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headings list	keywords list	title stringlengths 20 281	id stringlengths 20 20	toc stringlengths 57 522 ⌀	sections list	abstract list	summary list	year stringclasses 13 values
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "plant anatomy", "cell division analysis", "cell cycle and cell division", "plant cell biology", "cell processes", "brassica", "simulation and modeling", "developmental biology", "plant science", "model organisms", "experimental organism systems", "bioassays and physiological analysis", "emb...	Cell geometry determines symmetric and asymmetric division plane selection in Arabidopsis early embryos	journal.pcbi.1006771	null	[ [ "In plants , patterns of cell divisions combined with growth and differentiation determine the hierarchical organization into tissues and organs .", "Cells can proliferate via symmetric divisions while asymmetric divisions are mainly associated with initiation of new cell types , layers and developmental ...	[ "Plant tissue architecture and organ morphogenesis rely on the proper orientation of cell divisions .", "Previous attempts to predict division planes from cell geometry in plants mostly focused on 2D symmetric divisions .", "Using the stereotyped division patterns of Arabidopsis thaliana early embryogenesis , w...	[ "The proper positioning of division planes is key for correct development and morphogenesis of organs , in particular in plants were cellular walls prevent cell rearrangements .", "Elucidating how division planes are selected is therefore essential to decipher the cellular bases of plant morphogenesis .", "Prev...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunology/immune response", "immunology/innate immunity", "virology/effects of virus infection on host gene expression", "immunology/immunity to infections", "virology/host antiviral responses" ]	Interferon-β Pretreatment of Conventional and Plasmacytoid Human Dendritic Cells Enhances Their Activation by Influenza Virus	journal.ppat.1000193	null	[ [ "Dendritic cells ( DCs ) play a key role in the initiation and regulation of the immune system .", "They respond to various microbial stimuli by undergoing a process of activation that propels them to migrate to draining lymph nodes and endows them with the ability to efficiently activate T cells [1] , [2...	[ "Influenza virus produces a protein , NS1 , that inhibits infected cells from releasing type I interferon ( IFN ) and blocks maturation of conventional dendritic cells ( DCs ) .", "As a result , influenza virus is a poor activator of both mouse and human DCs in vitro .", "However , in vivo a strong immune respo...	[ "Influenza infection leads to a serious respiratory infection of the lung epithelium .", "Lying directly below the epithelial cells are immune system sentinels known as dendritic cells .", "These cells interact with the virus and carry parts of the virus to draining lymph nodes to activate killer T cells .", ...	2008
[ "Introduction", "Material and Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "parasitic diseases", "parasitic protozoans", "mutation", "protozoans", "leishmania", "cellular structures and organelles", "lipids", "sterols", "cell membranes", "biochemistry", "leishmania infantum", "point mutation", "cell biology", "genetics", "biolo...	Different Mutations in a P-type ATPase Transporter in Leishmania Parasites are Associated with Cross-resistance to Two Leading Drugs by Distinct Mechanisms	journal.pntd.0005171	null	[ [ "Protozoan parasites belonging to the Leishmania genus cause several vector-borne diseases collectively referred as leishmaniases .", "Currently , Leishmania species threaten ca .", "350 million people in 88 countries worldwide [1] .", "Control measures primarily rely on prevention and chemotherap...	[ "Leishmania infantum is an etiological agent of the life-threatening visceral form of leishmaniasis .", "Liposomal amphotericin B ( AmB ) followed by a short administration of miltefosine ( MF ) is a drug combination effective for treating visceral leishmaniasis in endemic regions of India .", "Resistance to MF...	[ "Miltefosine and amphotericin B are two leading molecules in the fight against the vector-borne disease Leishmaniasis .", "We demonstrate here that different point mutations in a P-type ATPase could play an important role in resistance , not only to miltefosine , but also to amphotericin B . Furthermore , macroph...	2016
[ "Introduction", "Results and discussion" ]	[ "taxonomy", "ecology and environmental sciences", "microbiome", "community structure", "microbiology", "phylogenetics", "data management", "information technology", "data processing", "microbial genomics", "computer and information sciences", "ecosystems", "medical microbiology", "behavior...	Two dynamic regimes in the human gut microbiome	journal.pcbi.1005364	null	[ [ "Microbial ecology has become an important branch of medical science [1] .", "Recent work has shown how each person maintains a fairly unique microbial fingerprint [2–4] , and that microbial dysbioses are often associated with shifts in health-status [5–8] .", "We now recognize that our microbiota are...	[ "The gut microbiome is a dynamic system that changes with host development , health , behavior , diet , and microbe-microbe interactions .", "Prior work on gut microbial time series has largely focused on autoregressive models ( e . g . Lotka-Volterra ) .", "However , we show that most of the variance in microb...	[ "Dynamics reveal crucial information about how a system functions .", "In this study , we develop an approach for disentangling two types of dynamics within the human gut microbiome .", "We find that autoregressive dynamics involve recovery from large deviations in community structure .", "These recovery proc...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell physiology", "cell death", "invertebrates", "autophagic cell death", "medicine and health sciences", "reproductive system", "rna interference", "gonads", "caenorhabditis", "cell processes", "animals", "germ cells", "dna damage", "animal models", "caenorhabditis elegans", "model o...	Autophagy of germ-granule components, PGL-1 and PGL-3, contributes to DNA damage-induced germ cell apoptosis in C. elegans	journal.pgen.1008150	null	[ [ "During mammalian germline development , the vast majority of germ cells are eliminated by apoptosis [1–5] .", "Studies in mouse models demonstrated that germ cell apoptosis following DNA damage requires the activities of the DNA damage response pathway and the p53 family members [6 , 7] .", "The majo...	[ "Germ granules , termed P granules in nematode C . elegans , are the germline-specific cytoplasmic structures widely observed from worms to humans .", "P granules are known to have critical functions for postembryonic germline development likely through regulating RNA metabolism .", "They are localized at the p...	[ "C . elegans provides a prime model for studying evolutionarily conserved biological mechanisms that control development and physiology .", "One of the conserved features of germ cells is the presence of germ granules , the germline-specific cytoplasmic structures observed in various organisms from worms to human...	2019
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "ecology", "evolutionary biology", "neuroscience" ]	Selection for Social Signalling Drives the Evolution of Chameleon Colour Change	journal.pbio.0060025	In dwarf chameleons, evolutionary shifts in the capacity for colour change are associated with increasingly conspicuous signals used in contests and courtship rather than by the need to match different backgrounds.	[ [ "The ability to change colour in response to environmental stimuli has evolved in numerous vertebrate and invertebrate lineages including fish [1–4] , amphibians [5 , 6] , reptiles [7] , crustaceans [8] , and cephalopods [9 , 10] .", "In most lineages , colour change occurs over a period of minutes or hou...	[ "Rapid colour change is a remarkable natural phenomenon that has evolved in several vertebrate and invertebrate lineages .", "The two principal explanations for the evolution of this adaptive strategy are ( 1 ) natural selection for crypsis ( camouflage ) against a range of different backgrounds and ( 2 ) selecti...	[ "The ability to change colour has evolved in numerous vertebrate and invertebrate groups , the most well-known of which are chameleons and cephalopods ( octopuses and their relatives ) .", "There is great variation among species , however , in the apparent capacity for colour change , ranging from limited changes...	2008
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "learning", "medicine and health sciences", "action potentials", "neural networks", "membrane potential", "social sciences", "electrophysiology", "neuroscience", "learning and memory", "surgical and invasive medical procedures", "optimization", "cognitive psychology", "mathematics", "funct...	Autonomous Optimization of Targeted Stimulation of Neuronal Networks	journal.pcbi.1005054	null	[ [ "Electrical stimulation of the brain is considered an effective strategy to manage the symptoms of an increasing range of neurological disorders like essential tremor [1 , 2] , dystonia [3] and Parkinson’s disease ( PD ) [4–7] , and as a possible means to artificially inject information into neural circuits ,...	[ "Driven by clinical needs and progress in neurotechnology , targeted interaction with neuronal networks is of increasing importance .", "Yet , the dynamics of interaction between intrinsic ongoing activity in neuronal networks and their response to stimulation is unknown .", "Nonetheless , electrical stimulatio...	[ "Electrical stimulation of the brain is increasingly used to alleviate the symptoms of a range of neurological disorders and as a means to artificially inject information into neural circuits in neuroprosthetic applications .", "Machine learning has been proposed to find optimal stimulation settings autonomously ...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "biology and life sciences", "medicine and health sciences" ]	Combined Inflammatory and Metabolic Defects Reflected by Reduced Serum Protein Levels in Patients with Buruli Ulcer Disease	journal.pntd.0002786	null	[ [ "Buruli ulcer disease ( BUD ) is a progressive ulceration of the skin that results from infection with Mycobacterium ulcerans [1] , [2] , [3] .", "BUD is associated with swamps , marshes and wetlands , with the most affected countries in Western Africa .", "The disease classically starts as a nodule ,...	[ "Buruli ulcer is a skin disease caused by Mycobacterium ulcerans that is spreading in tropical countries , with major public health and economic implications in West Africa .", "Multi-analyte profiling of serum proteins in patients and endemic controls revealed that Buruli ulcer disease down-regulates the circula...	[ "Buruli ulcer is a skin disease caused by inoculation of Mycobacterium ulcerans bacteria , which is emerging in tropical countries .", "Lesions typically start as nodules , which eventually open to form progressive , non-healing wounds .", "Although anti-mycobacterial antibiotics are efficient at stopping the i...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "chemical compounds", "enzymes", "salts", "enzymology", "phosphatases", "fungi", "model organisms", "experimental organism systems", "molecular biology techniques", "mapk signaling cascades", "saccharomyces", "research and analysis methods", "proteins", "hyperexpression techniques", "sul...	Inositol polyphosphates regulate and predict yeast pseudohyphal growth phenotypes	journal.pgen.1007493	null	[ [ "The transition from unicellular yeast to growth in multicellular filaments is characteristic of many fungi [1–4] .", "In the budding yeast Saccharomyces cerevisiae nitrogen limitation or growth in an alternate carbon source induces cell elongation , unipolar budding , and altered cell-cell adhesion , res...	[ "Pseudohyphal growth is a nutrient-regulated program in which budding yeast form multicellular filaments of elongated and connected cells .", "Filamentous growth is required for virulence in pathogenic fungi and provides an informative model of stress-responsive signaling .", "The genetics and regulatory networ...	[ "Changes in metabolite levels underlie important biological processes , including cellular responses to nutrient stress .", "One such response encompasses the nitrogen stress-induced transition of budding yeast cells into multicellular filaments , relevant as a model of directional growth and fungal pathogenesis ...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "milk", "body fluids", "immune physiology", "ruminants", "immunology", "antigenic variation", "diet", "vertebrates", "cloning", "animals", "mammals", "nutrition", "animal behavior", "mycoplasma", "molecular biology techniques", "zoology", "bacteria",...	Vpma phase variation is important for survival and persistence of Mycoplasma agalactiae in the immunocompetent host	journal.ppat.1006656	null	[ [ "Mycoplasmas are not only the smallest but also belong to the most successful bacterial pathogens that cause persistent and often difficult-to eradicate infections in humans and animals [1] .", "Although a number of mycoplasma diseases have a huge socio-economic significance , proper control strategies ar...	[ "Despite very small genomes , mycoplasmas retain large multigene families encoding variable antigens whose exact role in pathogenesis needs to be proven .", "To understand their in vivo significance , we used Mycoplasma agalactiae as a model exhibiting high-frequency variations of a family of immunodominant Vpma ...	[ "Though implicated to play important roles in mycoplasma pathogenicity , the biological significance of large multigene families causing phase variation of immunodominant surface antigens has never been directly proven .", "Using M . agalactiae and its Xer1-mediated high-frequency variation system of Vpma surface...	2017
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "animal diseases", "pathology and laboratory medicine", "infectious disease epidemiology", "influenza", "pathogens", "swine influenza", "microbiology", "orthomyxoviruses", "epidemiological methods and statistics", "ethnicities", "viruses", "rna viruses", "h1...	Role of genetic heterogeneity in determining the epidemiological severity of H1N1 influenza	journal.pcbi.1006069	null	[ [ "A central aim of epidemiological studies is to identify factors that place some populations at greater risk of contracting an infectious disease than others [1] .", "Such factors can be associated with each of the three legs of the “epidemiologic triad” for infectious diseases , the combination of an ext...	[ "Genetic differences contribute to variations in the immune response mounted by different individuals to a pathogen .", "Such differential response can influence the spread of infectious disease , indicating why such diseases impact some populations more than others .", "Here , we study the impact of population...	[ "Levels of immunity to strains of H1N1 influenza can vary , depending on the individual .", "This strongly influences how the disease spreads in a population .", "Accounting for such variations is a major challenge for the epidemiology of infectious diseases .", "We study the effect of population-level geneti...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunology/cellular microbiology and pathogenesis", "immunology/immunomodulation", "cell biology", "immunology/immune response", "microbiology/innate immunity", "infectious diseases/bacterial infections" ]	Variation of Neisseria gonorrhoeae Lipooligosaccharide Directs Dendritic Cell–Induced T Helper Responses	journal.ppat.1000625	null	[ [ "Neisseria gonorrhoeae ( gonococci , GC ) is the causative agent of gonorrhea , one of the main sexually transmitted diseases .", "Global incidence has been estimated at 62 million infected people annually [1] .", "Although gonorrhea can remain asymptomatic , complications of the disease include pelvi...	[ "Gonorrhea is one of the most prevalent sexually transmitted diseases in the world .", "A naturally occurring variation of the terminal carbohydrates on the lipooligosaccharide ( LOS ) molecule correlates with altered disease states .", "Here , we investigated the interaction of different stable gonoccocal LOS ...	[ "Neisseria gonorrhoeae is a species of Gram-negative bacteria responsible for the sexually transmitted disease gonorrhea .", "Although effective antibiotic treatments are available , little is known about the host immune response to this pathogen .", "Here , we analyzed three well-characterized gonococcal varia...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology/membranes and sorting", "infectious diseases/protozoal infections", "immunology/innate immunity", "cell biology/cellular death and stress responses" ]	Disruption of the Toxoplasma gondii Parasitophorous Vacuole by IFNγ-Inducible Immunity-Related GTPases (IRG Proteins) Triggers Necrotic Cell Death	journal.ppat.1000288	null	[ [ "The mouse is a natural intermediate host for Toxoplasma gondii , an apicomplexan parasite whose definitive host is the cat .", "Most T . gondii strains are not virulent for normal mice at low infective doses [1] , [2] .", "Following the development of a strongly IFNγ-dependent primary immunity , rapi...	[ "Toxoplasma gondii is a natural intracellular protozoal pathogen of mice and other small mammals .", "After infection , the parasite replicates freely in many cell types ( tachyzoite stage ) before undergoing a phase transition and encysting in brain and muscle ( bradyzoite stage ) .", "In the mouse , early imm...	[ "Toxoplasma gondii infects many warm-blooded animals , including approximately one quarter of the world's human population , residing life-long , usually asymptomatically , in cysts in the brain .", "If , however , the immune system is weakened for any reason , T . gondii can break out and cause life-threatening ...	2009
