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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", "Methods" ]	[ "medicine", "infectious diseases", "immune cells", "theoretical biology", "hiv", "t cells", "immunology", "biology", "viral diseases", "immune response" ]	Why Don't CD8+ T Cells Reduce the Lifespan of SIV-Infected Cells In Vivo?	journal.pcbi.1002200	null	[ [ "One of the most direct and convincing demonstrations of the importance of CD8+ T cells in controlling SIV infection in vivo is the observation that , on depleting CD8+ cells , SIV-1 viral load increases by 0 . 5–1 log .", "This observation has been made in both acute and chronic infection and has been re...	[ "In January 2010 two groups independently published the observation that the depletion of CD8+ cells in SIV-infected macaques had no detectable impact on the lifespan of productively infected cells .", "This unexpected observation led the authors to suggest that CD8+ T cells control SIV viraemia via non-lytic mec...	[ "Several studies have shown a role for CD8+ T cells in controlling SIV-infection .", "However , early last year two groups independently showed that depletion of CD8+ lymphocytes did not result in a measurable increase in the lifespan of productively infected cells , suggesting that direct cell killing may not be...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "public health and epidemiology", "global health", "immunology", "biology", "microbiology", "public health" ]	Dengue Virus Co-opts UBR4 to Degrade STAT2 and Antagonize Type I Interferon Signaling	journal.ppat.1003265	null	[ [ "Approximately fifty million dengue virus ( DENV ) infections occur annually with more than forty percent of the human population at risk of developing dengue fever ( DF ) or dengue hemorrhagic fever ( DHF ) .", "DF and its more severe form , DHF , are potentially fatal diseases caused by the four serotyp...	[ "An estimated 50 million dengue virus ( DENV ) infections occur annually and more than forty percent of the human population is currently at risk of developing dengue fever ( DF ) or dengue hemorrhagic fever ( DHF ) .", "Despite the prevalence and potential severity of DF and DHF , there are no approved vaccines ...	[ "Dengue virus ( DENV ) is the leading cause of mosquito-borne viral illness and death in humans .", "At present , there are no vaccines and no specific antiviral therapeutics to prevent or treat DENV infections .", "We previously described that the NS5 protein of DENV inhibits type I interferon signaling in vir...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "cell biology", "physiology", "microbiology", "chemical biology", "molecular biology", "eubacteria" ]	Protein Oxidation Implicated as the Primary Determinant of Bacterial Radioresistance	journal.pbio.0050092	A high intracellular concentration of manganese inDeinococcus radiodurans protects proteins, but not DNA, from ionizing radiation-induced oxidative damage. Protein protection may be critical to the known radiation resistance of these bacteria.	[ [ "The amount of DNA damage caused by a given dose of γ-radiation for resistant and sensitive bacteria is very similar [1 , 2] .", "Yet , the range of ionizing radiation ( IR ) resistances is large [1–3] , with a factor of 200 separating the most-resistant from the most-sensitive species [1] .", "For ex...	[ "In the hierarchy of cellular targets damaged by ionizing radiation ( IR ) , classical models of radiation toxicity place DNA at the top .", "Yet , many prokaryotes are killed by doses of IR that cause little DNA damage .", "Here we have probed the nature of Mn-facilitated IR resistance in Deinococcus radiodura...	[ "One original goal of radiobiology was to explain why cells are so sensitive to ionizing radiation ( IR ) .", "Early studies in bacteria incriminated DNA as the principal radiosensitive target , an assertion that remains central to modern radiation toxicity models .", "More recently , the emphasis has shifted t...	2007
[ "Introduction", "Results/Discussion", "Methods" ]	[ "genetics and genomics", "genetics and genomics/comparative genomics" ]	Nonsense-Mediated Decay Enables Intron Gain in Drosophila	journal.pgen.1000819	null	[ [ "Intron number is highly variable among eukaryotes , ranging from about a dozen in some fungi to more than 100 , 000 in the human genome .", "Comparative genomics across broad phylogenetic distances have identified the importance of both intron gain and loss to the establishment of this variation [1] .", ...	[ "Intron number varies considerably among genomes , but despite their fundamental importance , the mutational mechanisms and evolutionary processes underlying the expansion of intron number remain unknown .", "Here we show that Drosophila , in contrast to most eukaryotic lineages , is still undergoing a dramatic r...	[ "The surprising observation 30 years ago that genes are interrupted by non-coding introns changed our view of gene architecture .", "Intron number varies dramatically among species; ranging from nine introns/gene in humans to less than one in some simple eukyarotes .", "Here we ask where new introns come from a...	2010
[ "Introduction", "Results and Discussion", "Materials and Methods" ]	[ "invertebrates", "medicine and health sciences", "rna interference", "cell cycle and cell division", "cell processes", "animals", "animal models", "developmental biology", "drosophila melanogaster", "respiratory system", "model organisms", "stem cells", "membrane receptor signaling", "horm...	Snoo and Dpp Act as Spatial and Temporal Regulators Respectively of Adult Progenitor Cells in the Drosophila Trachea	journal.pgen.1005909	null	[ [ "Facultative stem cells have been defined as a particular class of differentiated cells that contribute to the structure and function of well-developed organs but remain multipotent; thus , upon damage due to either regular usage or injury they can proliferate and their progeny acquire the identities of diffe...	[ "Clusters of differentiated cells contributing to organ structures retain the potential to re-enter the cell cycle and replace cells lost during development or upon damage .", "To do so , they must be designated spatially and respond to proper activation cues .", "Here we show that in the case of Drosophila dif...	[ "An important feature of organs is their ability to maintain their structure and function in spite of natural or accidental cell loss .", "This capacity is often sustained by so-called stem cells , which are able to provide new cells of the different types in the organ .", "In addition , some specialized cells ...	2016
[ "Introduction", "Methods", "Results", "Discussion", "Conclusions" ]	[ "antimicrobials", "sequencing techniques", "medicine and health sciences", "pathology and laboratory medicine", "drugs", "tropical diseases", "microbiology", "genome sequencing", "bacterial diseases", "signs and symptoms", "ulcers", "antibiotics", "neglected tropical diseases", "pharmacolo...	Low incidence of recurrent Buruli ulcers in treated Australian patients living in an endemic region	journal.pntd.0006724	null	[ [ "Mycobacterium ulcerans ( M . ulcerans ) causes a necrotising infection of skin and soft-tissue known as Buruli ulcer . [1]", "Since the regular use of antibiotics for Buruli ulcer treatment in Australian populations was introduced at the turn of the century , treatment success rates have been very high ....	[ "We examined recurrent Buruli ulcer cases following treatment and assumed cure in a large cohort of Australian patients living in an endemic area .", "We report that while the recurrence rate was low ( 2 . 81 cases/year/1000 population ) , it remained similar to the estimated risk of primary infection within the ...	[ "Mycobacterium ulcerans ( M . ulcerans ) causes a necrotising infection of skin and soft-tissue known as Buruli ulcer .", "Since the regular use of antibiotics for Buruli ulcer treatment in Australian populations was introduced at the turn of the century , treatment success rates have been very high .", "Howeve...	2018
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "health promotion", "medicine and health sciences", "zika fever", "microcephaly", "pathology and laboratory medicine", "maternal health", "obstetrics and gynecology", "pathogens", "tropical diseases", "microbiology", "health care", "viruses", "developmental biology", "women's health", "r...	“Zika is everywhere”: A qualitative exploration of knowledge, attitudes and practices towards Zika virus among women of reproductive age in Iquitos, Peru	journal.pntd.0006708	null	[ [ "Zika is a vector-borne disease transmitted by a daytime biting mosquito of the Aedes species , predominantly Aedes aegypti [1] .", "Common Zika symptoms include rash , mild fever , headache and joint pain [1] .", "Zika has also been linked to severe neurological disorders , including microcephaly aff...	[ "Zika virus was reported in the rainforest city of Iquitos , Peru in 2016 .", "The potential associations between Zika and fetal neurological disorders were reported extensively in the media regarding neighboring Brazil , and led to great concern about the impact Zika could have on people’s health in Iquitos when...	[ "Zika virus is an arthropod-borne viral disease that has recently caused epidemics in many Latin American countries and is associated with adverse neurologic outcomes and fetal complications .", "Although the infection is typically mosquito-transmitted , infection is also possible via sexual transmission .", "T...