plant anatomy", "luciferase", "chemical compounds", "molecular probe techniques", "enzymes", "immunoblotting", "enzymology", "cloning", "carbohydrates", "organic compounds", "endosperm", "cereal crops", "plant science", "model organisms", "crops", "molecular biology techniques", "pl...	Maize opaque10 Encodes a Cereal-Specific Protein That Is Essential for the Proper Distribution of Zeins in Endosperm Protein Bodies	journal.pgen.1006270	null	[ [ "Cereal crops are major source of the world’s food supply [1 , 2] .", "Many storage proteins in cereal grains are valuable nitrogen sources for humans and livestock [3] .", "Prolamins are major storage proteins that occur only in cereal grain endosperm [4] .", "Studies of the protein storage mecha...	[ "Cereal storage proteins are major nitrogen sources for humans and livestock .", "Prolamins are the most abundant storage protein in most cereals .", "They are deposited into protein bodies ( PBs ) in seed endosperm .", "The inner structure and the storage mechanism for prolamin PBs is poorly understood .", ...	[ "Through the positional cloning of the maize classic endosperm mutant opaque10 ( o10 ) , we identified a novel protein critical for PB morphology .", "O10 is a fast-evolving cereal-specific gene with recent origin .", "A thorough characterization of its three functional domains revealed its important functions ...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "dna metabolism", "cancer genetics", "genetic mutation", "chromosome structure and function", "developmental biology", "organism development", "mutation types", "dna", "chromosome biology", "biology", "molecular biology", "aging", "biochemistry", "cell biology", "nucleic acids", "genet...	Replicative Age Induces Mitotic Recombination in the Ribosomal RNA Gene Cluster of Saccharomyces cerevisiae	journal.pgen.1002015	null	[ [ "One of the greatest risk factors associated with carcinogenesis is age .", "Cancer risk increases exponentially toward the end of life in humans and other mammalian species [1] .", "Somatic genetic changes contribute significantly to the development of most tumors .", "However , the rate at which...	[ "Somatic mutations contribute to the development of age-associated disease .", "In earlier work , we found that , at high frequency , aging Saccharomyces cerevisiae diploid cells produce daughters without mitochondrial DNA , leading to loss of respiration competence and increased loss of heterozygosity ( LOH ) in...	[ "There is a striking correlation between age and the onset of many diseases , such as cancer , suggesting that the aging process itself can contribute to their development .", "Cancer is a genetic disease caused by the accumulation of a series of deleterious somatic mutations leading to unchecked proliferation ."...	2011
[ "Introduction", "Material and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "ecology and environmental sciences", "tropical diseases", "sand flies", "parasitic diseases", "parasitic protozoans", "organisms", "protozoans", "leishmania", "neglected tropical diseases", "insect vectors", "research and analysis methods", "sequence analysis...	Identification of French Guiana sand flies using MALDI-TOF mass spectrometry with a new mass spectra library	journal.pntd.0007031	null	[ [ "Phlebotomine sand flies ( Diptera: Psychodidae: Phlebotominae ) are insects of great medical relevance because they are the most frequent vectors of leishmaniasis [1 , 2] and also transmit various other human pathogens including bacteria and viruses [3] .", "Leishmaniases are a range of diseases caused b...	[ "Phlebotomine sand flies are insects that are highly relevant in medicine , particularly as the sole proven vectors of leishmaniasis .", "Accurate identification of sand fly species is an essential prerequisite for eco-epidemiological studies aiming to better understand the disease .", "Traditional morphologica...	[ "Phlebotomine sand flies are small insects , mostly known for their role in the transmission of Leishmania parasites to humans and other mammals .", "In French Guiana , the main clinical form of the disease manifests as cutaneous lesions also called American cutaneous leishmaniasis .", "The transmission of Leis...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "biology", "microbiology", "parasitology" ]	Cure of Hookworm Infection with a Cysteine Protease Inhibitor	journal.pntd.0001680	null	[ [ "One of a number of soil-transmitted helminthiases ( STHs ) that is deeply rooted in poverty , hookworm disease afflicts as much as 10% of the world's population in sub-Saharan Africa , South America , and South and South-East Asia [1] , [2] , [3] .", "The principal etiological agents in humans are the ne...	[ "Hookworm disease is a major global health problem and principal among a number of soil-transmitted helminthiases ( STHs ) for the chronic disability inflicted that impacts both personal and societal productivity .", "Mass drug administration most often employs single-dose therapy with just two drugs of the same ...	[ "In spite of the enormous prevalence of hookworm disease , just two drugs , albendazole and mebendazole , are most commonly employed for treatment and control , and both belong to the same benzimidazole chemical class .", "There exists , therefore , a pressing need to develop new , safe and inexpensive agents for...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Dynamic Contacts of U2, RES, Cwc25, Prp8 and Prp45 Proteins with the Pre-mRNA Branch-Site and 3' Splice Site during Catalytic Activation and Step 1 Catalysis in Yeast Spliceosomes	journal.pgen.1005539	null	[ [ "The removal of introns from nuclear pre-mRNAs proceeds by way of two phosphoester transfer reactions and is catalyzed by the spliceosome , a large ribonucleoprotein ( RNP ) complex composed of the snRNPs U1 , U2 , U4/U6 and U5 and several proteins [1] .", "The spliceosome is a highly dynamic RNP machine ...	[ "Little is known about contacts in the spliceosome between proteins and intron nucleotides surrounding the pre-mRNA branch-site and their dynamics during splicing .", "We investigated protein-pre-mRNA interactions by UV-induced crosslinking of purified yeast Bact spliceosomes formed on site-specifically labeled p...	[ "The spliceosome is a highly dynamic RNP machine that during the catalytic cycle undergoes many changes in composition and conformation .", "The pre-catalytic Bact spliceosome contains the U2 , U6 and U5 snRNAs and ~40 proteins , which are evolutionarily conserved between budding yeast and metazoans .", "The Ba...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "neonatology", "urology", "medicine and health sciences", "maternal health", "obstetrics and gynecology", "geographical locations", "tropical diseases", "pediatrics", "treponematoses", "bacterial diseases", "women's health", "sexually transmitted diseases", "pregnancy", "neglected tropical...	Pregnancy outcomes and mother-to-child transmission rate in HTLV-1/2 infected women attending two public hospitals in the metropolitan area of Rio de Janeiro	journal.pntd.0007404	null	[ [ "Human T-lymphotropic virus types 1 and 2 ( HTLV-1/2 ) are human oncogenic retroviruses first identified in the early 1980’s [1] .", "There are six subtypes of HTLV-1 ( A to F ) , which have no impact on the clinical expression of the disease [2] .", "There are two other types of HTLV ( 3 and 4 ) ; bu...	[ "HTLV-1/2 are transmitted sexually , by whole cell blood products and from mother-to-child ( MTC ) , mainly through breastfeeding .", "HTLV-1/2 prevalence in pregnant women is high in Rio de Janeiro , however there were no local studies addressing the rate of adverse pregnancy outcomes ( APO ) and MTC transmissio...	[ "HTLV-1/2 are retroviruses transmitted by sex , blood products and from mother to child ( MTC ) , mainly through breastfeeding .", "There is currently no vaccine , treatment or cure .", "Although it’s mostly asymptomatic it can cause disabling and even lethal diseases in carriers .", "The prevalence of HTLV-1...	2019
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "action potentials", "diagnostic radiology", "functional magnetic resonance imaging", "membrane potential", "brain", "electrophysiology", "neuroscience", "magnetic resonance imaging", "simulation and modeling", "brain mapping", "electrocorticography", "neurona...	Neuronal synchrony and the relation between the blood-oxygen-level dependent response and the local field potential	journal.pbio.2001461	null	[ [ "Most measurements of activity in the living human brain arise from the responses of large populations of neurons , spanning the millimeter scale of functional magnetic resonance imaging ( fMRI ) and electrocorticography ( ECoG ) to the centimeter scale of electro- and magneto-encephalography ( EEG and MEG ) ...	[ "The most widespread measures of human brain activity are the blood-oxygen-level dependent ( BOLD ) signal and surface field potential .", "Prior studies report a variety of relationships between these signals .", "To develop an understanding of how to interpret these signals and the relationship between them ,...	[ "There are several methods for measuring activity in the living human brain .", "Here , we studied functional magnetic resonance imaging ( fMRI ) , which depends on the vascular response to neuronal activity , and surface field potentials , which measure electrical activity from many neurons .", "These two wide...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "acoustics", "medicine and health sciences", "neurochemistry", "body fluids", "classical mechanics", "fluid mechanics", "radii", "mechanical stress", "geometry", "neuroscience", "muscle contraction", "mathematics", "algebra", "sound pressure", "lymph", "muscle physiology", "neurochem...	Synchronization and Random Triggering of Lymphatic Vessel Contractions	journal.pcbi.1005231	null	[ [ "To maintain fluid homeostasis , interstitial fluid drains into the lymphatic system through initial lymphatic vessels that carry it to the collecting lymphatic vessels .", "The collecting lymphatic vessels transport the fluid ( known as lymph ) both passively and actively to lymph nodes and back to the s...	[ "The lymphatic system is responsible for transporting interstitial fluid back to the bloodstream , but unlike the cardiovascular system , lacks a centralized pump-the heart–to drive flow .", "Instead , each collecting lymphatic vessel can individually contract and dilate producing unidirectional flow enforced by ...	