Split (3)

train · 24.8k rows

headings list	keywords list	title stringlengths 20 281	id stringlengths 20 20	toc stringlengths 57 522 ⌀	sections list	abstract list	summary list	year stringclasses 13 values
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "computational biology/comparative sequence analysis", "computational biology/genomics", "evolutionary biology/evolutionary and comparative genetics" ]	Increased Expression and Protein Divergence in Duplicate Genes Is Associated with Morphological Diversification	journal.pgen.1000781	null	[ [ "Duplicate genes rarely exhibit de novo functions ( neofunctionalization ) ; more usually , the functions of the original gene are split into multiple functions among the duplicate genes ( subfunctionalization ) [1]–[5] .", "Such functionalization through gene duplication is considered to be an important ...	[ "The differentiation of both gene expression and protein function is thought to be important as a mechanism of the functionalization of duplicate genes .", "However , it has not been addressed whether expression or protein divergence of duplicate genes is greater in those genes that have undergone functionalizati...	[ "The relationship between morphological and molecular evolution is a central issue to the understanding of eukaryote evolution .", "In particular , there is much interest in how duplicate genes have contributed to morphological diversification during evolution .", "As a mechanism of functionalization of duplica...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "urology", "medicine and health sciences", "solomon islands", "immune physiology", "cost-effectiveness analysis", "economic analysis", "immunology", "tropical diseases", "geographical locations", "social sciences", "vanuatu", "treponematoses", "bacterial diseases", "sexually transmitted di...	The cost and cost-effectiveness of rapid testing strategies for yaws diagnosis and surveillance	journal.pntd.0005985	null	[ [ "Yaws is a non-venereal treponemal infection caused by Treponema pallidum subspecies pertenue affecting primarily the skin in the early stages and the bone and cartilage in the late stages .", "In 1950 , WHO estimated that 160 million people were infected with yaws .", "Between 2008 and 2012 more than...	[ "Yaws is a non-venereal treponemal infection caused by Treponema pallidum subspecies pertenue .", "The disease is targeted by WHO for eradication by 2020 .", "Rapid diagnostic tests ( RDTs ) are envisaged for confirmation of clinical cases during treatment campaigns and for certification of the interruption of ...	[ "Yaws is a non-venereal treponemal infection .", "The disease is targeted by WHO for eradication by 2020 .", "Testing is envisaged for diagnosis to confirm of clinical cases during treatment campaigns and for surveillance to certify the interruption of transmission .", "However resources available to the glob...	2017
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "body fluids", "chemical compounds", "liquid chromatography", "urine", "ultraviolet spectroscopy", "metabolites", "pharmaceutics", "drug administration", "sulfoxides", "pharmacology", "high performance liquid chromatography", "drug metabolism", "research and...	Assessment of serum pharmacokinetics and urinary excretion of albendazole and its metabolites in human volunteers	journal.pntd.0005945	null	[ [ "The neglected tropical diseases ( NTDs ) are a group of infections which affect the poorest regions of the world [1] .", "Among the NTDs , Soil-transmitted helminths ( STH , the roundworm Ascaris lumbricoides , the whipworm Trichuris trichiura and the two hookworm species Necator americanus and Ancylosto...	[ "Soil Transmitted Helminth ( STH ) infections negatively impact physical and mental development in human populations .", "Current WHO guidelines recommend morbidity control of these infections through mass drug administration ( MDA ) using albendazole ( ABZ ) or mebendazole .", "Despite major reductions in STH ...	[ "The soil-transmitted-helminths ( STH ) infections are produced by four species of parasites: Ascaris lumbricoides , Trichuris trichiura , and hookworm ( Necator americanus and Ancylostoma duodenale ) .", "These parasites are transmitted by eggs present in human faeces , which contaminate the environment in areas...	2018
[ "Introduction", "Results and Discussion", "Conclusions", "Materials and Methods" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "gene regulation", "pathogens", "microbiology", "dna transcription", "pseudomonas aeruginosa", "regulator genes", "genome analysis", "gene types", "bacteria", "bacterial pathogens", "pseudomonas", "genomics", "medical m...	Unravelling the Genome-Wide Contributions of Specific 2-Alkyl-4-Quinolones and PqsE to Quorum Sensing in Pseudomonas aeruginosa	journal.ppat.1006029	null	[ [ "Pseudomonas aeruginosa is a multi-antibiotic resistant pathogen commonly responsible for hospital-acquired infections and is the main cause of morbidity and mortality in cystic fibrosis [1] .", "The pathogenicity of P . aeruginosa is multifactorial and host specific relying on the coordinated production ...	[ "The pqs quorum sensing ( QS ) system is crucial for Pseudomonas aeruginosa virulence both in vitro and in animal models of infection and is considered an ideal target for the development of anti-virulence agents .", "However , the precise role played by each individual component of this complex QS circuit in the...	[ "Many bacterial pathogens control virulence gene expression and the development of antibiotic-resistant biofilms via intercellular communication through ‘quorum sensing’ ( QS ) .", "QS systems depend on the synthesis , secretion and perception of diffusible signalling molecules that enable bacteria to synchronize...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "biology and life sciences", "computer and information sciences", "medicine and health sciences" ]	Simulating Population Genetics of Pathogen Vectors in Changing Landscapes: Guidelines and Application with Triatoma brasiliensis	journal.pntd.0003068	null	[ [ "Human-induced landscape changes are increasingly recognized as important drivers of infectious disease outbreak and emergence events , resulting in significant threats to public health [1]–[3] .", "Worldwide the rapid modification of natural habitats has triggered intense research on the landscape epidem...	[ "Understanding the mechanisms that influence the population dynamics and spatial genetic structure of the vectors of pathogens infecting humans is a central issue in tropical epidemiology .", "In view of the rapid changes in the features of landscape pathogen vectors live in , this issue requires new methods that...	[ "Worldwide , humans are modifying landscapes at an unprecedented rate .", "These modifications have an influence on the ecology of pathogen vectors , yet this issue has received relatively little input from modeling research .", "The current study presents guidelines for the use of a modeling framework for the ...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases/neglected tropical diseases", "infectious diseases/tropical and travel-associated diseases", "genetics and genomics/comparative genomics", "genetics and genomics/functional genomics" ]	A Genomic-Based Approach Combining In Vivo Selection in Mice to Identify a Novel Virulence Gene in Leishmania	journal.pntd.0000248	null	[ [ "Leishmania protozoa are transmitted by the bite of an infected sandfly and cause a spectrum of diseases ranging from self-healing cutaneous lesions to fatal visceral infection [1] , [2] .", "There are an estimated 12 million cases in over 80 countries , with an annual incidence of 0 . 5 million new cases...	[ "Infection with Leishmania results in a broad spectrum of pathologies where L . infantum and L . donovani cause fatal visceral leishmaniasis and L . major causes destructive cutaneous lesions .", "The identification and characterization of Leishmania virulence genes may define the genetic basis for these differen...	[ "Parasites of the genus Leishmania cause a variety of human diseases that range from destructive skin lesions caused by L . major to visceral infections of the liver and spleen caused by L . donovani that result in death .", "The Leishmania genes responsible for these different pathologies are not known .", "In...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology/embryology", "genetics and genomics/animal genetics", "developmental biology/morphogenesis and cell biology", "genetics and genomics/gene expression", "developmental biology/pattern formation", "developmental biology/cell differentiation", "genetics and genomics/gene function", ...	A Negative Regulatory Loop between MicroRNA and Hox Gene Controls Posterior Identities in Caenorhabditis elegans	journal.pgen.1001089	null	[ [ "miRNAs are small endogenous RNA molecules found in most eukaryotic species that are involved in post-transcriptional regulation of genes required for cell fate determination , metabolism and carcinogenesis among other processes [1] .", "Like protein coding genes , miRNA genes are transcribed by RNA polym...	[ "MicroRNAs ( miRNAs ) have been found to regulate gene expression across eukaryotic species , but the function of most miRNA genes remains unknown .", "Here we describe how the analysis of the expression patterns of a well-conserved miRNA gene , mir-57 , at cellular resolution for every minute during early develo...	[ "miRNAs are small RNAs found in many multi-cellular species that inhibit gene expression .", "Many of them play important roles in cancer and cell fate determination , but the function of most miRNAs is uncertain .", "Using live cell imaging and automated expression analysis , we found a miRNA gene , mir-57 , i...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "in vitro", "immunology", "mus (mouse)", "homo (human)" ]	Epigenetic Control of the foxp3 Locus in Regulatory T Cells	journal.pbio.0050038	The transcription factor Foxp3 is a master switch for the regulatory T cell lineage. The authors show that the Foxp3 locus is epigenetically modified in stable regulatory T cells.	[ [ "Regulatory T cells ( Tregs ) , which have been shown to play a pivotal role in the maintenance of self-tolerance within the immune system , were described originally as CD4+ T cells constitutively expressing CD25 [1] .", "More recently , the forkhead transcription factor Foxp3 has been shown to be specif...	[ "Compelling evidence suggests that the transcription factor Foxp3 acts as a master switch governing the development and function of CD4+ regulatory T cells ( Tregs ) .", "However , whether transcriptional control of Foxp3 expression itself contributes to the development of a stable Treg lineage has thus far not b...	[ "Regulatory T cells play a pivotal role in the maintenance of self-tolerance within the immune system by preventing autoimmunity or excessive activation of the T cells that respond to pathogens ( naïve and effector T cells ) .", "They differentiate within the thymus , but can also be de novo induced in the rest o...	2007
[ "Introduction", "Results", "Discussion" ]	[ "genome-wide association studies", "body weight", "medicine and health sciences", "functional genomics", "physical activity", "mathematics", "physiological parameters", "statistics (mathematics)", "genome analysis", "obesity", "epigenomics", "research and analysis methods", "public and occup...	Genome-wide physical activity interactions in adiposity ― A meta-analysis of 200,452 adults	journal.pgen.1006528	null	[ [ "In recent decades , we have witnessed a global obesity epidemic that may be driven by changes in lifestyle such as easier access to energy-dense foods and decreased physical activity ( PA ) [1] .", "However , not everyone becomes obese in obesogenic environments .", "Twin studies suggest that changes...	[ "Physical activity ( PA ) may modify the genetic effects that give rise to increased risk of obesity .", "To identify adiposity loci whose effects are modified by PA , we performed genome-wide interaction meta-analyses of BMI and BMI-adjusted waist circumference and waist-hip ratio from up to 200 , 452 adults of ...	[ "Decline in daily physical activity is thought to be a key contributor to the global obesity epidemic .", "However , the impact of sedentariness on adiposity may be in part determined by a person’s genetic constitution .", "The specific genetic variants that are sensitive to physical activity and regulate adipo...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "phosphorylation", "medicine and health sciences", "protein interactions", "pathology and laboratory medicine", "chemical compounds", "pathogens", "microbiology", "viral structure", "hepatitis b virus", "electron cryo-microscopy", "viruses", "microscopy", "research and analysis methods", "...	Importin β Can Bind Hepatitis B Virus Core Protein and Empty Core-Like Particles and Induce Structural Changes	journal.ppat.1005802	null	[ [ "Viruses take advantage of host proteins throughout their lifecycle; here we investigate interactions between Hepatitis B Virus ( HBV ) and host proteins related to nuclear transport .", "HBV is an enveloped virus with an icosahedral core .", "Mature HBV cores , which consist of a relaxed circular dsD...	[ "Hepatitis B virus ( HBV ) capsids are found in many forms: immature single-stranded RNA-filled cores , single-stranded DNA-filled replication intermediates , mature cores with relaxed circular double-stranded DNA , and empty capsids .", "A capsid , the protein shell of the core , is a complex of 240 copies of co...	[ "Viruses take advantage of host proteins .", "During infection , DNA-filled Hepatitis B Virus ( HBV ) cores are ferried to the nucleus by a complex of importin α and importin β; importinβ alone does not bind mature cores .", "However , a surprisingly large amount of the HBV core protein accumulates in nuclei ."...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "trichuris", "parasitology", "nematoda", "biology and life sciences", "intestinal parasites", "animals", "organisms" ]	Hidden Population Structure and Cross-species Transmission of Whipworms (Trichuris sp.) in Humans and Non-human Primates in Uganda	journal.pntd.0003256	null	[ [ "Parasites that infect multiple host species are of particular concern because they are more likely to emerge than single-host parasites [1]–[4] .", "Moreover , multi-host parasites are difficult to control because reservoir hosts may serve as sources of re-infection for other populations in which the par...	[ "Whipworms ( Trichuris sp . ) are a globally distributed genus of parasitic helminths that infect a diversity of mammalian hosts .", "Molecular methods have successfully resolved porcine whipworm , Trichuris suis , from primate whipworm , T . trichiura .", "However , it remains unclear whether T . trichiura is ...	[ "Whipworms are a group of gastrointestinal worms that are both common and globally distributed .", "These parasites are known to stunt development , especially in school-aged children , and therefore hinder economic , social , and intellectual growth .", "Unfortunately , research on whipworms has lagged behind ...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Designing Molecular Dynamics Simulations to Shift Populations of the Conformational States of Calmodulin	journal.pcbi.1003366	null	[ [ "Protein behavior in solution may be manipulated and controlled through tailored structural perturbations [1] and rational control of the solution conditions [2] http://www . pnas . org/content/109/50/E3454 . full . pdfhtml .", "In the living cell , proteins adapt to particular subcellular compartments wh...	[ "We elucidate the mechanisms that lead to population shifts in the conformational states of calcium-loaded calmodulin ( Ca2+-CaM ) .", "We design extensive molecular dynamics simulations to classify the effects that are responsible for adopting occupied conformations available in the ensemble of NMR structures ."...	[ "Calmodulin ( CaM ) is involved in calcium signaling pathways in eukaryotic cells as an intracellular Ca2+ receptor .", "Exploiting pH differences in the cell , CaM performs a variety of functions by conveniently adopting different conformational states .", "We aim to reveal pH and ionic strength ( IS ) depende...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "medicine and health sciences", "reproductive system", "rna interference", "body fluids", "animals", "reproductive physiology", "epithelial cells", "epigenetics", "insect vectors", "infectious diseases", "genetic interference", "aedes aegypti", "animal cells", "gene expr...	