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "rna interference", "cell division analysis", "caenorhabditis", "cell cycle and cell division", "cell processes", "green fluorescent protein", "neuroscience", "animals", "animal models", "caenorhabditis elegans", "luminescent proteins", "model organisms", "experimental org...	Stochastic loss and gain of symmetric divisions in the C. elegans epidermis perturbs robustness of stem cell number	journal.pbio.2002429	null	[ [ "It is remarkable how biological systems manage to operate consistently despite facing several types of variation , including the intrinsic stochasticity in every molecular process .", "This ability of a given system to produce an invariable output in the presence of internal and external perturbations is...	[ "Biological systems are subject to inherent stochasticity .", "Nevertheless , development is remarkably robust , ensuring the consistency of key phenotypic traits such as correct cell numbers in a certain tissue .", "It is currently unclear which genes modulate phenotypic variability , what their relationship i...	[ "Organisms are exposed to both internal and external perturbations in every molecular process they go through , and robustness—the ability to maintain their systems unchanged—is crucial for their development and survival .", "However , the processes that keep the variability of cells as low as possible are barely...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "sequencing techniques", "invertebrates", "dengue virus", "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "microbiology", "vertebrates", "animals", "sequence assembly tools", "mammals", "viruses", "genomic databases", "rna viruses", "genome analysis", ...	Identification and Genomic Analysis of a Novel Group C Orthobunyavirus Isolated from a Mosquito Captured near Iquitos, Peru	journal.pntd.0004440	null	[ [ "The Orthobunyavirus genus comprises a diverse set of viral species , represented by multiple serogroups , including: Bunyamwera , California , Group C , and Simbu [1] .", "Their RNA genome includes three segments ( Small [S] , Medium [M] , and Large [L] ) .", "The L segment encodes a RNA polymerase (...	[ "Group C orthobunyaviruses are single-stranded RNA viruses found in both South and North America .", "Until very recently , and despite their status as important vector-borne human pathogens , no Group C whole genome sequences containing all three segments were available in public databases .", "Here we report ...	[ "Arthropod-borne viruses remain a significant cause of human and domestic animal disease and new viruses are constantly being discovered .", "RNA virus discovery and assembly remains a challenge due to highly polymorphic genomes , current lack of breadth and depth of publicly available viral genomes , and confoun...	2016
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "genetics and genomics/microbial evolution and genomics" ]	Evolution of a Bacterial Regulon Controlling Virulence and Mg2+ Homeostasis	journal.pgen.1000428	null	[ [ "The ability of an organism to orchestrate responses to environmental changes often depends on transcriptional regulatory proteins that control the expression of multiple genes .", "Related species typically rely on orthologous regulatory proteins to respond to a given stimulus .", "However , the exte...	[ "Related organisms typically rely on orthologous regulatory proteins to respond to a given signal .", "However , the extent to which ( or even if ) the targets of shared regulatory proteins are maintained across species has remained largely unknown .", "This question is of particular significance in bacteria du...	[ "Organisms often respond to environmental cues by modifying the patterns of expression of multiple genes .", "Related species typically rely on orthologous DNA-binding regulatory proteins to orchestrate the response to a given stimulus .", "However , it is unclear whether different organisms express similar or ...	2009
[ "Introduction", "Methods and models", "Results", "Discussion" ]	[ "invertebrates", "linguistics", "medicine and health sciences", "abdomen", "markov models", "nervous system", "social sciences", "mathematical models", "neuroscience", "animals", "animal models", "drosophila melanogaster", "model organisms", "mathematics", "experimental organism systems"...	Drosophila melanogaster grooming possesses syntax with distinct rules at different temporal scales	journal.pcbi.1007105	null	[ [ "Sequential animal behaviors are often composed of repetitions of simple subroutines .", "In driving motor action execution , nervous systems must integrate sensory information with internal priorities and dynamics .", "Both external and internal conditions contribute to sequence organization , but th...	[ "Mathematical modeling of behavioral sequences yields insight into the rules and mechanisms underlying sequence generation .", "Grooming in Drosophila melanogaster is characterized by repeated execution of distinct , stereotyped actions in variable order .", "Experiments demonstrate that , following stimulation...	[ "Analysis of temporally rich behavioral sequences provides a quantitative description of the rules underlying their generation .", "Drosophila melanogaster grooming behavior consists of many complex sequences involving repetitions of well-characterized actions .", "In this paper , we leverage advances in machin...	2019
[ "Introduction", "Models", "Results", "Discussion" ]	[ "recreation", "organismal evolution", "markov models", "statistics", "applied mathematics", "microbiology", "social sciences", "simulation and modeling", "algorithms", "mathematics", "network analysis", "microbial evolution", "population biology", "research and analysis methods", "comput...	Close spatial arrangement of mutants favors and disfavors fixation	journal.pcbi.1007212	null	[ [ "Cooperation is ubiquitous in the natural world ranging from microbial communities to human societies .", "Yet , it is seemingly against evolutionary theory , since cooperators forgo their own interest to benefit others whereas defectors pay nothing to get the benefit .", "The past two decades have se...	[ "Cooperation is ubiquitous across all levels of biological systems ranging from microbial communities to human societies .", "It , however , seemingly contradicts the evolutionary theory , since cooperators are exploited by free-riders and thus are disfavored by natural selection .", "Many studies based on evol...	[ "Evolutionary dynamics on networks are key for biological and social evolution .", "Typically , the clustering mutants on networks can dramatically alter the direction of selection .", "Previous studies on the assortment of mutants assume that individuals interact in a frequency-dependent way .", "It is hard ...	2019
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "chinchillas", "medicine and health sciences", "ears", "vertebrates", "neuroscience", "animals", "mammals", "primates", "animal models", "inner ear", "computational neuroscience", "experimental organism systems", "nerve fibers", "coding mechanisms", "old world monkeys", "research and a...	High-resolution frequency tuning but not temporal coding in the human cochlea	journal.pbio.2005164	null	[ [ "The cochlea decomposes sound into bands of frequencies and encodes the temporal waveform in these bands , generating frequency tuning and phase-locking in the auditory nerve ( AN ) .", "The relative roles of these two processes in human perception have long been debated [1 , 2] and would be clarified by ...	[ "Frequency tuning and phase-locking are two fundamental properties generated in the cochlea , enabling but also limiting the coding of sounds by the auditory nerve ( AN ) .", "In humans , these limits are unknown , but high resolution has been postulated for both properties .", "Electrophysiological recordings ...	[ "The coding of sounds by the cochlea depends on two primary properties: frequency selectivity , which refers to the ability to separate sounds into their different frequency components , and phase-locking , which refers to the neural coding of the temporal waveform of these components .", "These properties have b...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunology/immune response", "microbiology/innate immunity" ]	The Type III Secretion Effector NleE Inhibits NF-κB Activation	journal.ppat.1000743	null	[ [ "Enteropathogenic Escherichia coli ( EPEC ) belong to a group of pathogens defined by their ability to form “attaching and effacing” ( AE ) histopathology on intestinal epithelia .", "These pathogens employ their type III protein secretion system ( TTSS ) to inject ( translocate ) toxic proteins ( effecto...	[ "The complex host-pathogen interplay involves the recognition of the pathogen by the host's innate immune system and countermeasures taken by the pathogen .", "Detection of invading bacteria by the host leads to rapid activation of the transcription factor NF-κB , followed by inflammation and eradication of the i...	[ "The innate immune system senses intruding pathogens and in response , mounts an inflammatory reaction .", "Essential for this response is the activation of the transcription factor NF-κB , which mediates reprogramming of gene expression in the host .", "The bacteria Escherichia coli is usually a non-pathogenic...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "anatomy and physiology", "signaling in selected disciplines", "muscle", "animal models", "developmental biology", "model organisms", "molecular development", "musculoskeletal system", "signaling in cellular processes", "gene expression", "biology", "molecular biology", "biochemistry", "si...	Phosphorylation of the Drosophila melanogaster RNA–Binding Protein HOW by MAPK/ERK Enhances Its Dimerization and Activity	journal.pgen.1002632	null	[ [ "Regulation of gene expression at the level of RNA is often mediated through the activities of RNA-binding proteins ( RBPs ) , which control different aspects of RNA metabolism of target genes [1] , [2] .", "Drosophila melanogaster Held Out Wings ( HOW ) is an RBP that belongs to a family of evolutionaril...	[ "Drosophila melanogaster Held Out Wings ( HOW ) is a conserved RNA–binding protein ( RBP ) belonging to the STAR family , whose closest mammalian ortholog Quaking ( QKI ) has been implicated in embryonic development and nervous system myelination .", "The HOW RBP modulates a variety of developmental processes by ...	[ "Somatic muscles are huge cells that feature highly organized sarcomeric architecture , whose formation and maintenance are not fully understood .", "Multiple signals play a role in these cells , including the highly conserved MAPK/ERK pathway , which often serves as a cue for cellular proliferation or differenti...	2012