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "cell death", "cognitive neurology", "autophagic cell death", "medicine and health sciences", "neurodegenerative diseases", "cell processes", "sports and exercise medicine", "physical activity", "neuroscience", "biological locomotion", "animal models", "cognitive neuroscience", "model organi...	A Becn1 mutation mediates hyperactive autophagic sequestration of amyloid oligomers and improved cognition in Alzheimer's disease	journal.pgen.1006962	null	[ [ "Alzheimer’s disease ( AD ) is a neurodegenerative disorder characterized by protein aggregation and deposition , leading to progressive neuronal loss and cognitive decline among elderly populations [1] .", "Amyloid plaques and neurofibrillary tangles are the two primary hallmarks of AD pathology , and ag...	[ "Impairment of the autophagy pathway has been observed during the pathogenesis of Alzheimer’s disease ( AD ) , a neurodegenerative disorder characterized by abnormal deposition of extracellular and intracellular amyloid β ( Aβ ) peptides .", "Yet the role of autophagy in Aβ production and AD progression is comple...	[ "Accumulation of amyloid β peptides ( Aβ ) is a major cause of Alzheimer’s disease ( AD ) .", "Although many efforts have been made , no effective therapies are available to cure AD .", "Autophagy is a stress-induced pathway nerve cells use to dispose damaged structures , and may be a strategy to eliminate Aβ a...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "genetics and genomics/microbial evolution and genomics", "evolutionary biology/evolutionary and comparative genetics", "infectious diseases/neglected tropical diseases", "microbiology/microbial evolution and genomics", "immunology/immunity to infections", "infectious diseases/epidemiology and control of ...	Differential Gene Repertoire in Mycobacterium ulcerans Identifies Candidate Genes for Patho-Adaptation	journal.pntd.0000353	null	[ [ "Mycobacterium ulcerans is the etiologic agent of the emerging human disease Buruli ulcer , the third most common mycobacterial disease which occurs in more than 30 countries .", "It is associated with necrosis of subcutaneous tissues , mainly in the extremities of children , and often leads to severe dis...	[ "Based on large genomic sequence polymorphisms , several haplotypes belonging to two major lineages of the human pathogen Mycobacterium ulcerans could be distinguished among patient isolates from various geographic origins .", "However , the biological relevance of insertional/deletional diversity is not understo...	[ "The emerging human disease Buruli ulcer , caused by Mycobacterium ulcerans , is of increasing challenge for public health systems in many countries , mainly in West and Central sub-Saharan Africa .", "Genetic differentiation of patient isolates , a prerequisite for scientific studies on and intervention of disea...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "embryology", "developmental biology", "genetics", "biology", "gene function" ]	Arf4 Is Required for Mammalian Development but Dispensable for Ciliary Assembly	journal.pgen.1004170	null	[ [ "Cilia play diverse motility and sensory functions throughout the eukaryotic kingdom , but play especially critical roles in vertebrates where severe defects lead to embryonic lethality while mild defects cause a wide range of syndromes affecting every organ system .", "Both the motility and sensory funct...	[ "The primary cilium is a sensory organelle , defects in which cause a wide range of human diseases including retinal degeneration , polycystic kidney disease and birth defects .", "The sensory functions of cilia require specific receptors to be targeted to the ciliary subdomain of the plasma membrane .", "Arf4 ...	[ "Primary cilia are ubiquitous sensory organelles that play vital roles in an ever-growing class of human diseases termed ciliopathies including obesity , retinal degeneration and polycystic kidney disease .", "The proper function of the primary cilium relies on a cell's ability to target and concentrate specific ...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunity", "immunology", "biology", "microbiology", "immune system" ]	Neutrophils Promote Mycobacterial Trehalose Dimycolate-Induced Lung Inflammation via the Mincle Pathway	journal.ppat.1002614	null	[ [ "Mycobacterium tuberculosis ( Mtb ) is estimated to infect one-third of the world's population and is one of the most common causes of death by infectious diseases [1] .", "Infection by this bacterium mainly results in pulmonary disease , specifically the formation of granulomas , which are intended to wa...	[ "Trehalose 6 , 6′-dimycolate ( TDM ) , a cord factor of Mycobacterium tuberculosis ( Mtb ) , is an important regulator of immune responses during Mtb infections .", "Macrophages recognize TDM through the Mincle receptor and initiate TDM-induced inflammatory responses , leading to lung granuloma formation .", "A...	[ "Tuberculosis is one of the world's most pernicious diseases .", "Mycobacterium tuberculosis ( Mtb ) , the causative agent of tuberculosis , has a lipid-rich cell wall that contains immunostimulatory properties .", "One of the lipid cell wall components , trehalose 6 , 6′-dimycolate ( TDM ) , is a Mincle ligand...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "computer science/applications", "genetics and genomics/complex traits", "computational biology", "mathematics/statistics", "genetics and genomics/bioinformatics", "genetics and genomics/population genetics" ]	Rapid and Accurate Multiple Testing Correction and Power Estimation for Millions of Correlated Markers	journal.pgen.1000456	null	[ [ "Association studies have emerged as a powerful tool for discovering the genetic basis of human diseases [1]–[3] .", "With the development of sequencing and high-throughput genotyping technologies , the number of single nucleotide polymorphism ( SNP ) markers genotyped by current association studies is dr...	[ "With the development of high-throughput sequencing and genotyping technologies , the number of markers collected in genetic association studies is growing rapidly , increasing the importance of methods for correcting for multiple hypothesis testing .", "The permutation test is widely considered the gold standard...	[ "In genome-wide association studies , it is important to account for the fact that a large number of genetic variants are tested in order to adequately control for false positives .", "The simplest way to correct for multiple hypothesis testing is the Bonferroni correction , which multiplies the p-values by the n...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "body fluids", "tropical diseases", "geographical locations", "india", "parasitic diseases", "neglected tropical diseases", "molecular biology techniques", "extraction techniques", "research and analysis methods", "infectious diseases", "zoonoses", "artificial...	Validation of SYBR green I based closed tube loop mediated isothermal amplification (LAMP) assay and simplified direct-blood-lysis (DBL)-LAMP assay for diagnosis of visceral leishmaniasis (VL)	journal.pntd.0006922	null	[ [ "Visceral leishmaniasis ( VL ) is one of the most neglected infectious diseases with an annual incidence of 50 000 to 90 000 new cases worldwide [1] .", "Cases of VL are characterized by irregular bouts of fever , weight loss , hepatosplenomegaly , hypergammaglobulinemia , pancytopenia and anaemia .", ...	[ "The World Health Organization has targeted elimination of visceral leishmaniasis ( VL ) in the Indian subcontinent ( ISC ) by 2020 .", "Despite distinctive decline seen in the number of VL cases in ISC , there is still a quest for development of a diagnostic test which has the utility for detection of active inf...	[ "Definitive diagnosis of visceral leishmaniasis ( VL ) by demonstration of amastigotes by microscopy is invasive and risky .", "Serology based diagnosis using rK39 rapid diagnostic test ( RDT ) has excellent sensitivity of~97% when combined with clinical symptoms but is inconclusive for detection of active infect...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell death", "cellular stress responses", "animal genetics", "cancer genetics", "gene function", "animal models", "mitosis", "telomeres", "drosophila melanogaster", "model organisms", "cell division", "cell growth", "chromosome biology", "biology", "cell biology", "genetics", "molec...	Chk2 and p53 Are Haploinsufficient with Dependent and Independent Functions to Eliminate Cells after Telomere Loss	journal.pgen.1002103	null	[ [ "In the 1930s , seminal work from Hermann Muller and Barbara McClintock showed that the normal termini of linear chromosomes can be distinguished from ends produced by chromosome breakage [1] , [2] .", "Muller showed that normal ends did not participate in chromosome rearrangements induced by irradiation ...	[ "The mechanisms that cells use to monitor telomere integrity , and the array of responses that may be induced , are not fully defined .", "To date there have been no studies in animals describing the ability of cells to survive and contribute to adult organs following telomere loss .", "We developed assays to m...	[ "In this work , we describe two simple assays for examining the fate of cells that lose a telomere .", "We applied these assays to examine the role of DNA damage response genes in controlling the fate of such cells .", "The checkpoint kinase Chk2 is known to activate the p53 tumor suppressor to promote apoptosi...	2011
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Determinants of Visceral Leishmaniasis: A Case-Control Study in Gedaref State, Sudan	journal.pntd.0004187	null	[ [ "Visceral leishmaniasis ( VL ) is a devastating illness with a high case fatality rate when left untreated .", "Gedaref state is the main endemic area of VL in Sudan where the detection figures vary largely between villages in relation with average rainfall and altitude [1] .", "Villages with higher i...	[ "Improving knowledge on local determinants of visceral leishmaniasis ( VL ) is crucial to guide the development of relevant control strategies .", "This study aimed to identify individual and household level determinants of primary VL in 24 highly endemic villages of Tabarak Allah hospital’s catchment area , Geda...	[ "Visceral leishmaniasis ( VL ) , a fatal disease without treatment , is caused by a parasite ( Leishmania ) transmitted to humans through sandflies .", "Its epidemiology and the vectors involved in its transmission differ importantly between endemic zones .", "Preventive measures aim at reducing the parasite re...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "biotechnology", "medicine", "public health and epidemiology", "enzymes", "pest control", "global health", "neglected tropical diseases", "infectious diseases", "enzyme classes", "proteins", "biology", "public health", "agriculture", "biochemistry" ]	Pinpointing P450s Associated with Pyrethroid Metabolism in the Dengue Vector, Aedes aegypti: Developing New Tools to Combat Insecticide Resistance	journal.pntd.0001595	null	[ [ "Dengue fever , transmitted by Aedes mosquito vectors , is a major public health problem in over 100 countries with some 2 . 5 billion people at risk of the disease [1] .", "Prevention of the disease depends in large part on vector control , which relies heavily on the use of insecticides .", "Interve...	[ "Pyrethroids are increasingly used to block the transmission of diseases spread by Aedes aegypti such as dengue and yellow fever .", "However , insecticide resistance poses a serious threat , thus there is an urgent need to identify the genes and proteins associated with pyrethroid resistance in order to produce ...	[ "Dengue fever , transmitted by Aedes mosquito vectors , is a major public health problem in over 100 countries .", "Prevention of the disease relies heavily on the use of insecticides such as pyrethroids .", "Unfortunately , mosquitoes are becoming resistant to these insecticides so it is urgent to identify the...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "biology" ]	Thriving under Stress: Selective Translation of HIV-1 Structural Protein mRNA during Vpr-Mediated Impairment of eIF4E Translation Activity	journal.ppat.1002612	null	[ [ "Regulation of translation is a fundamental property of cell physiology .", "In dividing cells , mRNA translation is robust in the G1 growth phase , diminishes during the S phase , and is downregulated during the G2/M phase [1] , [2] , [3] .", "In the virus-infected cell , pathogen-associated molecula...	[ "Translation is a regulated process and is pivotal to proper cell growth and homeostasis .", "All retroviruses rely on the host translational machinery for viral protein synthesis and thus may be susceptible to its perturbation in response to stress , co-infection , and/or cell cycle arrest .", "HIV-1 infection...	[ "Retroviruses are intracellular parasites that utilize the host translation machinery to catalyze viral protein synthesis .", "The activity of the translation machinery fluctuates during cell cycle progression and is reduced in the G2/M phase .", "HIV-1 infection causes the cells to arrest in the G2/M phase , w...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "enteropathies", "infectious diseases", "medicine and health sciences", "radiology and imaging", "chagas disease", "diagnostic medicine", "diagnostic radiology", "emerging infectious diseases", "gastrointestinal motility disorders", "gastroenterology and hepatology", "vector-borne diseases", "...	Characterization of Digestive Involvement in Patients with Chronic T. cruzi Infection in Barcelona, Spain	journal.pntd.0003105	null	[ [ "Due to migratory flows , chronic Trypanosoma cruzi infection , or chronic Chagas disease ( CD ) , has become relatively common in traditionally non-endemic countries [1] .", "This symptomatic form of CD , which affects approximately 40% of patients , is characterized by cardiac and digestive complication...	[ "Digestive damage due to Chagas disease ( CD ) occurs in 15–20% of patients diagnosed as a result of peristaltic dysfunction in some endemic areas .", "The symptoms of chronic digestive CD are non-specific , and there are numerous confounders .", "Diagnosis of CD may easily be missed if symptoms are not evaluat...	[ "Digestive damage due to Chagas disease ( CD ) , which symptoms are non-specific , occurs in 15–20% of patients as a result of peristaltic dysfunction .", "The results of this study with 71 individuals with T . cruzi infection and 18 without it coming from Latin American countries and performed in a non endemic s...	2014