Identification and characterization of a mosquito-specific eggshell organizing factor in Aedes aegypti mosquitoes	journal.pbio.3000068	An RNAi functional screen of 40 Aedes aegypti genes specific to the mosquito lineage helped to identify EOF1, a protein that plays an essential role in mosquito eggshell formation and melanization.	[ [ "Developing new strategies for vector control is becoming critical because worldwide cases of Aedes aegypti-transmitted dengue and Zika virus infections have risen dramatically in the last decade [1–3] .", "Researchers have been investigating metabolic regulation of blood meal metabolism in A . aegypti mo...	[ "Mosquito-borne diseases are responsible for several million human deaths annually around the world .", "One approach to controlling mosquito populations is to disrupt molecular processes or antagonize novel metabolic targets required for the production of viable eggs .", "To this end , we focused our efforts o...	[ "Mosquito-borne pathogens infect millions of people worldwide , and the rise in insecticide resistance is exacerbating this problem .", "A new generation of environmentally safe insecticides will be essential to control insecticide-resistant mosquitoes .", "One potential route to such novel insecticide targets ...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "breast tumors", "engineering and technology", "signal processing", "signaling networks", "cancers and neoplasms", "simulation and modeling", "oncology", "optimization", "systems science", "mathematics", "network analysis", "research and analysis methods", "...	Data-driven reverse engineering of signaling pathways using ensembles of dynamic models	journal.pcbi.1005379	null	[ [ "Inferring the molecular circuits of the cell from experimental data is a fundamental question of systems biology .", "In particular , the identification of signaling and regulatory networks in healthy and diseased human cells is a powerful approach to unravel the mechanisms controlling biological homeost...	[ "Despite significant efforts and remarkable progress , the inference of signaling networks from experimental data remains very challenging .", "The problem is particularly difficult when the objective is to obtain a dynamic model capable of predicting the effect of novel perturbations not considered during model ...	[ "Signaling pathways play a key role in complex diseases such as cancer , for which the development of novel therapies is a difficult , expensive and laborious task .", "Computational models that can predict the effect of a new combination of drugs without having to test it experimentally can help in accelerating ...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Potential Role of a Bistable Histidine Kinase Switch in the Asymmetric Division Cycle of Caulobacter crescentus	journal.pcbi.1003221	null	[ [ "The function of the cell division cycle of both prokaryotes and eukaryotes is to produce two nearly identical copies of a progenitor cell .", "The two progeny cells have identical genomes ( modulo unavoidable mutations in the DNA replication process ) , and they are usually quite similar in all other asp...	[ "The free-living aquatic bacterium , Caulobacter crescentus , exhibits two different morphologies during its life cycle .", "The morphological change from swarmer cell to stalked cell is a result of changes of function of two bi-functional histidine kinases , PleC and CckA .", "Here , we describe a detailed mol...	[ "Recent evidence suggests that the transition of PleC from phosphatase to kinase is induced by its own substrate , DivK .", "Based on experimental clues , we propose a molecular mechanism to explain this substrate-induced conformational change in PleC .", "The general principles of thermodynamics , enzyme-subst...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/viral infections", "virology" ]	Genome-Wide Mutagenesis Reveals That ORF7 Is a Novel VZV Skin-Tropic Factor	journal.ppat.1000971	null	[ [ "Human varicella-zoster virus ( VZV ) is a widespread human alpha-herpesvirus , and the majority of the US population has been previously exposed [1] .", "VZV is the causative agent of chicken pox and shingles , the latter of which is associated with a significant incidence of post-herpetic neuralgia [2] ...	[ "The Varicella Zoster Virus ( VZV ) is a ubiquitous human alpha-herpesvirus that is the causative agent of chicken pox and shingles .", "Although an attenuated VZV vaccine ( v-Oka ) has been widely used in children in the United States , chicken pox outbreaks are still seen , and the shingles vaccine only reduces...	[ "The Varicella Zoster Virus ( VZV ) is the causative agent of chicken pox and shingles .", "The long-term efficacy of the current chickenpox vaccine is yet to be determined , and the current shingles vaccine fails to provide protective immunity for a substantial number of individuals .", "Shingles can also lead...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology/immunodeficiency viruses", "molecular biology/rna-protein interactions" ]	Controlling Cellular P-TEFb Activity by the HIV-1 Transcriptional Transactivator Tat	journal.ppat.1001152	null	[ [ "Synthesis of mRNAs by Pol II is tightly controlled at the step of transcription elongation by the positive transcription elongation factor b ( P-TEFb ) that is a cyclin-dependent kinase composed of Cdk9 and cyclin T1 ( CycT1 ) [1] , [2] , [3] , [4] , [5] .", "After transcription initiation and promoter c...	[ "The human immunodeficiency virus 1 ( HIV-1 ) transcriptional transactivator ( Tat ) is essential for synthesis of full-length transcripts from the integrated viral genome by RNA polymerase II ( Pol II ) .", "Tat recruits the host positive transcription elongation factor b ( P-TEFb ) to the HIV-1 promoter through...	[ "Expression and replication of the human immunodeficiency virus ( HIV ) is supported by the viral transcriptional transactivator ( Tat ) that recruits the host positive transcription elongation factor b ( P-TEFb ) to the promoter of the integrated viral genome .", "Here , we demonstrate that HIV Tat specifically ...	2010
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "biology", "veterinary science" ]	Ultra-Efficient PrPSc Amplification Highlights Potentialities and Pitfalls of PMCA Technology	journal.ppat.1002370	null	[ [ "Transmissible Spongiform Encephalopathies ( TSEs ) are progressive and fatal neurodegenerative disorders that include scrapie of sheep , bovine spongiform encephalopathy ( BSE ) of cattle and Creutzfeldt-Jakob disease ( CJD ) of humans [1] .", "The nature of the causal agent of TSEs has long been a matte...	[ "In order to investigate the potential of voles to reproduce in vitro the efficiency of prion replication previously observed in vivo , we seeded protein misfolding cyclic amplification ( PMCA ) reactions with either rodent-adapted Transmissible Spongiform Encephalopathy ( TSE ) strains or natural TSE isolates .", ...	[ "In an attempt to transpose to an in vitro system the particular sensitivity of the vole model to human and animal Transmissible Spongiform Encephalopathies ( TSEs ) , we first explored the suitability of vole brain homogenate as a substrate for PMCA .", "As well as observing the highly efficient replication of a...	2011
[ "Introduction", "Results/Discussion", "Methods" ]	[ "developmental biology/morphogenesis and cell biology", "computational biology/transcriptional regulation", "developmental biology/developmental evolution", "developmental biology/plant growth and development", "developmental biology/cell differentiation", "plant biology/plant growth and development", "...	Developmental Robustness by Obligate Interaction of Class B Floral Homeotic Genes and Proteins	journal.pcbi.1000264	null	[ [ "Depending on the nature of the interactions of their constituents , gene regulatory circuits can display a variety of dynamical behaviors ranging from simple steady states , to switching and multistability , to oscillations .", "Temporal or spatial patterning during development requires activation of gen...	[ "DEF-like and GLO-like class B floral homeotic genes encode closely related MADS-domain transcription factors that act as developmental switches involved in specifying the identity of petals and stamens during flower development .", "Class B gene function requires transcriptional upregulation by an autoregulatory...	[ "The development of organs , their position , and boundaries in multicellular organisms are defined by genes that can sustain their own activation over long periods of time , termed genetic switches .", "A good case in point is provided by the genetic machinery controlling the development of flowers in higher pla...	2009
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "fluorescence imaging", "medicine and health sciences", "fish", "immune cells", "pathology and laboratory medicine", "intracellular pathogens", "pathogens", "immunology", "microbiology", "vertebrates", "opportunistic infections", "animals", "animal models", "osteichthyes",...	The afc antifungal activity cluster, which is under tight regulatory control of ShvR, is essential for transition from intracellular persistence of Burkholderia cenocepacia to acute pro-inflammatory infection	journal.ppat.1007473	null	[ [ "B . cenocepacia belongs to the Burkholderia cepacia complex ( Bcc ) , currently encompassing 21 officially named species [1 , 2] .", "These opportunistic bacteria are notorious pathogens of cystic fibrosis ( CF ) patients [3 , 4] and are emerging as the culprit of serious infections in non-CF conditions ...	[ "The opportunistic pathogen Burkholderia cenocepacia is particularly life-threatening for cystic fibrosis ( CF ) patients .", "Chronic lung infections with these bacteria can rapidly develop into fatal pulmonary necrosis and septicaemia .", "We have recently shown that macrophages are a critical site for replic...	[ "Burkholderia cenocepacia is a bacterial pathogen that can infect cystic fibrosis patients , causing a chronic infection that can suddenly change to often fatal inflammatory necrotic pneumonia called cepacia syndrome .", "The transcriptional regulator ShvR controls the expression of a lipoprotein with antifungal ...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "muscle tissue", "cell differentiation", "developmental biology", "muscle proteins", "molecular motors", "actin motors", "muscle functions", "embryos", "morphogenesis", "motor proteins", "muscle physiology", "contractile proteins", "embryology", "muscle di...	A Differentiation Transcription Factor Establishes Muscle-Specific Proteostasis in Caenorhabditis elegans	journal.pgen.1006531	null	[ [ "Molecular chaperones are a diverse group of highly conserved proteins that evolved to cope with protein quality control challenges [1–3] .", "The cellular chaperone machinery is involved in a multitude of cellular functions , including de novo folding , assembly and disassembly of protein complexes , pro...	[ "Safeguarding the proteome is central to the health of the cell .", "In multi-cellular organisms , the composition of the proteome , and by extension , protein-folding requirements , varies between cells .", "In agreement , chaperone network composition differs between tissues .", "Here , we ask how chaperone...	[ "Molecular chaperones protect proteins from misfolding and aggregation .", "In multi-cellular organisms , the composition and expression levels of chaperones vary between tissues .", "However , little is known of how such differential expression is regulated .", "We hypothesized that the cellular differentiat...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "hiv infections", "medicine and health sciences", "immune cells", "microbiome", "pathology and laboratory medicine", "immune activation", "pathogens", "immunology", "microbiology", "retroviruses", "viruses", "immunodeficiency viruses", "rna viruses", "cytotoxic t cells", ...	Gut microbiota from high-risk men who have sex with men drive immune activation in gnotobiotic mice and in vitro HIV infection	journal.ppat.1007611	null	[ [ "Men who have sex with men ( MSM ) comprise over half of all people living with HIV in the United States and accounted for 67% of new U . S . infections in 2016 [1] .", "Prevention and treatment in the MSM population is of high priority in the effort to eradicate HIV/AIDS in the U . S . Identifying novel ...	[ "Men who have sex with men ( MSM ) have differences in immune activation and gut microbiome composition compared with men who have sex with women ( MSW ) , even in the absence of HIV infection .", "Gut microbiome differences associated with HIV itself when controlling for MSM , as assessed by 16S rRNA sequencing ...	[ "The communities of commensal microbes that colonize the human gut comprise the gut microbiome , which has been shown to play a significant role in shaping the immune system .", "Recent studies have reported a distinct gut microbiome composition in men who have sex with men ( MSM ) exhibiting HIV-risk behaviors w...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "dermatology", "public and occupational health", "infectious diseases", "medicine and health sciences", "epidemiology" ]	Contribution of the Community Health Volunteers in the Control of Buruli Ulcer in Bénin	journal.pntd.0003200	null	[ [ "Buruli ulcer ( BU ) , caused by Mycobacterium ulcerans , is an emerging neglected tropical disease .", "It is the third most common mycobacterial disease after tuberculosis and leprosy in immuno-competent persons in Bénin .", "The disease has been reported in more than 30 countries worldwide , but th...	[ "Buruli ulcer ( BU ) is a neglected tropical disease caused by Mycobacterium ulcerans .", "Usually BU begins as a painless nodule , plaque or edema , ultimately developing into an ulcer .", "The high number of patients presenting with ulcers in an advanced stage is striking .", "Such late presentation will co...	[ "Buruli ulcer ( BU ) is a neglected tropical disease caused by Mycobacterium ulcerans .", "Usually , the number of patients presenting with ulcers in an advanced stage is high .", "This complicates treatment and increases the risk of disabilities .", "The disease is endemic mainly in West Africa .", "The pr...	2014
[ "Introduction", "Material and methods", "Results", "Discussion" ]	[]	Immunosuppressive and angiogenic cytokine profile associated with Bartonella bacilliformis infection in post-outbreak and endemic areas of Carrion's disease in Peru	journal.pntd.0005684	null	[ [ "Carrion’s disease ( CD ) ( ORPHANET 64692 ) is a tropical , neglected poorest-linked illness , endemic in low-income areas of Peru , but also affecting specific areas of Ecuador and Colombia , with sporadic cases reported in Bolivia and Chile [1] .", "It is estimated that approximately 1 . 7 million of S...	[ "Analysis of immune responses in Bartonella bacilliformis carriers are needed to understand acquisition of immunity to Carrion’s disease and may allow identifying biomarkers associated with bacterial infection and disease phases .", "Serum samples from 144 healthy subjects from 5 villages in the North of Peru col...	[ "Carrion’s disease is a neglected vector-borne disease limited to vulnerable population of Ecuador , Colombia and specially Peru .", "This illness consist in two distinct phases , the Oroya fever and Peruvian wart , but exist a high percentage of asymptomatic carriers in endemic areas that should be detected in o...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Distinct and Cooperative Activities of HESO1 and URT1 Nucleotidyl Transferases in MicroRNA Turnover in Arabidopsis	journal.pgen.1005119	null	[ [ "The three major types of small RNAs in eukaryotes , microRNAs ( miRNAs ) , small interfering RNAs ( siRNAs ) and piwi-interacting RNAs ( piRNAs ) , impact many biological processes such as development , self/non-self recognition , genome stability , and adaption to environment .", "Given the widespread a...	[ "3’ uridylation is increasingly recognized as a conserved RNA modification process associated with RNA turnover in eukaryotes .", "2’-O-methylation on the 3’ terminal ribose protects micro ( mi ) RNAs from 3’ truncation and 3’ uridylation in Arabidopsis .", "Previously , we identified HESO1 as the nucleotidyl t...	[ "The tailing of RNAs with non-templated uridines , known as uridylation , is often associated with RNA degradation .", "We previously identified HESO1 as a nucleotidyl transferase that uridylates microRNAs ( miRNAs ) to lead to their degradation in Arabidopsis .", "But HESO1 cannot account for all the miRNA uri...	2015