[ "Introduction", "Methods", "Discussion" ]	[ "physiology/sensory systems", "neuroscience/sensory systems", "computational biology" ]	Power Efficiency of Outer Hair Cell Somatic Electromotility	journal.pcbi.1000444	null	[ [ "Outer hair cells ( OHC ) in the mammalian cochlea are essential to the remarkable sensitivity of hearing .", "These highly specialized cells actively feed mechanical power into the organ of Corti and amplify its mechanical vibrations in response to sound [1]–[5] .", "How this is achieved at auditory ...	[ "Cochlear outer hair cells ( OHCs ) are fast biological motors that serve to enhance the vibration of the organ of Corti and increase the sensitivity of the inner ear to sound .", "Exactly how OHCs produce useful mechanical power at auditory frequencies , given their intrinsic biophysical properties , has been a ...	[ "The sense of hearing is exquisitely sensitive to quiet sounds due to active mechanical amplification of sound-induced vibrations by hair cells within the inner ear .", "In mammals , the amplification is due to the motor action of “outer hair cells” that feed mechanical power into the cochlea .", "How outer hai...	2009
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "pathology and laboratory medicine", "cestodes", "light microscopy", "parasitic diseases", "animals", "morphometry", "microscopy", "fresh water", "research facilities", "research and analysis methods", "hydrology", "imaging techniques", "f...	Eggs as a Suitable Tool for Species Diagnosis of Causative Agents of Human Diphyllobothriosis (Cestoda)	journal.pntd.0004721	null	[ [ "Human infections with gastrointestinal helminths are usually diagnosed when their eggs are found in stool samples .", "Therefore , examination of stool and detection of parasite eggs is used as a non-invasive method for detection of infections [1] .", "Some of the helminth parasites are relatively ea...	[ "Tapeworms of the order Diphyllobothriidea are parasites of tetrapods and several species may infect man and cause neglected human disease called diphyllobothriosis .", "Identification of human-infecting diphyllobothriid cestodes is difficult because of their morphological uniformity , which concerns also their e...	[ "More than 2 , 000 eggs of 8 species of diphyllobothriid cestodes infecting humans were compared .", "Combination of morphometrical and ultrastructural ( surface morphology ) data made it possible to distinguish all species ." ]	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "small intestine", "cellular stress responses", "animal genetics", "genetic mutation", "anatomy and physiology", "gene function", "animal models", "genetics of disease", "physiological processes", "immunochemistry", "model organisms", "nutrition", "homeostasis", "gastroentero...	A Mouse Model of Acrodermatitis Enteropathica: Loss of Intestine Zinc Transporter ZIP4 (Slc39a4) Disrupts the Stem Cell Niche and Intestine Integrity	journal.pgen.1002766	null	[ [ "The rare pseudo-dominant genetic disease acrodermatitis enteropathica ( AE ) is thought to be caused by the inefficient absorption of dietary zinc [1] .", "AE occurs at a frequency 1 in 500 , 000 and symptoms in humans usually develop soon after birth in bottle fed infants or after weaning in breast fed ...	[ "Mutations in the human Zip4 gene cause acrodermatitis enteropathica , a rare , pseudo-dominant , lethal genetic disorder .", "We created a tamoxifen-inducible , enterocyte-specific knockout of this gene in mice which mimics this human disorder .", "We found that the enterocyte Zip4 gene in mice is essential th...	[ "Loss-of-function of the zinc transporter ZIP4 in the mouse intestine mimics the lethal human disease acrodermatitis enteropathica .", "This is a rare disease in humans that is not well understood .", "Our studies demonstrate the paramount importance of ZIP4 in the intestine in this disease and reveal that a ro...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "neurological disorders/neuromuscular diseases", "molecular biology/dna replication", "molecular biology/recombination", "genetics and genomics/disease models", "molecular biology/dna repair" ]	Expanded CAG/CTG Repeat DNA Induces a Checkpoint Response That Impacts Cell Proliferation in Saccharomyces cerevisiae	journal.pgen.1001339	null	[ [ "Repetitive DNA is found dispersed throughout eukaryotic genomes , and in some cases is central to key biological processes such as chromosome segregation and chromosome end protection [1] .", "Repeat tracts are usually sites of variation among individuals , with some classes of repeats expanding to sizes...	[ "Repetitive DNA elements are mutational hotspots in the genome , and their instability is linked to various neurological disorders and cancers .", "Although it is known that expanded trinucleotide repeats can interfere with DNA replication and repair , the cellular response to these events has not been characteri...	[ "Expansion of a CAG/CTG trinucleotide repeat is the causative mutation for multiple neurodegenerative diseases , including Huntington's disease , myotonic dystrophy , and multiple types of spinocerebellar ataxias .", "Two reasons for the cell death that occurs in these diseases are toxicity of the repeat-containi...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "bacteriology", "organismal evolution", "microbial metabolism", "microbial mutation", "population genetics", "metabolic networks", "microbiology", "bacterial biochemistry", "escherichia coli", "parallel evolution", "mutation", "prokaryotic models", "model organisms", "microbial evolution",...	Metabolic Erosion Primarily Through Mutation Accumulation, and Not Tradeoffs, Drives Limited Evolution of Substrate Specificity in Escherichia coli	journal.pbio.1001789	During long-term evolution of Escherichia coli, nutrient specialization is primarily driven by the accumulation of neutral mutations, rather than by tradeoffs, and can also be accompanied by general catabolic improvements.	[ [ "Evolving populations face the fundamental dilemma that there is no single phenotype that is optimal in all environments .", "When an evolving population occupies the same selective environment for an extended period of time , no advantage is realized by maintaining fitness on resources it no longer encou...	[ "Evolutionary adaptation to a constant environment is often accompanied by specialization and a reduction of fitness in other environments .", "We assayed the ability of the Lenski Escherichia coli populations to grow on a range of carbon sources after 50 , 000 generations of adaptation on glucose .", "Using di...	[ "Adaptation to a single constant environment is commonly expected to result in decreased performance in alternative conditions , or specialization .", "It has been proposed that , rather than occurring through the neutral accumulation of mutations in unused alternative pathways , this happens because loss of thes...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Proportionality: A Valid Alternative to Correlation for Relative Data	journal.pcbi.1004075	null	[ [ "Relative abundance measurements are common in molecular biology: nucleic acids typically have to be provided at a set concentration for sequencing or microarray analysis; sequencing methods report a large but finite total of reads , of which any particular sequence is a proportion .", "Sometimes , resear...	[ "In the life sciences , many measurement methods yield only the relative abundances of different components in a sample .", "With such relative—or compositional—data , differential expression needs careful interpretation , and correlation—a statistical workhorse for analyzing pairwise relationships—is an inapprop...	[ "Relative abundance data is common in the life sciences , but appreciation that it needs special analysis and interpretation is scarce .", "Correlation is popular as a statistical measure of pairwise association but should not be used on data that carry only relative information .", "Using timecourse yeast gene...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "molecular biology/rna-protein interactions", "evolutionary biology/genomics", "evolutionary biology/bioinformatics", "computational biology/genomics", "genetics and genomics/bioinformatics" ]	Human miRNA Precursors with Box H/ACA snoRNA Features	journal.pcbi.1000507	null	[ [ "Small nucleolar RNAs ( snoRNAs ) and microRNAs ( miRNAs ) are two classes of abundant non-coding regulatory RNAs that carry out fundamental cellular activities but that have only been comprehensively investigated in recent years .", "SnoRNAs are small RNA molecules of approximately 60–300 nucleotides in ...	[ "MicroRNAs ( miRNAs ) and small nucleolar RNAs ( snoRNAs ) are two classes of small non-coding regulatory RNAs , which have been much investigated in recent years .", "While their respective functions in the cell are distinct , they share interesting genomic similarities , and recent sequencing projects have iden...	[ "The major functions known for RNA were long believed to be either messenger RNAs , which function as intermediates between genes and proteins , or ribosomal RNAs and transfer RNAs which carry out the translation process .", "In recent years , however , newly discovered classes of small RNAs have been shown to pl...	2009