[ "Introduction", "Materials and methods", "Discussion" ]	[ "medicine and health sciences", "ecology and environmental sciences", "respiratory infections", "influenza", "atmospheric science", "pulmonology", "systems science", "mathematics", "humidity", "infectious diseases", "computer and information sciences", "nonlinear systems", "soil science", ...	Predictability in process-based ensemble forecast of influenza	journal.pcbi.1006783	null	[ [ "Influenza imposes a tremendous toll on global public health due to its recurrent worldwide spread and associated heavy morbidity and mortality burden [1] .", "To better prepare for and mitigate future outbreaks , accurate forecasts of influenza transmission are needed .", "Over the last few years , a...	[ "Process-based models have been used to simulate and forecast a number of nonlinear dynamical systems , including influenza and other infectious diseases .", "In this work , we evaluate the effects of model initial condition error and stochastic fluctuation on forecast accuracy in a compartmental model of influen...	[ "Mathematical models are now used to forecast infectious disease incidence at the population scale .", "By better understanding how errors in prediction systems are introduced , grow and impact the predictability of infectious disease , forecast accuracy could be improved .", "Here we explore the growth pattern...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "microbiology/microbial physiology and metabolism", "microbiology/cellular microbiology and pathogenesis" ]	Feedback Inhibition in the PhoQ/PhoP Signaling System by a Membrane Peptide	journal.pgen.1000788	null	[ [ "Many prokaryotes inhabit multiple niches with disparate environmental conditions and challenges for proliferation .", "Not surprisingly , they have evolved a plethora of regulatory circuits that enable them to adapt to these environments .", "One important and extensively studied example is the signa...	[ "The PhoQ/PhoP signaling system responds to low magnesium and the presence of certain cationic antimicrobial peptides .", "It regulates genes important for growth under these conditions , as well as additional genes important for virulence in many gram-negative pathogens .", "PhoQ is a sensor kinase that phosph...	[ "The proteins PhoQ and PhoP comprise an environmental sensing system that has been extensively studied in numerous bacteria , including Salmonella typhimurium and Escherichia coli .", "The PhoQ/PhoP system is stimulated by conditions of low extracellular magnesium or the presence of certain cationic antimicrobial...	2009
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "veterinary diseases", "pest control", "african trypanosomiasis", "zoonotic diseases", "neglected tropical diseases", "veterinary science", "integrated control", "agriculture", "trypanosomiasis" ]	The Sequential Aerosol Technique: A Major Component in an Integrated Strategy of Intervention against Riverine Tsetse in Ghana	journal.pntd.0002135	null	[ [ "In sub-Saharan Africa the tsetse fly ( Genus: Glossina ) is the cyclical vector of trypanosomosis , a disease of livestock and humans , caused by unicellular parasites of the genus Trypanosoma .", "Whilst the human form of the disease no longer appears to be a major public health issue in Ghana [1]–[3] ,...	[ "An integrated strategy of intervention against tsetse flies was implemented in the Upper West Region of Ghana ( 9 . 62°–11 . 00° N , 1 . 40°–2 . 76° W ) , covering an area of ≈18 , 000 km2 within the framework of the Pan-African Tsetse and Trypanosomosis Eradication Campaign .", "Two species were targeted: Gloss...	[ "We document the impact of an integrated strategy of intervention against riverine tsetse flies in the Upper West Region of Ghana within the framework of the Pan-African Tsetse and Trypanosomosis Eradication Campaign , in an area of ≈18 , 000 km2 .", "The strategy included a sequential aerosol technique ( SAT ) c...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "parallel evolution", "mutation", "forms of evolution", "adaptation", "medical microbiology", "microbial evolution", "biology", "evolutionary biology", "microbiology", "evolutionary processes", "evolutionary genetics", "evolutionary theory" ]	Quantifying the Adaptive Potential of an Antibiotic Resistance Enzyme	journal.pgen.1002783	null	[ [ "Adaptation of asexual organisms to their environment is driven by the successive fixation of mutations that increase fitness .", "The effect-size of beneficial mutations varies and the distribution of beneficial fitness effects ( DBFE ) influences dynamics , outcome and repeatability of adaptation [1]–[5...	[ "For a quantitative understanding of the process of adaptation , we need to understand its “raw material , ” that is , the frequency and fitness effects of beneficial mutations .", "At present , most empirical evidence suggests an exponential distribution of fitness effects of beneficial mutations , as predicted ...	[ "Although mutations with positive effect on fitness are rare , they contribute disproportionally to evolution , because they are favored by natural selection .", "Because they are rare and hard to study experimentally , little is known about the frequency and variation in fitness effects of beneficial mutations ,...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	The Exosome Component Rrp6 Is Required for RNA Polymerase II Termination at Specific Targets of the Nrd1-Nab3 Pathway	journal.pgen.1004999	null	[ [ "The exosome is a 3’-5’ exonuclease complex involved in termination of short RNAs , RNA quality control surveillance , and RNA degradation in both the cytoplasm and the nucleus .", "The core RNA exosome is a multi-subunit complex that has been proposed to channel the substrate to the catalytic subunit Dis...	[ "The exosome and its nuclear specific subunit Rrp6 form a 3’-5’ exonuclease complex that regulates diverse aspects of RNA biology including 3’ end processing and degradation of a variety of noncoding RNAs ( ncRNAs ) and unstable transcripts .", "Known targets of the nuclear exosome include short ( <1000 bp ) RNAP...	[ "RNAPII is responsible for transcription of protein-coding genes and short , regulatory RNAs .", "In Saccharomyces cerevisiae , termination of RNAPII-transcribed RNAs ≤1000 bases requires the NNS complex ( comprised of Nrd1 , Nab3 , and Sen1 ) , processing by the exosome , and the nuclear specific catalytic subun...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases/viral infections" ]	Prediction of Dengue Disease Severity among Pediatric Thai Patients Using Early Clinical Laboratory Indicators	journal.pntd.0000769	null	[ [ "Dengue fever ( DF ) and dengue hemorrhagic fever ( DHF ) , the more severe form of dengue illness , are re-emerging viral diseases [1] .", "Dengue is endemic in countries in tropical and subtropical areas .", "Dengue viruses are transmitted through the bite of an infected mosquito [2] .", "Illnes...	[ "Dengue virus is endemic in tropical and sub-tropical resource-poor countries .", "Dengue illness can range from a nonspecific febrile illness to a severe disease , Dengue Shock Syndrome ( DSS ) , in which patients develop circulatory failure .", "Earlier diagnosis of severe dengue illnesses would have a substa...	[ "Patients with severe dengue illness typically develop complications in the later stages of illness , making early clinical management of all patients with suspected dengue infection difficult .", "An early prediction tool to identify which patients will have a severe dengue illness will improve the utilization o...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "biology" ]	Defective Repair of Oxidative Base Lesions by the DNA Glycosylase Nth1 Associates with Multiple Telomere Defects	journal.pgen.1003639	null	[ [ "All eukaryotic linear chromosome ends consist of complex nucleoprotein structures , called telomeres .", "Telomeres are composed of tandem repeat sequences 5′- ( TTAGGG ) n-3′ whose lengths vary from about 10 kbps in humans to up to 100 kbps in mice .", "In mammals , telomere DNA is bound by the shel...	[ "Telomeres are chromosome end structures and are essential for maintenance of genome stability .", "Highly repetitive telomere sequences appear to be susceptible to oxidative stress-induced damage .", "Oxidation may therefore have a severe impact on telomere integrity and function .", "A wide spectrum of oxid...	[ "Oxidative stress causes DNA base damage that is mainly repaired by base excision repair pathway , where a DNA glycosylase initiates the recognition and removal of specific base damage .", "Mammalian telomeres are composed of repetitive purine and pyrimidine bases , TTAGGG , which are prone to damage by oxidation...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/comparative genomics", "evolutionary biology/evolutionary and comparative genetics", "computational biology/comparative sequence analysis", "genetics and genomics/chromosome biology", "evolutionary biology/genomics", "computational biology/genomics", "computational biology", "ge...	Silent but Not Static: Accelerated Base-Pair Substitution in Silenced Chromatin of Budding Yeasts	journal.pgen.1000247	null	[ [ "The ends of chromosomes in yeasts , vertebrates , Drosophila , and eukaryotic pathogens such as Plasmodim falciparum diverge more rapidly than the rest of their genomes [1] .", "In budding yeasts of the genus Saccharomyces , chromosome ends contain a high density of repeated sequences and relatively few ...	[ "Subtelomeric DNA in budding yeasts , like metazoan heterochromatin , is gene poor , repetitive , transiently silenced , and highly dynamic .", "The rapid evolution of subtelomeric regions is commonly thought to arise from transposon activity and increased recombination between repetitive elements .", "However ...	[ "Many plants , fungi , pathogens , and animals have chromosome regions that are silenced .", "Special proteins change the chromosome structure in these domains , turning genes off or lowering their expression levels .", "We found an increased frequency of DNA mutations in these silenced regions of closely relat...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "model organisms", "genetics", "biology", "genetics and genomics" ]	Bmps and Id2a Act Upstream of Twist1 To Restrict Ectomesenchyme Potential of the Cranial Neural Crest	journal.pgen.1002710	null	[ [ "The neural crest is a transient , migratory cell population that arises at the boundary between the neural and non-neural ectoderm [1] .", "Although both cranial and trunk neural crest cells differentiate into non-ectomesenchyme derivatives , such as neurons , glia and pigment cells , CNCCs also generate...	[ "Cranial neural crest cells ( CNCCs ) have the remarkable capacity to generate both the non-ectomesenchyme derivatives of the peripheral nervous system and the ectomesenchyme precursors of the vertebrate head skeleton , yet how these divergent lineages are specified is not well understood .", "Whereas studies in ...	[ "A fascinating question of vertebrate development is how a single cell population—the cranial neural crest—creates such different types of structures as the peripheral nervous system and head skeleton .", "To date , the molecular signals that instruct neural crest cells to develop into head skeleton at the expens...	2012
[ "Introduction", "Results and Discussion", "Methods" ]	[ "evolutionary biology", "evolutionary biology/paleontology" ]	Predation upon Hatchling Dinosaurs by a New Snake from the Late Cretaceous of India	journal.pbio.1000322	A new snake from Upper Cretaceous rocks in India is found with hatchling sauropod dinosaurs, demonstrating that large, gape-limited snakes were probably capable of taking in moderate-sized vertebrate prey.	[ [ "Snakes are limbless reptiles that first appeared in the fossil record in the middle of the Cretaceous , approximately 98 million years ago [1] .", "Most species of living snakes are macrostomatans , which consume large prey items using a specialized gape achieved via a posteriorly displaced jaw joint , i...	[ "Derived large-mouthed snakes ( macrostomatans ) possess numerous specializations in their skull and lower jaws that allow them to consume large vertebrate prey .", "In contrast , basal snakes lack these adaptations and feed primarily on small prey items .", "The sequence of osteological and behavioral modifica...	[ "Snakes first appear in the fossil record towards the end of the dinosaur era , approximately 98 million years ago .", "Snake fossils from that time are fragmentary , usually consisting of parts of the backbone .", "Relatively complete snake fossils preserving skulls and occasionally hindlimbs are quite rare an...	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "children", "medicine and health sciences", "chemical compounds", "swallowing", "tropical diseases", "parasitic diseases", "organic compounds", "pediatrics", "physiological processes", "age groups", "pharmaceutics", "drug administration", "neglected tropical diseases", "families", "publi...	Risk of adverse swallowing events and choking during deworming for preschool-aged children	journal.pntd.0006578	null	[ [ "Soil-transmitted helminthiasis ( STH ) is a group of parasitic diseases caused by the nematode worms Ascaris lumbricoides ( roundworm ) , Trichuris trichiura ( whipworm ) , Ancylostoma duodenale and Necator americanus ( hookworm ) .", "The worms are transmitted to humans through fecal contamination of so...	[ "In areas where the prevalence of soil-transmitted helminthiasis ( STH ) is >20% , the World Health Organization ( WHO ) recommends that deworming medication be given periodically to preschool-age children .", "To reduce risk of choking-related deaths in children <3 years old , WHO recommends that deworming table...	[ "To improve the health of young children with intestinal worm infections , the World Health Organization recommends that they periodically receive deworming medication .", "The medicines are safe and effective but young children occasionally choke on the chewable tablets .", "Rarely , this results in death .", ...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology and life sciences", "microbiology", "virology" ]	Aminoterminal Amphipathic α-Helix AH1 of Hepatitis C Virus Nonstructural Protein 4B Possesses a Dual Role in RNA Replication and Virus Production	journal.ppat.1004501	null	[ [ "Hepatitis C virus ( HCV ) infection is a leading cause of chronic hepatitis , liver cirrhosis and hepatocellular carcinoma worldwide , with a peak of the disease burden expected in around 10 years from now [1] .", "HCV and GB virus B have been classified in the Hepacivirus genus within the Flaviviridae f...	[ "Nonstructural protein 4B ( NS4B ) is a key organizer of hepatitis C virus ( HCV ) replication complex formation .", "In concert with other nonstructural proteins , it induces a specific membrane rearrangement , designated as membranous web , which serves as a scaffold for the HCV replicase .", "The N-terminal ...	[ "With an estimated 180 million chronically infected individuals , hepatitis C virus ( HCV ) is a leading cause of chronic hepatitis , liver cirrhosis and hepatocellular carcinoma worldwide .", "HCV is a positive-strand RNA virus that builds its replication complex on rearranged intracellular membranes , designate...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/microbial evolution and genomics", "genetics and genomics", "microbiology" ]	Co-Orientation of Replication and Transcription Preserves Genome Integrity	journal.pgen.1000810	null	[ [ "The fundamental processes of replication and transcription take place on the same template efficiently and accurately , requiring them to be coordinated with each other to avoid potential conflicts .", "In cells growing rapidly , both replication and transcription of ribosomal RNA ( rRNA ) genes , and ma...	[ "In many bacteria , there is a genome-wide bias towards co-orientation of replication and transcription , with essential and/or highly-expressed genes further enriched co-directionally .", "We previously found that reversing this bias in the bacterium Bacillus subtilis slows replication elongation , and we propos...	[ "An important feature of genome organization is that transcription and replication are selectively co-oriented .", "This feature helps to avoid conflicts between head-on replication and transcription .", "The precise consequences of the conflict and how it affects genome organization remain to be understood .",...	2010