[ "Introduction", "Results", "Discussion", "Conclusion", "Materials and methods" ]	[ "invertebrates", "cell death", "rna interference", "nuclear staining", "molecular probe techniques", "cell cycle and cell division", "cell processes", "animals", "cell differentiation", "developmental biology", "epigenetics", "molecular biology techniques", "planarians", "research and anal...	Hippo signaling controls cell cycle and restricts cell plasticity in planarians	journal.pbio.2002399	null	[ [ "The same developmental processes that drive embryogenesis also regulate the constant cell renewal required throughout the natural life span of the organism .", "Successful cell renewal relies on multiple events , including proliferation and differentiation of progenitor cell populations and death of unne...	[ "The Hippo pathway plays a key role in regulating cell turnover in adult tissues , and abnormalities in this pathway are consistently associated with human cancers .", "Hippo was initially implicated in the control of cell proliferation and death , and its inhibition is linked to the expansion of stem cells and p...	[ "Constant cell renewal is required to maintain healthy organs during adult homeostasis .", "The highly conserved Hippo signaling pathway is essential for the regulation of basic cell behaviors that underlie tissue renewal , including cell proliferation , cell differentiation , and cell death .", "The Hippo prot...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology" ]	Eurasian-Origin Gene Segments Contribute to the Transmissibility, Aerosol Release, and Morphology of the 2009 Pandemic H1N1 Influenza Virus	journal.ppat.1002443	null	[ [ "Influenza A viruses pose a global threat to human health .", "They circulate in animal hosts and can reassort to generate a virus to which the human population is naïve , creating a potential pandemic threat .", "Efficient person-to-person transmission of influenza A viruses via RDs is a feature of s...	[ "The epidemiological success of pandemic and epidemic influenza A viruses relies on the ability to transmit efficiently from person-to-person via respiratory droplets .", "Respiratory droplet ( RD ) transmission of influenza viruses requires efficient replication and release of infectious influenza particles into...	[ "Influenza A viruses spread rapidly from person-to-person via respiratory droplets ( RDs ) .", "In this study we used a ferret model to explore viral functions involved in RD transmission of influenza viruses .", "The 2009 pandemic H1N1 ( pH1N1 ) virus originated by reassortment of a North American triple reass...	2011
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "body fluids", "pathology and laboratory medicine", "pathogens", "animal models of disease", "microbiology", "animals", "viruses", "animal models", "multivariate analysis", "model organisms", "mathematics", "rna viruses", "statistics (math...	Altered vector competence in an experimental mosquito-mouse transmission model of Zika infection	journal.pntd.0006350	null	[ [ "Zika virus ( ZIKV ) , a member of the flaviviridae family , was originally isolated from a sentinel monkey in the Zika forest of Uganda in 1947 [1] .", "The first case of ZIKV infection in humans was reported in Nigeria in 1954 [2] .", "For half a century , serologic evidence suggests that the virus ...	[ "Few animal models of Zika virus ( ZIKV ) infection have incorporated arthropod-borne transmission .", "Here , we establish an Aedes aegypti mosquito model of ZIKV infection of mice , and demonstrate altered vector competency among three strains , ( Orlando , ORL , Ho Chi Minh , HCM , and Patilas , PAT ) .", "A...	[ "Zika virus ( ZIKV ) , an emerging flavivirus , is associated with severe clinical outcomes , including Guillain-Barre syndrome and birth defects .", "Transmission of ZIKV is primarily mosquito-borne , but the complete transmission cycle from mammalian host to mosquito and back to mammalian host has not yet been ...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine" ]	Dengue Infection and Miscarriage: A Prospective Case Control Study	journal.pntd.0001637	null	[ [ "Each year there is an estimated 100 million dengue infections [1] , 500 thousand hospitalisations due to severe dengue illness [2] and 25 thousand dengue deaths [1] worldwide .", "Dengue's geographical reach is expanding [3] due in part to the complex interplay of climate warming [4] coupled with travel ...	[ "Dengue is the most prevalent mosquito borne infection worldwide .", "Vertical transmissions after maternal dengue infection to the fetus and pregnancy losses in relation to dengue illness have been reported .", "The relationship of dengue to miscarriage is not known .", "We aimed to establish the relationshi...	[ "Dengue is the most prevalent mosquito-borne infection with two billion of the world's population at risk and 100 million infections every year .", "Dengue is increasingly important due to expansion in the vector's range , increased population density in endemic areas from urbanisation , social and environment ch...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "cell physiology", "urology", "medicine and health sciences", "genetic networks", "gene regulation", "cancers and neoplasms", "genitourinary tract tumors", "epithelial cells", "oncology", "prostate cancer", "network analysis", "genome analysis", "cellular structures and organelles", "cytos...	A Network Biology Approach Identifies Molecular Cross-Talk between Normal Prostate Epithelial and Prostate Carcinoma Cells	journal.pcbi.1004884	null	[ [ "Prostate Cancer is the most common cancer in males .", "It is characterized by a considerable molecular and phenotypic heterogeneity that results in radically different clinical outcomes [1] .", "The role of tumour microenvironment in the development of cancer is crucial .", "More specifically , ...	[ "The advent of functional genomics has enabled the genome-wide characterization of the molecular state of cells and tissues , virtually at every level of biological organization .", "The difficulty in organizing and mining this unprecedented amount of information has stimulated the development of computational me...	[ "In the current era of cancer research , stimulated by the release of the entire human genome , it has become increasingly clear that to understand cancer we need to understand how the many thousands of genes and proteins involved interact .", "Modern techniques have enabled the collection of unprecedented amount...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases", "infectious disease immunology", "medicine and health sciences", "immune evasion", "major histocompatibility complex", "genetics of the immune system", "clinical immunology", "biology and life sciences", "immunology", "viral diseases", "cytomegalovirus infection", "immun...	Specific Dysregulation of IFNγ Production by Natural Killer Cells Confers Susceptibility to Viral Infection	journal.ppat.1004511	null	[ [ "Natural killer ( NK ) cells are pivotal for both the destruction of virally-infected cells and for the cytolysis of certain tumor cells [1] .", "These processes are dependent on the interaction of NK cell receptors with their cognate ligands on target cells .", "NK cell responses are controlled by th...	[ "Natural Killer ( NK ) cells contribute to the control of viral infection by directly killing target cells and mediating cytokine release .", "In C57BL/6 mice , the Ly49H activating NK cell receptor plays a key role in early resistance to mouse cytomegalovirus ( MCMV ) infection through specific recognition of th...	[ "Cytomegalovirus ( CMV ) is a ubiquitous herpesvirus that largely infects the human population leading to a significant cause of disease and death in the immunocompromised and elderly .", "The study of CMV in animal models has helped understand the pathogenic consequences of CMV infection and adds substantial und...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases/neglected tropical diseases" ]	Host Gene Expression Profiling of Dengue Virus Infection in Cell Lines and Patients	journal.pntd.0000086	null	[ [ "Although dengue-related disease results in an estimated 50–100 million cases of dengue fever and 250 , 000 to 500 , 000 cases of dengue hemorrhagic fever/dengue shock syndrome each year [1] , [2] , a clear understanding of dengue pathogenesis remains elusive .", "Dengue virus is an enveloped , positive-s...	[ "Despite the seriousness of dengue-related disease , with an estimated 50–100 million cases of dengue fever and 250 , 000–500 , 000 cases of dengue hemorrhagic fever/dengue shock syndrome each year , a clear understanding of dengue pathogenesis remains elusive .", "Because of the lack of a disease model in animal...	[ "Dengue is the most prevalent mosquito-born viral disease affecting humans , yet there is , at present , no drug treatment for the disease nor are there any validated host targets for therapeutic intervention .", "Using microarray technology to monitor the response of virtually every human gene , we aimed to iden...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology/virion structure, assembly, and egress", "virology" ]	Intracellular Proton Conductance of the Hepatitis C Virus p7 Protein and Its Contribution to Infectious Virus Production	journal.ppat.1001087	null	[ [ "Hepatitis C virus ( HCV ) primarily infects human hepatocytes and results in a severe liver disease manifested by chronic inflammation , progressive fibrosis and development of hepatocellular carcinoma .", "The virus is highly successful in evading the host innate and adaptive immune systems [1] .", ...	[ "The hepatitis C virus ( HCV ) p7 protein is critical for virus production and an attractive antiviral target .", "p7 is an ion channel when reconstituted in artificial lipid bilayers , but channel function has not been demonstrated in vivo and it is unknown whether p7 channel activity plays a critical role in vi...	[ "The hepatitis C virus ( HCV ) is the most common cause of chronic liver disease .", "Current therapy is only partially effective and fraught with side effects .", "A greater understanding of viral replication and new virus particle formation is thus important for developing new therapeutic targets .", "The H...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "cell biology/cell signaling", "cell biology/morphogenesis and cell biology", "plant biology/plant cell biology", "cell biology", "developmental biology/pattern formation", "developmental biology/plant growth and development", "cell biology/membranes and sorting", "plant bio...	A Rho Scaffold Integrates the Secretory System with Feedback Mechanisms in Regulation of Auxin Distribution	journal.pbio.1000282	In plants, auxin distribution and tissue patterning are coordinated via a feedback loop involving the auxin-regulated cell polarity factor ICR1 and the secretory machinery.	[ [ "ROP ( Rho of Plants ) , also known as RAC GTPases , have been implicated as master regulators of cell polarity [1] , [2] .", "In their GTP-bound , active state , ROPs interact with downstream effector proteins to regulate organization of actin and microtubules ( MT ) , vesicle trafficking , production of...	[ "Development in multicellular organisms depends on the ability of individual cells to coordinate their behavior by means of small signaling molecules to form correctly patterned tissues .", "In plants , a unique mechanism of directional transport of the signaling molecule auxin between cells connects cell polarit...	[ "The coordination of different cells during pattern formation is a fundamental process in the development of multicellular organisms .", "In plants , a unique mechanism of directional transport of the signaling molecule auxin between cells demonstrates the importance of cell polarity for tissue patterning .", "...	2010
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "clinical immunology", "sexually transmitted diseases", "immunologic subspecialties", "neglected tropical diseases", "immunology", "viral diseases", "neuroimmunology", "immunomodulation" ]	Ciclosporin A Proof of Concept Study in Patients with Active, Progressive HTLV-1 Associated Myelopathy/Tropical Spastic Paraparesis	journal.pntd.0001675	null	[ [ "An estimated 20 million people are infected with HTLV-1 worldwide [1] of which approximately 8% ( ∼2 million ) will develop HTLV-1-associated diseases , most notably adult T-cell leukaemia/lymphoma ( ATLL ) [2] , HTLV-1-associated myelopathy/tropical spastic paraparesis ( HAM/TSP ) [3] , HTLV-1-associated uv...	[ "Patients with HTLV-1-associated myelopathy/tropical spastic paraparesis ( HAM/TSP ) become progressively impaired , with chronic pain , immobility and bladder , bowel and sexual dysfunction .", "Tested antiretroviral therapies have not been effective and most patients are offered a short course of corticosteroid...	[ "HTLV-1 is a retrovirus transmitted through body fluids that is commonly seen in the West Indies , South America and Southern Japan but rarely in the UK .", "Although most patients remain healthy carriers , HTLV-1 causes serious conditions such as adult T cell leukaemia/lymphoma ( ATLL ) and HTLV-1-associated mye...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/protozoal infections", "molecular biology", "cell biology/gene expression", "microbiology/parasitology" ]	Surface Co-Expression of Two Different PfEMP1 Antigens on Single Plasmodium falciparum-Infected Erythrocytes Facilitates Binding to ICAM1 and PECAM1	journal.ppat.1001083	null	[ [ "Plasmodium falciparum is the most pathogenic human malaria parasite and a major cause of morbidity and mortality in Africa .", "Its pathogenesis is closely associated with the adhesive properties of the variable erythrocyte surface antigens , PfEMP1 , encoded by the var gene family [1] .", "These adh...	[ "The Plasmodium falciparum erythrocyte membrane protein 1 ( PfEMP1 ) antigens play a major role in cytoadhesion of infected erythrocytes ( IE ) , antigenic variation , and immunity to malaria .", "The current consensus on control of variant surface antigen expression is that only one PfEMP1 encoded by one var gen...	[ "Plasmodium falciparum is the most pathogenic human malaria parasite and its virulence has been linked to its capacity to express different adhesion proteins that enable the developing parasitized erythrocyte to bind to capillaries of the host , thereby avoiding removal by the spleen .", "Each parasite has approx...	2010
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases", "computer and information sciences", "medicine and health sciences", "systems science", "mathematics", "population modeling", "influenza", "biology and life sciences", "infectious disease modeling", "computational biology", "nonlinear dynamics", "viral diseases", "phys...	Impact of Different Oseltamivir Regimens on Treating Influenza A Virus Infection and Resistance Emergence: Insights from a Modelling Study	journal.pcbi.1003568	null	[ [ "Besides influenza vaccination , neuraminidase inhibitors are currently the most effective pharmaceutical intervention recommended to reduce the burden of seasonal or pandemic influenza [1] , [2] , [3] , [4] , [5] , [6] .", "Two neuraminidase inhibitors are widely marketed: nebulised zanamivir ( Glaxo Wel...	[ "Several studies have proven oseltamivir to be efficient in reducing influenza viral titer and symptom intensity .", "However , the usefulness of oseltamivir can be compromised by the emergence and spread of drug-resistant virus .", "The selective pressure exerted by different oseltamivir therapy regimens have ...	[ "Oseltamivir is currently the most commonly used drug against influenza but the emergence and spread of oseltamivir-resistant virus is threatening its usefulness .", "A previously published study quantified the risk of drug-resistance emergence and spread .", "In this work we investigate under what conditions d...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genome-wide association studies", "mutation", "genetics", "population genetics", "population biology", "biology", "human genetics", "genetics of disease" ]	Analysis of the Genetic Basis of Disease in the Context of Worldwide Human Relationships and Migration	journal.pgen.1003447	null	[ [ "Analyzing the impact of human migration on genetic disease susceptibility is critical to the understanding of complex disease .", "Moving to new environments causes adaptation , which can also affect disease susceptibility .", "The availability of methods to measure genomic differences between worldw...	[ "Genetic diversity across different human populations can enhance understanding of the genetic basis of disease .", "We calculated the genetic risk of 102 diseases in 1 , 043 unrelated individuals across 51 populations of the Human Genome Diversity Panel .", "We found that genetic risk for type 2 diabetes and p...	[ "The environment humans inhabit has changed many times in the last 100 , 000 years .", "Migration and dynamic local environments can lead to genetic adaptations favoring beneficial traits .", "Many genes responsible for these adaptations can alter disease susceptibility .", "Genes can also affect disease susc...	2013