[ "For decades , cardiovascular physiology has been an area of intense research , and we have a fundamental understanding of the mechanisms the heart uses to drive blood flow through the distributed network of vessels in the body .", "The lymphatic system is now receiving similar attention as more is learned about ...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The Orphan Gene dauerless Regulates Dauer Development and Intraspecific Competition in Nematodes by Copy Number Variation	journal.pgen.1005146	null	[ [ "Phenotypic ( developmental ) plasticity describes the ability of an individual organism to develop distinct phenotypes from the same genotype .", "Besides numerous examples in plants and insects , nematode dauer development represents one key example of phenotypic plasticity ( Fig 1 ) [1] .", "The ne...	[ "Many nematodes form dauer larvae when exposed to unfavorable conditions , representing an example of phenotypic plasticity and a major survival and dispersal strategy .", "In Caenorhabditis elegans , the regulation of dauer induction is a model for pheromone , insulin , and steroid-hormone signaling .", "Recen...	[ "The nematode dauer stage represents the major survival and dispersal strategy , and had a remarkable impact in the evolutionary and ecological success of nematodes .", "Our recent work in Pristionchus pacificus revealed substantial natural variation in various aspects of dauer development , i . e . pheromone pro...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "biogeography", "ecology and environmental sciences", "medicine and health sciences", "parasite evolution", "population genetics", "parasitic diseases", "parasitic protozoans", "parasitology", "protozoans", "forms of dna", "dna", "population biology", "research and analysis methods", "sequ...	New insights into Trypanosoma cruzi evolution, genotyping and molecular diagnostics from satellite DNA sequence analysis	journal.pntd.0006139	null	[ [ "Trypanosoma cruzi , the causative agent of Chagas disease , has been subdivided into seven Discrete Typing Units ( DTUs ) , TcI-TcVI and Tcbat , which have been associated with different geographic distribution and transmission cycles [1–4] .", "Historically , the genetic diversity displayed by T . cruzi...	[ "Trypanosoma cruzi has been subdivided into seven Discrete Typing Units ( DTUs ) , TcI-TcVI and Tcbat .", "Two major evolutionary models have been proposed to explain the origin of hybrid lineages , but while it is widely accepted that TcV and TcVI are the result of genetic exchange between TcII and TcIII strains...	[ "Trypanosoma cruzi , the causative agent of Chagas disease , is a genetically complex protozoan parasite .", "T . cruzi strains have been classified into seven Discrete Typing Units ( DTUs ) , TcI-TcVI and Tcbat , which have been associated with different geographic distribution and transmission cycles .", "Two...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious disease epidemiology", "epidemiology" ]	Epidemiology of Visceral Leishmaniasis in Georgia	journal.pntd.0002725	null	[ [ "In recent years reports have emerged of increased leishmaniasis transmission in Europe [1] , drug resistant leishmaniasis has spread further [2] , and the spread of HIV/leishmaniasis co-infection is a trend of particular concern [3] , [4] .", "Visceral Leishmaniasis ( VL ) is mainly caused by two species...	[ "This study investigated the transmission and prevalence of Leishmania parasite infection of humans in two foci of Visceral Leishmaniasis ( VL ) in Georgia , the well known focus in Tbilisi in the East , and in Kutaisi , a new focus in the West of the country .", "The seroprevalence of canine leishmaniasis was in...	[ "Leishmaniasis is a disease complex of various clinical manifestations caused by infection with protozoan parasites ( Leishmania spp ) .", "It is transmitted through the bite of infected sand flies ( Phlebotomus or Lutzomyia spp ) and dogs are the main reservoir host for the Leishmania infantum species described ...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "viral immune evasion", "virology", "biology", "microbiology" ]	Early Low-Titer Neutralizing Antibodies Impede HIV-1 Replication and Select for Virus Escape	journal.ppat.1002721	null	[ [ "Much of what is known about virus-host interactions underlying HIV-1 persistence and pathogenesis in humans has come from quantitative measurements and mathematical modeling of viral replication dynamics and virus evolution in response to selective pressures , including antiretroviral drug therapy and adapti...	[ "Single genome sequencing of early HIV-1 genomes provides a sensitive , dynamic assessment of virus evolution and insight into the earliest anti-viral immune responses in vivo .", "By using this approach , together with deep sequencing , site-directed mutagenesis , antibody adsorptions and virus-entry assays , we...	[ "Characterizing early adaptive immune responses to HIV-1 can inform studies of virus persistence , pathogenesis and natural history and can guide rational vaccine design .", "Previous studies examined the role of neutralizing antibodies ( Nab ) in acute and chronic HIV-1 infection but not against the precise enve...	2012
[ "Introduction", "Models", "Results", "Discussion" ]	[]	Neural Sequence Generation Using Spatiotemporal Patterns of Inhibition	journal.pcbi.1004581	null	[ [ "From the kingfisher’s dive to the performance of a piano concerto , sequences of stereotyped actions are central to the everyday lives of humans and animals .", "One of the most well-studied behavioral sequences in nature is birdsong , and the physiology underlying HVC ( the songbird analogue of mammalia...	[ "Stereotyped sequences of neural activity are thought to underlie reproducible behaviors and cognitive processes ranging from memory recall to arm movement .", "One of the most prominent theoretical models of neural sequence generation is the synfire chain , in which pulses of synchronized spiking activity propag...	[ "Sequences of stereotyped actions are central to the everyday lives of humans and animals .", "It was hypothesized over half a century ago that these behaviors were enabled by linking together groups of neurons ( or “cell assemblies” ) into a feedforward chain using correlation-based learning rules .", "These c...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biophysics/theory and simulation", "cell biology/membranes and sorting", "diabetes and endocrinology/obesity", "computational biology/metabolic networks", "computational biology/molecular dynamics", "computational biology/systems biology" ]	Association of Lipidome Remodeling in the Adipocyte Membrane with Acquired Obesity in Humans	journal.pbio.1000623	The authors describe a new approach to studying cellular lipid profiles and propose a compensatory mechanism that may help maintain the normal membrane function of adipocytes in the context of obesity.	[ [ "Obesity is characterized by excess body fat , which is predominantly stored in the", "adipose tissue .", "Obesity is considered one of the pathological features of metabolic", "syndrome ( MetS ) , which also includes insulin resistance , hypertension , and", "dyslipidemia [1] .", "Althoug...	[ "Identification of early mechanisms that may lead from obesity towards", "complications such as metabolic syndrome is of great interest .", "Here we performed", "lipidomic analyses of adipose tissue in twin pairs discordant for obesity but", "still metabolically compensated .", "In parallel we studied mor...	[ "Obesity is characterized by excess body fat , which is predominantly stored in the", "adipose tissue .", "When adipose tissue expands too much it stops storing lipid", "appropriately .", "The excess lipid accumulates in organs such as muscle , liver , and", "pancreas , causing metabolic disease .", "In...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "bacteriology", "microbiology", "host-pathogen interaction", "animal models", "caenorhabditis elegans", "prokaryotic models", "model organisms", "microbial evolution", "bacterial pathogens", "microbial pathogens", "biology", "pathogenesis", "gram negative", "genetic screens", "genetics",...	Genome-Wide Identification of Pseudomonas aeruginosa Virulence-Related Genes Using a Caenorhabditis elegans Infection Model	journal.ppat.1002813	null	[ [ "Pseudomonas aeruginosa , an opportunistic Gram-negative human pathogen , is one of the leading causes of hospital-acquired infections .", "In the context of a breakdown in host defenses , it is capable of infecting a plethora of tissue types , causing both acute and chronic infections .", "Burn victi...	[ "Pseudomonas aeruginosa strain PA14 is an opportunistic human pathogen capable of infecting a wide range of organisms including the nematode Caenorhabditis elegans .", "We used a non-redundant transposon mutant library consisting of 5 , 850 clones corresponding to 75% of the total and approximately 80% of the non...	[ "Pseudomonas aeruginosa is an opportunistic human pathogen that can also infect a wide range of model organisms , including the nematode Caenorhabditis elegans .", "To identify P . aeruginosa genes that play key roles in the pathogenic process , we performed a screen for mutants that exhibited reduced ability to ...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Activation of the Cph1-Dependent MAP Kinase Signaling Pathway Induces White-Opaque Switching in Candida albicans	journal.ppat.1003696	null	[ [ "The yeast Candida albicans is a member of the microbiota in the gastrointestinal and genitourinary tracts of most healthy persons , but it can also cause superficial as well as life-threatening systemic infections when host defenses are compromised .", "Morphological transitions play a major role in the ...	[ "Depending on the environmental conditions , the pathogenic yeast Candida albicans can undergo different developmental programs , which are controlled by dedicated transcription factors and upstream signaling pathways .", "C . albicans strains that are homozygous at the mating type locus can switch from the norma...	[ "The pathogenic yeast Candida albicans can switch from the white yeast form to the mating-competent opaque form .", "Opaque cells are less virulent than white cells , but they can avoid recognition by phagocytes , indicating that white-opaque switching has evolved as an adaptation mechanism of C . albicans to spe...