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics and genomics/complex traits", "genetics and genomics/gene expression", "computational biology/transcriptional regulation" ]	Joint Genetic Analysis of Gene Expression Data with Inferred Cellular Phenotypes	journal.pgen.1001276	null	[ [ "Many interesting traits are heritable , and have a strong genetic component .", "In simple cases , such as Mendelian diseases , the genetic cause can be found with linkage methods , and many trait genes have been mapped to date [1] .", "More recently , association mapping studies have focused on comp...	[ "Even within a defined cell type , the expression level of a gene differs in individual samples .", "The effects of genotype , measured factors such as environmental conditions , and their interactions have been explored in recent studies .", "Methods have also been developed to identify unmeasured intermediate...	[ "The first step in transmitting heritable information , expressing RNA molecules , is highly regulated and depends on activations of specific pathways and regulatory factors .", "The state of the cell is hard to measure , making it difficult to understand what drives the changes in the gene expression .", "To c...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Conservative Sex and the Benefits of Transformation in Streptococcus pneumoniae	journal.ppat.1003758	null	[ [ "Natural transformation is an important cause of genome evolution in bacteria , but the evolutionary factors maintaining natural transformation , or competence , in bacteria remain uncertain [1] , [2] , [3] , [4] .", "Transformation is widely believed to have evolved to facilitate adaptation , especially ...	[ "Natural transformation has significant effects on bacterial genome evolution , but the evolutionary factors maintaining this mode of bacterial sex remain uncertain .", "Transformation is hypothesized to have both positive and negative evolutionary effects on bacteria .", "It can facilitate adaptation by combin...	[ "Transformation of environmental DNA can provide bacteria with a means to adapt quickly to a changing environment .", "While this can benefit microbes by facilitating the spread of antibiotic resistance , it can also be harmful if it causes the loss of beneficial alleles from a population .", "Therefore , it is...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "immune cells", "immunology", "microbiology", "host-pathogen interaction", "gynecologic infections", "bacterial diseases", "infectious diseases", "medical microbiology", "microbial pathogens", "biology", "pathogenesis", "immunopathology", "listeriosis" ]	Listeria monocytogenes Cytoplasmic Entry Induces Fetal Wastage by Disrupting Maternal Foxp3+ Regulatory T Cell-Sustained Fetal Tolerance	journal.ppat.1002873	null	[ [ "Listeria monocytogenes ( Lm ) is a ubiquitous human pathogen with a unique predisposition for invasive disseminated infection during pregnancy that represents a significant etiology of spontaneous abortion , stillbirth , and neonatal infection [1] , [2] .", "Although many Lm-specific proteins required fo...	[ "Although the intracellular bacterium Listeria monocytogenes has an established predilection for disseminated infection during pregnancy that often results in spontaneous abortion or stillbirth , the specific host-pathogen interaction that dictates these disastrous complications remain incompletely defined .", "H...	[ "Pregnant women are uniquely susceptible to the bacterium Listeria monocytogenes that preferentially lives inside infected cells .", "Since infection during pregnancy often triggers prematurity , abortion , or stillbirth , we propose that understanding how these complications occur represent important prerequisit...	2012
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "blood cells", "invertebrates", "medicine and health sciences", "rift valley fever virus", "body fluids", "immune cells", "pathology and laboratory medicine", "european union", "pathogens", "immunology", "geographical locations", "microbiology", "cloning", "saliva", "animals", "viruses...	Transmission of Rift Valley fever virus from European-breed lambs to Culex pipiens mosquitoes	journal.pntd.0006145	null	[ [ "RVFV is a mosquito-borne zoonotic bunyavirus that predominantly affects domesticated and wild ruminants .", "Near simultaneous abortions of gestating sheep and high numbers of newborn lamb fatalities are characteristic features of RVF outbreaks .", "Human infections generally result in a self-resolvi...	[ "Rift Valley fever virus ( RVFV ) is a mosquito-borne bunyavirus of the genus Phlebovirus that is highly pathogenic to ruminants and humans .", "The disease is currently confined to Africa and the Arabian Peninsula , but globalization and climate change may facilitate introductions of the virus into currently una...	[ "The consequences of first introductions of mosquito-borne viruses into previously unaffected areas depend on environmental factors , the availability of susceptible hosts and local vector populations .", "We have previously demonstrated that sheep breeds native to the Netherlands are highly susceptible to Rift V...	2017
[ "Introduction", "Results", "Discussion", "Material and methods" ]	[ "invertebrates", "medicine and health sciences", "gustatory system", "nervous system", "neuronal differentiation", "social sciences", "neuroscience", "animals", "cell differentiation", "animal models", "developmental biology", "drosophila melanogaster", "model organisms", "experimental org...	The Drosophila fussel gene is required for bitter gustatory neuron differentiation acting within an Rpd3 dependent chromatin modifying complex	journal.pgen.1007940	null	[ [ "During development , the TGF-ß superfamily plays an important role in cell proliferation , differentiation , apoptosis , cell adhesion , wound healing , bone morphogenesis and cell motility [1] .", "Accordingly , there are multiple inhibitory factors taking care of proper regulation of TGF-ß pathways .",...	[ "Members of the Ski/Sno protein family are classified as proto-oncogenes and act as negative regulators of the TGF-ß/BMP-pathways in vertebrates and invertebrates .", "A newly identified member of this protein family is fussel ( fuss ) , the Drosophila homologue of the human functional Smad suppressing elements (...	[ "Ski/Sno proteins have been discovered as proto-oncogenes transforming chicken fibroblasts into cancer cells .", "They have been found to be ubiquitously expressed in embryonic and adult tissues and to interfere with TGF-ß/BMP signaling .", "More recently , a group of proteins has been discovered which belongs ...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases", "biology and life sciences", "microbiology", "medicine and health sciences" ]	Programmed Ribosomal Frameshift Alters Expression of West Nile Virus Genes and Facilitates Virus Replication in Birds and Mosquitoes	journal.ppat.1004447	null	[ [ "West Nile virus ( WNV ) is a flavivirus that circulates in a bird-mosquito enzootic cycle with humans and horses as incidental hosts [1] .", "It belongs to the Japanese encephalitis subgroup that also includes Japanese encephalitis virus ( JEV ) , St Louis encephalitis virus , and Murray Valley encephali...	[ "West Nile virus ( WNV ) is a human pathogen of significant medical importance with close to 40 , 000 cases of encephalitis and more than 1 , 600 deaths reported in the US alone since its first emergence in New York in 1999 .", "Previous studies identified a motif in the beginning of non-structural gene NS2A of e...	[ "Programmed ribosomal frameshift ( PRF ) is a strategy used by some viruses to regulate expression of viral genes and/or generate additional gene products for the benefit of the virus .", "Encephalitic flaviruses from Japanese encephalitis virus serogroup encode PRF motif in the beginning of nonstructural gene NS...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "systems biology", "biochemistry", "proteomics", "biology", "molecular cell biology", "microbiology" ]	Metabolic Reprogramming during Purine Stress in the Protozoan Pathogen Leishmania donovani	journal.ppat.1003938	null	[ [ "Leishmania are protozoan parasites that are a significant human health burden , afflicting approximately 12 million people in 88 countries worldwide [1] .", "These parasites cause a spectrum of diseases in humans ranging from cutaneous ulcerative lesions that can be localized or diffuse; disfiguring muco...	[ "The ability of Leishmania to survive in their insect or mammalian host is dependent upon an ability to sense and adapt to changes in the microenvironment .", "However , little is known about the molecular mechanisms underlying the parasite response to environmental changes , such as nutrient availability .", "...	[ "Leishmania , the cause of a deadly spectrum of diseases in humans , surmounts a number of environmental challenges , including changes in the availability of salvageable nutrients , to successfully colonize its host .", "Adaptation to environmental stress is clearly of significance in parasite biology , but the ...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "dimers (chemical physics)", "taxonomy", "medicine and health sciences", "crystal structure", "pathology and laboratory medicine", "bacteriophages", "pathogens", "condensed matter physics", "microbiology", "staphylococcus aureus", "viruses", "phylogenetics", "data management", "phylogeneti...	Convergent evolution involving dimeric and trimeric dUTPases in pathogenicity island mobilization	journal.ppat.1006581	null	[ [ "The staphylococcal pathogenicity islands ( SaPIs ) are virus satellites that carry and disseminate virulence genes in Staphylococcus aureus .", "They reside passively in the host chromosome under the control of Stl , a global SaPI-encoded repressor .", "Following infection by a helper phage , they ex...	[ "The dUTPase ( Dut ) enzymes , encoded by almost all free-living organisms and some viruses , prevent the misincorporation of uracil into DNA .", "We previously proposed that trimeric Duts are regulatory proteins involved in different cellular processes; including the phage-mediated transfer of the Staphylococcus...	[ "Understanding bacterial horizontal gene transfer is vital for establishing how toxins and antibiotic resistance genes are disseminated .", "Bacteriophage and pathogenicity islands make up key components of the wider horizontal transfer map .", "SaPIs are clinically relevant pathogenicity islands , residing pas...	2017
[ "Introduction", "Results and discussion", "Materials and methods" ]	[ "medicine and health sciences", "microbiology", "parasitic diseases", "parasitic protozoans", "protozoan life cycles", "cell differentiation", "developmental biology", "trypomastigotes", "protozoans", "epimastigotes", "genomics", "gene expression", "life cycles", "comparative genomics", ...	Comparative transcriptome profiling of virulent and non-virulent Trypanosoma cruzi underlines the role of surface proteins during infection	journal.ppat.1006767	null	[ [ "Trypanosoma cruzi is the etiological agent of Chagas disease , a disease affecting at least 8 million people throughout Latin America and for which there are only two drugs available , both with poor efficacy and harmful side effects ( http://www . who . int/mediacentre/factsheets/fs340/en/ ) .", "T . cr...	[ "Trypanosoma cruzi , the protozoan that causes Chagas disease , has a complex life cycle involving several morphologically and biochemically distinct stages that establish intricate interactions with various insect and mammalian hosts .", "It has also a heterogeneous population structure comprising strains with d...	[ "Chagas disease , caused by the protozoan parasite Trypanosoma cruzi , is an infection that occurs in several Latin American countries , resulting in a mild illness or in severe damage of the heart and intestinal tract .", "Such a broad spectrum of clinical manifestations observed in Chagas disease patients is li...	2017
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[]	De Novo Assembly of a Field Isolate Genome Reveals Novel Plasmodium vivax Erythrocyte Invasion Genes	journal.pntd.0002569	null	[ [ "Despite being responsible for several million cases of clinical malaria every year , we still know very little about the biology of Plasmodium vivax .", "An important limitation of P . vivax research is the lack of continuous in vitro propagation that hampers development of functional assays and collecti...	[ "Recent sequencing of Plasmodium vivax field isolates and monkey-adapted strains enabled characterization of SNPs throughout the genome .", "These analyses relied on mapping short reads onto the P . vivax reference genome that was generated using DNA from the monkey-adapted strain Salvador I . Any genomic locus d...	[ "Plasmodium vivax is responsible for most malaria cases outside Africa , but is poorly understood , as the parasite is difficult to study in vitro .", "Genome sequencing studies offer a novel and exciting opportunity to better understand this parasite but , so far , have directly mapped reads onto the reference g...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "microbiology/plant-biotic interactions", "plant biology/plant-biotic interactions" ]	Autoacetylation of the Ralstonia solanacearum Effector PopP2 Targets a Lysine Residue Essential for RRS1-R-Mediated Immunity in Arabidopsis	journal.ppat.1001202	null	[ [ "To defend themselves against pathogen infection , plants have evolved a bipartite , inducible innate immune system that efficiently recognizes and wards off pathogens [1]–[3] .", "Perception of conserved molecules , essential to many pathogens and called pathogen-associated molecular patterns ( PAMPs ) ,...	[ "Type III effector proteins from bacterial pathogens manipulate components of host immunity to suppress defence responses and promote pathogen development .", "In plants , host proteins targeted by some effectors called avirulence proteins are surveyed by plant disease resistance proteins referred to as “guards” ...	[ "Plant and animal bacterial pathogens have evolved to produce virulence factors , called type III effectors , which are injected into host cells to suppress host defences and provide an environment beneficial for pathogen growth .", "Type III effectors from pathogenic bacteria display enzymatic activities , often...	2010
[ "Introduction", "Results/Discussion", "Methods" ]	[ "computational biology/molecular dynamics", "biophysics", "biochemistry", "computational biology" ]	Induced Effects of Sodium Ions on Dopaminergic G-Protein Coupled Receptors	journal.pcbi.1000884	null	[ [ "G-protein coupled receptors ( GPCR ) are highly sophisticated signal transduction machines able to respond to extracellular stimulus by activating diverse intracellular signaling pathways .", "Recent research in this field is unveiling the complexity of the mechanisms involved , which are far from being ...	[ "G-protein coupled receptors , the largest family of proteins in the human genome , are involved in many complex signal transduction pathways , typically activated by orthosteric ligand binding and subject to allosteric modulation .", "Dopaminergic receptors , belonging to the class A family of G-protein coupled ...	[ "G-protein coupled receptors represent more than 50% of the current drug targets , hence playing a crucial role in drug discovery today .", "A deeper understanding of G-protein coupled receptor functioning and modulation will help in the development of new drugs that are able to interact with such systems in a mo...	2010