[ "Introduction", "Results and Discussion", "Materials and Methods", "Acknowledgments" ]	[ "biomacromolecule-ligand interactions", "biochemistry", "medicinal chemistry", "proteins", "protein structure", "biology and life sciences", "chemistry", "physical sciences", "computational biology", "biophysics", "molecular biology", "macromolecular structure analysis", "biophysical simulat...	Structure-Based Druggability Assessment of the Mammalian Structural Proteome with Inclusion of Light Protein Flexibility	journal.pcbi.1003741	null	[ [ "The majority of small molecule drug discovery efforts towards new , unprecedented biological targets do not progress past high-throughput screening or hit-to-lead optimization due to lack of pursuable chemical matter [1] , [2] .", "To counter this , drug discovery groups increasingly use druggability ana...	[ "Advances reported over the last few years and the increasing availability of protein crystal structure data have greatly improved structure-based druggability approaches .", "However , in practice , nearly all druggability estimation methods are applied to protein crystal structures as rigid proteins , with prot...	[ "Advances reported over the last few years and the increasing availability of protein crystal structure data have greatly improved structure-based druggability approaches .", "These algorithms predict our ability to discover small molecule drugs for protein targets and can help in identifying promising new biolog...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Achnowledgments" ]	[ "virology/immune evasion", "virology/effects of virus infection on host gene expression", "virology/virulence factors and mechanisms", "virology/emerging viral diseases" ]	Steric Shielding of Surface Epitopes and Impaired Immune Recognition Induced by the Ebola Virus Glycoprotein	journal.ppat.1001098	null	[ [ "EBOV is an enveloped , negative-stranded RNA virus , a member of the family Filoviridae , and the causative agent of Ebola viral hemorrhagic fever .", "To date , five subtypes of EBOV have been identified: Zaire , Sudan , Côte d'Ivoire , Reston and Bundibugyo .", "EBOV Zaire is the most pathogenic su...	[ "Many viruses alter expression of proteins on the surface of infected cells including molecules important for immune recognition , such as the major histocompatibility complex ( MHC ) class I and II molecules .", "Virus-induced downregulation of surface proteins has been observed to occur by a variety of mechanis...	[ "The Ebola virus ( EBOV ) is a highly pathogenic virus that infects humans and non-human primates , causing severe disease or death in the majority of these cases .", "The interaction of this virus with its host on a cellular level is only just beginning to be understood .", "EBOV , like many viruses , affects ...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/viral infections", "virology/virulence factors and mechanisms" ]	PB1-F2 Proteins from H5N1 and 20th Century Pandemic Influenza Viruses Cause Immunopathology	journal.ppat.1001014	null	[ [ "For the first time in more than 40 years , a novel influenza virus has emerged from an animal reservoir and caused a human pandemic [1] .", "In contrast to the three pandemics of the 20th century , most disease from the novel H1N1 pandemic influenza virus has been mild [2] .", "The reasons for this d...	[ "With the recent emergence of a novel pandemic strain , there is presently intense interest in understanding the molecular signatures of virulence of influenza viruses .", "PB1-F2 proteins from epidemiologically important influenza A virus strains were studied to determine their function and contribution to virul...	[ "There is presently great interest in understanding how influenza viruses cause disease .", "In this paper , we explore the role of the influenza virus PB1-F2 protein in disease .", "We show that the ability of the protein to cause cell death is mediated through a mitochondrial death pathway controlled by prote...	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "viral vaccines", "medicine and health sciences", "rift valley fever virus", "immune physiology", "enzyme-linked immunoassays", "pathology and laboratory medicine", "pathogens", "immunology", "microbiology", "cloning", "vaccines", "preventive medicine", "viruses", "lymph nodes", "rna vir...	Rift Valley Fever Vaccine Virus Clone 13 Is Able to Cross the Ovine Placental Barrier Associated with Foetal Infections, Malformations, and Stillbirths	journal.pntd.0004550	null	[ [ "Rift Valley fever ( RVF ) is a peracute or acute zoonotic disease of ruminants caused by the mosquito-borne RVF virus ( RVFV ) , which belongs to the genus Phlebovirus within the family Bunyaviridae .", "Outbreaks of the disease are typically reported during climatic conditions that favour the breeding o...	[ "Rift Valley fever virus ( RVFV ) is a mosquito-borne pathogen that affects domesticated ruminants and occasionally humans .", "Classical RVF vaccines are based on formalin-inactivated virus or the live-attenuated Smithburn strain .", "The inactivated vaccine is highly safe but requires multiple administrations...	[ "Rift Valley fever virus is a mosquito-borne virus that causes severe disease in young ruminants and occasionally humans .", "The virus is largely confined to the African continent , but mosquito vectors associated with transmission of RVFV are globally prevalent .", "There are no vaccines fully registered for ...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience/theoretical neuroscience" ]	Tag-Trigger-Consolidation: A Model of Early and Late Long-Term-Potentiation and Depression	journal.pcbi.1000248	null	[ [ "Changes in the connection strength between neurons in response to appropriate", "stimulation are thought to be the physiological basis for learning and memory", "formation [1] , [2] .", "A minimal requirement for proper memory function", "is that these changes , once they are induced , persis...	[ "Changes in synaptic efficacies need to be long-lasting in order to serve as a", "substrate for memory .", "Experimentally , synaptic plasticity exhibits phases", "covering the induction of long-term potentiation and depression ( LTP/LTD ) during", "the early phase of synaptic plasticity , the setting of sy...	[ "Humans and animals learn by changing the strength of connections between neurons ,", "a phenomenon called synaptic plasticity .", "These changes can be induced by rather", "short stimuli ( lasting sometimes only a few seconds ) but should then be stable", "for months or years in order to be useful for long...	2008
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "trophozoites", "parasite groups", "protein interactions", "giardia", "biological cultures", "dna-binding proteins", "parasitic protozoans", "parasitology", "cell differentiation", "developmental biology", "apicomplexa", "molecular motors", "protozoans", "caco-2 cells", "motor proteins",...	Characterization of the Giardia intestinalis secretome during interaction with human intestinal epithelial cells: The impact on host cells	journal.pntd.0006120	null	[ [ "Giardia intestinalis is an intestinal protozoan parasite causing 280 million human diarrheal cases ( giardiasis ) annually [1] .", "Giardia has two life-cycle stages: infectious cysts and disease-causing trophozoites [2] .", "Trophozoites move by flagella and adhere to intestinal epithelial cells ( I...	[ "Giardia intestinalis is a non-invasive protozoan parasite that causes giardiasis in humans , the most common form of parasite-induced diarrhea .", "Disease mechanisms are not completely defined and very few virulence factors are known .", "To identify putative virulence factors and elucidate mechanistic pathwa...	[ "Giardia intestinalis is a major contributor to the enormous burden of diarrheal diseases with 280 million symptomatic human infections ( giardiasis ) per year , mainly in children .", "Nonetheless , there is poor insight into how Giardia causes disease; it is not invasive and very few virulence factors are known...	2017
[ "Introduction", "Model", "Results", "Discussion" ]	[ "developmental biology", "organism development", "biology", "computational biology" ]	Branch Mode Selection during Early Lung Development	journal.pcbi.1002377	null	[ [ "Branched structures are ubiquitous in nature , and the mechanism of their formation has been investigated for decades both in experimental [1]–[3] and theoretical studies [4] , [5] .", "Studies some 50 years ago showed that the dimension of the airway in adult lungs depends exponentially on the branch or...	[ "Many organs of higher organisms , such as the vascular system , lung , kidney , pancreas , liver and glands , are heavily branched structures .", "The branching process during lung development has been studied in great detail and is remarkably stereotyped .", "The branched tree is generated by the sequential ,...	[ "Most organs of higher organisms , such as the vascular system , lung , kidney , pancreas , liver and glands , are heavily branched structures .", "The branching process during lung development has been studied in great detail and is remarkably stereotyped .", "The branched tree is generated by the sequential ,...	2012
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "enzyme-linked immunoassays", "immune physiology", "enzymes", "immunology", "enzymology", "trichinella", "parasitic diseases", "animals", "nematode infections", "serine proteases", "developmental biology", "trichinellosis", "antibodies", ...	Characterization of a Trichinella spiralis putative serine protease. Study of its potential as sero-diagnostic tool	journal.pntd.0006485	null	[ [ "Trichinellosis is an important food-borne parasitic disease worldwide .", "Trichinella infection occurs by ingesting raw or undercooked meat containing Trichinella muscle larvae [1] .", "T . spiralis is the main etiological agent of trichinellosis [2] .", "Outbreak of human trichinellosis was rec...	[ "Trichinellosis is a serious zoonositc parasitosis worldwide .", "Because its clinical manifestations aren’t specific , the diagnosis of trichinellosis is not easy to be made .", "Trichinella spiralis muscle larva ( ML ) excretory–secretory ( ES ) antigens are the most widely applied diagnostic antigens for hum...	[ "Trichinellosis is an important parasitic zoonosis , and has a public health hazard and an economic impact on the safety of animal food .", "The diagnosis of trichinellosis is difficult and it is often misdiagnosed .", "There is an evident 2–3 week window stage between clinical manifestations and the anti-Trich...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "body fluids", "pathology and laboratory medicine", "pathogens", "immunology", "tropical diseases", "microbiology", "retroviruses", "viruses", "immunodeficiency viruses", "bacterial diseases", "rna viruses", "signs and symptoms", "genome analysis", "bacter...	In Vivo Molecular Dissection of the Effects of HIV-1 in Active Tuberculosis	journal.ppat.1005469	null	[ [ "One and a half million deaths are attributed to nine million new cases of active tuberculosis ( TB ) per annum [1] .", "Most individuals infected with Mycobacterium tuberculosis ( Mtb ) do not develop disease , but co-infection with Human immunodeficiency virus ( HIV ) -1 substantially increases this ris...	[ "Increased risk of tuberculosis ( TB ) associated with HIV-1 infection is primarily attributed to deficient T helper ( Th ) 1 immune responses , but most people with active TB have robust Th1 responses , indicating that these are not sufficient to protect against disease .", "Recent findings suggest that favourab...	[ "HIV-1 infected people have substantially increased risk of tuberculosis ( TB ) leading to a large burden of disease worldwide .", "We aimed to investigate how HIV-1 causes this effect by altering human immune responses .", "We measured the products of all immune genes at injection sites of sterilized TB under ...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "group-specific staining", "medicine and health sciences", "reproductive system", "hematoxylin staining", "alleles", "epithelial cells", "germ cells", "oocytes", "forms of dna", "paleontology", "dna", "paleogenetics", "research and analysis methods", "specimen preparation and treatment", ...	Control of Oocyte Reawakening by Kit	journal.pgen.1006215	null	[ [ "Primordial follicles are the reserve precursor pool for maturing follicles throughout reproductive life [1] .", "Primordial follicles are reawakened via an ovarian-intrinsic ( gonadotropin independent ) process whereby they are selected from the quiescent reserve into the growing follicle pool [2 , 3] ."...	[ "In mammals , females are born with finite numbers of oocytes stockpiled as primordial follicles .", "Oocytes are “reawakened” via an ovarian-intrinsic process that initiates their growth .", "The forkhead transcription factor Foxo3 controls reawakening downstream of PI3K-AKT signaling .", "However , the iden...	[ "In mammals , oocyte reawakening controls female fertility , the onset of the menopause , and thus , overall aging .", "We demonstrate here through complementary genetic experiments that Kit is the upstream receptor regulating oocyte reawakening .", "Although other cell surface receptors have been proposed as c...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Molecular Detection and Identification of Spotted Fever Group Rickettsiae in Ticks Collected from the West Bank, Palestinian Territories	journal.pntd.0004348	null	[ [ "Tick-borne spotted fever group ( SFG ) rickettsioses are caused by obligate intracellular Gram-negative bacteria belonging to the genus Rickettsia [1] .", "Feeding ticks can transmit these microorganisms to humans and animals .", "Various vertebrates are suspected to serve as reservoirs for Rickettsi...	[ "Tick-borne rickettsioses are caused by obligate intracellular bacteria belonging to the spotted fever group ( SFG ) rickettsiae .", "Although Spotted Fever is prevalent in the Middle East , no reports for the presence of tick-borne pathogens are available or any studies on the epidemiology of this disease in the...	[ "Tick borne rickettsial diseases may have similar clinical characteristics , yet epidemiologically and etiologically different diseases .", "To date , no studies have been conducted to detect potential tick vectors of rickettsiae in the West Bank .", "Therefore , we aimed to identify tick species and to determi...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "chemical compounds", "pathogens", "immunology", "microbiology", "neisseria gonorrhoeae", "esters", "membrane proteins", "mutation", "outer membrane proteins", "cellular structures and organelles", "bacteria", "bacterial ...	The novel interaction between Neisseria gonorrhoeae TdfJ and human S100A7 allows gonococci to subvert host zinc restriction	journal.ppat.1007937	null	[ [ "The obligate human pathogen Neisseria gonorrhoeae , the etiological agent of the eponymous sexually-transmitted infection ( STI ) gonorrhea , poses a growing threat to global health .", "In 2017 , the World Health Organization ( WHO ) estimated over 100 million new cases of gonorrhea , with surveillance ...	[ "Neisseria gonorrhoeae causes the sexually-transmitted infection gonorrhea , a global disease that is difficult to treat and for which there is no vaccine .", "This pathogen employs an arsenal of conserved outer membrane proteins called TonB-dependent transporters ( TdTs ) that allow the gonococcus to overcome nu...	[ "Neisseria gonorrhoeae causes the common sexually-transmitted infection gonorrhea .", "This bacteria’s ability to rapidly acquire antibiotic resistance factors , coupled with the lack of any effective vaccine to prevent infection , has resulted in a disease that poses a global threat and may become untreatable ."...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public health and epidemiology", "infectious disease epidemiology", "spatial epidemiology", "bacterial diseases", "neglected tropical diseases", "infectious disease control", "spatial analysis", "human geography", "disease mapping", "geography", "infectious diseases", "disease e...	Leptospirosis in American Samoa – Estimating and Mapping Risk Using Environmental Data	journal.pntd.0001669	null	[ [ "Leptospirosis is the most common bacterial zoonosis around the world [1] , and its emergence has been linked to many environmental and ecological drivers of disease transmission .", "Varying environmental health hazards operate in different settings , and include climate , flooding , land use , urbanisat...	[ "The recent emergence of leptospirosis has been linked to many environmental drivers of disease transmission .", "Accurate epidemiological data are lacking because of under-diagnosis , poor laboratory capacity , and inadequate surveillance .", "Predictive risk maps have been produced for many diseases to identi...	[ "Leptospirosis is the most common bacterial infection transmitted from animals to humans .", "Infected animals excrete the bacteria in their urine , and humans can become infected through contact with animals or a contaminated environment such as water and soil .", "Environmental factors are important in determ...	2012