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infographics", "medicine and health sciences", "genetic networks", "breast tumors", "cancers and neoplasms", "random variables", "covariance", "oncology", "mathematics", "pharmaceutics", "network analysis", "genome analysis", "pharmacology", "computer and information sciences", "gene ex...	Pathway-Based Genomics Prediction using Generalized Elastic Net	journal.pcbi.1004790	null	[ [ "Previous approaches that combine gene interaction data with genomic features can be roughly divided into three categories .", "The first category focuses on feature modification , with the most popular approach being dimensionality reduction by grouping genes together according to functional categories ....	[ "We present a novel regularization scheme called The Generalized Elastic Net ( GELnet ) that incorporates gene pathway information into feature selection .", "The proposed formulation is applicable to a wide variety of problems in which the interpretation of predictive features using known molecular interactions ...	[ "The low costs of sequencing and other high-throughput technologies have made available large amounts of data to address molecular biology problems .", "However , often this means thousands of measurements , for example on gene expression , are assayed for a much smaller number of samples .", "The imbalance com...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "nuclear staining", "pathology and laboratory medicine", "pathogens", "immunology", "microbiology", "light microscopy", "viruses", "rna viruses", "immunoprecipitation", "microscopy", "confocal microscopy", "stat proteins", "research and analysis methods", ...	HCV and flaviviruses hijack cellular mechanisms for nuclear STAT2 degradation: Up-regulation of PDLIM2 suppresses the innate immune response	journal.ppat.1007949	null	[ [ "Host cells sense the presence of an infecting virus using pathogen pattern recognition receptors which initiate signaling pathways that converge on the activation of NF-κB and the IRF family of transcription factors leading to the production and secretion of cytokines , type I ( IFNα and IFNβ ) and type III ...	[ "Host encounters with viruses lead to an innate immune response that must be rapid and broadly targeted but also tightly regulated to avoid the detrimental effects of unregulated interferon expression .", "Viral stimulation of host negative regulatory mechanisms is an alternate method of suppressing the host inna...	[ "The response of cells to an invading pathogen must be swift and well controlled because of the detrimental effects of chronic inflammation .", "However , viruses often hijack host control mechanisms .", "HCV and flaviviruses are known to suppress the innate immune response in cells by a variety of mechanisms ....	2019
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "genetics and genomics/population genetics", "genetics and genomics/gene expression" ]	Effects of cis and trans Genetic Ancestry on Gene Expression in African Americans	journal.pgen.1000294	null	[ [ "Admixed populations are uniquely useful for analyzing the genetic contribution to phenotypic differences among humans .", "Phenotypic differences that are observed among human populations may have systematic non-genetic causes , such as differences in environment [1] , [2] .", "However , in an admixe...	[ "Variation in gene expression is a fundamental aspect of human phenotypic variation .", "Several recent studies have analyzed gene expression levels in populations of different continental ancestry and reported population differences at a large number of genes .", "However , these differences could largely be d...	[ "Variation in gene expression is a fundamental aspect of human phenotypic variation , and understanding how this variation is apportioned among human populations is an important aim .", "Previous studies have compared gene expression levels between distinct populations , but it is unclear whether the differences ...	2008
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "physics", "general physics", "computational neuroscience", "interdisciplinary physics", "biology", "computational biology", "sensory systems" ]	Coordinated Optimization of Visual Cortical Maps (II) Numerical Studies	journal.pcbi.1002756	null	[ [ "In the primary visual cortex of primates and carnivores , functional architecture can be characterized by maps of various stimulus features such as orientation preference ( OP ) , ocular dominance ( OD ) , spatial frequency , or direction preference [1]–[21] .", "Many attempts have been made to explain a...	[ "In the juvenile brain , the synaptic architecture of the visual cortex remains in a state of flux for months after the natural onset of vision and the initial emergence of feature selectivity in visual cortical neurons .", "It is an attractive hypothesis that visual cortical architecture is shaped during this ex...	[ "Neurons in the visual cortex of carnivores , primates and their close relatives form spatial representations or maps of multiple stimulus features .", "In part ( I ) of this study we theoretically predicted maps that are optima of a variety of optimization principles .", "When analyzing the joint optimization ...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "animal models", "model organisms", "biology", "microbiology", "bacterial pathogens", "pathogenesis" ]	InlA Promotes Dissemination of Listeria monocytogenes to the Mesenteric Lymph Nodes during Food Borne Infection of Mice	journal.ppat.1003015	null	[ [ "L . monocytogenes are facultative intracellular bacteria that cause food borne disease in humans ranging in severity from mild , self-limiting gastroenteritis to life-threatening sepsis and meningoencephalitis [1]–[3] .", "The factors that determine host resistance to intestinal infection and subsequent ...	[ "Intestinal Listeria monocytogenes infection is not efficient in mice and this has been attributed to a low affinity interaction between the bacterial surface protein InlA and E-cadherin on murine intestinal epithelial cells .", "Previous studies using either transgenic mice expressing human E-cadherin or mouse-a...	[ "Ingestion of Listeria monocytogenes-contaminated food can be life-threatening for immune compromised individuals , can cause severe gastroenteritis in otherwise healthy people , and is also thought to occur frequently with little consequence .", "The factors that determine susceptibility to this infection are un...	2012
[ "Introduction", "Results/Discussion", "Methods" ]	[ "evolutionary biology", "genetics and genomics/population genetics", "evolutionary biology/animal genetics", "evolutionary biology/evolutionary ecology" ]	Genetic Tests for Ecological and Allopatric Speciation in Anoles on an Island Archipelago	journal.pgen.1000929	null	[ [ "Speciation generates biodiversity and is therefore a key process in evolution and ecology , and the relative importance of factors contributing to speciation in sexually reproducing animals , such as genetic drift in spatial isolation , natural selection , sexual selection and mutation-order , remains an act...	[ "From Darwin's study of the Galapagos and Wallace's study of Indonesia , islands have played an important role in evolutionary investigations , and radiations within archipelagos are readily interpreted as supporting the conventional view of allopatric speciation .", "Even during the ongoing paradigm shift toward...	[ "Over the last 150 years , since Darwin's study of islands and his “Origin of Species , ” island archipelagos have played a central role in the understanding of evolution and how species multiply ( speciation ) .", "Islands epitomise the conventional view of geographic ( allopatric ) speciation , where genomes di...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases", "veterinary diseases", "zoonoses", "medicine and health sciences", "neurology", "neurodegenerative diseases", "biology and life sciences", "veterinary science", "prion diseases" ]	Sialylation of Prion Protein Controls the Rate of Prion Amplification, the Cross-Species Barrier, the Ratio of PrPSc Glycoform and Prion Infectivity	journal.ppat.1004366	null	[ [ "Prion disease is a family of lethal , neurodegenerative maladies that can be sporadic , inheritable or transmissible in origin [1] .", "The key molecular event underlying prion diseases involves conformational change of the normal , cellular form of the prion protein denoted PrPC into the disease-associa...	[ "The central event underlying prion diseases involves conformational change of the cellular form of the prion protein ( PrPC ) into the disease-associated , transmissible form ( PrPSc ) .", "PrPC is a sialoglycoprotein that contains two conserved N-glycosylation sites .", "Among the key parameters that control ...	[ "The central event underlying prion diseases involves conformational change of the cellular form of the prion protein ( PrPC ) into disease-associated , transmissible form ( PrPSc ) .", "The amino acid sequence of PrPC and strain-specific structure of PrPSc are among the key parameters that control prion replicat...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "meiosis", "chromosome structure and function", "microbiology", "mitosis", "model organisms", "cell division", "tetrahymena thermophila", "chromosome biology", "protozoan models", "biology", "cell biology", "cytogenetic techniques", "genetics", "molecular cell biology", "cytogenetics", ...	A Single Cohesin Complex Performs Mitotic and Meiotic Functions in the Protist Tetrahymena	journal.pgen.1003418	null	[ [ "Cohesin is a ring-shaped protein complex which holds sister chromatids together to prevent their untimely separation prior to anaphase ( see [1] ) .", "It consists of four core components , Smc1 and Smc3 , Scc3 , and a member of the conserved α-kleisin family of proteins , Mdc1/Rad21/Scc1 in mitotic cell...	[ "The cohesion of sister chromatids in the interval between chromosome replication and anaphase is important for preventing the precocious separation , and hence nondisjunction , of chromatids .", "Cohesion is accomplished by a ring-shaped protein complex , cohesin; and its release at anaphase occurs when separase...	