[ "Introduction", "Results/Discussion", "Methods" ]	[ "physics", "biophysic al simulations", "biology", "computational biology", "biophysics simulations", "biophysics" ]	Membrane Sculpting by F-BAR Domains Studied by Molecular Dynamics Simulations	journal.pcbi.1002892	null	[ [ "Interplay between cellular membranes and their peripheral proteins drives many cellular processes , including cell division , growth , movement and cell-cell communication [1]–[6] .", "During their lifetime and often with the help of membrane peripheral proteins , eukaryotic cells dynamically sculpt thei...	[ "Interplay between cellular membranes and their peripheral proteins drives many processes in eukaryotic cells .", "Proteins of the Bin/Amphiphysin/Rvs ( BAR ) domain family , in particular , play a role in cellular morphogenesis , for example curving planar membranes into tubular membranes .", "However , it is ...	[ "To generate organelles , eukaryotic cells sculpt their membranes into compartments , often employing proteins as chaperones , for example , F-BAR domains .", "The latter induce formation of tubular and vesicular membranes .", "Functional and structural studies suggest that F-BAR domains sculpt membranes throug...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Computational Optogenetics: Empirically-Derived Voltage- and Light-Sensitive Channelrhodopsin-2 Model	journal.pcbi.1003220	null	[ [ "Quantitative biophysical approaches have strong traditions in neural and cardiac electrophysiology [1]–[4] .", "The dynamic and highly nonlinear process of cellular excitation is still successfully captured today by Hodgkin and Huxley's empirical modeling framework from 1952 [4] , even though the complex...	[ "Channelrhodospin-2 ( ChR2 ) , a light-sensitive ion channel , and its variants have emerged as new excitatory optogenetic tools not only in neuroscience , but also in other areas , including cardiac electrophysiology .", "An accurate quantitative model of ChR2 is necessary for in silico prediction of the respons...	[ "Optogenetics , the use of light-sensitive ion channels for stimulation of mammalian cells and tissues , offers specificity and superior precision of control compared to traditional chemical or electrical means of stimulation .", "In particular , Channelrhodospin-2 ( ChR2 ) , a light-sensitive ion channel , origi...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	A Trypanosomatid Iron Transporter that Regulates Mitochondrial Function Is Required for Leishmania amazonensis Virulence	journal.ppat.1005340	null	[ [ "Leishmania spp .", ", parasitic protozoa from the Trypanosomatidae family , cause a broad spectrum of human diseases collectively referred to as leishmaniasis .", "An estimated 12 million people worldwide are infected with these parasites , with another 350 million at risk of infection [1] .", "I...	[ "Iron , an essential co-factor of respiratory chain proteins , is critical for mitochondrial function and maintenance of its redox balance .", "We previously reported a role for iron uptake in differentiation of Leishmania amazonensis into virulent amastigotes , by a mechanism that involves reactive oxygen specie...	[ "Leishmaniasis is a serious parasitic disease that affects 12 million people worldwide , with clinical manifestations ranging from self-healing cutaneous lesions to deadly visceralizing disease .", "A vaccine is not available , and new and less toxic drugs against this protozoan parasite are urgently needed .", ...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "biotechnology", "engineering and technology", "mitochondrial dna", "genomic library construction", "sequence assembly tools", "plant science", "genome analysis", "forms of dna", "plant genomics", "mitochondria", "energy-producing organelles", "bioenergetics", "dna", "molecular biology tec...	The alternative reality of plant mitochondrial DNA: One ring does not rule them all	journal.pgen.1008373	null	[ [ "Unlike the relatively simple mitochondrial genomes of animals , the genomes of non-parasitic flowering plant mitochondria are large and complex [1–8] .", "They exhibit extensive variation in size [191 kb–11 , 319 kb] , sequence arrangement , and repeat content , yet coding sequences are highly conserved ...	[ "Plant mitochondrial genomes are usually assembled and displayed as circular maps based on the widely-held view across the broad community of life scientists that circular genome-sized molecules are the primary form of plant mitochondrial DNA , despite the understanding by plant mitochondrial researchers that this ...	[ "Plant mitochondrial genomes are commonly depicted in research articles and textbooks as circular molecules that are the size of the genome .", "Although research on mitochondrial DNA ( mtDNA ) over the past few decades has revealed that genome-sized circles are exceedingly rare and that alternative forms of mtDN...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/animal genetics", "developmental biology/morphogenesis and cell biology", "cell biology", "cell biology/developmental molecular mechanisms", "pathology/histopathology", "cell biology/membranes and sorting", "genetics and genomics/disease models", "genetics and genomics/gene func...	Phosphoinositide Regulation of Integrin Trafficking Required for Muscle Attachment and Maintenance	journal.pgen.1001295	null	[ [ "Myofibers are large , highly differentiated contractile cells that rely on strong extracellular attachments to preserve their integrity during force-generating muscle contractions .", "Myofiber attachments are mediated by integrin adhesion complexes ( IACs ) composed of α- and β- transmembrane heterodime...	[ "Muscles must maintain cell compartmentalization when remodeled during development and use .", "How spatially restricted adhesions are regulated with muscle remodeling is largely unexplored .", "We show that the myotubularin ( mtm ) phosphoinositide phosphatase is required for integrin-mediated myofiber attachm...	[ "Muscles require strong extracellular attachments to preserve cellular integrity during force-generating contractions .", "Integrin transmembrane receptors mediate muscle attachments at highly localized sites , but how this pattern of attachments is continuously maintained with muscle use is not understood .", ...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "parasite groups", "medicine and health sciences", "plasmodium", "tropical diseases", "geographical locations", "vector-borne diseases", "database searching", "parasitic diseases", "parasitic protozoans", "parasitology", "apicomplexa", "plasmodium vivax", "protozoans", "africa", "researc...	Growing evidence of Plasmodium vivax across malaria-endemic Africa	journal.pntd.0007140	null	[ [ "Significant funding increases for global malaria control between 2005 and 2010 facilitated a rapid decrease in the burden of malaria , with an estimated 37% reduction in case incidence and a 60% drop in mortality from 2000 to 2015 [1] .", "During this period , malaria control programmes focused on scalin...	[ "Effective malaria control strategies require an accurate understanding of the epidemiology of locally transmitted Plasmodium species .", "Compared to Plasmodium falciparum infection , Plasmodium vivax has a lower asexual parasitaemia , forms dormant liver-stages ( hypnozoites ) , and is more transmissible .", ...	[ "Plasmodium vivax malaria presents challenges for malaria elimination distinct from those of the other human malarias .", "Patients become symptomatic at lower asexual parasitaemia , making it harder to diagnose , and its dormant stages in the liver give rise to multiple clinical attacks unless treated with an 8-...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "virology/vaccines", "virology/immunodeficiency viruses", "virology/new therapies, including antivirals and immunotherapy", "virology/mechanisms of resistance and susceptibility, including host genetics", "infectious diseases/hiv infection and aids", "immunology/immunity to infections", "virology/host a...	Selective Transmission of R5 HIV-1 over X4 HIV-1 at the Dendritic Cell–T Cell Infectious Synapse Is Determined by the T Cell Activation State	journal.ppat.1000279	null	[ [ "HIV-1 infects T cells and monocyte lineage cells , including macrophages and dendritic cells ( DCs ) , through CD4 , the primary receptor for entry .", "The cellular tropism of HIV-1 , i . e . , macrophage ( M ) -tropic or T-cell line ( T ) -tropic , is determined by chemokine receptors .", "Dependin...	[ "Dendritic cells ( DCs ) are essential antigen-presenting cells for the induction of T cell immunity against HIV .", "On the other hand , due to the susceptibility of DCs to HIV infection , virus replication is strongly enhanced in DC–T cell interaction via an immunological synapse formed during the antigen prese...	[ "The cellular tropism of HIV-1 is determined by the binding of HIV-1 envelope to chemokine coreceptors , CCR5 or CXCR4 , in addition to a major entry receptor , CD4 .", "The mystery still now is that despite the mixed infection of CCR5-utilizing ( R5 ) and CXCR4-utilizing ( X4 ) HIV-1 in many AIDS patients , R5 i...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/bacterial infections", "microbiology/cellular microbiology and pathogenesis", "infectious diseases/gastrointestinal infections", "cell biology/cytoskeleton" ]	The IpaC Carboxyterminal Effector Domain Mediates Src-Dependent Actin Polymerization during Shigella Invasion of Epithelial Cells	journal.ppat.1000271	null	[ [ "Shigella , the causative agent of bacillary dysentery , uses a T3S apparatus to invade epithelial cells [1] , [2] .", "Actin reorganization during Shigella entry involves Rho GTPases as well as the activation of the Src tyrosine kinase [3] , [4] .", "Using fibroblastic cells derived from Abl knock-ou...	[ "Shigella , the causative agent of bacillary dysentery , invades epithelial cells by locally reorganizing the actin cytoskeleton .", "Shigella invasion requires actin polymerization dependent on the Src tyrosine kinase and a functional bacterial type III secretion ( T3S ) apparatus .", "Using dynamic as well as...	[ "Type III secretion systems ( T3SS ) are present in a wide range of Gram-negative bacteria that are pathogenic to humans , animals , and plants .", "These molecular devices allow the injection of bacterial virulence factors into host cells to manipulate various cellular functions .", "T3SSs share similar functi...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "animal models", "genome expression analysis", "drosophila melanogaster", "model organisms", "chromosome biology", "gene expression", "genetics", "epigenetics", "biology", "genomics", "genetics and genomics" ]	Enrichment of HP1a on Drosophila Chromosome 4 Genes Creates an Alternate Chromatin Structure Critical for Regulation in this Heterochromatic Domain	journal.pgen.1002954	null	[ [ "In eukaryotes , initial gene regulation is achieved through the interaction of transcription factors and the transcriptional machinery with DNA packaged into chromatin .", "The basic unit of chromatin is the nucleosome , 147 bp of DNA wrapped around a histone octamer [1] , [2] .", "Post-translational...	[ "Chromatin environments differ greatly within a eukaryotic genome , depending on expression state , chromosomal location , and nuclear position .", "In genomic regions characterized by high repeat content and high gene density , chromatin structure must silence transposable elements but permit expression of embed...	[ "How DNA is packaged into chromatin has profound implications for gene regulation .", "While certain chromatin conformations are accessible to RNA polymerase and allow expression , other chromatin structures prevent transcription .", "In many genomes , genes that need to be expressed and repetitive sequences th...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "rna", "molecular cell biology", "rna processing", "virulence factors and mechanisms", "nucleic acids", "virology", "biology", "microbiology", "molecular biology" ]	A Viral Nuclear Noncoding RNA Binds Re-localized Poly(A) Binding Protein and Is Required for Late KSHV Gene Expression	journal.ppat.1002300	null	[ [ "Kaposi's Sarcoma-Associated Herpesvirus ( KSHV ) is the causative agent of several human cancers and immunoproliferative disorders , including Kaposi's Sarcoma , Multicentric Castleman's Disease and Primary Effusion Lymphoma [1] , [2] .", "Like other herpesviruses , KSHV infection is characterized by two...	[ "During the lytic phase of infection , the gamma herpesvirus Kaposi's Sarcoma-Associated Herpesvirus ( KSHV ) expresses a highly abundant , 1 . 1 kb nuclear noncoding RNA of unknown function .", "We observe that this polyadenylated nuclear ( PAN ) RNA avidly binds host poly ( A ) -binding protein C1 ( PABPC1 ) , ...	[ "Almost all eukaryotic messenger RNAs ( mRNAs ) have a string of 150–200 adenylates at the 3′ end .", "This poly ( A ) tail has been implicated as important for regulating mRNA translation , stability and export .", "During the lytic phase of infection of Kaposi's Sarcoma-Associated Herpesvirus ( KSHV ) , a non...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "spectrometric identification of proteins", "cancer genetics", "model organisms", "proteomic databases", "enzyme regulation", "enzymes", "genetics", "yeast and fungal models", "biology", "saccharomyces cerevisiae", "proteomics", "protein abundance" ]	Distinct SUMO Ligases Cooperate with Esc2 and Slx5 to Suppress Duplication-Mediated Genome Rearrangements	journal.pgen.1003670	null	[ [ "The human genome contains many “at-risk” sequences that are prone to mutations including diverse repeated sequences , segmental duplications and regions of copy number variations [1] , [2] .", "Such repetitive sequence elements can cause genome rearrangements through non-allelic homologous recombination ...	[ "Suppression of duplication-mediated gross chromosomal rearrangements ( GCRs ) is essential to maintain genome integrity in eukaryotes .", "Here we report that SUMO ligase Mms21 has a strong role in suppressing GCRs in Saccharomyces cerevisiae , while Siz1 and Siz2 have weaker and partially redundant roles .", ...	[ "The human genome contains many “at-risk” sequences that are prone to mutations , including diverse repeated sequences , segmental duplications and regions of copy number variations .", "Such repetitive sequence elements can cause genome rearrangements through non-allelic homologous recombination ( NAHR ) and man...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "bacteriology", "antimicrobials", "innate immune system", "medicine and health sciences", "immune cells", "cytokines", "pathology and laboratory medicine", "pathogens", "immunology", "microbiology", "developmental biology", "secretion systems", "signs and symptoms", "micro...	The Host Protein Calprotectin Modulates the Helicobacter pylori cag Type IV Secretion System via Zinc Sequestration	journal.ppat.1004450	null	[ [ "Helicobacter pylori is a Gram-negative bacterial pathogen that colonizes half of the world's population and contributes to a variety of disease outcomes , including peptic or duodenal ulcer disease , gastric adenocarcinoma , and mucosal-associated lymphoid tissue ( MALT ) lymphoma [1] .", "The most commo...	[ "Transition metals are necessary for all forms of life including microorganisms , evidenced by the fact that 30% of all proteins are predicted to interact with a metal cofactor .", "Through a process termed nutritional immunity , the host actively sequesters essential nutrient metals away from invading pathogenic...	[ "Helicobacter pylori is a bacterium that colonizes the stomach and causes gastric diseases .", "Some strains of H . pylori possess a secretion system that has the capacity to inject a cancer-causing protein into host cells .", "The activity of this secretion system contributes to the development of inflammation...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "microbiology/environmental microbiology", "evolutionary biology/microbial evolution and genomics", "genetics and genomics/gene discovery", "genetics and genomics/comparative genomics", "genetics and genomics/gene expression", "molecular biology/recombination", "computational biology/comparative sequenc...	Alliance of Proteomics and Genomics to Unravel the Specificities of Sahara Bacterium Deinococcus deserti	journal.pgen.1000434	null	[ [ "The surface sands of hot arid deserts are exposed to intense ultraviolet ( UV ) radiation , cycles of extreme temperatures , and desiccation .", "Nevertheless , an extensive diversity of bacterial species has been identified in such extreme and nutrient-poor environments [1] , [2] .", "To better unde...	[ "To better understand adaptation to harsh conditions encountered in hot arid deserts , we report the first complete genome sequence and proteome analysis of a bacterium , Deinococcus deserti VCD115 , isolated from Sahara surface sand .", "Its genome consists of a 2 . 8-Mb chromosome and three large plasmids of 32...	[ "D . deserti belongs to the Deinococcaceae , a family of bacteria characterized by an exceptional ability to withstand the lethal effects of DNA-damaging agents , including ionizing radiation , UV light , and desiccation .", "It was isolated from Sahara surface sands , an extreme and nutrient-poor environment , r...	2009