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell physiology", "carbohydrate metabolism", "medicine and health sciences", "chemical compounds", "microbiology", "enzymology", "carbohydrates", "cell metabolism", "parasitic diseases", "protozoan life cycles", "glucose metabolism", "organic compounds", "glucose", "developmental biology"...	Deletion of transketolase triggers a stringent metabolic response in promastigotes and loss of virulence in amastigotes of Leishmania mexicana	journal.ppat.1006953	null	[ [ "Leishmania are parasitic protozoa that cause a wide spectrum of diseases including a self-healing cutaneous form , a disfiguring mucocutaneous form and severe , often fatal , visceral leishmaniasis .", "The individual clinical manifestation and severity of the disease depends on the causative Leishmania ...	[ "Transketolase ( TKT ) is part of the non-oxidative branch of the pentose phosphate pathway ( PPP ) .", "Here we describe the impact of removing this enzyme from the pathogenic protozoan Leishmania mexicana .", "Whereas the deletion had no obvious effect on cultured promastigote forms of the parasite , the Δtkt...	[ "Leishmania parasites endanger over 1 billion people worldwide , infecting 300 , 000 people and causing 20 , 000 deaths annually .", "In this study , we scrutinized metabolism in Leishmania mexicana after deletion of the gene encoding transketolase ( TKT ) , an enzyme involved in sugar metabolism via the pentose ...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "sequencing techniques", "medicine and health sciences", "immune cells", "immunology", "simulation and modeling", "alternative splicing", "mathematics", "statistics (mathematics)", "distribution curves", "molecular biology techniques", "rna sequencing", "research and analysis ...	Stochastic principles governing alternative splicing of RNA	journal.pcbi.1005761	null	[ [ "Most genes of eukaryotic organisms , unlike those of prokaryotes , may each generate multiple different mature transcript isoforms which can encode proteins with distinct or even opposing functions [1–6] .", "It has also been shown that the dominance of the major transcript isoform from a single gene may...	[ "The dominance of the major transcript isoform relative to other isoforms from the same gene generated by alternative splicing ( AS ) is essential to the maintenance of normal cellular physiology .", "However , the underlying principles that determine such dominance remain unknown .", "Here , we analyzed the ph...	[ "Alternative RNA splicing within eukaryotic cells enables each gene to generate multiple different mature transcripts which further encode proteins with distinct or even opposing functions .", "The relative frequencies of the transcript isoforms generated by a particular gene are essential to the maintenance of n...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Sustained Pax6 Expression Generates Primate-like Basal Radial Glia in Developing Mouse Neocortex	journal.pbio.1002217	"Humanizing" the expression of the transcription factor Pax6 in cortical progenitors in the developing mouse brain is sufficient to endow these progenitors with a primate-like proliferative capacity.	[ [ "The evolutionary expansion of the mammalian neocortex is thought to be primarily the consequence of the increasing proliferative capacity of cortical stem and progenitor cells during development [1–9] .", "Recent studies have progressively focused on differences between species regarding the type , abund...	[ "The evolutionary expansion of the neocortex in mammals has been linked to enlargement of the subventricular zone ( SVZ ) and increased proliferative capacity of basal progenitors ( BPs ) , notably basal radial glia ( bRG ) .", "The transcription factor Pax6 is known to be highly expressed in primate , but not mo...	[ "During development , neural progenitors generate all cells that make up the mammalian brain .", "Differences in brain size among the various mammalian species are attributed to differences in the abundance and proliferative capacity of a specific class of neural progenitors called basal progenitors .", "Among ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "signal transduction", "signaling in cellular processes", "molecular cell biology", "mechanisms of signal transduction", "signaling pathways", "biology", "microbiology", "microbial growth and development" ]	A Dynamic Response Regulator Protein Modulates G-Protein–Dependent Polarity in the Bacterium Myxococcus xanthus	journal.pgen.1002872	null	[ [ "In living organisms , cell polarization underlies many developmental and cellular processes , such as budding in yeast , cell migration and bacterial differentiation [1]–[3] .", "In eukaryotic cells , polarization mechanisms ensure the asymmetric positioning of subcellular organelles and its transmission...	[ "Migrating cells employ sophisticated signal transduction systems to respond to their environment and polarize towards attractant sources .", "Bacterial cells also regulate their polarity dynamically to reverse their direction of movement .", "In Myxococcus xanthus , a GTP-bound Ras-like G-protein , MglA , acti...	[ "Migrating cells have evolved a molecular compass to rapidly respond to environmental signals .", "During chemotaxis , small G-proteins and their regulators are activated and determine a leading cell edge towards attractant molecules .", "Bacteria also move across surfaces in a directed manner .", "The rod-sh...	2012
[ "Introduction", "Methods", "Results" ]	[ "medicine and health sciences", "epidemiology" ]	Epidemiological Trends of Dengue Disease in Thailand (2000–2011): A Systematic Literature Review	journal.pntd.0003241	null	[ [ "Dengue is a global arboviral disease affecting humans .", "The primary vector is the Aedes aegypti ( Linnaeus ) mosquito .", "Dengue is present in the tropical and subtropical regions of the Americas , the eastern Mediterranean , Africa , and the World Health Organization ( WHO ) Western Pacific and ...	[ "A literature survey and analysis was conducted to describe the epidemiology of dengue disease in Thailand reported between 2000 and 2011 .", "The literature search identified 610 relevant sources , 40 of which fulfilled the inclusion criteria defined in the review protocol .", "Peaks in the number of cases occ...	[ "We conducted this comprehensive systematic review to determine the impact of dengue disease in Thailand for the period 2000–2011 , and to identify future research priorities .", "Well-defined methods were used to search and identify relevant published research , according to predetermined inclusion criteria .", ...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Developing a Molecular Roadmap of Drug-Food Interactions	journal.pcbi.1004048	null	[ [ "Drugs and plant-based foods ( i . e . fruits , vegetables and beverages derived from them , referred to simply as “food” throughout the rest of the document ) manifest an intricate relationship in human health and have a complementary effect in disease prevention and therapy .", "In many diseases , such ...	[ "Recent research has demonstrated that consumption of food -especially fruits and vegetables- can alter the effects of drugs by interfering either with their pharmacokinetic or pharmacodynamic processes .", "Despite the recognition of such drug-food associations as an important element for successful therapeutic ...	[ "Vegetables and fruits that are otherwise considered beneficial to our health can have serious consequences in medical care .", "Interference of plant-based foods with drug performance and pharmacological activity may potentially contribute to an increased risk of side effects or treatment failure .", "A well-k...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	A Randomized Controlled Trial of Increased Dose and Frequency of Albendazole with Standard Dose DEC for Treatment of Wuchereria bancrofti Microfilaremics in Odisha, India	journal.pntd.0003583	null	[ [ "The Global Lymphatic Filariasis Elimination Programme ( GPELF ) had its inception in 1998 following agreements between the World Health Organization and the international pharmaceutical companies GlaxoSmithKline ( GSK ) and Merck to donate supplies of , respectively , albendazole and ivermectin for the progr...	[ "Although current programmes to eliminate lymphatic filariasis have made significant progress it may be necessary to use different approaches to achieve the global goal , especially where compliance has been poor and ‘hot spots’ of continued infection exist .", "In the absence of alternative drugs , the use of hi...	[ "In order to achieve global elimination of lymphatic filariasis , it may be necessary to consider alternative approaches to mass treatment using higher or more frequent dosing with the existing drugs used in the programmes .", "Outside Africa , the drugs used are albendazole and diethylcarbamazine given annually ...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "antimicrobials", "medicine and health sciences", "pathology and laboratory medicine", "gene regulation", "pathogens", "regulatory proteins", "drugs", "microbiology", "dna-binding proteins", "antifungals", "mutation", "fungi", "experimental organism systems", "transcription factors", "ph...	An acquired mechanism of antifungal drug resistance simultaneously enables Candida albicans to escape from intrinsic host defenses	journal.ppat.1006655	null	[ [ "The yeast Candida albicans is a member of the microbiota of the oral cavity and the gastrointestinal and genitourinary tracts in most healthy persons .", "When host defenses are compromised , C . albicans can also cause symptomatic infections , which range from superficial skin or mucosal infections to l...	[ "The opportunistic fungal pathogen Candida albicans frequently produces genetically altered variants to adapt to environmental changes and new host niches in the course of its life-long association with the human host .", "Gain-of-function mutations in zinc cluster transcription factors , which result in the cons...	[ "The yeast Candida albicans is part of the normal microflora of most healthy persons , but it can also cause symptomatic infections when host defenses are compromised .", "C . albicans frequently generates genetically altered variants that are better adapted to changes in its environment during colonization and i...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "infectious diseases", "none", "cell biology", "immunology", "microbiology", "mus (mouse)", "eubacteria" ]	Bacterial Ligands Generated in a Phagosome Are Targets of the Cytosolic Innate Immune System	journal.ppat.0030051	null	[ [ "Macrophages are highly phagocytic cells that can act as benign scavengers , sentinels of microbial infection , and hosts to intracellular pathogens [1] .", "However , a key property of macrophages is their capacity to be immunologically activated by cytokines such as interferon ( IFN ) –γ .", "Subseq...	[ "Macrophages are permissive hosts to intracellular pathogens , but upon activation become microbiocidal effectors of innate and cell-mediated immunity .", "How the fate of internalized microorganisms is monitored by macrophages , and how that information is integrated to stimulate specific immune responses is not...	[ "Innate immune recognition of microorganisms has a direct impact on the type and the magnitude of the immune response elicited .", "While recognition of microorganisms relies on receptors that sense pathogen-associated molecular patterns , ( PAMPs ) , it was reasonable to suspect that immune cells could discrimin...	2007
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "phosphorylation", "medicine and health sciences", "immune cells", "3' utr", "immunology", "messenger rna", "signal inhibition", "untranslated regions", "sequence motif analysis", "research and analysis methods", "sequence analysis", "white blood cells", "animal cells", "p...	Novel AU-rich proximal UTR sequences (APS) enhance CXCL8 synthesis upon the induction of rpS6 phosphorylation	journal.pgen.1008077	null	[ [ "Translation is an essential step in protein synthesis .", "Mechanisms that regulate the rate of translation determine the expression levels of a large fraction of the genome .", "This was revealed by metabolic pulse labeling of global cellular mRNA and protein synthesis rates [1] .", "Consistentl...	[ "The role of ribosomal protein S6 ( rpS6 ) phosphorylation in mRNA translation remains poorly understood .", "Here , we reveal a potential role in modulating the translation rate of chemokine ( C-X-C motif ) ligand 8 ( CXCL8 or Interleukin 8 , IL8 ) .", "We observed that more CXCL8 protein was being secreted fr...	[ "Ribosomal protein S6 ( rpS6 ) is a component of the cell translation system .", "This system produces proteins based on the instructions found on messenger ribonucleic acids or mRNAs .", "The activity of rpS6 is modified via the attachment of phosphate groups .", "This rpS6 “phosphorylation” regulates cell s...	2019
[ "Background", "Methods", "Results", "Discussion" ]	[]	Molecular Epidemiology of Rabies Viruses Circulating in Two Rabies Endemic Provinces of Laos, 2011–2012: Regional Diversity in Southeast Asia	journal.pntd.0003645	null	[ [ "Globally , an estimated 60 , 000 people die of rabies annually , and more than 31 , 000 of these deaths occur in Asia [1 , 2] .", "Among various Asian regions , the countries of the Association of South East Asian Nations ( ASEAN ) have been working towards substantial economic development .", "A cal...	[ "Although rabies is endemic in Laos , genetic characterization of the viruses in this country is limited .", "There are growing concerns that development in the region may have increased transport of dog through Laos for regional dog meat consumption , and that this may cause spillover of the viruses from dogs br...	[ "Laos is a land-locked rabies-endemic country in Southeast Asia that is surrounded by five rabies-endemic countries .", "Thus , there is increasing concern that the epidemiology of rabies in Laos is influenced by infrastructure development and economic activities , including international transport of dogs for me...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "immune physiology", "spleen", "immunology", "cancers and neoplasms", "oncology", "hematologic cancers and related disorders", "animal models", "model organisms", "epigenetics", "dna", "cytotoxic t cells", "lymphomas", "mam...	Dnmt3a Is a Haploinsufficient Tumor Suppressor in CD8+ Peripheral T Cell Lymphoma	journal.pgen.1006334	null	[ [ "DNA methylation is an epigenetic modification involved in transcriptional regulation of gene expression .", "Three catalytically active DNA methyltransferases—Dnmt1 , Dnmt3a , and Dnmt3b—are involved in the generation and maintenance of DNA methylation in mammalian cells .", "Dnmt3a and Dnmt3b are cl...	[ "DNA methyltransferase 3A ( DNMT3A ) is an enzyme involved in DNA methylation that is frequently mutated in human hematologic malignancies .", "We have previously shown that inactivation of Dnmt3a in hematopoietic cells results in chronic lymphocytic leukemia in mice .", "Here we show that 12% of Dnmt3a-deficie...	[ "Global deregulation of cytosine methylation is an epigenetic hallmark of hematologic malignancies that may promote tumorigenesis by silencing tumor suppressor genes , upregulating oncogenes , and inducing genomic instability .", "DNA methyltransferase 3a ( DNMT3A ) is one of the three catalytically active enzyme...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/protozoal infections", "infectious diseases/neglected tropical diseases", "genetics and genomics/comparative genomics", "infectious diseases/gastrointestinal infections" ]	Draft Genome Sequencing of Giardia intestinalis Assemblage B Isolate GS: Is Human Giardiasis Caused by Two Different Species?	journal.ppat.1000560	null	[ [ "Giardia intestinalis ( syn G . duodenalis and G . lamblia ) is a major contributor to the enormous burden of diarrheal diseases , as causes of morbidity and mortality worldwide .", "The human prevalence rates range from 2–7% in developed countries to 20–30% in most developing countries [1] .", "Infec...	[ "Giardia intestinalis is a major cause of diarrheal disease worldwide and two major Giardia genotypes , assemblages A and B , infect humans .", "The genome of assemblage A parasite WB was recently sequenced , and the structurally compact 11 . 7 Mbp genome contains simplified basic cellular machineries and metabol...	[ "Giardia intestinalis is a major contributor to the enormous burden of diarrheal diseases with 250 million symptomatic infections per year , and it is part of the WHO neglected disease initiative .", "Nonetheless , there is poor insight into how Giardia causes disease; it is not invasive , secretes no known toxin...	2009