[ "Introduction", "Results", "Discussion", "Material and methods" ]	[ "blood cells", "innate immune system", "medicine and health sciences", "immune physiology", "cytokines", "pathology and laboratory medicine", "respiratory infections", "immune cells", "pathogens", "immunology", "microbiology", "pulmonology", "pseudomonas aeruginosa", "animal models", "pn...	Interleukin-36γ and IL-36 receptor signaling mediate impaired host immunity and lung injury in cytotoxic Pseudomonas aeruginosa pulmonary infection: Role of prostaglandin E2	journal.ppat.1006737	null	[ [ "Pseudomonas aeruginosa is a Gram-negative bacterium that causes acute nosocomial infection as well as chronic infection in immunocompromised hosts .", "Infection with P . aeruginosa can lead to sepsis , pneumonia , and lung injury , which are often severe and life threatening [1] .", "Poor clinical o...	[ "Pseudomonas aeruginosa is a Gram-negative pathogen that can lead to severe infection associated with lung injury and high mortality .", "The interleukin ( IL ) -36 cytokines ( IL-36α , IL-36β and IL-36γ ) are newly described IL-1 like family cytokines that promote inflammatory response via binding to the IL-36 r...	[ "Pneumonia caused by Pseudomonas aeruginosa is a serious infection resulting in significant lung injury and mortality in susceptible hosts .", "The first line of defense in P . aeruginosa lung infection are neutrophils and macrophages , which play a pivotal role in the rapid clearance of pathogens from the lung ....	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "infectious disease epidemiology", "epidemiology", "dengue fever", "neglected tropical diseases" ]	Symptomatic Versus Inapparent Outcome in Repeat Dengue Virus Infections Is Influenced by the Time Interval between Infections and Study Year	journal.pntd.0002357	null	[ [ "Dengue is a major health problem globally , with more than 40% of the world's population at risk and over a hundred countries affected by epidemics [1] .", "In the past 50 years , the incidence of dengue has increased considerably , affecting tens of millions of people annually .", "Dengue is caused ...	[ "Four dengue virus serotypes ( DENV1-4 ) circulate globally , causing more human illness than any other arthropod-borne virus .", "Dengue can present as a range of clinical manifestations from undifferentiated fever to Dengue Fever to severe , life-threatening syndromes .", "However , most DENV infections are i...	[ "The four serotypes of the mosquito-borne dengue virus ( DENV ) infect an estimated 100 million humans annually , resulting in tens of millions of dengue cases and hundreds of thousands of cases of severe disease .", "However , infection with DENV does not always lead to clinical signs , and a large proportion of...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "mitogenic signaling", "fungal genetics", "microbiology", "fungi", "mapk signaling cascades", "protein kinase signaling cascade", "mycology", "ascomycetes", "molds (fungi)", "fungal biochemistry", "signal transduction", "cell biology", "neurospora crassa", "genetics", "biology and life s...	Fungal Communication Requires the MAK-2 Pathway Elements STE-20 and RAS-2, the NRC-1 Adapter STE-50 and the MAP Kinase Scaffold HAM-5	journal.pgen.1004762	null	[ [ "Intercellular communication is critical for the survival of simple unicellular organisms such as bacteria and yeasts and is central for the development and function of multicellular plant and animal systems [1]–[4] .", "Cell-cell signaling and somatic cell fusion is also required to develop the interconn...	[ "Intercellular communication is critical for the survival of unicellular organisms as well as for the development and function of multicellular tissues .", "Cell-to-cell signaling is also required to develop the interconnected mycelial network characteristic of filamentous fungi and is a prerequisite for symbioti...	[ "Appropriate cellular responses to external stimuli depend on the highly orchestrated activity of interconnected signaling cascades .", "One crucial level of control arises from the formation of discrete complexes through scaffold proteins that bind multiple components of a given pathway .", "Central for our un...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/viral infections", "virology", "computational biology/systems biology", "immunology/innate immunity" ]	Host Defense against Viral Infection Involves Interferon Mediated Down-Regulation of Sterol Biosynthesis	journal.pbio.1000598	Upon infection, our immune cells produce a small protein called interferon, which in turn signals a protective response through a series of biochemical reactions that involves lowering the cells' ability to make cholesterol by targeting a gene essential for controlling the pathway for cholesterol metabolism.	[ [ "Sterols and fatty acids are common intermediary metabolites that play key roles in many biological pathways involved in inflammatory diseases such as atherosclerosis and chronic heart disease [1]–[4] .", "Significantly , mounting evidence shows a connection between innate immune signaling processes and t...	[ "Little is known about the protective role of inflammatory processes in modulating lipid metabolism in infection .", "Here we report an intimate link between the innate immune response to infection and regulation of the sterol metabolic network characterized by down-regulation of sterol biosynthesis by an interfe...	[ "Currently , little is known about the crosstalk between the body's immune and metabolic systems that occurs after viral infection .", "This work uncovers a previously unappreciated physiological role for the cholesterol-metabolic pathway in protecting against infection that involves a molecular link with the pro...	2011
[ "Introduction", "Methods", "Results", "Discussion", "Conclusion" ]	[ "schistosoma", "invertebrates", "children", "medicine and health sciences", "body fluids", "clinical research design", "education", "helminths", "sociology", "tropical diseases", "geographical locations", "social sciences", "parasitic diseases", "animals", "urine", "age groups", "res...	Safety, efficacy and acceptability of praziquantel in the treatment of Schistosoma haematobium in pre-school children of Kwale County, Kenya	journal.pntd.0006852	null	[ [ "Human schistosomiasis is a major neglected public health problem caused by trematodes of the genus Schistosoma .", "Over 200 million people are infected globally , with 85% of these cases living in Sub-Saharan Africa [1] .", "In Kenya , nearly 6 million people are infected and an additional 15 millio...	[ "The recommended strategy for control of schistosomiasis is preventive chemotherapy with praziquantel ( PZQ ) .", "Pre-school children ( PSC ) are excluded from population treatment programs .", "In high endemic areas , these children are also at risk , and require treatment with PZQ .", "The Government of Ke...	[ "Control of schistosome infections is through treatment of infected people with a single dose of the anti-helminth drug praziquantel ( PZQ ) which is safe , highly efficacious , and can reverse schistosome-related morbidity particularly in the early stages of disease progression .", "However pre-school children a...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology and life sciences", "immunology" ]	T Cell Inactivation by Poxviral B22 Family Proteins Increases Viral Virulence	journal.ppat.1004123	null	[ [ "Smallpox was among the deadliest infectious diseases in history and its eradication is a landmark in medicine .", "However , loss of orthopoxvirus ( OPXV ) -specific immunity facilitates the accidental introduction of zoonotic OPXV such as monkeypox virus ( MPXV ) and cowpox virus ( CPXV ) which cannot b...	[ "Infections with monkeypox , cowpox and weaponized variola virus remain a threat to the increasingly unvaccinated human population , but little is known about their mechanisms of virulence and immune evasion .", "We now demonstrate that B22 proteins , encoded by the largest genes of these viruses , render human T...	[ "We discovered that the largest gene in the genome of monkeypox viruses and several related viruses , including the virus causing smallpox , but not vaccine strains , encode a protein ( B22 ) that renders the cellular immune system non-responsive .", "A particularly novel aspect of this work is that B22 proteins ...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "medicine and health sciences", "rna interference", "classical mechanics", "pathology and laboratory medicine", "caenorhabditis", "gene regulation", "pathogens", "enzymes", "microbiology", "enzymology", "mechanical stress", "animals", "pseudomonas aeruginosa", "animal mo...	