[ "During cell division , identical DNA molecules , packaged in the sister chromatids of a chromosome , must be distributed to daughter cells .", "The cohesion of sister chromatids in the interval between DNA replication and mitotic anaphase is important for preventing the precocious separation , and hence nondisju...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Power Laws for Heavy-Tailed Distributions: Modeling Allele and Haplotype Diversity for the National Marrow Donor Program	journal.pcbi.1004204	null	[ [ "Allele and Haplotype diversity are fundamental properties in the domain of population genetics for describing the general characteristics of any population of diploid organisms .", "In the context of hematopoietic stem cell transplant ( HSCT ) matching , proper estimates of allele and haplotype diversity...	[ "Measures of allele and haplotype diversity , which are fundamental properties in population genetics , often follow heavy tailed distributions .", "These measures are of particular interest in the field of hematopoietic stem cell transplant ( HSCT ) .", "Donor/Recipient suitability for HSCT is determined by Hu...	[ "The distribution of haplotypes and species tend to be heavy tailed .", "The heavy tail is expected from theoretical considerations and is observed in most populations .", "Accurate measures of diversity are difficult to achieve given that a limited number of common haplotypes represent the majority of the popu...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion", "Conclusion" ]	[ "public health and epidemiology/infectious diseases", "public health and epidemiology/environmental health" ]	Family Relationship, Water Contact and Occurrence of Buruli Ulcer in Benin	journal.pntd.0000746	null	[ [ "Mycobacterium ulcerans disease , commonly named Buruli Ulcer ( BU ) , is the most common mycobacterial disease in the world after leprosy and tuberculosis .", "This emerging disease has been reported in more than 30 countries in Africa , Latin America , Oceania and Asia [1] causing immense human sufferin...	[ "Mycobacterium ulcerans disease ( Buruli ulcer ) is the most widespread mycobacterial disease in the world after leprosy and tuberculosis .", "How M . ulcerans is introduced into the skin of humans remains unclear , but it appears that individuals living in the same environment may have different susceptibilities...	[ "Mycobacterium ulcerans disease ( Buruli ulcer ) is the most widespread mycobacterial disease in the world after leprosy and tuberculosis .", "How M . ulcerans is introduced into the skin of humans remains unclear , but it appears that individuals living in the same environment may have different susceptibilities...	2010
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "complement system", "medicine and health sciences", "gut bacteria", "toxins", "pathology and laboratory medicine", "immune physiology", "gene regulation", "pathogens", "immunology", "toxicology", "toxic agents", "regulator genes", "gene types", "infectious disease control", "bacteria", ...	CdtR Regulates TcdA and TcdB Production in Clostridium difficile	journal.ppat.1005758	null	[ [ "C . difficile antibiotic-associated diarrhoea is a toxin mediated disease [1 , 2] .", "During infection , TcdA , TcdB and CDT are secreted into the colonic epithelium by this bacterium , leading to diarrhoea that can progress to serious , life threatening inflammatory diseases , including pseudomembranou...	[ "Clostridium difficile is a global health burden and the leading cause of antibiotic-associated diarrhoea worldwide , causing severe gastrointestinal disease and death .", "Three well characterised toxins are encoded by this bacterium in two genetic loci , specifically , TcdB ( toxin B ) and TcdA ( toxin A ) in t...	[ "Clostridium difficile is the leading cause of antibiotic-associated diarrhoea .", "The TcdB , TcdA and binary toxins produced by C . difficile are encoded in two genomically distinct loci: TcdB and TcdA in the Pathogenicity Locus ( PaLoc ) and binary toxin ( CDT ) in the CDT locus ( CdtLoc ) .", "Toxin product...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	A Genetic Approach to the Recruitment of PRC2 at the HoxD Locus	journal.pgen.1003951	null	[ [ "Polycomb group ( PcG ) proteins are essential for proper development of most eukaryotic organisms .", "The founding member ( Polycomb ) was characterized genetically as a repressor of Drosophila homeotic genes [1] and subsequent studies have established these proteins as key organizers of the epigenome (...	[ "Polycomb group ( PcG ) proteins are essential for the repression of key factors during early development .", "In Drosophila , the polycomb repressive complexes ( PRC ) associate with defined polycomb response DNA elements ( PREs ) .", "In mammals , however , the mechanisms underlying polycomb recruitment at ta...	[ "Hox genes are essential for the proper organization of structures along the developing vertebrate body axis .", "These genes must be activated at a precise time and their premature transcription is deleterious to the organism .", "Early on , Hox gene clusters are covered by Polycomb Repressive protein Complexe...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Salmonella Modulation of Host Cell Gene Expression Promotes Its Intracellular Growth	journal.ppat.1003668	null	[ [ "Bacterial pathogens that have sustained long-standing associations with their hosts have developed complex functional interfaces shaped by the concerted activities of molecules from the host and the pathogen [1]–[4] .", "For many pathogens , this functional interface is largely dependent on the activity ...	[ "Salmonella Typhimurium has evolved a complex functional interface with its host cell largely determined by two type III secretion systems ( T3SS ) , which through the delivery of bacterial effector proteins modulate a variety of cellular processes .", "We show here that Salmonella Typhimurium infection of epithe...	[ "Essential for the ability of Salmonella Typhimurium to cause disease is the function of a type III secretion system ( T3SS ) encoded within its pathogenicity island 1 ( SPI-1 ) , which through the delivery of bacterial effector proteins modulates a variety of cellular functions .", "This study reports that the i...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biology", "computational biology", "metabolic networks" ]	Identification of Biochemical Network Modules Based on Shortest Retroactive Distances	journal.pcbi.1002262	null	[ [ "Hierarchical modularity has emerged as an organizational principle of biochemical networks , where larger less cohesive clusters of network components ( e . g . metabolic enzymes or signaling molecules ) comprise functionally distinct sub-clusters [1] , [2] .", "For example , Ihmels and coworkers analyze...	[ "Modularity analysis offers a route to better understand the organization of cellular biochemical networks as well as to derive practically useful , simplified models of these complex systems .", "While there is general agreement regarding the qualitative properties of a biochemical module , there is no clear con...	[ "Mathematical models are powerful tools to understand and predict the behavior of complex systems .", "However , the complexity presents many challenges in developing such models .", "In the case of a biological cell , a fully detailed and comprehensive model of a major function such as signaling and metabolism...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "prokaryotic models", "model organisms", "rna processing", "gene expression", "genetics", "bacillus subtilis", "biology", "microbiology", "microbial growth and development", "genetics and genomics", "rna stability" ]	Global Regulatory Functions of the Staphylococcus aureus Endoribonuclease III in Gene Expression	journal.pgen.1002782	null	[ [ "Bacteria are highly adaptive organisms that are able to rapidly alter their gene expression in response to environmental changes .", "In addition to transcriptional control , regulation of RNA decay has emerged as a major pathway in fast adaptive processes .", "Changes in RNA turnover facilitate stre...	[ "RNA turnover plays an important role in both virulence and adaptation to stress in the Gram-positive human pathogen Staphylococcus aureus .", "However , the molecular players and mechanisms involved in these processes are poorly understood .", "Here , we explored the functions of S . aureus endoribonuclease II...	[ "Control of mRNA stability is crucial for bacteria to survive and rapidly adapt to environmental changes and stress conditions .", "The molecular players and the degradation pathways involved in these adaptive processes are poorly understood in Staphylococcus aureus .", "The universally conserved double-strand-...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "blood cells", "phosphorylation", "cell death", "medicine and health sciences", "immune cells", "immunology", "cell processes", "microbiology", "messenger rna", "parasitic diseases", "parasitic protozoans", "protozoan life cycles", "developmental biology", "protozoans", "leishmania", "...	Leishmania donovani induced Unfolded Protein Response delays host cell apoptosis in PERK dependent manner	journal.pntd.0006646	null	[ [ "Leishmania ability to defy the host immune response is a major cause for persistence of Leishmaniasis .", "Parasite modulates host in various aspects and hampers the activation of adaptive immune responses against infection [1] .", "Expression of LPG on parasite surface and TLR 2 modulates the host i...	[ "Endoplasmic reticulum ( ER ) stress generated unfolded stress response ( UPR ) is a basic survival mechanism which protects cell under unfavourable conditions .", "Leishmania parasite modulates host macrophages in various ways to ensure its survival .", "Modulation of PI3K-Akt pathway in delayed apoptotic indu...	[ "Visceral Leishmaniasis or Kala-azar is one of the severe tropical neglected parasitic diseases caused by Leishmania donovani in Indian subcontinent .", "Modulation of host in terms of delayed apoptotic induction is one of the aspects which favours disease establishment; however the mechanism is not clearly under...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biophysics", "biochemistry", "biology" ]	Structural Insights Into DNA Repair by RNase T—An Exonuclease Processing 3′ End of Structured DNA in Repair Pathways	journal.pbio.1001803	Structure analysis of the exonuclease RNase T reveals that it also functions in DNA repair pathways where it binds and processes bulge, bubble, and Y-structured DNA to trim the DNA 3′ ends.	