[ "Introduction", "Results and Discussion", "Materials and Methods" ]	[ "sequencing techniques", "medicine and health sciences", "cell cycle and cell division", "cell processes", "fibroblasts", "genome sequencing", "mutation", "stem cells", "induced pluripotent stem cells", "connective tissue cells", "molecular biology techniques", "research and analysis methods",...	Mutational History of a Human Cell Lineage from Somatic to Induced Pluripotent Stem Cells	journal.pgen.1005932	null	[ [ "From the moment of fertilisation , as each cell divides random mutations occur which are fixed and inherited by daughter cells .", "Most of these variants have little , if any , physiological consequence but contribute to genetic diversity within tissues .", "A small proportion will contribute to pat...	[ "The accuracy of replicating the genetic code is fundamental .", "DNA repair mechanisms protect the fidelity of the genome ensuring a low error rate between generations .", "This sustains the similarity of individuals whilst providing a repertoire of variants for evolution .", "The mutation rate in the human ...	[ "The mutation load of human tissues is unknown and represents the genetic divergence from the fertilised egg .", "Reprogramming of somatic cells generates induced pluripotent stem cells ( iPSCs ) , a cell type being considered for clinical applications .", "We generated iPSCs from tissues of healthy individuals...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "neuroscience/behavioral neuroscience", "molecular biology/rna-protein interactions", "physiology/neuronal signaling mechanisms", "genetics and genomics/disease models", "neurological disorders/developmental and pediatric neurology", "neuroscience/neurobiology of disease and regeneration" ]	A Mouse Model of the Human Fragile X Syndrome I304N Mutation	journal.pgen.1000758	null	[ [ "Missense mutations have been especially informative for establishing links between genetics and protein function in human disease .", "For example , missense mutations have advanced our understanding of the relationship between autism and mutations in genes including neuroligin-3 [1] , [2] , neurexin-1 [...	[ "The mental retardation , autistic features , and behavioral abnormalities characteristic of the Fragile X mental retardation syndrome result from the loss of function of the RNA–binding protein FMRP .", "The disease is usually caused by a triplet repeat expansion in the 5′UTR of the FMR1 gene .", "This leads t...	[ "Missense mutations in human genes provide valuable insight into the genetic causes of disease .", "Fragile X Syndrome ( FXS ) , a common genetic cause of autism and mental retardation , is usually caused by transcriptional silencing of the FMR1 gene .", "The potential importance of single patient with a missen...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "invertebrates", "medicine and health sciences", "sleep", "neuroscience", "biological locomotion", "biomechanics", "animals", "animal models", "physiological processes", "drosophila melanogaster", "model organisms", "chronobiology", "drosophila", "neuroimaging", "research and analysis me...	Allatostatin A Signalling in Drosophila Regulates Feeding and Sleep and Is Modulated by PDF	journal.pgen.1006346	null	[ [ "Neuropeptides and peptide hormones transfer a wide variety of neuronal or physiological information from one cell to the other by activating specific receptors on their target cells [1] .", "Most if not all peptides are pleiotropic and can orchestrate diverse physiological , neuronal or behavioural proce...	[ "Feeding and sleep are fundamental behaviours with significant interconnections and cross-modulations .", "The circadian system and peptidergic signals are important components of this modulation , but still little is known about the mechanisms and networks by which they interact to regulate feeding and sleep .",...	[ "Feeding and sleep are fundamental behaviours that are controlled by diverse neuropeptides .", "While feeding is associated with wake periods , sleep prevents feeding .", "Both feeding and sleep are timed to specific parts of the day by internal clocks , presumably to optimise behaviour and metabolic processes ...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "animal models", "developmental biology", "zebrafish", "animal genetics", "cancer genetics", "model organisms", "gene expression", "genetics", "biology", "molecular cell biology", "genetics of disease", "dna transcription" ]	Mutations in LRRC50 Predispose Zebrafish and Humans to Seminomas	journal.pgen.1003384	null	[ [ "Human testicular germ cell tumors ( TGCT ) [MIM 613190] affect 1 in 500 Caucasian men .", "Current clinical classification recognizes five main subcategories with diverse clinical manifestations , genomic constitution and pathology [1] .", "TGCTs have their origin in the oncogenic counterparts of cel...	[ "Seminoma is a subclass of human testicular germ cell tumors ( TGCT ) , the most frequently observed cancer in young men with a rising incidence .", "Here we describe the identification of a novel gene predisposing specifically to seminoma formation in a vertebrate model organism .", "Zebrafish carrying a heter...	[ "Testicular Germ Cell Tumors are frequently occurring tumors , affecting 1 in 500 individuals .", "Of this diverse group , the subtype seminoma is most prevalent and is the most common tumor type found in men aged 20–40 years of age .", "In contrast to other frequently occurring tumor types , there is very litt...	2013
[ "Introduction", "Materials and methods", "Results", "Discussion", "Conclusion" ]	[ "guinea", "medicine and health sciences", "toxins", "pathology and laboratory medicine", "tropical diseases", "geographical locations", "vertebrates", "social sciences", "animals", "mammals", "toxicology", "toxic agents", "social geography", "neglected tropical diseases", "lassa fever", ...	Rodent control to fight Lassa fever: Evaluation and lessons learned from a 4-year study in Upper Guinea	journal.pntd.0006829	null	[ [ "Lassa fever is a viral haemorrhagic fever caused by an arenavirus , which was first discovered in Nigeria in 1969 [1 , 2] .", "The disease is endemic in West African countries , including Sierra Leone , Liberia , Guinea , southern Mali , northern Cote d’Ivoire and Nigeria [3–6] .", "Lassa fever recen...	[ "Lassa fever is a viral haemorrhagic fever caused by an arenavirus .", "The disease is endemic in West African countries , including Guinea .", "The rodents Mastomys natalensis and Mastomys erythroleucus have been identified as Lassa virus reservoirs in Guinea .", "In the absence of a vaccine , rodent control...	[ "In the absence of a Lassa fever vaccine , rodent control is the primary prevention option .", "An effective rodent control intervention must understand human behaviour towards the rodent such as: human–rodent interactions , cohabitation , and local rodent control measures .", "We conducted a rodent control int...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	VAPB/ALS8 MSP Ligands Regulate Striated Muscle Energy Metabolism Critical for Adult Survival in Caenorhabditis elegans	journal.pgen.1003738	null	[ [ "ALS is a lethal neurodegenerative disease characterized by the combined degeneration of lower and upper motor neurons [1] .", "Most ALS cases occur sporadically , but about 10% are familial .", "These genetic cases are caused by mutations in multiple genes , including in the Vapb ( VAMP/synaptobrevin...	[ "Mutations in VAPB/ALS8 are associated with amyotrophic lateral sclerosis ( ALS ) and spinal muscular atrophy ( SMA ) , two motor neuron diseases that often include alterations in energy metabolism .", "We have shown that C . elegans and Drosophila neurons secrete a cleavage product of VAPB , the N-terminal major...	[ "ALS patients often present with systemic alterations in energy metabolism , such as dyslipidemia and hypermetabolism of unknown origin .", "Reduction of Vapb function is thought to cause motor neuron disease in ALS8 patients and may predispose individuals to ALS , in general .", "We have shown that neurons sec...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases/protozoal infections", "infectious diseases/neglected tropical diseases", "biochemistry", "molecular biology" ]	Influence of Ecto-Nucleoside Triphosphate Diphosphohydrolase Activity on Trypanosoma cruzi Infectivity and Virulence	journal.pntd.0000387	null	[ [ "Trypanosoma cruzi is the etiologic agent of Chagas disease , an endemic zoonosis present in some countries of South and Central Americas .", "WHO estimates suggested that 100 million people remain at risk of acquiring this infection [1] .", "There are no vaccines or effective treatment for this disea...	[ "The protozoan Trypanosoma cruzi is the causative agent of Chagas disease .", "There are no vaccines or effective treatment , especially in the chronic phase when most patients are diagnosed .", "There is a clear necessity to develop new drugs and strategies for the control and treatment of Chagas disease .", ...	[ "The protozoan Trypanosoma cruzi is the causative agent of Chagas disease , an endemic zoonosis present in some countries of South and Central Americas .", "The World Health Organization estimates that 100 million people are at risk of acquiring this disease .", "The infection affects mainly muscle tissues in t...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "rna", "signal transduction", "medicine and health sciences", "cell biology", "nucleic acids", "cell adhesion", "pathology and laboratory medicine", "virology", "biology and life sciences", "microbiology", "molecular cell biology", "pathogenesis" ]	Coxsackievirus-Induced miR-21 Disrupts Cardiomyocyte Interactions via the Downregulation of Intercalated Disk Components	journal.ppat.1004070	null	[ [ "microRNAs ( miRNAs ) are endogenous gene regulators functioning through targeting messenger RNAs ( mRNAs ) [1] .", "Their capability of targeting several genes simultaneously enables their vast involvement in physiological and pathological conditions [2] , including cardiac dysfunctions and viral infecti...	[ "Intercalated disks ( ICDs ) are substantial connections maintaining cardiac structures and mediating signal communications among cardiomyocytes .", "Deficiency in ICD components such as desmosomes , fascia adherens and gap junctions leads to heart dysfunction .", "Coxsackievirus B3 ( CVB3 ) infection induces c...	[ "Coxsackievirus B3 ( CVB3 ) is one of most common causes of heart inflammation and failure .", "However , the mechanism by which CVB3 induces cardiac damage has not been fully elucidated .", "Particularly , the involvement of microRNAs ( miRNAs ) , a family of small RNAs controlling the progression of a wide ra...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "biology" ]	Distinct Binding and Immunogenic Properties of the Gonococcal Homologue of Meningococcal Factor H Binding Protein	journal.ppat.1003528	null	[ [ "The Gram negative bacterium Neisseria meningitidis is part of the normal human nasopharyngeal flora in up to 40% of healthy individuals [1] , [2] and a leading cause of sepsis and meningitis worldwide , with a case fatality rate from septicaemia of approximately 10% [3] , [4] .", "Because of the non-spec...	[ "Neisseria meningitidis is a leading cause of sepsis and meningitis .", "The bacterium recruits factor H ( fH ) , a negative regulator of the complement system , to its surface via fH binding protein ( fHbp ) , providing a mechanism to avoid complement-mediated killing .", "fHbp is an important antigen that eli...	[ "Neisseria meningitidis is a major cause of sepsis and meningitis in young children and adolescents .", "Although vaccines are currently available against several serogroups , a broadly effective vaccine against serogroup B is still needed .", "Factor H binding protein ( fHbp ) can bind the human complement reg...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "protein metabolism", "ruminants", "mitochondrial dna", "vertebrates", "animals", "mammals", "animal models", "model organisms", "experimental organism systems", "forms of dna", "mitochondria", "dna", "bioenergetics", "molecular biology techniques", "cellular structures and organelles", ...	Bovine and murine models highlight novel roles for SLC25A46 in mitochondrial dynamics and metabolism, with implications for human and animal health	journal.pgen.1006597	null	[ [ "Mitochondria are eukaryotic organelles with a wide range of functions .", "In addition to delivery of energy to cells via oxidative phosphorylation ( OXPHOS ) , they are involved in various other bioenergetic reactions , including Krebs cycle , β-oxidation of fatty acids and heme biosynthesis .", "Fu...	[ "Neuropathies are neurodegenerative diseases affecting humans and other mammals .", "Many genetic causes have been identified so far , including mutations of genes encoding proteins involved in mitochondrial dynamics .", "Recently , the “Turning calves syndrome” , a novel sensorimotor polyneuropathy was describ...	[ "Mitochondria are essential organelles , the site of numerous biochemical reactions , with a critical role in delivering energy to cells , particularly in the nervous system .", "Consequently , disrupted mitochondrial function often results in neurodegenerative diseases , in humans and in other mammals .", "Her...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "computer science", "cell biology", "neurological disorders", "ophthalmology", "computational biology", "neuroscience" ]	A Computational Framework for Ultrastructural Mapping of Neural Circuitry	journal.pbio.1000074	A framework for analysis of terabyte-scale serial-section transmission electron microscopic (ssTEM) datasets overcomes computational barriers and accelerates high-resolution tissue analysis, providing a practical way of mapping complex neural circuitry and an effective screening tool for neurogenetics.	[ [ "Is ssTEM really necessary ?", "Why can't we deduce networks from physiology , confocal imaging , or behavior ?", "The answer is that potential network motifs derived by these methods are not unique .", "Diversity in potential network topologies is so high [17 , 26] that only anatomical ground tru...	[ "Circuitry mapping of metazoan neural systems is difficult because canonical neural regions ( regions containing one or more copies of all components ) are large , regional borders are uncertain , neuronal diversity is high , and potential network topologies so numerous that only anatomical ground truth can resolve...	[ "Building an accurate neural network diagram of the vertebrate nervous system is a major challenge in neuroscience .", "Diverse groups of neurons that function together form complex patterns of connections often spanning large regions of brain tissue , with uncertain borders .", "Although serial-section transmi...	2009