Stress-responsive and metabolic gene regulation are altered in low S-adenosylmethionine	journal.pgen.1007812	null	[ [ "Cellular functions are profoundly affected by metabolic state .", "For example , transcriptional regulation can be linked to metabolism through the modification of chromatin by methylation [1] .", "Using the methyl groups produced by the 1-carbon cycle ( 1CC ) and donated by S-adenosylmethionine ( SA...	[ "S-adenosylmethionine ( SAM ) is a donor which provides the methyl groups for histone or nucleic acid modification and phosphatidylcholine production .", "SAM is hypothesized to link metabolism and chromatin modification , however , its role in acute gene regulation is poorly understood .", "We recently found t...	[ "Animals respond to stress by activating suites of protective genes .", "A specific metabolite , S-adenosylmethionine ( SAM ) , influences how these genes are activated in a variety of stress conditions .", "SAM is produced by the 1-carbon cycle and is the major donor for methylation reactions .", "Thus , SAM...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "phosphorylation", "innate immune system", "medicine and health sciences", "immune physiology", "cytokines", "pathology and laboratory medicine", "gene regulation", "pathogens", "immunology", "microbiology", "viruses", "developmental biology", "dna viruses", "molecular development", "mol...	Human Cytomegalovirus Immediate-Early 1 Protein Rewires Upstream STAT3 to Downstream STAT1 Signaling Switching an IL6-Type to an IFNγ-Like Response	journal.ppat.1005748	null	[ [ "Janus kinase-signal transducer and activator of transcription ( JAK-STAT ) signaling pathways are the principal means by which responses to dozens of cytokines , growth factors and other extracellular molecules are transduced from the cell surface to the nucleus .", "Although all JAK-STAT pathways share ...	[ "The human cytomegalovirus ( hCMV ) major immediate-early 1 protein ( IE1 ) is best known for activating transcription to facilitate viral replication .", "Here we present transcriptome data indicating that IE1 is as significant a repressor as it is an activator of host gene expression .", "Human cells induced ...	[ "Our previous work has shown that the human cytomegalovirus ( hCMV ) major immediate-early 1 protein ( IE1 ) modulates host cell signaling pathways involving proteins of the signal transducer and activator of transcription ( STAT ) family .", "IE1 has also long been known to facilitate viral replication by activa...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology/cell differentiation", "developmental biology/developmental evolution", "evolutionary biology/developmental evolution" ]	Cheating by Exploitation of Developmental Prestalk Patterning in Dictyostelium discoideum	journal.pgen.1000854	null	[ [ "Cooperative behaviors are susceptible to exploitation by cheaters – individuals that do not pay the full cost of cooperation , but reap the benefits [1] and thus take advantage of other cooperative individuals ( victims ) .", "Cheating is predicted to affect the relative fitness of any interacting partne...	[ "The cooperative developmental system of the social amoeba Dictyostelium discoideum is susceptible to exploitation by cheaters—strains that make more than their fair share of spores in chimerae .", "Laboratory screens in Dictyostelium have shown that the genetic potential for facultative cheating is high , and fi...	[ "Cooperative systems are susceptible to exploitation by cheaters who enjoy the benefits of cooperation without paying the costs .", "Such conflict is seen in biological systems at every level from individual genes within a cell to individuals within societies .", "The social amoebae Dictyostelium discoideum hav...	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "computer and information sciences", "medicine and health sciences", "population modeling", "biology and life sciences", "infectious disease modeling", "computational biology", "computerized simulations", "malaria", "parasitic diseases" ]	Seasonally Dependent Relationships between Indicators of Malaria Transmission and Disease Provided by Mathematical Model Simulations	journal.pcbi.1003812	null	[ [ "Evaluating the effectiveness of malaria control interventions on the basis of their impact on transmission is increasingly important as countries consider elimination as well as malaria control .", "However , direct measurement of transmission , such as by the entomological inoculation rate ( EIR ) ( a m...	[ "Evaluating the effectiveness of malaria control interventions on the basis of their impact on transmission as well as impact on morbidity and mortality is becoming increasingly important as countries consider pre-elimination and elimination as well as disease control .", "Data on prevalence and transmission are ...	[ "While malaria is still a major public health problem in many parts of the world , control programs have greatly reduced the burden of disease in recent years and many countries are now considering the goal of elimination .", "Unfortunately , malaria transmission becomes more difficult to measure when it is low b...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology", "biology", "microbiology" ]	Vpu Binds Directly to Tetherin and Displaces It from Nascent Virions	journal.ppat.1003299	null	[ [ "Tetherin is an antiviral protein that can inhibit the release of a broad-spectrum of enveloped viruses , including retroviruses [1]–[7] , filoviruses [4] , [8]–[10] , arenaviruses [9] , [10] , rhabdoviruses [11] and herpesviruses [6] , [12] .", "The Tetherin protein is a type-II single-pass transmembrane...	[ "Tetherin ( Bst2/CD317/HM1 . 24 ) is an interferon-induced antiviral host protein that inhibits the release of many enveloped viruses by tethering virions to the cell surface .", "The HIV-1 accessory protein , Vpu , antagonizes Tetherin through a variety of proposed mechanisms , including surface downregulation a...	[ "At the cell surface , HIV-1 particles are assembled and then released to infect new cells .", "However , an anti-viral host restriction factor , Tetherin , can tether outgoing virions to the infected cell surface , preventing their dissemination .", "HIV-1 overcomes this block through the expression of the vir...	2013
[ "Introduction", "Model", "Results", "Discussion" ]	[ "organismal evolution", "theoretical biology", "microbial evolution", "biology", "evolutionary biology", "microbiology", "evolutionary theory", "evolutionary developmental biology" ]	Differences in Cell Division Rates Drive the Evolution of Terminal Differentiation in Microbes	journal.pcbi.1002468	null	[ [ "The reproduction and development of differentiated multicellular organisms follows a complex iterative pattern .", "Almost all differentiated multicellular organisms develop from a single pluripotent germ cell that divides and differentiates .", "Although terminally differentiated somatic cells conta...	[ "Multicellular differentiated organisms are composed of cells that begin by developing from a single pluripotent germ cell .", "In many organisms , a proportion of cells differentiate into specialized somatic cells .", "Whether these cells lose their pluripotency or are able to reverse their differentiated stat...	[ "The evolution of multicellularity is one of the most fascinating topics of evolutionary biology .", "Without multicellularity the incredible diversity of extant life would not be possible .", "In many multicellular organisms with specialized cells , some cell types become terminally differentiated ( somatic ce...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "rna interference", "gene function", "gene expression", "muscle fibers", "biology", "molecular biology", "rna", "rna processing", "cell biology", "nucleic acids", "genetic screens", "genetics", "cellular types", "molecular cell biology", "genetics and genomics" ]	Muscle-Specific Splicing Factors ASD-2 and SUP-12 Cooperatively Switch Alternative Pre-mRNA Processing Patterns of the ADF/Cofilin Gene in Caenorhabditis elegans	journal.pgen.1002991	null	[ [ "Alternative pre-mRNA processing is a major way to produce a number of different mRNAs and proteins from one gene [1] , [2] .", "Recent transcriptome analyses by deep sequencing estimated that more than 90% of human multi-exon genes undergo alternative processing and most alternative processing events are...	[ "Pre–mRNAs are often processed in complex patterns in tissue-specific manners to produce a variety of protein isoforms from single genes .", "However , mechanisms orchestrating the processing of the entire transcript are not well understood .", "Muscle-specific alternative pre–mRNA processing of the unc-60 gene...	[ "Muscle is a specialized organ with specialized contractile apparatuses .", "A number of genes encoding contractile apparatus-related proteins undergo muscle-specific pre–mRNA processing .", "However , the molecular mechanisms and consequences of muscle-specific alternative pre–mRNA processing remain largely un...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience/neuronal signaling mechanisms", "neuroscience/neuronal and glial cell biology", "neuroscience/theoretical neuroscience" ]	The Role of Ongoing Dendritic Oscillations in Single-Neuron Dynamics	journal.pcbi.1000493	null	[ [ "The dendritic tree contributes significantly to the elementary computations a neuron can perform , both by its intricate morphology and its composition of voltage-gated ionic conductances [1] .", "Such active conductances can underlie a wide variety of dynamical behaviors , amongst others dendritic spike...	