[ "Introduction", "Results", "Discussion", "Conclusion", "Materials and Methods" ]	[ "genome-wide association studies", "cancer genetics", "genetic mutation", "genomics", "genetic association studies", "human genetics", "genetics", "gene regulation", "epigenetics", "molecular genetics", "biology", "computational biology", "molecular cell biology", "population biology", "...	Comprehensive Functional Annotation of 77 Prostate Cancer Risk Loci	journal.pgen.1004102	null	[ [ "The basic goal of research into human genetics is to connect variation at the genetic level with variation in organismal and cellular phenotype .", "Until recently , inferences about such connections have been limited to the kind associated with heritable disorders and developmental syndromes .", "Su...	[ "Genome-wide association studies ( GWAS ) have revolutionized the field of cancer genetics , but the causal links between increased genetic risk and onset/progression of disease processes remain to be identified .", "Here we report the first step in such an endeavor for prostate cancer .", "We provide a compreh...	[ "In the following work we provide a complete summary annotation of functional hypotheses relating to risk identified by genome wide association studies of prostate cancer .", "In addition , we present new genome-wide profiles for H3K27-acetylation and TCF7L2 binding in LNCaP cells .", "We also introduce the con...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "protein interactions", "pathology and laboratory medicine", "pathogens", "microbiology", "cancers and neoplasms", "notch signaling", "viruses", "oncology", "dna viruses", "sequence motif analysis", "human papillomavirus", "research and analysis methods", "s...	Association of papillomavirus E6 proteins with either MAML1 or E6AP clusters E6 proteins by structure, function, and evolutionary relatedness	journal.ppat.1006781	null	[ [ "Papillomaviruses are a large group of viruses with hundreds of different fully sequenced types and additional types partially characterized by metagenomic sequencing [1–4] .", "All papillomaviruses express early genes E1 and E2 that are necessary for viral transcriptional control and DNA replication , as...	[ "Papillomavirus E6 proteins bind to LXXLL peptide motifs displayed on targeted cellular proteins .", "Alpha genus HPV E6 proteins associate with the cellular ubiquitin ligase E6AP ( UBE3A ) , by binding to an LXXLL peptide ( ELTLQELLGEE ) displayed by E6AP , thereby stimulating E6AP ubiquitin ligase activity .", ...	[ "Papillomaviruses are a large family of viruses with great medical and veterinary importance .", "This study explores the viral E6 oncoproteins from diverse papillomavirus genera to determine how E6 distinguishes in interaction between cellular proteins .", "E6 proteins have been previously found to interact wi...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Distributed Fading Memory for Stimulus Properties in the Primary Visual Cortex	journal.pbio.1000260	The brain has a one-back memory for visual stimuli. Neural responses to an image contain as much information about the current image as it does about another image presented immediately before.	[ [ "A number of analysis methods have been designed to investigate how neuronal spiking activity correlates to sensory stimulation or behavior and , as expected , many relations have been found .", "All of the following variables—firing rates [1]–[4] and the synchronization [4]–[7] and the differential timin...	[ "It is currently not known how distributed neuronal responses in early visual areas carry stimulus-related information .", "We made multielectrode recordings from cat primary visual cortex and applied methods from machine learning in order to analyze the temporal evolution of stimulus-related information in the s...	[ "Researchers usually assume that neuronal responses carry primarily information about the stimulus that evoked these responses .", "We show here that , when multiple images are shown in a fast sequence , the response to an image contains as much information about the preceding image as about the current one .", ...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "neurological disorders/alzheimer disease" ]	Lysosomal Dysfunction Promotes Cleavage and Neurotoxicity of Tau In Vivo	journal.pgen.1001026	null	[ [ "Tauopathies , including Alzheimer's disease , are characterized by abnormal intraneuronal accumulation of the microtubule-associated protein tau .", "The identification of dominant mutations in the gene encoding tau in hereditary tauopathies ( frontotemporal dementia with Parkinsonism linked to chromosom...	[ "Expansion of the lysosomal system , including cathepsin D upregulation , is an early and prominent finding in Alzheimer's disease brain .", "Cell culture studies , however , have provided differing perspectives on the lysosomal connection to Alzheimer's disease , including both protective and detrimental influen...	[ "Neurodegenerative disorders , like Alzheimer's disease , are a devastating group of conditions that exact a heavy toll on patients and their families .", "These disorders also represent a significant and growing public health challenge as our population ages because no effective treatments are available .", "R...	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "rift valley fever", "public health and epidemiology", "epidemiology", "infectious disease epidemiology", "neglected tropical diseases", "viral diseases" ]	Postepidemic Analysis of Rift Valley Fever Virus Transmission in Northeastern Kenya: A Village Cohort Study	journal.pntd.0001265	null	[ [ "Rift Valley Fever ( RVF ) is a life-threatening , mosquito-borne zoonotic disease found in many areas of sub-Saharan Africa and the Middle East [1] .", "Because Rift Valley fever virus ( RVFV ) readily infects both humans and their livestock , RVF poses a severe , dual threat to public health and to live...	[ "In endemic areas , Rift Valley fever virus ( RVFV ) is a significant threat to both human and animal health .", "Goals of this study were to measure human anti-RVFV seroprevalence in a high-risk area following the 2006–2007 Kenyan Rift Valley Fever ( RVF ) epidemic , to identify risk factors for interval serocon...	[ "RVFV infection causes significant disease in both human and animal populations , resulting in significant agricultural , economic and public health consequences .", "We conducted a cohort study on residents of a high-risk area to measure human anti-RVFV seroprevalence , to identify risk factors , and to estimate...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "nucleic acids", "dna", "dna repair", "biology", "molecular cell biology" ]	Ddc2 Mediates Mec1 Activation through a Ddc1- or Dpb11-Independent Mechanism	journal.pgen.1004136	null	[ [ "The DNA damage response pathways coordinate DNA repair , replication and cell-cycle progression to maintain genome integrity [1] , [2] .", "Initiation of DNA damage responses requires two evolutionarily conserved phosphoinositide 3-kinase ( PI3K ) -related protein kinases: ATM and ATR .", "While ATM ...	[ "The protein kinase Mec1 ( ATR ortholog ) and its partner Ddc2 ( ATRIP ortholog ) play a key role in DNA damage checkpoint responses in budding yeast .", "Previous studies have established the model in which Ddc1 , a subunit of the checkpoint clamp , and Dpb11 , related to TopBP1 , activate Mec1 directly and cont...	[ "When DNA replication is blocked and DNA damage occurs , checkpoints arrest the cell cycle in eukaryotic cells , allowing DNA replication and repair to take place .", "The major regulators of the DNA damage checkpoint response are the phosphoinositide 3-kinase ( PI3K ) -related protein kinases , including ATM and...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	A GDF5 Point Mutation Strikes Twice - Causing BDA1 and SYNS2	journal.pgen.1003846	null	[ [ "Growth and Differentiation Factor 5 ( GDF5 ) , which is also known as Cartilage-Derived Morphogenetic Protein 1 ( CDMP1 ) belongs to the Transforming Growth Factor Beta superfamily ( TGFB ) and the subordinated group of Bone Morphogenetic Proteins ( BMPs ) [1] .", "GDF5 has a fundamental role during limb...	[ "Growth and Differentiation Factor 5 ( GDF5 ) is a secreted growth factor that belongs to the Bone Morphogenetic Protein ( BMP ) family and plays a pivotal role during limb development .", "GDF5 is a susceptibility gene for osteoarthritis ( OA ) and mutations in GDF5 are associated with a wide variety of skeletal...	[ "Mutations can be generally classified in loss- or gain-of-function mutations depending on their specific pathomechanism .", "Here we report on a GDF5 mutation , p . W414R , which is associated with brachydactyly type A1 ( BDA1 ) and Multiple Synostoses Syndrome 2 ( SYNS2 ) .", "Interestingly , whereas shorteni...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology/host invasion and cell entry", "cell biology", "virology" ]	Vesicular Stomatitis Virus Enters Cells through Vesicles Incompletely Coated with Clathrin That Depend upon Actin for Internalization	journal.ppat.1000394	null	[ [ "Clathrin-mediated endocytosis is the major transport pathway from the plasma membrane to early endosomes .", "In this process , the plasma membrane typically invaginates into a clathrin-coated pit , in which adaptor molecules bridge the interaction of clathrin with cargo .", "During invagination , th...	[ "Many viruses that enter cells by clathrin-dependent endocytosis are significantly larger than the dimensions of a typical clathrin-coated vesicle .", "The mechanisms by which viruses co-opt the clathrin machinery for efficient internalization remain uncertain .", "Here we examined how clathrin-coated vesicles ...	[ "Clathrin-dependent endocytosis accounts for the majority of uptake from the plasma membrane .", "However , many viruses that infect cells through an endocytic route are larger than the dimensions of a typical clathrin-coated vesicle .", "Working with vesicular stomatitis virus , we determined how this cargo en...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "computational biology/systems biology", "computational biology" ]	Identifying Causal Genes and Dysregulated Pathways in Complex Diseases	journal.pcbi.1001095	null	[ [ "Complex diseases are typically caused by combinations of molecular perturbations that might vary strongly in different patients , yet dys-regulate the same component of a cellular system [1] .", "In recent years , whole-genome gene expression sets have increasingly been used to search for markers , allow...	[ "In complex diseases , various combinations of genomic perturbations often lead to the same phenotype .", "On a molecular level , combinations of genomic perturbations are assumed to dys-regulate the same cellular pathways .", "Such a pathway-centric perspective is fundamental to understanding the mechanisms of...	[ "It is now being recognized that complex diseases should be studied from the perspective of dys-regulated pathways and processes rather than individual genes .", "Indeed , various combinations of molecular perturbations might lead to the same disease .", "In such cases , responses to these perturbations are exp...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Resistance to Gray Leaf Spot of Maize: Genetic Architecture and Mechanisms Elucidated through Nested Association Mapping and Near-Isogenic Line Analysis	journal.pgen.1005045	null	[ [ "Plants resist attack by many plant pathogens by inducing localized cell death .", "This strategy can provide effective defense against pathogens that require living host tissue ( biotrophs or hemibiotrophs ) and is the basis for most monogenic resistance .", "However , it is not effective for pathoge...	[ "Gray leaf spot ( GLS ) , caused by Cercospora zeae-maydis and Cercospora zeina , is one of the most important diseases of maize worldwide .", "The pathogen has a necrotrophic lifestyle and no major genes are known for GLS .", "Quantitative resistance , although poorly understood , is important for GLS manageme...	[ "Gray leaf spot ( GLS ) , a necrotrophic , foliar fungal disease of maize , contributes to maize yield losses worldwide .", "We identified and characterized regions of the maize genome that confer resistance to GLS and gained insight into the mechanisms associated with these quantitative trait loci ( QTL ) .", ...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "flow cytometry", "cell death", "medicine and health sciences", "immune physiology", "pathology and laboratory medicine", "pathogens", "cell processes", "immunology", "microbiology", "light microscopy", "viral structure", "scanning confocal microscopy", "plasmid construction", "viruses", ...	Ebola virus requires a host scramblase for externalization of phosphatidylserine on the surface of viral particles	journal.ppat.1006848	null	[ [ "Ebola virus ( EBOV ) , a member of the family Filoviridae , is an enveloped , single-stranded , negative-sense RNA virus that causes severe hemorrhagic fever with a high mortality rate in humans and nonhuman primates [1] .", "Currently , there are no FDA-approved therapeutics to treat EBOV infection [2] ...	[ "Cell surface receptors for phosphatidylserine contribute to the entry of Ebola virus ( EBOV ) particles , indicating that the presence of phosphatidylserine in the envelope of EBOV is important for the internalization of EBOV particles .", "Phosphatidylserine is typically distributed in the inner layer of the pl...	[ "Although Ebola virus causes severe hemorrhagic fever with a high mortality rate , there are no approved therapeutics .", "The viral entry process is one of the targets for antiviral development .", "Previous studies suggest that binding of phosphatidylserine , a component of the viral envelop , to the receptor...	2018
[ "Introduction", "Results", "Discussion", "Materials & methods" ]	[ "medicine and health sciences", "neuromuscular junctions", "nervous system", "skeletal muscles", "electrophysiology", "neuroscience", "macroglial cells", "surgical and invasive medical procedures", "motor neurons", "respiratory system", "schwann cells", "bioassays and physiological analysis", ...	Blocking skeletal muscle DHPRs/Ryr1 prevents neuromuscular synapse loss in mutant mice deficient in type III Neuregulin 1 (CRD-Nrg1)	journal.pgen.1007857	null	[ [ "Like all chemical synapses in the brain , the NMJ–the synaptic connections between motor neurons and skeletal muscles–is assembled as a tripartite structure that includes a presynaptic motor nerve terminal , a postsynaptic muscle cell and a terminal Schwann cell , which caps the motor nerve terminal .", ...	[ "Schwann cells are integral components of vertebrate neuromuscular synapses; in their absence , pre-synaptic nerve terminals withdraw from post-synaptic muscles , leading to muscle denervation and synapse loss at the developing neuromuscular junction ( NMJ ) .", "Here , we report a rescue of muscle denervation an...	[ "Nerve cells ( neurons ) communicate with each other through specialized focal connections called synapses .", "Synapses are commonly assembled into a tripartite structure composed of pre- and post-synaptic neurons , and a glial cell that is closely associated with both pre- and post-synaptic components .", "At...	2019