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "action potentials", "nervous system", "membrane potential", "social sciences", "electrophysiology", "neuroscience", "ganglion cells", "vision", "neuronal tuning", "animal cells", "cellular neuroscience", "psychology", "cell biology", "anatomy", "synapse...	A model for the origin and development of visual orientation selectivity	journal.pcbi.1007254	null	[ [ "Response properties in the visual system undergo a remarkable change in the transition from subcortical pathways to cortex .", "Cortical neurons are selective for stimulus characteristics such as contour orientation , motion direction and depth .", "In primate and carnivore subcortical neurons , by c...	[ "Orientation selectivity is a key property of primary visual cortex that contributes , downstream , to object recognition .", "The origin of orientation selectivity , however , has been debated for decades .", "It is known that on- and off-centre subcortical pathways converge onto single neurons in primary visu...	[ "Many neurons in mammalian primary visual cortex are highly selective for the orientation of visual contours and can therefore contribute to object recognition .", "Orientation selectivity depends on on- and off-centre retinal neurons that respond , respectively , to light and dark .", "We describe a signal-pro...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular cell biology", "neuroscience", "biochemistry", "biology" ]	A Neurotoxic Glycerophosphocholine Impacts PtdIns-4, 5-Bisphosphate and TORC2 Signaling by Altering Ceramide Biosynthesis in Yeast	journal.pgen.1004010	null	[ [ "Remodeling of lipid species is required for maintaining normal cellular function and disruptions in lipid homeostasis are believed to contribute to aberrant cellular processes and toxicity associated with specific diseases [1] .", "Although significant advances have been made in characterizing the change...	[ "Unbiased lipidomic approaches have identified impairments in glycerophosphocholine second messenger metabolism in patients with Alzheimer's disease .", "Specifically , we have shown that amyloid-β42 signals the intraneuronal accumulation of PC ( O-16:0/2:0 ) which is associated with neurotoxicity .", "Similar ...	[ "Accelerated cognitive decline in Alzheimer's patients is associated with distinct changes in the abundance of choline-containing lipids belonging to the platelet activating factor family .", "In particular , PC ( O-16:0/2:0 ) or C16:0 platelet activating factor ( PAF ) , is specifically elevated in brains of Alz...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "animal diseases", "crystal structure", "condensed matter physics", "electron cryo-microscopy", "animal models", "animal prion diseases", "model organisms", "microscopy", "protein structure", "crystallography", "immunologic techniques", "zoology", "research ...	The Structural Architecture of an Infectious Mammalian Prion Using Electron Cryomicroscopy	journal.ppat.1005835	null	[ [ "Little is known about the structure of the infectious prion protein , the infectious agent causing prion diseases such as sheep and goat scrapie , bovine spongiform encephalopathy or “mad cow disease” , chronic wasting disease in cervids ( deer , elk , moose , and reindeer ) , and Creutzfeldt-Jakob disease i...	[ "The structure of the infectious prion protein ( PrPSc ) , which is responsible for Creutzfeldt-Jakob disease in humans and bovine spongiform encephalopathy , has escaped all attempts at elucidation due to its insolubility and propensity to aggregate .", "PrPSc replicates by converting the non-infectious , cellul...	[ "The structure of the infectious prion ( PrPSc ) , which is responsible for Creutzfeldt-Jakob disease in humans and bovine spongiform encephalopathy , has escaped all attempts at elucidation due to its propensity to aggregate .", "Here , we use the repetitive organization inherent in amyloid fibrils to analyze th...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry/molecular evolution" ]	Thermodynamic Stability of Histone H3 Is a Necessary but not Sufficient Driving Force for its Evolutionary Conservation	journal.pcbi.1001042	null	[ [ "In eukaryotes , histone and non-histone proteins package genomic DNA into higher order chromatin structures .", "These higher order structures control the accessibility of genomic DNA to various cellular machineries that perform transcription , replication , repair and recombination .", "The fundamen...	[ "Determining the forces that conserve amino acid positions in proteins across species is a fundamental pursuit of molecular evolution .", "Evolutionary conservation is driven by either a protein's function or its thermodynamic stability .", "Highly conserved histone proteins offer a platform to evaluate these d...	[ "Most proteins fold to a well-defined , three-dimensional structure , which can be delineated into the protein surface and its buried core .", "When comparing amino acid sequences of the same protein from different organisms , we would expect to find certain residue positions conserved due to the importance of th...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biogeography", "ecology and environmental sciences", "population genetics", "geographical locations", "social sciences", "census", "research design", "animal behavior", "molecular biology techniques", "population biology", "zoology", "research and analysis methods", "europe", "geography",...	Estimating recent migration and population-size surfaces	journal.pgen.1007908	null	[ [ "MAPS estimates demography using the number of Pairwise Shared Coalescence ( PSC ) segments of different lengths shared between individuals .", "We define a PSC segment between ( haploid ) individuals to be a genomic segment with a single coalescent time across its length ( Fig 1A ) .", "Long PSC ( lP...	[ "In many species a fundamental feature of genetic diversity is that genetic similarity decays with geographic distance; however , this relationship is often complex , and may vary across space and time .", "Methods to uncover and visualize such relationships have widespread use for analyses in molecular ecology ,...	[ "We introduce a novel statistical method to infer migration rates and population sizes across space in recent time periods .", "Our approach builds upon the previously developed EEMS method , which infers effective migration rates under a dense lattice .", "Similarly , we infer demographic parameters under a la...	2019
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "taxonomy", "chemical bonding", "medicine and health sciences", "shrews", "membrane potential", "vertebrates", "electrophysiology", "mice", "diet", "animals", "mammals", "neuroscience", "receptor potentials", "phylogenetics", "data management", "nutrition", "phylogenetic analysis", ...	Molecular mechanism of the tree shrew’s insensitivity to spiciness	journal.pbio.2004921	null	[ [ "Many plants contain pungent chemicals that deter animals from consuming them .", "Particularly , the genus Capsicum encompasses 22 wild species and produces a capsaicinoid called capsaicin , which is a pungent substance [1 , 2] .", "One of these species , the chili pepper , is a low shrub with capsai...	[ "Spicy foods elicit a pungent or hot and painful sensation that repels almost all mammals .", "Here , we observe that the tree shrew ( Tupaia belangeri chinensis ) , which possesses a close relationship with primates and can directly and actively consume spicy plants .", "Our genomic and functional analyses rev...	[ "Most mammals cannot tolerate the pungent sensation , such as that evoked by eating chili peppers .", "Here , we show that unexpectedly , the tree shrew , a mammal closely related to primates , can consume pungent plants .", "We determined that this tolerance is caused by an amino acid change in the tree shrew’...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Utilization of an Eilat Virus-Based Chimera for Serological Detection of Chikungunya Infection	journal.pntd.0004119	null	[ [ "The genus Alphavirus in the family Togaviridae is comprised of small , enveloped viruses with single-stranded , positive-sense RNA genomes 11–12 kb in length [1] .", "The genus includes 31 recognized species classified into eleven complexes based on antigenic and/or genetic similarities [2–4] , with most...	[ "In December of 2013 , chikungunya virus ( CHIKV ) , an alphavirus in the family Togaviridae , was introduced to the island of Saint Martin in the Caribbean , resulting in the first autochthonous cases reported in the Americas .", "As of January 2015 , local and imported CHIKV has been reported in 50 American cou...	[ "We have developed an innovative approach to production of alphavirus antigens for use in diagnostic assays that results in reduced production complexity as well as improved sensitivity in application .", "By generating recombinant viruses that contain the structural protein genes of pathogenic alphaviruses and t...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "chemical bonding", "crystal structure", "absorption spectroscopy", "condensed matter physics", "crystallography", "thermodynamics", "hydrogen bonding", "selectins", "physical chemistry", "research and analysis methods", "contractile proteins", "actins", "solid state physics", "proteins", ...	Unraveling the mechanism of the cadherin-catenin-actin catch bond	journal.pcbi.1006399	null	[ [ "The development and maintenance of tissues in multicellular organisms requires a diverse array of structural elements that link cells to each other and to the extracellular matrix [1 , 2] .", "For epithelial tissues the main players in cell-cell adhesion are the proteins of the adherens junction complex:...	[ "The adherens junctions between epithelial cells involve a protein complex formed by E-cadherin , β-catenin , α-catenin and F-actin .", "The stability of this complex was a puzzle for many years , since in vitro studies could reconstitute various stable subsets of the individual proteins , but never the entirety ...	[ "Epithelial cells that line the surface of cavities in the human body are held together by groups of proteins known as adherens junctions .", "The cells are always under some level of mechanical tension , and the resulting forces can play a major role in determining junction stability .", "Our work provides a t...	2018
[ "Introduction", "Methods", "Results", "Discussion", "Conclusions" ]	[ "schistosoma", "invertebrates", "schistosoma mansoni", "helminths", "gene regulation", "dna-binding proteins", "animals", "dna transcription", "dna replication", "genome analysis", "dna", "epigenetics", "chromatin", "promoter regions", "genomics", "chromosome biology", "proteins", ...	Histone deacetylase inhibition modulates histone acetylation at gene promoter regions and affects genome-wide gene transcription in Schistosoma mansoni	journal.pntd.0005539	null	[ [ "It has been widely recognized in recent years that epigenetic effectors of chromatin remodeling are promising targets for therapeutic intervention , because they play a key role in epigenetic regulation of gene expression in all eukaryotes [1 , 2] .", "For schistosomiasis , new therapeutic interventions ...	[ "Schistosomiasis is a parasitic disease infecting hundreds of millions of people worldwide .", "Treatment depends on a single drug , praziquantel , which kills the Schistosoma spp .", "parasite only at the adult stage .", "HDAC inhibitors ( HDACi ) such as Trichostatin A ( TSA ) induce parasite mortality in v...	[ "Human schistosomiasis is a disease caused by the parasite Schistosoma spp .", "that affects over 230 million people worldwide .", "Treatment depends on a single drug , praziquantel , and the search for new drugs calls for exploiting strategies that are successful for other pathologies such as cancer , includin...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biophysics/macromolecular assemblies and machines", "biophysics/theory and simulation", "biophysics/protein folding" ]	Multi-Scale Simulations Provide Supporting Evidence for the Hypothesis of Intramolecular Protein Translocation in GroEL/GroES Complexes	journal.pcbi.1000006	null	[ [ "Proteins that have not yet folded to their native state may interfere with the machinery of the cell .", "For this reason , prokaryotic and eukaryotic cells have evolved special macro-molecular “chaperone” complexes that capture and refold partially folded proteins , thereby preventing them from indulgin...	[ "The biological function of chaperone complexes is to assist the folding of non-native proteins .", "The widely studied GroEL chaperonin is a double-barreled complex that can trap non-native proteins in one of its two barrels .", "The ATP-driven binding of a GroES cap then results in a major structural change o...	[ "Chaperonin complexes capture proteins that have not yet reached their functional ( “native” ) state .", "Non-native proteins cannot perform their function correctly and threaten the survival of the cell .", "The chaperonins help these proteins to reach their native state .", "The prokaryotic GroEL-GroES chap...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "reproductive system", "body fluids", "pathology and laboratory medicine", "pathogens", "microbiology", "vertebrates", "viral structure", "animals", "mammals", "reproductive physiology", "retroviruses", "primates", "immunodeficiency viruses", "viruses", ...	Increases in Endogenous or Exogenous Progestins Promote Virus-Target Cell Interactions within the Non-human Primate Female Reproductive Tract	journal.ppat.1005885	null	[ [ "Globally , male-to-female mucosal transmission accounts for the majority of recent HIV-1 infections ( 60% ) [1] .", "Numerous factors may increase HIV-1 acquisition risk in women , including stage of HIV-1 infection and viral load of the partner , co-infections with sexually transmitted infections , cerv...	[ "Currently , there are mounting data suggesting that HIV-1 acquisition in women can be affected by the use of certain hormonal contraceptives .", "However , in non-human primate models , endogenous or exogenous progestin-dominant states are shown to increase acquisition .", "To gain mechanistic insights into th...	[ "Sexual transmission accounts for over 80% of all HIV-1 infections , with half of new infections occurring in women .", "Epidemiological studies suggest that certain hormonal contraceptives may be associated with increased HIV-1 acquisition .", "A hormonal influence of vaginal HIV acquisition is supported by st...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "public health", "medicine", "infectious diseases", "public health and epidemiology", "epidemiology", "neglected tropical diseases", "parasitic diseases" ]	Human and Canine Echinococcosis Infection in Informal, Unlicensed Abattoirs in Lima, Peru	journal.pntd.0001462	null	[ [ "Canine echinococcosis is caused by the adult stage of the tapeworm Echinococcus granulosus; infected dogs are the source of infection for human cystic hydatid disease ( CHD ) , a serious public health problem in farming regions around the world [1] , [2] .", "In the domestic life cycle of E . granulosus ...	[ "Echinococcus granulosus infections are a major public health problem in livestock-raising regions around the world .", "The life cycle of this tapeworm is sustained between dogs ( definitive host , canine echinococcosis ) , and herbivores ( intermediary host , cystic hydatid disease ) .", "Humans may also deve...	[ "Echinococcus granulosus infections are a major public health problem in livestock-raising regions around the world .", "This parasite is transmitted by dogs , and humans could be accidentally infected , developing cystic lesions in internal organs after several years of infection .", "The risk of infection has...	2012