[ "The dendritic tree contributes significantly to the elementary computations a neuron performs while converting its synaptic inputs into action potential output .", "Traditionally , these computations have been characterized as both temporally and spatially localized .", "Under this localist account , neurons c...	[ "A central issue in biology is how local processes yield global consequences .", "This is especially relevant for neurons since these spatially extended cells process local synaptic inputs to generate global action potential output .", "The dendritic tree of a neuron , which receives most of the inputs , expres...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular biology/dna replication", "genetics and genomics/microbial evolution and genomics", "molecular biology/recombination", "molecular biology/chromosome structure", "genetics and genomics/chromosome biology", "genetics and genomics", "genetics and genomics/bioinformatics", "molecular biology/dn...	The Baker's Yeast Diploid Genome Is Remarkably Stable in Vegetative Growth and Meiosis	journal.pgen.1001109	null	[ [ "Mutations can arise in genomes as the result of errors that occur during DNA replication , and the repair of DNA lesions [1] , [2] .", "Mutations such as base substitutions , small insertions and deletions , and large-scale rearrangements are raw materials for adaptive evolution [3]–[5]; however , the de...	[ "Accurate estimates of mutation rates provide critical information to analyze genome evolution and organism fitness .", "We used whole-genome DNA sequencing , pulse-field gel electrophoresis , and comparative genome hybridization to determine mutation rates in diploid vegetative and meiotic mutation accumulation ...	[ "Mutations result from errors that occur during DNA metabolism .", "They provide the raw materials for evolution , can affect organism fitness , and have been shown to accumulate in organisms during asexual growth .", "During a sexual life cycle , mutations can be removed by recombination and mating .", "Whil...	2010
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "flow cytometry", "medicine and health sciences", "immune cells", "gene regulation", "immunology", "bone marrow cells", "animal models", "micrornas", "model organisms", "granulocytes", "experimental organism systems", "neutrophils", "research and analysis methods", "white ...	MiR-125a Is a critical modulator for neutrophil development	journal.pgen.1007027	null	[ [ "Neutrophils , also known as polymorphonuclear leukocytes ( PMNs ) , are the most abundant granulocytes which play a crucial role in immune defense and inflammatory reaction .", "Given that the post-mitotic nature of mature neutrophils , they have short lives about only a few days [1] and need to be regen...	[ "MicroRNAs are universal post-transcriptional regulators in genomes .", "They have the ability of buffering gene expressional programs , contributing to robustness of biological systems and playing important roles in development , physiology and diseases .", "Here , we identified a microRNA , miR-125a , as a po...	[ "MicroRNAs are critical epigenetic modulators in development , physiology and disease processes .", "Many miRNAs are involved in immune cell development and function , like miR-150 for B cells , miR-181a for T cells .", "However , studies of miRNAs involvement in granulocyte development and function and related...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "computational neuroscience", "biology", "sensory systems", "neuroscience" ]	Efficient Sparse Coding in Early Sensory Processing: Lessons from Signal Recovery	journal.pcbi.1002372	null	[ [ "In the last decades a large body of research has been devoted to explain the nature of neural representations .", "Since experimental manipulation of the stimuli has the most direct impact on the sensory responses , most of our knowledge comes from studies about the early stages of sensory systems .", ...	[ "Sensory representations are not only sparse , but often overcomplete: coding units significantly outnumber the input units .", "For models of neural coding this overcompleteness poses a computational challenge for shaping the signal processing channels as well as for using the large and sparse representations in...	[ "Neural systems favor overcomplete sparse codes in which the number of potential output neurons may exceed the number of input neurons , but only a small subset of neurons become actually active .", "We argue that efficient use of such large dimensional overcomplete sparse codes requires structural sparsity by co...	2012
[ "Introduction", "Materials and methods", "Results and discussion", "Conclusions and future directions" ]	[ "parasite evolution", "vertebrates", "parasitic protozoans", "mammals", "animals", "parasitology", "organisms", "trypanosoma brucei", "protozoans", "molecular biology techniques", "cellular structures and organelles", "research and analysis methods", "kinetoplasts", "camels", "artificial...	Multiple evolutionary origins of Trypanosoma evansi in Kenya	journal.pntd.0005895	null	[ [ "Trypanosoma evansi is an important disease-causing parasite of livestock in many African , Asian and South American countries .", "T . evansi belongs to a group of five closely related named taxa of various ranks found in a wide diversity of mammalian hosts; Trypanosoma brucei brucei , T . b .", "gam...	[ "Trypanosoma evansi is the parasite causing surra , a form of trypanosomiasis in camels and other livestock , and a serious economic burden in Kenya and many other parts of the world .", "Trypanosoma evansi transmission can be sustained mechanically by tabanid and Stomoxys biting flies , whereas the closely relat...	[ "Trypanosoma evansi is an important pathogen of the camel and other livestock where it is a causative agent of surra ( an economically burdensome disease ) .", "The T . evansi is found in Kenya and the rest of the world .", "This study indicates that T . evansi originated recently from multiple Trypanosoma bruc...	2017
[ "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "classical mechanics", "abdomen", "diagnostic radiology", "vibration", "social sciences", "electromagnetic radiation", "muscle contraction", "mechanical energy", "animal behavior", "synchrotron radiation", "zoology", "research and analysis methods", "muscle ...	Planthopper bugs use a fast, cyclic elastic recoil mechanism for effective vibrational communication at small body size	journal.pbio.3000155	Planthopper insects produce fast abdominal twerks for vibrational communication through the substrate, employing a novel vibratory organ that uses two reciprocal elastic recoil mechanisms to generate fast cyclical motion.	[ [ "We begin by characterising the morphology of the newly-described snapping organ in our model species , Agalmatium bilobum ( Fulgoromorpha: Issidae ) .", "The snapping organ can be found dorsally on each side of the body at the junction between the metathorax and the abdomen , spanning the first two abdom...	[ "Vibrations through substrates are an important source of information for diverse organisms , from nematodes to elephants .", "The fundamental challenge for small animals using vibrational communication is to move their limited mass fast enough to provide sufficient kinetic energy for effective information transf...	[ "Animals use substrate-borne vibrations for eavesdropping and communication over an immense range of body size—from elephants to nematodes .", "Vibrational communication is especially challenging for small animals because of the high mechanical power that is needed to transmit information effectively over extende...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	KRN4 Controls Quantitative Variation in Maize Kernel Row Number	journal.pgen.1005670	null	[ [ "Understanding the genetic and molecular basis of grain yield is necessary to guide breeding efforts towards the development of high-yielding maize hybrids .", "Kernel row number ( KRN ) in maize is one of the most important yield components and a significant breeding target .", "During the domesticat...	[ "Kernel row number ( KRN ) is an important component of yield during the domestication and improvement of maize and controlled by quantitative trait loci ( QTL ) .", "Here , we fine-mapped a major KRN QTL , KRN4 , which can enhance grain productivity by increasing KRN per ear .", "We found that a ~3-Kb intergen...	[ "Maize ( Zea mays L . ) is one of the world's most important sources of calories for humans .", "With an expanding global population , the demands for maize-derived food , feed , and fuel are rapidly increasing .", "To meet these needs , geneticists and breeders are facing the challenge of enhancing grain yield...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "evolutionary biology/animal genetics", "evolutionary biology/evolutionary and comparative genetics", "infectious diseases/neglected tropical diseases", "molecular biology/molecular evolution", "infectious diseases/protozoal infections", "infectious diseases/epidemiology and control of infectious diseases...	Phylogeography and Genetic Variation of Triatoma dimidiata, the Main Chagas Disease Vector in Central America, and Its Position within the Genus Triatoma	journal.pntd.0000233	null	[ [ "American trypanosomiasis or Chagas disease is widespread in Latin America from Mexico to Chile and southern Argentina .", "Although present estimates of 10 to 12 million people infected with the haemoflagellate protozoan species Trypanosoma cruzi represent 6–8 million fewer cases than those reported in t...	