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "body fluids", "microbiome", "pathology and laboratory medicine", "pathogens", "bladder", "microbiology", "urine", "animal models", "bacterial diseases", "model organisms", "experimental organism systems", "kidneys", "bacterial pathogens", "microbial genom...	Transient microbiota exposures activate dormant Escherichia coli infection in the bladder and drive severe outcomes of recurrent disease	journal.ppat.1006238	null	[ [ "Many disease-causing microorganisms can inhabit the human body asymptomatically , but factors that activate potentially pathogenic reservoirs to cause disease are not well understood .", "After an initial infection , some pathogens establish states of latency that can reactivate to cause recurrent sympto...	[ "Pathogens often inhabit the body asymptomatically , emerging to cause disease in response to unknown triggers .", "In the bladder , latent intracellular Escherichia coli reservoirs are regarded as likely origins of recurrent urinary tract infection ( rUTI ) , a problem affecting millions of women worldwide .", ...	[ "Millions of women suffer from recurrent urinary tract infections ( rUTI ) and the only treatment option is prophylactic antibiotics , which contributes to antibiotic resistance .", "In experimental models , Escherichia coli , the dominant UTI pathogen , establishes reservoirs inside the bladder lining; it is bel...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "cell biology", "computational biology", "molecular biology", "genetics and genomics" ]	Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation	journal.pbio.0060245	Analyzing the temporal order of DNA replication across the genome during embryonic stem cell differentiation reveals stable boundaries between coordinately replicated regions that consolidate into fewer, larger domains during differentiation.	[ [ "Despite our rapidly expanding knowledge of the structure and function of eukaryotic chromatin at the individual nucleosome level , little is known about the higher-order organization of chromosomes [1] .", "DNA replication provides an excellent forum with which to investigate these levels of chromosome o...	[ "DNA replication in mammals is regulated via the coordinate firing of clusters of replicons that duplicate megabase-sized chromosome segments at specific times during S-phase .", "Cytogenetic studies show that these “replicon clusters” coalesce as subchromosomal units that persist through multiple cell generation...	[ "Microscopy studies have suggested that chromosomal DNA is composed of multiple , megabase-sized segments , each replicated at different times during S-phase of the cell cycle .", "However , a molecular definition of these coordinately replicated sequences and the stability of the boundaries between them has not ...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "mammals", "computational biology", "vertebrates", "homo (human)", "genetics and genomics" ]	Global Discriminative Learning for Higher-Accuracy Computational Gene Prediction	journal.pcbi.0030054	null	[ [ "Prediction of protein-coding genes in eukaryotes involves correctly identifying splice sites and translation initiation and stop signals in DNA sequences .", "There are two main gene prediction methods .", "Ab initio methods rely exclusively on intrinsic structural features of genes , such as frequen...	[ "Most ab initio gene predictors use a probabilistic sequence model , typically a hidden Markov model , to combine separately trained models of genomic signals and content .", "By combining separate models of relevant genomic features , such gene predictors can exploit small training sets and incomplete annotation...	[ "We describe a new approach to statistical learning for sequence data that is broadly applicable to computational biology problems and that has experimentally demonstrated advantages over current hidden Markov model ( HMM ) -based methods for sequence analysis .", "The methods we describe in this paper , implemen...	2007
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Validation of Two Rapid Diagnostic Tests for Visceral Leishmaniasis in Kenya	journal.pntd.0002441	null	[ [ "Visceral Leishmaniasis ( VL ) , also known as kala-azar , is a systemic parasitic disease transmitted through the bite of an infected phlebotomine sandfly .", "It is usually fatal if left untreated .", "This neglected disease affects mainly the poorest communities in Brazil , South Asia ( India , Ban...	[ "Visceral leishmaniasis ( VL ) is a systemic parasitic disease that is fatal unless treated .", "In Kenya , national VL guidelines rely on microscopic examination of spleen aspirate to confirm diagnosis .", "As this procedure is invasive , it cannot be safely implemented in peripheral health structures , where ...	[ "Visceral Leishmaniasis ( VL ) is potentially fatal if not treated promptly .", "Its diagnosis is based on the presence of parasites in spleen or bone marrow aspirates .", "These are invasive and risky procedures .", "Simple , rapid and non-invasive diagnostic tests are needed , notably in rural settings .", ...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "bacteriology", "cell motility", "swimming", "medicine and health sciences", "rna interference", "pathology and laboratory medicine", "pathogens", "microbiology", "biological locomotion", "parasitic protozoans", "biomechanics", "protozoan life cycles", "developmental biology", "trypomastig...	Use of chiral cell shape to ensure highly directional swimming in trypanosomes	journal.pcbi.1005353	null	[ [ "Many swimming microorganisms and cells swim along helical paths; examples come from all scales of microscopic life , including the multicellular zooplankton Ploesoma[1] , ciliates like Paramecium[2] , and bacteria like Caulobacter[3] .", "This has been recognised for over a century[1] , and a helical pat...	[ "Swimming cells typically move along a helical path or undergo longitudinal rotation as they swim , arising from chiral asymmetry in hydrodynamic drag or propulsion bending the swimming path into a helix .", "Helical paths are beneficial for some forms of chemotaxis , but why asymmetric shape is so prevalent when...	[ "Swimming cells often follow a helical swimming path , however the advantage of helical paths over a simple straight line path is not clear .", "To analyse this phenomenon , I analysed the swimming of the human parasites Trypanosoma brucei ( which causes sleeping sickness/trypanosomiasis ) and Leishmania mexicana...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	A RecA Protein Surface Required for Activation of DNA Polymerase V	journal.pgen.1005066	null	[ [ "The Escherichia coli RecA protein is the prototype of a bacterial recombinase common to every species of free-living bacteria [1–3] .", "Homologs of RecA protein exist in all classes of organisms , where they play central roles in homologous genetic recombination and recombinational DNA repair .", "R...	[ "DNA polymerase V ( pol V ) of Escherichia coli is a translesion DNA polymerase responsible for most of the mutagenesis observed during the SOS response .", "Pol V is activated by transfer of a RecA subunit from the 3'-proximal end of a RecA nucleoprotein filament to form a functional complex called DNA polymeras...	[ "DNA polymerase V from the bacterium Escherichia coli is one of a class of DNA polymerases that replicate DNA inaccurately .", "They thus generate mutations at elevated levels .", "Whereas this might seem incongruous with the goal of accurate transmission of genetic information from one generation to the next ,...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Chemotherapy of Second Stage Human African Trypanosomiasis: Comparison between the Parenteral Diamidine DB829 and Its Oral Prodrug DB868 in Vervet Monkeys	journal.pntd.0003409	null	[ [ "Diamidinesare widely used in the control of both animal and human infectious diseases .", "Diminazeneaceturate , a diamidine primarily utilized in livestock , has demonstrated activity against Babesia ( bovis and bigemina ) and a variety of animal-infective trypanosomes .", "Pentamidineis an aliphati...	[ "Human African trypanosomiasis ( HAT , sleeping sickness ) ranks among the most neglected tropical diseases based on limited availability of drugs that are safe and efficacious , particularly against the second stage ( central nervous system [CNS] ) of infection .", "In response to this largely unmet need for new...	[ "Treatment of human African trypanosomiasis ( HAT , sleeping sickness ) suffers from a shortage of medicines that are both effective , especially against the second ( late ) stage of the disease , and safe for patients .", "The development of new HAT medicines also has been significantly influenced by the perceiv...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Loss- and Gain-of-Function Approaches Indicate a Dual Role Exerted by Regulatory T Cells in Pulmonary Paracoccidioidomycosis	journal.pntd.0004189	null	[ [ "Regulatory T cells ( Tregs ) were initially considered a Foxp3-expressing CD4+CD25+ T cell subset involved in maintenance of immune tolerance by suppressing T cell responses against self-antigens .", "Nevertheless , recent studies have also clearly revealed their crucial role in modulating immunity durin...	[ "Paracoccidioidomycosis ( PCM ) , is a pulmonary fungal disease whose severity depends on the adequate development of T cell immunity .", "Although regulatory T ( Treg ) cells were shown to control immunity against PCM , deleterious or protective effects were described in different experimental settings .", "To...	[ "Paracoccidioidomycosis ( PCM ) , the most relevant deep mycosis in Latin America , is caused by the fungus Paracoccidioides brasiliensis .", "The involvement of regulatory T ( Treg ) cells in the immunity against PCM has been previously demonstrated , however its underlying mechanisms are still to be elucidated ...	2015
[ "Introduction", "Results and discussion", "Materials and methods" ]	[ "bacteriology", "medicine and health sciences", "aeromonas hydrophila", "crystal structure", "pathology and laboratory medicine", "monomers", "pathogens", "vibrio", "condensed matter physics", "microbiology", "electron cryo-microscopy", "hormones", "membrane proteins", "secretion systems",...	Structure and assembly of pilotin-dependent and -independent secretins of the type II secretion system	journal.ppat.1007731	null	[ [ "Pathogenic bacteria commonly employ the Type II Secretion System ( T2SS ) for the release of protein toxins .", "In many cases these proteins are fundamentally responsible for the pathologies associated with infection including attachment , invasion and defense against host responses [1] .", "Vibrio ...	[ "The type II secretion system ( T2SS ) is a cell envelope-spanning macromolecular complex that is prevalent in Gram-negative bacterial species .", "It serves as the predominant virulence mechanism of many bacteria including those of the emerging human pathogens Vibrio vulnificus and Aeromonas hydrophila .", "Th...	[ "Vibrio vulnificus and Aeromonas hydrophila are two bacterial species that are emerging as significant human pathogens .", "The major virulence mechanism utilized by these species is the Type II secretion system ( T2SS ) that functions in exporting toxic proteins produced by the bacterium into the infected indivi...	2019
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "public health and epidemiology", "infectious disease epidemiology", "statistics", "microbiology", "spatial epidemiology", "geoinformatics", "mathematics", "population modeling", "neglected tropical diseases", "population biology", "infectious disease control", "epidemiological m...	The Effects of City Streets on an Urban Disease Vector	journal.pcbi.1002801	null	[ [ "In the context of increasing urbanization worldwide [1]–[4] , vector-borne diseases , a significant burden to human and animal populations [5] , are quickly emerging in cities [6] and require the adaptation of control strategies to densely populated and highly interconnected environments .", "Notable exa...	[ "With increasing urbanization vector-borne diseases are quickly developing in cities , and urban control strategies are needed .", "If streets are shown to be barriers to disease vectors , city blocks could be used as a convenient and relevant spatial unit of study and control .", "Unfortunately , existing spat...	[ "Chagas disease is a major parasitic disease in Latin America .", "It is transmitted by Triatoma infestans an insect common in Arequipa , the second largest city in Peru .", "We propose a method to demonstrate that streets strongly affect the spatial distribution of infestation by this insect in Arequipa .", ...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "medicine and health sciences", "nervous system", "electrophysiology", "neuroscience", "animals", "animal models", "developmental biology", "drosophila melanogaster", "model organisms", "synaptic plasticity", "experimental organism systems", "muscle functions", "drosophila...	Kek-6: A truncated-Trk-like receptor for Drosophila neurotrophin 2 regulates structural synaptic plasticity	journal.pgen.1006968	null	[ [ "Brain plasticity , neurotrophism in development , structural and synaptic plasticity during learning and long-term memory in humans critically depend on the receptor TrkB binding its neurotrophin ( NT ) ligand BDNF [1 , 2] .", "During development , NTs and Trks regulate neuronal number and connectivity; ...	[ "Neurotrophism , structural plasticity , learning and long-term memory in mammals critically depend on neurotrophins binding Trk receptors to activate tyrosine kinase ( TyrK ) signaling , but Drosophila lacks full-length Trks , raising the question of how these processes occur in the fly .", "Paradoxically , trun...	[ "A long-standing paradox had been to explain how brain structural plasticity , learning and long-term memory might occur in Drosophila in the absence of canonical Trk receptors for neurotrophin ( NT ) ligands .", "NTs link structure and function in the brain enabling adjustments in cell number , dendritic , axona...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "fungal genetics", "sequence assembly tools", "genome analysis", "sequence motif analysis", "epigenetics", "structural genomics", "chromatin", "research and analysis methods", "sequence analysis", "genomic libraries", "mycology", "genomics", "bioinformatics", "chromosome biology", "gene ...	Repeat elements organise 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae	journal.pgen.1007467	null	[ [ "The three-dimensional organisation of chromatin within the nucleus is increasingly seen as a key contributor to the regulation of gene expression [1–3] .", "Eukaryotes share a common hierarchical organisation within the nucleus , where individual nucleosomes aggregate to form chromatin fibres , those fib...	[ "Structural features of genomes , including the three-dimensional arrangement of DNA in the nucleus , are increasingly seen as key contributors to the regulation of gene expression .", "However , studies on how genome structure and nuclear organisation influence transcription have so far been limited to a handful...	[ "How a genome folds within a nucleus can contribute to the regulation of gene expression .", "There is now considerable interest in understanding how the three-dimensional structure of a genome is maintained and how this structure influences biological processes .", "However , most studies on these phenomena fo...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases", "veterinary diseases", "zoonoses", "medicine and health sciences", "clinical immunology", "leishmaniasis", "neglected tropical diseases", "biology and life sciences", "immunology", "tropical diseases", "veterinary science", "immune response" ]	Matrix Metalloproteinase 9 Production by Monocytes is Enhanced by TNF and Participates in the Pathology of Human Cutaneous Leishmaniasis	journal.pntd.0003282	null	[ [ "Human cutaneous leishmaniasis ( CL ) caused by Leishmania braziliensis infection is characterized by the presence of one or more ulcerated lesions with raised borders and few parasites [1] .", "Early after infection , most patients develop lymphadenopathy , followed by the appearance of a papule at the b...	[ "Cutaneous leishmaniasis ( CL ) due to L . braziliensis infection is characterized by a strong inflammatory response with high levels of TNF and ulcer development .", "Less attention has been given to the role of mononuclear phagocytes to this process .", "Monocytes constitute a heterogeneous population subdivi...	[ "To examine the participation of MMP-9 in the pathogenesis of L . braziliensis infection , we realized a cross-sectional study with CL patients in an early phase of the disease or with a classical ulcer , and healthy controls .", "We evaluated the frequency of MMP-9 in monocyte subsets and its mechanism of produc...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Antibodies, western blotting, Seprion ELISA", "Immunohistochemistry and confocal microscopy", "TUNEL assay", "ECG evaluation in conscious mice", "MRI measurement", "Statistical analysis" ]	[ "molecular neuroscience", "medicine and health sciences", "clinical genetics", "genetic dominance", "clinical medicine", "genetics", "biology and life sciences", "molecular genetics", "genetic diseases", "autosomal dominant diseases", "neuroscience", "molecular biology", "cardiology" ]	Dysfunction of the CNS-Heart Axis in Mouse Models of Huntington's Disease	journal.pgen.1004550	null	[ [ "Huntington's disease ( HD ) is an inherited neurodegenerative disorder caused by the expansion of a polyglutamine ( polyQ ) stretch within the huntingtin protein ( HTT ) .", "It is characterized by neurological symptoms and brain pathology , particularly neurodegeneration in the basal ganglia and cerebra...	[ "Cardiac remodelling and contractile dysfunction occur during both acute and chronic disease processes including the accumulation of insoluble aggregates of misfolded amyloid proteins that are typical features of Alzheimer's , Parkinson's and Huntington's disease ( HD ) .", "While HD has been described mainly as ...	