[ [ "It is well known that DNA repair mechanisms maintain genomic integrity and are essential for cell survival .", "Damaged DNA can be restored by a variety of DNA repair processes , such as direct reversal , base excision , nucleotide excision , mismatch , and recombination repair pathways [1] .", "Alth...	[ "DNA repair mechanisms are essential for preservation of genome integrity .", "However , it is not clear how DNA are selected and processed at broken ends by exonucleases during repair pathways .", "Here we show that the DnaQ-like exonuclease RNase T is critical for Escherichia coli resistance to various DNA-da...	[ "DNA repair relies on various enzymes , including exonucleases that bind and trim DNA at broken ends .", "However , we know little about how an exonuclease precisely selects and trims a DNA broken end in specific repair pathways .", "In this study , the enzyme RNase T , previously known for its involvement in p...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/gene function", "neuroscience/neuronal signaling mechanisms" ]	Macoilin, a Conserved Nervous System–Specific ER Membrane Protein That Regulates Neuronal Excitability	journal.pgen.1001341	null	[ [ "One of the most striking innovations in Metazoa is a nervous system with specialized nerve cells , pre- and post-synaptic structures , and associated signaling molecules .", "Neuronal signaling depends on complexes of multipass transmembrane proteins such as ion channels and G-protein-coupled receptors ....	[ "Genome sequence comparisons have highlighted many novel gene families that are conserved across animal phyla but whose biological function is unknown .", "Here , we functionally characterize a member of one such family , the macoilins .", "Macoilins are characterized by several highly conserved predicted trans...	[ "The human genome project has given us a catalog of the genes that make a human; however , the function of about 40% of these genes remains elusive .", "Many of these mysterious genes have relatives in simpler organisms like worms and flies , where their function can be studied much more easily than in a mammal ....	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "hematologic cancers and related disorders", "developmental biology", "leukemias", "medicine and health sciences", "cancer genetics", "hematopoietic stem cells", "lymphoblastic leukemia", "stem cells", "animal cells", "cell biology", "genetics", "biology and life sciences", "cellular types",...	SCL, LMO1 and Notch1 Reprogram Thymocytes into Self-Renewing Cells	journal.pgen.1004768	null	[ [ "An important attribute of stem cell populations is the capacity to self-renew indefinitely both in normal development and during the process of cell transformation .", "Cancer stem cells , initially identified in acute myeloblastic leukemias [1] , can self-renew indefinitely to propagate and maintain the...	[ "The molecular determinants that render specific populations of normal cells susceptible to oncogenic reprogramming into self-renewing cancer stem cells are poorly understood .", "Here , we exploit T-cell acute lymphoblastic leukemia ( T-ALL ) as a model to define the critical initiating events in this disease ."...	[ "Deciphering the initiating events in lymphoid leukemia is important for the development of new therapeutic strategies .", "In this manuscript , we define oncogenic reprogramming as the process through which non-self-renewing progenitors are converted into pre-leukemic stem cells with sustained self-renewal capac...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biotechnology", "nucleocapsid", "viral classification", "plant biology", "macromolecular assemblies", "microbiology", "viral structure", "chemical biology", "plant science", "rna viruses", "viruslike particles", "crops", "protein structure", "viral core", "proteins", "cryobiology", ...	Three-dimensional Structure of Victorivirus HvV190S Suggests Coat Proteins in Most Totiviruses Share a Conserved Core	journal.ppat.1003225	null	[ [ "The encapsidated , double-stranded ( ds ) RNA viruses infect a wide range of hosts including bacteria , plants , fungi , insects , and humans and other vertebrates [1] , [2] .", "Viruses that infect and replicate in fungi ( mycoviruses ) have no known natural vectors and are spread vertically or horizont...	[ "Double-stranded ( ds ) RNA fungal viruses are currently assigned to six different families .", "Those from the family Totiviridae are characterized by nonsegmented genomes and single-layer capsids , 300–450 Å in diameter .", "Helminthosporium victoriae virus 190S ( HvV190S ) , prototype of recently recognized ...	[ "Of the known dsRNA fungal viruses , the best characterized is Saccharomyces cerevisiae virus L-A ( ScV-L-A ) , prototype of the genus Totivirus , family Totiviridae .", "Until the current study , there have been no subnanometer structures of dsRNA fungal viruses from the genus Victorivirus , which is the largest...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Reconstructible Phylogenetic Networks: Do Not Distinguish the Indistinguishable	journal.pcbi.1004135	null	[ [ "As an example , consider again networks N1 and N2 in Fig . 1 , which display the same trees 𝓣 ( N ) = {T1 , T2 , T3} .", "( In the following , 𝓣 ( N ) denotes the set of trees displayed by N .", ") By displaying the same trees , these networks display the same clades , the same triples , the same q...	[ "Phylogenetic networks represent the evolution of organisms that have undergone reticulate events , such as recombination , hybrid speciation or lateral gene transfer .", "An important way to interpret a phylogenetic network is in terms of the trees it displays , which represent all the possible histories of the ...	[ "We consider here an elementary question for the inference of phylogenetic networks: what networks can be reconstructed .", "Indeed , whereas in theory it is always possible to reconstruct a phylogenetic tree , given sufficient data for this task , the same does not hold for phylogenetic networks: most notably , ...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Stochastic Modeling of Mouse Motor Activity under Deep Brain Stimulation: The Extraction of Arousal Information	journal.pcbi.1003883	null	[ [ "Deep Brain Stimulation is currently being used in the treatment of Parkinson’s Disease , Disorders of Consciousness ( DoC ) and clinical depression [1–3] .", "The possibility that Deep Brain Stimulation ( DBS ) could be used to enhance brain arousal is a subject of immense interest , e . g . , in traumat...	[ "In the present paper , we quantify , with a rigorous approach , the nature of motor activity in response to Deep Brain Stimulation ( DBS ) , in the mouse .", "DBS is currently being used in the treatment of a broad range of diseases , but its underlying principles are still unclear .", "Because mouse movement ...	[ "Brainstem and thalamic regulation of arousal has been studied experimentally since the mid 20-th century .", "Today , Deep Brain Stimulation ( DBS ) is used in the treatment of movement disorders , chronic pain , clinical depression , amongst others .", "At present , the proper choice of DBS parameters ( frequ...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "biotechnology", "genome-wide association studies", "ecology and environmental sciences", "quantitative trait loci", "plant physiology", "plant science", "rice", "genetically modified plants", "materials science", "experimental organism systems", "genome analysis", "trait locus analysis", "p...	Genetic control of the root system in rice under normal and drought stress conditions by genome-wide association study	journal.pgen.1006889	null	[ [ "Rice ( Oryza sativa L . ) is the staple food crop that feeds a large segment of the world’s population [1] .", "Owing to the climate change and shortage of freshwater , drought has been the most critical environmental stress influencing agriculture worldwide , particularly regarding the productivity of f...	[ "A variety of adverse conditions including drought stress severely affect rice production .", "Root system plays a critical role in drought avoidance , which is one of the major mechanisms of drought resistance .", "In this study , we adopted genome-wide association study ( GWAS ) to dissect the genetic basis c...	[ "Drought stress is a key environmental factor that severely reduces crop yield all over the world .", "The root system plays a critical role in the drought avoidance of crops , but the genetic basis of the root system in soil conditions has seldom been investigated in rice .", "We analyzed the genetic control o...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "biotechnology", "plant anatomy", "engineering and technology", "gene regulation", "hormones", "plant science", "rice", "plant hormones", "genetically modified plants", "experimental organism systems", "plants", "genetic engineering", "research and analysis methods", "bioengineering", "g...	SPOC domain-containing protein Leaf inclination3 interacts with LIP1 to regulate rice leaf inclination through auxin signaling	journal.pgen.1007829	null	[ [ "Rice is one of the most important crops in the world and breeding rice varieties with ideal architecture is a vital strategy for improvement of grain yields [1 , 2] .", "Leaf is the main organ for photosynthesis and its development is crucial for the yield potential .", "Leaf inclination indicates th...	[ "Leaf angle is an important agronomic trait and influences crop architecture and yield .", "Studies have demonstrated the roles of phytohormones , particularly auxin and brassinosteroids , and various factors in controlling leaf inclination .", "However , the underlying mechanism especially the upstream regulat...	[ "Leaf angle is a major trait of ideal architecture of crops that associates with photosynthetic efficiency and yields .", "Studies of the underlying mechanism will greatly help to improve the crop yield .", "Phytohormones especially auxin and brassinosteroids play crucial roles in regulating the leaf inclinatio...	2018