[ "Among Chagas disease triatomine vectors , the largest genus , Triatoma , includes species of high public health interest .", "Triatoma dimidiata , the main vector throughout Central America and up to Ecuador , presents extensive phenotypic , genotypic , and behavioral diversity in sylvatic , peridomestic and dom...	[ "Chagas disease is a serious parasitic disease of Latin America .", "Human contamination in poor rural or periurban areas is mainly attributed to haematophagous triatomine insects .", "Triatoma includes important vector species , as T . dimidiata in Central and Meso-America .", "DNA sequences , phylogenetic m...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/gene expression", "genetics and genomics/complex traits", "genetics and genomics/disease models", "molecular biology/dna methylation", "genetics and genomics/epigenetics", "developmental biology/developmental molecular mechanisms" ]	Maternal Ethanol Consumption Alters the Epigenotype and the Phenotype of Offspring in a Mouse Model	journal.pgen.1000811	null	[ [ "While it is well-recognized that gestational exposure to environmental triggers can lead to compromised fetal development and adult disease in humans [1] , the underlying molecular mechanisms remain unknown .", "There is increasing evidence in animal models that environmental factors can affect gene expr...	[ "Recent studies have shown that exposure to some nutritional supplements and chemicals in utero can affect the epigenome of the developing mouse embryo , resulting in adult disease .", "Our hypothesis is that epigenetics is also involved in the gestational programming of adult phenotype by alcohol .", "We have ...	[ "In humans it has been known for some time that exposure to environmental insults during pregnancy can harm a developing fetus and have life-long effects on the individual's health .", "A well known example is fetal alcohol syndrome , where the children of mothers that consume large amounts of alcohol during preg...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunology/leukocyte development", "immunology/innate immunity", "cell biology/membranes and sorting", "infectious diseases/protozoal infections", "microbiology/cellular microbiology and pathogenesis" ]	The Leishmania donovani Lipophosphoglycan Excludes the Vesicular Proton-ATPase from Phagosomes by Impairing the Recruitment of Synaptotagmin V	journal.ppat.1000628	null	[ [ "Phagocytosis consists in the uptake and destruction of invading microorganisms , thereby playing an essential role in host defense against infection [1] .", "Following internalization , microbes end up in a vacuole , the phagosome , which engages in a maturation process involving highly regulated fusion ...	[ "We recently showed that the exocytosis regulator Synaptotagmin ( Syt ) V is recruited to the nascent phagosome and remains associated throughout the maturation process .", "In this study , we investigated the possibility that Syt V plays a role in regulating interactions between the phagosome and the endocytic o...	[ "Upon their internalization by macrophages , Leishmania donovani promastigotes inhibit phagolysosome biogenesis .", "This inhibition is mediated by the virulence glycolipid lipophosphoglycan ( LPG ) , attached to the promastigote surface .", "We recently showed that the exocytosis regulator Synaptotagmin ( Syt ...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology/microbial growth and development", "infectious diseases/viral infections", "virology/host invasion and cell entry", "genetics and genomics/functional genomics" ]	A Kinome RNAi Screen Identified AMPK as Promoting Poxvirus Entry through the Control of Actin Dynamics	journal.ppat.1000954	null	[ [ "In order to successfully infect cells , viruses must remodel the cellular environment to allow for the reallocation of resources to viral production .", "Poxviruses are large double stranded ( ds ) DNA viruses that have a sophisticated lifecycle characterized by a number of temporally regulated steps .",...	[ "Poxviruses include medically important human pathogens , yet little is known about the specific cellular factors essential for their replication .", "To identify genes essential for poxvirus infection , we used high-throughput RNA interference to screen the Drosophila kinome for factors required for vaccinia inf...	[ "Entry is a vital step in establishing viral infection , providing a potential therapeutic target .", "Many viruses co-op one of the various cellular endocytic routes for entry , making the host factors that contribute to these processes essential for efficient infection .", "In particular , vaccinia , the prot...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases", "plasmodium", "physiology", "microbiology", "eukaryotes", "homo (human)" ]	Plasmodium falciparum Regulatory Subunit of cAMP-Dependent PKA and Anion Channel Conductance	journal.ppat.0040019	null	[ [ "Plasmodium falciparum is the species responsible for the lethal form of malaria [1] .", "The disease is caused by the developmental cycle of the blood stage of the parasite [2] .", "Their proliferation within the red blood cells ( RBCs ) requires amino acids from the degradation of haemoglobin , but ...	[ "Malaria symptoms occur during Plasmodium falciparum development into red blood cells .", "During this process , the parasites make substantial modifications to the host cell in order to facilitate nutrient uptake and aid in parasite metabolism .", "One significant alteration that is required for parasite devel...	[ "By replicating within red blood cells malaria parasites are largely hidden from immune recognition , but within mature erythrocytes nutrients are limiting and accumulation of potentially hazardous metabolic end products can rapidly become critical .", "In order to survive within red blood cells malaria parasites...	2008
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "ecology and environmental sciences", "water resources", "helminths", "tropical diseases", "hookworms", "parasitic diseases", "animals", "physiological processes", "ascaris", "ascaris lumbricoides", "neglected tropical diseases", "medical ri...	Prevalence, intensity and associated risk factors of soil transmitted helminth infections: A comparison between Negritos (indigenous) in inland jungle and those in resettlement at town peripheries	journal.pntd.0007331	null	[ [ "Cultural , socio-economic and environmental changes affect the pattern of diseases and health persistence within a population [1] .", "According to palaeoparasitology history , intestinal parasites , particularly soil-transmitted helminths ( STH ) had co-evolved together with humans since the very beginn...	[ "Formerly known as the Malaysian hunter gatherers , the Negrito Orang Asli ( OA ) were heavily dependent on the forest for sustenance and early studies indicated high prevalence of intestinal parasitism .", "Initiation of a redevelopment program in the 1970s aimed to demarginalize the OA was expected to reduce so...	[ "Pattern of diseases in a community are associated with changes of culture , socio-economic and environmental conditions .", "In Malaysia , while transition towards modernity by socio-economic development has shown significant reduction in intestinal parasitism in the general population , no significant differenc...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "vesicles", "cell processes", "microbiology", "viral structure", "epithelial cells", "golgi apparatus", "plants", "cellular structures and organelles", "endosomes", "animal cells", "proteins", "biological tissue", "tomatoes", "cell membranes", "virions",...	Intracellular trafficking of begomoviruses in the midgut cells of their insect vector	journal.ppat.1006866	null	[ [ "Insects transmit the majority of plant viruses [1–3] .", "The process of virus transmission by an insect vector varies based on how the virus is acquired , retained , and inoculated into plants .", "Some plant viruses , such as members of the genera Caulimovirus , Cucumovirus and Potyvirus , are tran...	[ "Begomoviruses are exclusively transmitted by whiteflies in a persistent circulative manner and cause considerable economic losses to crop production worldwide .", "Previous studies have shown that begomoviruses accumulate in vesicle-like structures in whitefly midgut cells and that clathrin-mediated endocytosis ...	[ "Many plant viruses are vectored by insects in a persistent circulative manner .", "In this process , the transport of virus from the gut lumen into the hemolymph of the vector is an important step .", "Identification of vector components involved in this transport process could lead to new strategies to combat...	2018