[ "Huntington's disease ( HD ) is a neurodegenerative disorder for which the mutation results in an extra-long tract of glutamines that causes the huntingtin protein to aggregate .", "It is characterized by neurological symptoms and brain pathology that is associated with nuclear and cytoplasmic aggregates and with...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Human Enterovirus Nonstructural Protein 2CATPase Functions as Both an RNA Helicase and ATP-Independent RNA Chaperone	journal.ppat.1005067	null	[ [ "For both cells and viruses , the functionality of RNA molecules usually requires correct folding into proper tertiary structures and the association with correct RNA-binding proteins [1 , 2] .", "To make the scenario more complex , RNA molecules frequently function via transient base pairing with target ...	[ "RNA helicases and chaperones are the two major classes of RNA remodeling proteins , which function to remodel RNA structures and/or RNA-protein interactions , and are required for all aspects of RNA metabolism .", "Although some virus-encoded RNA helicases/chaperones have been predicted or identified , their RNA...	[ "Enteroviruses contain a large number of closely related human pathogens , including poliovirus , EV71 , and coxsackie viruses , and cause ~3 billion infections annually .", "Among the nonstructural proteins of enteroviruses or picornaviruses , protein 2CATPase is the most conserved and complex but the least unde...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "auditory system", "computational neuroscience", "biology", "sensory systems", "neuroscience", "coding mechanisms" ]	Sparse Codes for Speech Predict Spectrotemporal Receptive Fields in the Inferior Colliculus	journal.pcbi.1002594	null	[ [ "Our remarkable ability to interpret the highly structured sounds in our everyday environment suggests that auditory processing in the brain is somehow specialized for natural sounds .", "Many authors have postulated that the brain tries to transmit and encode information efficiently , so as to minimize t...	[ "We have developed a sparse mathematical representation of speech that minimizes the number of active model neurons needed to represent typical speech sounds .", "The model learns several well-known acoustic features of speech such as harmonic stacks , formants , onsets and terminations , but we also find more ex...	[ "The receptive field of a neuron can be thought of as the stimulus that most strongly causes it to be active .", "Scientists have long been interested in discovering the underlying principles that determine the structure of receptive fields of cells in the auditory pathway to better understand how our brains proc...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunity", "virology", "biology", "microbiology" ]	Viral Mediated Redirection of NEMO/IKKγ to Autophagosomes Curtails the Inflammatory Cascade	journal.ppat.1002517	null	[ [ "Transcription factor NF-κB activates the expression of numerous target genes , most of which are involved in regulating innate and adaptive immune responses [1] , [2] .", "It is activated in response to a variety of stimuli , which include pathogen-associated molecular patterns ( PAMPs ) and proinflammat...	[ "The early host response to viral infections involves transient activation of pattern recognition receptors leading to an induction of inflammatory cytokines such as interleukin-1β ( IL-1β ) and tumor necrosis factor α ( TNFα ) .", "Subsequent activation of cytokine receptors in an autocrine and paracrine manner ...	[ "Upon viral infection cells immediately induce an innate immune response which involves the production of inflammatory cytokines .", "These cytokines activate specific receptors on infected and surrounding cells leading to local signal amplification as well as signal broadcasting beyond the original site of infec...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "developmental biology/morphogenesis and cell biology", "genetics and genomics/functional genomics", "genetics and genomics/disease models", "genetics and genomics/genetics of disease", "genetics and genomics" ]	Genome-Wide Profiling of p63 DNA–Binding Sites Identifies an Element that Regulates Gene Expression during Limb Development in the 7q21 SHFM1 Locus	journal.pgen.1001065	null	[ [ "The p63 protein encoded by the TP63 gene is a transcription factor of the p53 family and functions as a master regulator of ectodermal development .", "The key function of p63 during ectodermal development is underscored by phenotypic features in p63 knockout mice [1] , [2] and in p63 knock-down zebrafis...	[ "Heterozygous mutations in p63 are associated with split hand/foot malformations ( SHFM ) , orofacial clefting , and ectodermal abnormalities .", "Elucidation of the p63 gene network that includes target genes and regulatory elements may reveal new genes for other malformation disorders .", "We performed genome...	[ "Mammalian embryonic development requires precise control of gene expression in the right place at the right time .", "One level of control of gene expression is through cis-regulatory elements controlled by transcription factors .", "Deregulation of gene expression by mutations in such cis-regulatory elements ...	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "parasite groups", "plasmodium", "gene regulation", "parasitology", "dna transcription", "histone modification", "developmental biology", "apicomplexa", "sequence motif analysis", "epigenetics", "chromatin", "research and analysis methods", "sequence analysis", "transcriptional control", ...	Predicting gene expression in the human malaria parasite Plasmodium falciparum using histone modification, nucleosome positioning, and 3D localization features	journal.pcbi.1007329	null	[ [ "Plasmodium falciparum is the deadliest species of malaria parasite , responsible for 445 , 000 deaths in 2016 [1] .", "As resistance to antimalarial drugs spreads , demand for novel antimalarials increases .", "Designing such novel drugs would require an improved understanding of the biology of this ...	[ "Empirical evidence suggests that the malaria parasite Plasmodium falciparum employs a broad range of mechanisms to regulate gene transcription throughout the organism’s complex life cycle .", "To better understand this regulatory machinery , we assembled a rich collection of genomic and epigenomic data sets , in...	[ "The parasite responsible for the most lethal form of malaria , Plasmodium falciparum , employs a variety of mechanisms to modify the expression of its genes throughout its complex life cycle .", "In this work , we gather a rich collection of data describing various aspects of the gene regulatory apparatus in P ....	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "veterinary diseases", "zoonotic diseases", "leishmaniasis", "biology", "zoology", "veterinary science", "parasitology" ]	Canine Antibody Response to Phlebotomus perniciosus Bites Negatively Correlates with the Risk of Leishmania infantum Transmission	journal.pntd.0001344	null	[ [ "Leishmania infantum ( syn . Leishmania chagasi ) is a protozoan parasite that causes zoonotic leishmaniasis , including the life-threatening visceral form , occurring also in the Mediterranean Basin .", "Parasites are transmitted by the bite of infected phlebotomine sand flies to dogs , the major host an...	[ "Phlebotomine sand flies are blood-sucking insects that can transmit Leishmania parasites .", "Hosts bitten by sand flies develop an immune response against sand fly salivary antigens .", "Specific anti-saliva IgG indicate the exposure to the vector and may also help to estimate the risk of Leishmania spp .", ...	[ "Leishmania infantum is the causative agent of zoonotic visceral leishmaniasis in the Mediterranean Basin and Phlebotomus perniciosus serve as the major vector .", "In the endemic foci , Leishmania parasites are transmitted mostly to dogs , the main reservoir host , and to humans .", "We studied the canine humo...	2011
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "physical sciences", "chemistry", "biology and life sciences", "medicine and health sciences" ]	Synergy Testing of FDA-Approved Drugs Identifies Potent Drug Combinations against Trypanosoma cruzi	journal.pntd.0002977	null	[ [ "The need for new more effective drugs to treat Chagas disease has not been matched by drug discovery efforts .", "An estimated 8 million people have chronic infection with the etiologic agent , Trypanosoma cruzi [1] .", "Existing treatments consist of two nitroaromatic compounds ( benznidazole and ni...	[ "An estimated 8 million persons , mainly in Latin America , are infected with Trypanosoma cruzi , the etiologic agent of Chagas disease .", "Existing antiparasitic drugs for Chagas disease have significant toxicities and suboptimal effectiveness , hence new therapeutic strategies need to be devised to address thi...	[ "Chronic infection with Trypanosoma cruzi causes progressive damage to the heart and other organs that is fatal in about 30% of cases .", "Known as Chagas disease , this is a major public health problem in Latin America .", "The existing medicines were developed over forty years ago and are not widely used beca...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "b vitamins", "medicine and health sciences", "pathology and laboratory medicine", "chemical compounds", "hela cells", "pathogens", "biological cultures", "microbiology", "organic compounds", "cholines", "viruses", "rna viruses", "cell cultures", "cellular structures and organelles", "re...	Phospholipid synthesis fueled by lipid droplets drives the structural development of poliovirus replication organelles	journal.ppat.1007280	null	[ [ "The positive strand RNA ( ( + ) RNA ) viruses of eukaryotes universally assemble their RNA replication machinery in association with specialized membranous domains , featuring unique lipid and protein composition [1–3] .", "It is hypothesized that membranes may facilitate replication by increasing local ...	[ "Rapid development of complex membranous replication structures is a hallmark of picornavirus infections .", "However , neither the mechanisms underlying such dramatic reorganization of the cellular membrane architecture , nor the specific role of these membranes in the viral life cycle are sufficiently understoo...	[ "The cellular pathways hijacked to support viral replication may provide a promising class of targets for anti-viral therapeutics , which will be effective against broad groups of viruses relying on the same cellular pathways , and will likely be refractory to the development of resistance since cellular factors ar...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "gene regulation", "cell cycle and cell division", "membrane staining", "cell processes", "dna-binding proteins", "hormones", "dna transcription", "membrane proteins", "plant science", "plant hormones", "cellular structures and organelles", "research and analysis methods", "cytokinins", "s...	Cytokinin stabilizes WUSCHEL by acting on the protein domains required for nuclear enrichment and transcription	journal.pgen.1007351	null	[ [ "Plant meristem development depends largely on positional information .", "Determining how cells interpret positional cues to regulate gene expression is central to cell fate specification during pattern formation .", "The concentration of transcription factors ( TFs ) in developmental fields have bee...	[ "Concentration-dependent transcriptional regulation and the spatial regulation of transcription factor levels are poorly studied in plant development .", "WUSCHEL , a stem cell-promoting homeodomain transcription factor , accumulates at a higher level in the rib meristem than in the overlying central zone , which...	[ "Stem cell regulation is critical for the development of all organisms , and plants have particularly unique stem cell populations that are maintained throughout their lifespan at the tips of both the shoots and roots .", "Proper spatial and temporal regulation of gene expression by mobile proteins is essential f...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "protein metabolism", "gene regulation", "regulatory proteins", "enzymology", "dna-binding proteins", "metabolomics", "metabolites", "enzyme metabolism", "transcription factors", "enzyme chemistry", "proteins", "enzyme regulation", "gene expression", "biochemistry", "nitrogen metabolism"...	Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast	journal.pcbi.1005297	null	[ [ "Cells sense and react to extracellular stimuli with coordinated intracellular responses conveying transcriptional , protein and metabolic changes [1–3] .", "The continuous technological advances over the last few decades has contributed to the advent of the omics era with quantitative measurements of hun...	[ "Cells react to extracellular perturbations with complex and intertwined responses .", "Systematic identification of the regulatory mechanisms that control these responses is still a challenge and requires tailored analyses integrating different types of molecular data .", "Here we acquired time-resolved metabo...	[ "Phosphorylation is a broad regulatory mechanism with implications in nearly all processes of the cell .", "However , a global understanding of possible regulatory mechanisms remains elusive .", "In this study , we examined the potential regulatory role of kinases , phosphatases and transcription-factors in yea...	2017
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "liver", "enzymes", "cancer treatment", "enzymology", "signaling networks", "cancers and neoplasms", "endocrine physiology", "oncology", "network analysis", "growth factors", "epidermal growth factor", "computer and information sciences", "animal cells", "...	Cell signaling heterogeneity is modulated by both cell-intrinsic and -extrinsic mechanisms: An integrated approach to understanding targeted therapy	journal.pbio.2002930	null	[ [ "Normal cell signaling is significantly altered in cancer as a result of genetic and epigenetic changes , facilitating uncontrolled proliferation and cell survival [1 , 2] .", "Targeted therapies directly exploit these alterations by blocking the activity of specific proteins typically mutated or abnormal...	[ "During the last decade , our understanding of cancer cell signaling networks has significantly improved , leading to the development of various targeted therapies that have elicited profound but , unfortunately , short-lived responses .", "This is , in part , due to the fact that these targeted therapies ignore ...	[ "A signaling pathway is a network of molecules in a cell that is typically initiated by stimuli ( e . g . , microenvironmental cues ) acting on receptors and internal signaling molecules to determine cell fate .", "Signaling pathways in cancer cells are different from those in normal cells , and this difference h...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "deletion mutation", "reactive oxygen species", "medicine and health sciences", "rna interference", "physiological processes", "mutation", "developmental biology", "organism development", "mitochondria", "epigenetics", "bioenergetics", "cellular structures and organelles", "mutant strains", ...	Activation of DAF-16/FOXO by reactive oxygen species contributes to longevity in long-lived mitochondrial mutants in Caenorhabditis elegans	journal.pgen.1007268	null	[ [ "Mitochondria serve a variety of critical functions within the cell including energy production , intracellular signaling and metabolism .", "Accordingly , major disruptions of mitochondrial function lead to detrimental effects including lethality .", "In contrast , mild disruption of mitochondrial fu...	[ "Mild deficits in mitochondrial function have been shown to increase lifespan in multiple species including worms , flies and mice .", "Here , we study three C . elegans mitochondrial mutants ( clk-1 , isp-1 and nuo-6 ) to identify overlapping genetic pathways that contribute to their longevity .", "We find tha...	[ "The use of genetic model organisms has permitted the identification of a large number of genes that influence longevity .", "These genes have been grouped into different pathways of lifespan extension , which have been proposed to modulate longevity by distinct mechanisms .", "In this work , we explore the mec...	2018

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