[ "Introduction", "Methods", "Results and discussion" ]	[ "schistosoma", "invertebrates", "schistosoma mansoni", "protein interactions", "helminths", "dna-binding proteins", "animals", "fungi", "model organisms", "immunoprecipitation", "experimental organism systems", "molecular biology techniques", "co-immunoprecipitation", "research and analysi...	Analysis of the interactome of Schistosoma mansoni histone deacetylase 8	journal.pntd.0006089	null	[ [ "Schistosomiasis is a neglected tropical parasitic disease of major public health importance [1–3] caused by blood flukes of the Schistosoma spp .", ", with 258 million people requiring treatment worldwide , and 780 million at risk of infection ( http://www . who . int/mediacentre/factsheets/fs115/en/ ) ....	[ "Histone deacetylase 8 from Schistosoma mansoni ( SmHDAC8 ) is essential to parasite growth and development within the mammalian host and is under investigation as a target for the development of selective inhibitors as novel schistosomicidal drugs .", "Although some protein substrates and protein partners of hum...	[ "Using a target-based strategy to develop new drugs for the treatment of schistosomiasis we had earlier identified Schistosoma mansoni histone deacetylase 8 ( SmHDAC8 ) as essential for parasite development and survival in the mammalian host .", "Selective inhibitors of this enzyme show promise as lead compounds ...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "phosphorylation", "urology", "keratinocytes", "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "microbiology", "cell differentiation", "epithelial cells", "viruses", "developmental biology", "immunoprecipitation", "dna viruses", "sexually transmitted disea...	Post-Transcriptional Regulation of KLF4 by High-Risk Human Papillomaviruses Is Necessary for the Differentiation-Dependent Viral Life Cycle	journal.ppat.1005747	null	[ [ "The life cycle of human papillomaviruses is dependent upon host cell replication , differentiation and cellular gene expression [1 , 2] .", "HPVs infect stratified squamous epithelia through small wounds that expose basal cells to entry .", "Upon entry , viral genomes are maintained as low copy nucle...	[ "Human papillomaviruses ( HPVs ) are epithelial tropic viruses that link their productive life cycles to the differentiation of infected host keratinocytes .", "A subset of the over 200 HPV types , referred to as high-risk , are the causative agents of most anogenital malignancies .", "HPVs infect cells in the ...	[ "Viruses that induce persistent infections often alter the expression and activities of cellular transcription factors to regulate their productive life cycles .", "Human papillomaviruses ( HPVs ) are epithelial tropic viruses that link their productive life cycles to the differentiation of infected host keratino...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "amorphous solids", "medicine and health sciences", "health services research", "sociology", "geographical locations", "tropical diseases", "social sciences", "ebola hemorrhagic fever", "anthropology", "neuroscience", "glass", "herbs", "health care", "cognitive psychology", "drug licensi...	Preparing towards Preventing and Containing an Ebola Virus Disease Outbreak: What Socio-cultural Practices May Affect Containment Efforts in Ghana?	journal.pntd.0004852	null	[ [ "Ebola Virus Disease ( EVD ) is a condition with high infectivity and case fatality rate .", "The case fatality rate of the 2014 EVD epidemic was initially estimated as 70% at the beginning of the epidemic [1 , 2] .", "However , the case fatality declined with the establishment of treatment centres an...	[ "Ebola Virus Disease ( EVD ) is a condition with high fatality .", "Though the disease is deadly , taking precautions to reduce contact with infected people and their secretions can prevent cross- infection .", "In the 2014 EVD outbreak , socio-cultural factors were identified to be responsible for the spread o...	[ "The 2014 Ebola Virus Disease outbreak emerged as the most devastating outbreaks in recent history .", "This outbreak spread across continents with West Africa remaining the epicenter .", "Although , the three most affected countries have been declared Ebola free , the recent re-emergence of cases in Sierra Leo...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell death", "medicine and health sciences", "nervous system", "cell processes", "diet", "microglial cells", "physiological processes", "developmental biology", "nutrition", "homeostasis", "microscopy", "research and analysis methods", "animal cells", "gene expression", "scanning electr...	Proximal recolonization by self-renewing microglia re-establishes microglial homeostasis in the adult mouse brain	journal.pbio.3000134	null	[ [ "Microglia are resident parenchymal macrophages in the central nervous system ( CNS ) .", "Along with the perivascular , meningeal , and choroid plexus macrophages , these cells govern the innate immunity of the CNS [1] .", "Apart from their primary function in immune surveillance , microglia also per...	[ "Microglia are resident immune cells that play critical roles in maintaining the normal physiology of the central nervous system ( CNS ) .", "Remarkably , microglia have an intrinsic capacity to repopulate themselves after acute ablation .", "However , the underlying mechanisms that drive such restoration remai...	[ "Microglia are the brain’s primary immune sentinels .", "After being seeded in the central nervous system ( CNS ) during embryonic development , microglia form an evenly distributed grid-like population in the adult brain .", "In the adult , microglia have the remarkable ability to regenerate and restore their ...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "immunology/antigen processing and recognition", "immunology/immunity to infections", "computational biology" ]	T-Cell Epitope Prediction: Rescaling Can Mask Biological Variation between MHC Molecules	journal.pcbi.1000327	null	[ [ "In order to make the prediction values comparable between each MHC molecule , it is recommended that the MHC-peptide binding affinity scores are rescaled [28]; this is explicitly implemented in NetCTL .", "The method of rescaling involves obtaining the predicted binding affinities of 500 , 000 random nat...	[ "Theoretical methods for predicting CD8+ T-cell epitopes are an important tool in vaccine design and for enhancing our understanding of the cellular immune system .", "The most popular methods currently available produce binding affinity predictions across a range of MHC molecules .", "In comparing results betw...	[ "The use of prediction software has become an important tool in increasing our knowledge of infectious disease .", "It allows us to predict the interaction of molecules involved in an immune response , thereby significantly shortening the lengthy process of experimental elucidation .", "A high proportion of thi...	2009
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell cycle and cell division", "cell processes", "brassica", "bryology", "plant physiology", "notch signaling", "plant science", "model organisms", "experimental organism systems", "plants", "nonvascular plants", "arabidopsis thaliana", "research and analysis methods", "animal studies", ...	Control of proliferation in the haploid meristem by CLE peptide signaling in Marchantia polymorpha	journal.pgen.1007997	null	[ [ "Land plants have evolved unique peptide hormones to control various physiological processes including development and stress responses [1 , 2] .", "A notable example is CLE ( CLAVATA3/EMBRYO SURROUNDING REGION-related ) family peptides involved in various developmental contexts in flowering plants , such...	[ "The homeostasis of meristems in flowering plants is maintained by cell-to-cell communication via CLE ( CLAVATA3/EMBRYO SURROUNDING REGION-related ) peptide hormones .", "In contrast , cell signals that regulate meristem activity remains elusive in bryophytes that maintain apical meristems in the gametophyte ( ha...	[ "Land plants undergo an alternation of generations where both haploid and diploid phases develop multicellular bodies .", "Their growth relies on the activity of meristems at the growing tips of their bodies .", "Here we show a CLE peptide hormone acts as an intercellular signal controlling proliferative activi...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "humoral immunity", "medicine and health sciences", "pathology and laboratory medicine", "immunology", "microbiology", "animal models", "model organisms", "research and analysis methods", "animal models of infection", "inflammation", "viral immune evasion", "mouse models", "pathogenesis", ...	Rift Valley Fever Virus Encephalitis Is Associated with an Ineffective Systemic Immune Response and Activated T Cell Infiltration into the CNS in an Immunocompetent Mouse Model	journal.pntd.0002874	null	[ [ "Rift Valley fever virus ( RVFV ) is a zoonotic arbovirus that has serious public health , veterinary and economic impacts throughout Africa and the Arabian Peninsula .", "RVFV outbreaks are often triggered by periods of heavy rain and the subsequent emergence of RVFV-infected mosquitoes , and are charact...	[ "Rift Valley fever virus ( RVFV ) causes outbreaks of severe disease in livestock and humans throughout Africa and the Arabian Peninsula .", "In people , RVFV generally causes a self-limiting febrile illness but in a subset of individuals , it progresses to more serious disease .", "One manifestation is a delay...	[ "Rift Valley fever virus ( RVFV ) is a mosquito-borne virus that causes severe disease in people and livestock throughout Africa and the Arabian Peninsula .", "Human disease is usually self-limiting , but a small proportion of individuals develop fatal encephalitis .", "The role of the host immune response in d...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "acceleration", "ornithology", "medicine and health sciences", "ecology and environmental sciences", "dynamics", "classical mechanics", "bird flight", "vertebrates", "starlings", "biological locomotion", "animals", "flight (biology)", "animal anatomy", "zoology", "birds", "wings", "c...	Physics-based simulations of aerial attacks by peregrine falcons reveal that stooping at high speed maximizes catch success against agile prey	journal.pcbi.1006044	null	[ [ "The stoop is a remarkable attack strategy used by peregrine falcons Falco peregrinus , and a range of other raptors [1–4] .", "It involves a steep , controlled dive in which the attacker strikes its prey at high-speed with a massive blow in mid-air [1] .", "The high momentum of the attacker places it...	[ "The peregrine falcon Falco peregrinus is renowned for attacking its prey from high altitude in a fast controlled dive called a stoop .", "Many other raptors employ a similar mode of attack , but the functional benefits of stooping remain obscure .", "Here we investigate whether , when , and why stooping promot...	[ "Peregrine falcons are famed for their high-speed , high-altitude stoops .", "Hunting prey at perhaps the highest speed of any animal places a stooping falcon under extraordinary physical , physiological , and cognitive demands , yet it remains unknown how this behavioural strategy promotes catch success .", "B...	2018