[ "Introduction", "Results/Discussion", "Methods", "Supporting Information" ]	[ "viruses", "infectious diseases", "computational biology", "homo (human)", "eubacteria" ]	The Landscape of Human Proteins Interacting with Viruses and Other Pathogens	journal.ppat.0040032	null	[ [ "Infectious diseases result in millions of deaths each year .", "Millions of dollars are spent annually to better understand how pathogens infect their hosts and to identify potential targets for therapeutics .", "An important aspect of any host-pathogen system is the mechanism by which a pathogen is ...	[ "Infectious diseases result in millions of deaths each year .", "Mechanisms of infection have been studied in detail for many pathogens .", "However , many questions are relatively unexplored .", "What are the properties of human proteins that interact with pathogens ?", "Do pathogens interact with certain ...	[ "Many pathogens , such as viruses and bacteria , cause disease in humans .", "Pathogen infections result in illness and death for millions of people each year .", "Pathogens communicate with human cells through physical interactions with various human proteins on the surface of the cell and within the interior ...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "physiological processes", "developmental biology", "reproductive system", "anatomy", "fertilization", "ecology", "natural selection", "sexual selection", "sexual conflict", "speciation", "physiology", "biology and life sciences", "sexual reproduction", "evolutionary biology", "evolution...	Intense Sperm-Mediated Sexual Conflict Promotes Reproductive Isolation in Caenorhabditis Nematodes	journal.pbio.1001915	Sperm from other species invade female tissues to cause sterility and death, helping to keep nematode species boundaries intact.	[ [ "Rarely do reproductive interests of males and females perfectly align .", "Sexual selection can accelerate the evolution of the traits and molecules mediating reproductive encounters , and this can lead to sexual conflict [1] , [2] .", "Components of the reproductive system that mediate male-female i...	[ "Conflict between the sexes over reproductive interests can drive rapid evolution of reproductive traits and promote speciation .", "Here we show that inter-species mating between Caenorhabditis nematodes sterilizes maternal individuals .", "The principal effectors of male-induced harm are sperm cells , which i...	[ "The sexes have divergent reproductive interests , and conflict arising from this disparity can drive the rapid evolution of reproductive traits and promote speciation .", "Here we describe a unique reproductive barrier in Caenorhabditis nematodes that is induced by sperm .", "We found that mating between speci...	2014
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "leptospira", "pathology and laboratory medicine", "infectious disease epidemiology", "pathogens", "tropical diseases", "microbiology", "geographical locations", "vertebrates", "seychelles", "animals", "mammals", "dogs", "bacterial diseases", "neglected tr...	Human leptospirosis in Seychelles: A prospective study confirms the heavy burden of the disease but suggests that rats are not the main reservoir	journal.pntd.0005831	null	[ [ "Zoonoses are known to contribute to approximately 60% of human infectious diseases and represent 75% of emerging diseases [1] .", "Among them , leptospirosis is considered as one of the most prevalent bacterial zoonotic disease worldwide [2] , as well as a ( re ) emerging disease [3] .", "It is consi...	[ "Leptospirosis is a bacterial zoonosis caused by pathogenic Leptospira for which rats are considered as the main reservoir .", "Disease incidence is higher in tropical countries , especially in insular ecosystems .", "Our objectives were to determine the current burden of leptospirosis in Seychelles , a country...	[ "Leptospirosis is an emerging environmental infectious disease caused by corkscrew shaped bacteria called Leptospira .", "Humans usually get infected during recreational or work-related outdoor activities through contact with urine excreted by animal reservoirs .", "As a zoonotic disease , leptospirosis is a go...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Alcohol-Induced Histone Acetylation Reveals a Gene Network Involved in Alcohol Tolerance	journal.pgen.1003986	null	[ [ "Drug tolerance and dependence are two key components in the development of drug addiction .", "These drug responses are believed to arise from common homeostatic adaptations in the brain that oppose the effects of the drug [1] , [2] .", "Tolerance in particular is a reduction in drug sensitivity in r...	[ "Sustained or repeated exposure to sedating drugs , such as alcohol , triggers homeostatic adaptations in the brain that lead to the development of drug tolerance and dependence .", "These adaptations involve long-term changes in the transcription of drug-responsive genes as well as an epigenetic restructuring of...	[ "Alcoholism is a complex condition of compulsive alcohol use that results in devastating physical and social consequences .", "The development of this affliction is believed to arise in part by homeostatic adaptations in the brain that lead to the development of alcohol tolerance and dependence .", "These adapt...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "enzyme-linked immunoassays", "protein interactions", "pathology and laboratory medicine", "eukaryotic membrane proteins", "pathogens", "microbiology", "staphylococcus aureus", "membrane proteins", "physiological processes", "immunologic techniques", "cellular s...	Flotillin scaffold activity contributes to type VII secretion system assembly in Staphylococcus aureus	journal.ppat.1006728	null	[ [ "Scaffold proteins , which are responsible for tethering proteins and facilitating multi-enzymatic biological reactions [1–3] , are found ubiquitously in eukaryotic and prokaryotic cells .", "These proteins were first identified in eukaryotic cells , where they have been traditionally studied .", "The...	[ "Scaffold proteins are ubiquitous chaperones that promote efficient interactions between partners of multi-enzymatic protein complexes; although they are well studied in eukaryotes , their role in prokaryotic systems is poorly understood .", "Bacterial membranes have functional membrane microdomains ( FMM ) , a s...	[ "The recently discovered functional membrane microdomains ( FMM ) of prokaryotic cells contain a protein homologous to the scaffold protein flotillin found in eukaryotic lipid rafts .", "It remains to be elucidated whether , like their eukaryotic counterparts , flotillin homolog proteins have a scaffold function ...	2017
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "biology", "computational biology" ]	Prediction of Drug Combinations by Integrating Molecular and Pharmacological Data	journal.pcbi.1002323	null	[ [ "In the past decades , targeted therapies modulating specific targets were considerably successful .", "However , recently , the rate of new drug approvals is slowing down despite increasing research budgets for drug discovery .", "One reason for this is that most human diseases are caused by complex ...	[ "Combinatorial therapy is a promising strategy for combating complex disorders due to improved efficacy and reduced side effects .", "However , screening new drug combinations exhaustively is impractical considering all possible combinations between drugs .", "Here , we present a novel computational approach to...	[ "The combination of distinct drugs in combinatorial therapy can help to improve therapeutic efficacy by overcoming the redundancy and robustness of pathogenic processes , or by lowering the risk of side effects .", "However , identification of effective drug combinations is cumbersome , considering the possible s...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "plant science", "rice", "cereals", "plant growth and development", "crops", "genetics", "plant genetics", "biology", "crop genetics", "morphogenesis", "agriculture" ]	DWARF TILLER1, a WUSCHEL-Related Homeobox Transcription Factor, Is Required for Tiller Growth in Rice	journal.pgen.1004154	null	[ [ "Rice is one of the most important crops in the world and feeds more than half of the world population .", "Thousands of years of domestication and breeding have selected many desirable traits in rice , including a plant architecture optimized for grain yield and quality .", "A mature rice plant has a...	[ "Unlike many wild grasses , domesticated rice cultivars have uniform culm height and panicle size among tillers and the main shoot , which is an important trait for grain yield .", "However , the genetic basis of this trait remains unknown .", "Here , we report that DWARF TILLER1 ( DWT1 ) controls the developme...	[ "Plant architecture is important for crop yield .", "In most plants , branches grow smaller than the main shoot , largely due to the ‘apical dominance’ .", "However , in several cereal crops , including rice , wheat , and barley , the branches ( tillers ) have a height and size indistinguishable from the main s...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "evolutionary biology", "evolutionary biology/evolutionary and comparative genetics" ]	The Mating-Type Chromosome in the Filamentous Ascomycete Neurospora tetrasperma Represents a Model for Early Evolution of Sex Chromosomes	journal.pgen.1000030	null	[ [ "Many diverse systems for sex determination have evolved in plants and animals [1]–[3] .", "One involves physically distinct sex chromosomes , a system thought to have evolved independently many times by suppression of recombination around the sex determination genes , followed by differentiation and dege...	[ "We combined gene divergence data , classical genetics , and phylogenetics to study the evolution of the mating-type chromosome in the filamentous ascomycete Neurospora tetrasperma .", "In this species , a large non-recombining region of the mating-type chromosome is associated with a unique fungal life cycle whe...	[ "In fungi , mating occurs between individuals of alternative mating-types and there is no dichotomy of individuals into two morphologically different sexes .", "Nevertheless , in this paper we show that chromosomal regions controlling mating-type identity in fungi share features with the more complex sex chromoso...	2008
[ "Introduction", "Material and methods", "Results", "Discussion" ]	[ "typhus", "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "tropical diseases", "microbiology", "geographical locations", "parasitic diseases", "brucellosis", "bacterial diseases", "signs and symptoms", "neglected tropical diseases", "ethiopia", "bacteria",...	Community-based prevalence of typhoid fever, typhus, brucellosis and malaria among symptomatic individuals in Afar Region, Ethiopia	journal.pntd.0006749	null	[ [ "Sub-Saharan Africa is plagued by a myriad of infectious diseases posing significant public health and economic challenges .", "In addition , the often non-specific clinical signs of these diseases and the scarcity of proper diagnostic tools are the major challenges for health professionals in properly di...	[ "In sub-Saharan Africa , where there is the scarcity of proper diagnostic tools , febrile illness related symptoms are often misdiagnosed as malaria .", "Information on causative agents of febrile illness related symptoms among pastoral communities in Ethiopia have rarely been described .", "In this a community...	[ "Many diseases such as typhoid fever , typhus , brucellosis and malaria show common symptoms such as fever , headache , joint pain and back pain .", "Hence , in countries where there is a problem of appropriate laboratory based diagnostic tools , health workers cannot properly diagnose these diseases and provide ...	2018
[ "Introduction", "Results and discussion", "Methods" ]	[ "taxonomy", "ecology and environmental sciences", "ecological niches", "microbiome", "microbiology", "random variables", "covariance", "multivariate analysis", "data management", "mathematics", "statistics (mathematics)", "algebra", "microbial genomics", "research and analysis methods", ...	Variable habitat conditions drive species covariation in the human microbiota	journal.pcbi.1005435	null	[ [ "Species in an ecosystem interact with each other and with their environment .", "Both types of interactions leave an imprint on the composition and diversity of a community .", "Two species competing for exactly the same resources engage in a struggle for existence [1] .", "In the end , one speci...	[ "Two species with similar resource requirements respond in a characteristic way to variations in their habitat—their abundances rise and fall in concert .", "We use this idea to learn how bacterial populations in the microbiota respond to habitat conditions that vary from person-to-person across the human populat...	[ "The human body is inhabited by a vast number of microorganisms comprising the human microbiota .", "The species composition of the microbiota varies considerably from person-to-person and the relative abundances of some species rise and fall in concert .", "We introduce a mathematical model where differences i...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biotechnology", "invertebrates", "engineering and technology", "caenorhabditis", "social sciences", "neuroscience", "animals", "animal models", "caenorhabditis elegans", "model organisms", "odorants", "materials science", "experimental organism systems", "interneurons", "genetic enginee...	Molecular and cellular modulators for multisensory integration in C. elegans	journal.pgen.1007706	null	[ [ "An environment is often represented by numerous sensory cues .", "In order to better survive , an animal often needs to detect and process simultaneously present sensory cues to make a behavioral decision [1–8] .", "Because integrating multiple sensory cues generates a more accurate evaluation of the...	[ "In the natural environment , animals often encounter multiple sensory cues that are simultaneously present .", "The nervous system integrates the relevant sensory information to generate behavioral responses that have adaptive values .", "However , the neuronal basis and the modulators that regulate integrated...	[ "The present study characterizes the modulation of a behavioral decision in C . elegans when the worm is presented with a food lawn that is paired with a repulsive smell .", "We show that multiple specific sensory neurons and interneurons play roles in making the decision .", "We also identify several modulator...	2019
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "cardiovascular anatomy", "congenital anomalies", "gene regulation", "regulatory proteins", "dna-binding proteins", "respiratory system", "transcription factors", "proteins", "gene expression", "congenital disorders", "clinical genetics", "biochemistry", "th...	De novo variants in congenital diaphragmatic hernia identify MYRF as a new syndrome and reveal genetic overlaps with other developmental disorders	journal.pgen.1007822	null	[ [ "Congenital diaphragmatic hernia ( CDH ) is a severe developmental disorder affecting 1 in 3000 live births [1 , 2] .", "It is characterized by defects in diaphragm that allow the abdominal viscera to move into the thoracic cavity and is associated with pulmonary hypoplasia and in some cases pulmonary hyp...	[ "Congenital diaphragmatic hernia ( CDH ) is a severe birth defect that is often accompanied by other congenital anomalies .", "Previous exome sequencing studies for CDH have supported a role of de novo damaging variants but did not identify any recurrently mutated genes .", "To investigate further the genetics ...	[ "Congenital diaphragmatic hernia ( CDH ) is a life-threatening condition affecting about 1 every 3000 newborns .", "Although the role of genetics in the pathogenesis of CDH has been well established , only a handful of disease genes have been identified so far .", "We and other have previously shown that de nov...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "biogeography", "medicine and health sciences", "ecology and environmental sciences", "geographical locations", "tropical diseases", "parasitic diseases", "north america", "neglected tropical diseases", "infectious disease control", "caribbean", "public and occupational health", "infectious di...	Geospatial-temporal distribution of Tegumentary Leishmaniasis in Colombia (2007–2016)	journal.pntd.0006419	null	[ [ "Leishmaniasis , considered one of the most neglected diseases worldwide , is a grouping of parasitic pathologies caused by protozoans of the Leishmania genus , and transmitted to humans primarily by insects of the Psychodidae family [1] .", "Leishmaniasis displays a wide range of manifestations and clini...	[ "Tegumentary Leishmaniasis ( TL ) is a neglected disease with worldwide distribution and considered a public health problem , especially in Latin America .", "In Colombia , the governmental epidemiological surveillance system ( SIVIGILA ) is responsible for collecting information on the presentation of cases of T...	[ "Colombia is among the countries with the highest number of Tegumentary Leishmaniasis cases worldwide .", "Despite public health efforts , and the existence of a national epidemiological surveillance system , articulated with the regional SisLeish system , the trends followed by the disease’s prevalence and incid...	2018

Subsets and Splits

No community queries yet

The top public SQL queries from the community will appear here once available.