[ "Introduction", "Materials and methods", "Results", "Discussion", "Conclusion" ]	[ "medicine and health sciences", "african trypanosomiasis", "variant genotypes", "tropical diseases", "geographical locations", "parasitic diseases", "parasitic protozoans", "genetic mapping", "protozoans", "neglected tropical diseases", "molecular genetics", "molecular biology techniques", "...	A polymorphism in the haptoglobin, haptoglobin related protein locus is associated with risk of human sleeping sickness within Cameroonian populations	journal.pntd.0005979	null	[ [ "The study was conducted in three active sleeping sickness foci of the forest region of Southern Cameroon ( Fig 1 ) .", "The Cameroonian population is made up of more than 240 ethnic groups that can be grouped into Bantu ( e . g . : Beti , Bassa , Bakundu , Maka , Douala , Pygmie ) , Semi Bantu ( e . g . ...	[ "Human African Trypanosomiasis ( HAT ) is a neglected disease targeted for elimination as a public health problem by 2020 .", "Elimination requires a better understanding of the epidemiology and clinical evolution of HAT .", "In addition to the classical clinical evolution of HAT , asymptomatic carriers and spo...	[ "Human African trypanosomiasis ( HAT ) or sleeping sickness is a neglected tropical disease targeted for elimination by 2020 .", "This elimination requires a better understanding of the epidemiology and clinical evolution of this disease .", "Beside the classical clinical evolution , asymptomatic carriers , ser...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "functional genomics", "cell biology", "chromosome biology", "viral persistence and latency", "virology", "viruses and cancer", "genetics", "biology and life sciences", "microbiology", "genomics" ]	LANA Binds to Multiple Active Viral and Cellular Promoters and Associates with the H3K4Methyltransferase hSET1 Complex	journal.ppat.1004240	null	[ [ "Eukaryotic DNA is packaged into chromatin which plays a central role in the regulation of all DNA processes including replication , transcription , and repair .", "Chromatin contains nucleosomes with DNA wrapped around the core histones H2A , H2B , H3 , and H4 .", "Nucleosomes carry epigenetic inform...	[ "Kaposi's sarcoma-associated herpesvirus ( KSHV ) is a γ-herpesvirus associated with KS and two lymphoproliferative diseases .", "Recent studies characterized epigenetic modification of KSHV episomes during latency and determined that latency-associated genes are associated with H3K4me3 while most lytic genes are...	[ "KSHV is a DNA tumor virus which is associated with Kaposi's sarcoma and some lymphoproliferative diseases .", "During latent infection , the viral genome persists as circular extrachromosomal DNA in the nucleus and expresses a very limited number of viral proteins , including LANA , a multi-functional protein ."...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	CXCL9 Contributes to Antimicrobial Protection of the Gut during Citrobacter rodentium Infection Independent of Chemokine-Receptor Signaling	journal.ppat.1004648	null	[ [ "The intestinal tract is a site of continuous interaction between host and microbe .", "Tight regulation of immune surveillance and activation maintains the integrity of this interface during non-infectious periods while preserving the ability to launch immediate action upon pathogen exposure .", "Che...	[ "Chemokines have been shown to be effective bactericidal molecules against a variety of bacteria and fungi in vitro .", "These direct antimicrobial effects are independent of their chemotactic activities involving immunological receptors .", "However , the direct biological role that these proteins may play in ...	[ "Host defense peptides are an essential part of the innate immune response to pathogens , particularly at mucosal surfaces .", "Some chemokines , previously known for their ability to recruit immune cells to a site of inflammation , have been identified to have direct antimicrobial activity in vitro against a var...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "mental health", "pharmacology", "drosophila", "neuroscience", "molecular biology", "genetics and genomics" ]	Drug-Induced Epigenetic Changes Produce Drug Tolerance	journal.pbio.0050265	Tolerance to solvents of abuse--at least inDrosophila--is due to epigenetic modification of theslo potassium channel gene.	[ [ "Drug tolerance can be defined as reduced responsiveness to an effect of a drug caused by prior exposure to the drug [1] .", "With regard to recreational drugs , tolerance can cause an increase in self-administration and thereby speed the user down the path to addiction and/or to overdose .", "Most or...	[ "Tolerance to drugs that affect neural activity is mediated , in part , by adaptive mechanisms that attempt to restore normal neural excitability .", "Changes in the expression of ion channel genes are thought to play an important role in these neural adaptations .", "The slo gene encodes the pore-forming subun...	[ "A startlingly large number of adolescents abuse organic solvent inhalants , common components of glues , paints , and cleaning solutions .", "Our focus is on the molecular basis of tolerance—reduced response to a drug over time—which promotes increased drug consumption and accelerates the process of addiction ."...	2007
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blastocysts", "cell physiology", "cell death", "medicine and health sciences", "gene regulation", "cell cycle and cell division", "regulatory proteins", "cell processes", "dna-binding proteins", "endocrine physiology", "cell polarity", "developmental biology", "growth factors", "transcrip...	Four simple rules that are sufficient to generate the mammalian blastocyst	journal.pbio.2000737	null	[ [ "At compaction , E2 . 5–E3 . 0 , the outer cells of the embryo become polarized , express the transcription factor Cdx2 , and differentiate into TE .", "At E3 . 0 , the apical membrane of outer cells expresses several proteins that have a known role in cell polarity [9–13] .", "The acquisition of pola...	[ "Early mammalian development is both highly regulative and self-organizing .", "It involves the interplay of cell position , predetermined gene regulatory networks , and environmental interactions to generate the physical arrangement of the blastocyst with precise timing .", "However , this process occurs in th...	[ "The first 4 . 5 days of mammalian embryo development proceeds without maternal information and is remarkably robust to perturbations .", "For example , if an early embryo is cut in half , it produces 2 perfectly patterned , smaller embryos .", "Where does the information guiding this development come from ?", ...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "biotechnology", "reverse transcriptase-polymerase chain reaction", "plant anatomy", "engineering and technology", "symbiosis", "root nodules", "cell signaling", "root hairs", "plant science", "genetically modified plants", "molecular biology techniques", "plants", "calcium signaling", "ge...	LACK OF SYMBIONT ACCOMMODATION controls intracellular symbiont accommodation in root nodule and arbuscular mycorrhizal symbiosis in Lotus japonicus	journal.pgen.1007865	null	[ [ "Legumes can establish a symbiotic association with nitrogen-fixing bacteria through the formation of symbiotic root nodules .", "Nodulation is initiated by the rhizobia-derived lipo-chitooligosaccharidic nodulation ( Nod ) factors that trigger transient increases in calcium influx levels accompanied with...	[ "Nitrogen-fixing rhizobia and arbuscular mycorrhizal fungi ( AMF ) form symbioses with plant roots and these are established by precise regulation of symbiont accommodation within host plant cells .", "In model legumes such as Lotus japonicus and Medicago truncatula , rhizobia enter into roots through an intracel...	[ "Symbiosis between plants and beneficial microbes such as nitrogen-fixing bacteria and arbuscular mycorrhizal fungi has enabled plant colonization of new environments .", "Root nodule symbiosis with nitrogen-fixing rhizobia enables sessile plants to survive in a nitrogen-deficient environment .", "To establish ...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "microbial metabolism", "mycology", "medical microbiology", "biology", "microbiology", "pathogenesis", "fungal physiology" ]	Regulation of Sulphur Assimilation Is Essential for Virulence and Affects Iron Homeostasis of the Human-Pathogenic Mould Aspergillus fumigatus	journal.ppat.1003573	null	[ [ "Aspergillus fumigatus is an opportunistic fungal pathogen that may cause invasive infections in immunocompromised patients .", "During the last decades the incidence rate of invasive pulmonary aspergillosis ( IPA ) , the most severe infection caused by this mould [1] , has dramatically increased which ma...	[ "Sulphur is an essential element that all pathogens have to absorb from their surroundings in order to grow inside their infected host .", "Despite its importance , the relevance of sulphur assimilation in fungal virulence is largely unexplored .", "Here we report a role of the bZIP transcription factor MetR in...	[ "Invasive pulmonary aspergillosis ( IPA ) is a life-threatening disease that affects primarily immunosuppressed patients .", "During the last decades the incidence of this disease that is accompanied by high mortality rates has increased .", "Since opportunistic pathogenic fungi , unlike other pathogens , do no...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "lipids", "microbial physiology", "proteins", "protein structure", "biology", "microbiology", "host-pathogen interaction", "bacterial pathogens" ]	Discovery of a Siderophore Export System Essential for Virulence of Mycobacterium tuberculosis	journal.ppat.1003120	null	[ [ "Iron is an essential micronutrient for most forms of life on earth because of its vital role as a redox cofactor of proteins required for critical cellular processes .", "Pathogenic bacteria have evolved an array of intricate mechanisms to scavenge limited iron from the host [1] .", "Mycobacterium tu...	[ "Iron is an essential nutrient for most bacterial pathogens , but is restricted by the host immune system .", "Mycobacterium tuberculosis ( Mtb ) utilizes two classes of small molecules , mycobactins and carboxymycobactins , to capture iron from the human host .", "Here , we show that an Mtb mutant lacking the ...	[ "In the late 19th century the French physician Armand Trousseau recognized that treating anemic tuberculosis patients with iron salts exacerbated the disease .", "In 1911 Twort postulated that mycobacteria produce an essential growth factor which was identified in 1953 as mycobactin .", "The hydrophobic mycobac...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "decision making", "japan", "geographical locations", "india", "neuroscience", "indonesia", "cognition", "infectious disease control", "infectious diseases", "epidemiology", "people and places", "infectious disease surveillance", "philippines", "asia", "...	Dengue Sentinel Traveler Surveillance: Monthly and Yearly Notification Trends among Japanese Travelers, 2006–2014	journal.pntd.0004924	null	[ [ "Dengue is a mosquito-borne febrile viral disease that is endemic in over 100 countries in tropical and subtropical regions with notifications increasing 30-fold over the last 50 years , affecting an estimated 100 million people annually [1–3] .", "Over these decades , it has become apparent that dengue s...	[ "Dengue is becoming an increasing threat to non-endemic countries .", "In Japan , the reported number of imported cases has been rising , and the first domestic dengue outbreak in nearly 70 years was confirmed in 2014 , highlighting the need for greater situational awareness and better-informed risk assessment ."...	[ "With increasing globalization , the threat of dengue is rising in areas that were previously unaffected .", "Japan has been experiencing a rise in notifications of imported cases , and in 2014 confirmed the first domestic outbreak in nearly 70 years .", "Such events prompted the country to more actively utiliz...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "skin infections", "leishmaniasis", "neglected tropical diseases" ]	Cytotoxic T Cells Mediate Pathology and Metastasis in Cutaneous Leishmaniasis	journal.ppat.1003504	null	[ [ "CD8+ T cells contribute to the control of pathogens by cytokine production , cytolytic activity or both .", "In the case of intracellular parasites , the production of IFN-γ by CD8+ T cells is protective , while in viral infections CD8+ T cells provide protection by inducing cytokine production and killi...	[ "Disease progression in response to infection can be strongly influenced by both pathogen burden and infection-induced immunopathology .", "While current therapeutics focus on augmenting protective immune responses , identifying therapeutics that reduce infection-induced immunopathology are clearly warranted .", ...	[ "Leishmaniasis is a parasitic disease where the host immune response plays an essential role in pathogenesis .", "However , the mechanisms promoting immunopathology in patients are still unclear .", "We performed gene expression profiling of skin lesions from cutaneous leishmaniasis patients and normal skin and...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "toxins", "pathology and laboratory medicine", "membrane potential", "tropical diseases", "electrophysiology", "toxic agents", "toxicology", "bacterial diseases", "neglected tropical diseases", "cellular structures and organelles", "thermodynamics", "infectiou...	Membrane perturbing properties of toxin mycolactone from Mycobacterium ulcerans	journal.pcbi.1005972	null	[ [ "Buruli ulcer ( BU ) is a cutaneous disease caused by Mycobacterium ulcerans .", "The presence of necrosis , which is accompanied by surprisingly little inflammation or pain , is considered the most characteristic clinical presentation of BU disease [1–3] .", "The macrolide exotoxin mycolactone , whic...	[ "Mycolactone is the exotoxin produced by Mycobacterium ulcerans and is the virulence factor behind the neglected tropical disease Buruli ulcer .", "The toxin has a broad spectrum of biological effects within the host organism , stemming from its interaction with at least two molecular targets and the inhibition o...	[ "Mycolactone is a macrolide exotoxin secreted by Mycobacterium ulcerans , which causes a skin disease called Buruli ulcer , a neglected emerging disease .", "It is the third most common mycobacterial disease after tuberculosis and leprosy .", "Studies have shown how mycolactone plays a pivotal role in Buruli ul...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Self-organization in Balanced State Networks by STDP and Homeostatic Plasticity	journal.pcbi.1004420	null	[ [ "Distributions of synaptic weights are known to have a large influence on the dynamics and information-processing properties of neural circuits [1–5] .", "Recent electrophysiological studies have shown that the distributions of the amplitudes of excitatory postsynaptic potentials ( EPSPs ) in cortical [6 ...	[ "Structural inhomogeneities in synaptic efficacies have a strong impact on population response dynamics of cortical networks and are believed to play an important role in their functioning .", "However , little is known about how such inhomogeneities could evolve by means of synaptic plasticity .", "Here we pre...	[ "It is widely believed that the structure of neuronal circuits plays a major role in brain functioning .", "Although the full synaptic connectivity for larger populations is not yet assessable even by current experimental techniques , available data show that neither synaptic strengths nor the number of synapses ...	2015
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "blood cells", "medicine and health sciences", "cellular stress responses", "immune cells", "pathology and laboratory medicine", "pathogens", "cell processes", "immunology", "microbiology", "parasitic diseases", "parasitic protozoans", "protozoan life cycles", "developmental biology", "pro...	Quantitative proteomic analysis of amastigotes from Leishmania (L.) amazonensis LV79 and PH8 strains reveals molecular traits associated with the virulence phenotype	journal.pntd.0006090	null	[ [ "Leishmaniasis is an antropozoonosis that affects around 12 million people in 98 different countries in Europe , Africa , Asia and America [1] .", "More than 1 , 5 million new cases are reported every year , 0 , 7 to 1 , 2 of them of the tegumentary forms and 0 , 2 to 0 , 4 million of the visceral form [1...	[ "Leishmaniasis is an antropozoonosis caused by Leishmania parasites that affects around 12 million people in 98 different countries .", "The disease has different clinical forms , which depend mainly on the parasite genetics and on the immunologic status of the host .", "The promastigote form of the parasite is...	[ "Leishmaniasis is an antropozoonosis caused by Leishmania parasites that affects around 12 million people in 98 different countries .", "Cutaneous leishmaniasis caused by Leishmania amazonensis can have different clinical forms and severities depending on the parasite strain .", "We have here shown that two Lei...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "pathogens", "immunology", "microbiology", "staphylococcus aureus", "immune receptor signaling", "membrane receptor signaling", "hypoxia", "bacteria", "neutrophils", "bacterial pathogens", ...	Opposing roles of Toll-like receptor and cytosolic DNA-STING signaling pathways for Staphylococcus aureus cutaneous host defense	journal.ppat.1006496	null	[ [ "Cells of the innate immune system , including macrophages and neutrophils , are tasked with initiating the rapid and robust response to invading microbial pathogens .", "Armed with a variety of pattern recognition receptors ( PRRs ) , these sentinel cells sense pathogen associated molecular patterns ( PA...	[ "Successful host defense against pathogens requires innate immune recognition of the correct pathogen associated molecular patterns ( PAMPs ) by pathogen recognition receptors ( PRRs ) to trigger the appropriate gene program tailored to the pathogen .", "While many PRR pathways contribute to the innate immune res...	[ "Individual pathogen associated molecular patterns ( PAMPs ) induce gene expression in immune cells through distinct signaling pathways to protect cells from infection .", "However , pathogens typically possess many PAMPs , and the precise contribution of each PAMP to the gene expression program elicited by a liv...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "cell physiology", "carbohydrate metabolism", "cell motility", "medicine and health sciences", "chemical compounds", "cardiovascular anatomy", "oxygen", "cell cycle and cell division", "cell processes", "carbohydrates", "cell metabolism", "organic compounds", "glucose", "glucose metabolism...	Blood vessel tortuosity selects against evolution of aggressive tumor cells in confined tissue environments: A modeling approach	journal.pcbi.1005635	null	[ [ "Cancer is a disease of multicellular regulation , in which malfunctioning cells can break free of homeostatic regulations imposed by the host environment [1] .", "One of the main characteristics of cancer is the increased proliferation and mutation of cancerous cells due to malfunctioning control of grow...	[ "Cancer is a disease of cellular regulation , often initiated by genetic mutation within cells , and leading to a heterogeneous cell population within tissues .", "In the competition for nutrients and growth space within the tumors the phenotype of each cell determines its success .", "Selection in this process...	[ "Multicellular organisms control their cells to facilitate higher level function of the whole organism .", "In tumors , this control is lost and cells are allowed to enhance their fitness by , for example , increased proliferation .", "Tumor cells continue to change their behavior through accumulating mutations...	2017

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