[ "Introduction", "Materials and methods", "Results", "Discussion", "Conclusions and recommendations" ]	[ "medicine and health sciences", "face", "niger", "tropical diseases", "geographical locations", "surgical and invasive medical procedures", "health care", "bacterial diseases", "neglected tropical diseases", "africa", "veterinary science", "public and occupational health", "infectious diseas...	Estimated incidence and Prevalence of noma in north central Nigeria, 2010–2018: A retrospective study	journal.pntd.0007574	null	[ [ "Noma is a disease of the orofacial region that has been unanimously described as devastating , mutilating , destructive and debilitating due to its appearance and the nature of spread of the acute necrotizing lesion which runs fulminating courses .", "Alternatively known as Stomatitis gangrenosa or Cancr...	[ "Noma is a spreading and fulminant disease believed to be native to Sub-Saharan Africa over the last decade and associated with low socioeconomic status of citizens of the region .", "Within this noma belt , most epidemiological reports regarding the disease have emanated from the north western region of Nigeria ...	[ "Noma , a devouring disease of the orofacial complex , is commonly associated with poverty and impoverished regions of the world especially Sub-Saharan Africa termed the noma belt region of the world .", "With more reports advocating for full inclusion of noma in the WHO Neglected Tropical Diseases ( NTDs ) progr...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genome expression analysis", "animal genetics", "functional genomics", "gene regulation", "dna transcription", "histone modification", "animal models", "drosophila melanogaster", "model organisms", "molecular genetics", "epigenetics", "epigenomics", "chromatin", "gene expression", "biol...	Cohesin and Polycomb Proteins Functionally Interact to Control Transcription at Silenced and Active Genes	journal.pgen.1003560	null	[ [ "The cohesin complex that encircles DNA is named for its role in mediating sister chromatid cohesion [1] .", "Cohesin has four subunits: the Smc1 and Smc3 structural maintenance of chromosomes proteins , Rad21 , a kleisin protein , and Stromalin ( SA ) .", "Cohesin is loaded onto chromosomes by the ko...	[ "Cohesin is crucial for proper chromosome segregation but also regulates gene transcription and organism development by poorly understood mechanisms .", "Using genome-wide assays in Drosophila developing wings and cultured cells , we find that cohesin functionally interacts with Polycomb group ( PcG ) silencing p...	[ "An important task for the cohesin protein complex that binds chromosomes is to ensure equal distribution of chromosomes into the daughter cells when a cell divides .", "Small changes in cohesin activity , however , can alter gene activity without affecting chromosome distribution , and disrupt physical and menta...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "auditory system", "computational neuroscience", "psychoacoustics", "biology", "sensory systems", "sensory perception", "neuroscience" ]	Music in Our Ears: The Biological Bases of Musical Timbre Perception	journal.pcbi.1002759	null	[ [ "A fundamental role of auditory perception is to infer the likely source of a sound; for instance to identify an animal in a dark forest , or to recognize a familiar voice on the phone .", "Timbre , often referred to as the color of sound , is believed to play a key role in this recognition process [1] ."...	[ "Timbre is the attribute of sound that allows humans and other animals to distinguish among different sound sources .", "Studies based on psychophysical judgments of musical timbre , ecological analyses of sound's physical characteristics as well as machine learning approaches have all suggested that timbre is a ...	[ "Music is a complex acoustic experience that we often take for granted .", "Whether sitting at a symphony hall or enjoying a melody over earphones , we have no difficulty identifying the instruments playing , following various beats , or simply distinguishing a flute from an oboe .", "Our brains rely on a numbe...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "enzyme-linked immunoassays", "pathology and laboratory medicine", "molecular probe techniques", "pathogens", "immunology", "biological cultures", "microbiology", "immunoblotting", "salmonellosis", "bacterial diseases", "physio...	The Prostaglandin E2-EP3 Receptor Axis Regulates Anaplasma phagocytophilum-Mediated NLRC4 Inflammasome Activation	journal.ppat.1005803	null	[ [ "Rickettsial diseases are arthropod-borne illnesses caused by obligate intracellular bacteria grouped in the order Rickettsiales [1 , 2] .", "They include:", "( i ) rickettsioses due to bacteria of the genus Rickettsia , including the spotted fever and the typhus group;", "( ii ) scrub typhus due ...	[ "Rickettsial agents are sensed by pattern recognition receptors but lack pathogen-associated molecular patterns commonly observed in facultative intracellular bacteria .", "Due to these molecular features , the order Rickettsiales can be used to uncover broader principles of bacterial immunity .", "Here , we us...	[ "Elimination of bacteria is orchestrated by the immune system .", "Intracellular bacteria are generally recognized by cytosolic molecules named Nod-like receptors ( NLRs ) .", "One such protein scaffold that senses needle-like structures and globular proteins , namely , the bacterial type III secretion ( T3SS )...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Inhibition of Translation Initiation by Protein 169: A Vaccinia Virus Strategy to Suppress Innate and Adaptive Immunity and Alter Virus Virulence	journal.ppat.1005151	null	[ [ "The study of virus-host interactions continues to provide valuable information about the complex relationships between cells and pathogens .", "Large DNA viruses , in particular , encode many proteins that modify the intracellular environment to promote viral survival , replication and spread .", "Va...	[ "Vaccinia virus ( VACV ) is the prototypic orthopoxvirus and the vaccine used to eradicate smallpox .", "Here we show that VACV strain Western Reserve protein 169 is a cytoplasmic polypeptide expressed early during infection that is excluded from virus factories and inhibits the initiation of cap-dependent and ca...	[ "Long after smallpox was eradicated by vaccination with vaccinia virus , the study of this virus continues to reveal novel aspects of the interactions between a virus and the host in which it replicates .", "In this work we investigated the function of a previously uncharacterized VACV protein , called 169 .", ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "oncology", "developmental biology", "medicine and health sciences", "cell biology", "genetics", "biology and life sciences", "molecular cell biology" ]	Hyperactivated Wnt Signaling Induces Synthetic Lethal Interaction with Rb Inactivation by Elevating TORC1 Activities	journal.pgen.1004357	null	[ [ "The Retinoblastoma protein Rb is a tumor suppressor inactivated in a broad spectrum of cancers [1] , [2] .", "Rb functions mainly through binding to the E2F family of transcription factors and regulating the expression of diverse cellular targets involved in cell cycle regulation , DNA replication and re...	[ "Inactivation of the Rb tumor suppressor can lead to increased cell proliferation or cell death depending on specific cellular context .", "Therefore , identification of the interacting pathways that modulate the effect of Rb loss will provide novel insights into the roles of Rb in cancer development and promote ...	[ "Inactivation of Rb tumor suppressor is common in cancers .", "Therefore , identification of genes and pathways that are synthetic lethal with Rb will provide new insights into the role of Rb in cancer development and promote the development of novel therapeutic approaches .", "Here we identified a novel synthe...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "death rates", "invertebrates", "dengue virus", "medicine and health sciences", "pathology and laboratory medicine", "demography", "china", "atmospheric science", "pathogens", "geographical locations", "microbiology", "animals", "viruses", "seasons", "summer", "developmental biology", ...	The interplay of climate, intervention and imported cases as determinants of the 2014 dengue outbreak in Guangzhou	journal.pntd.0005701	null	[ [ "As the most important mosquito-borne disease globally , the incidence of dengue has increased 30-fold in the past 50 years [1] .", "In 2013 alone , dengue was responsible for 576 , 900 years of premature life lost and 1 . 14 million disability-adjusted life-years globally [2] .", "However , dengue wa...	[ "Dengue is a fast spreading mosquito-borne disease that affects more than half of the population worldwide .", "An unprecedented outbreak happened in Guangzhou , China in 2014 , which contributed 52 percent of all dengue cases that occurred in mainland China between 1990 and 2015 .", "Our previous analysis , ba...	[ "An unprecedented dengue outbreak occurred in Guangzhou , 2014 , with 38 , 036 reported cases in contrast to 73 , 179 cases in all of mainland China from 1990 to 2015 .", "In an earlier analysis using a deterministic model , we concluded the early timing of local transmission to be the most important determinant ...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "medicine and health sciences", "lysosomes", "caenorhabditis", "light microscopy", "animals", "animal models", "developmental biology", "guanine nucleotide exchange factors", "caenorhabditis elegans", "model organisms", "microscopy", "experimental organism systems", "confo...	Function and regulation of the Caenorhabditis elegans Rab32 family member GLO-1 in lysosome-related organelle biogenesis	journal.pgen.1007772	null	[ [ "Caenorhabditis elegans gut granules are lysosome related organelles ( LROs ) [1] , cell type-restricted compartments with diverse functions that share characteristics with conventional lysosomes [2] .", "These conspicuous intestine-specific compartments contain birefringent and autofluorescent material [...	[ "Cell type-specific modifications of conventional endosomal trafficking pathways lead to the formation of lysosome-related organelles ( LROs ) .", "C . elegans gut granules are intestinally restricted LROs that coexist with conventional degradative lysosomes .", "The formation of gut granules requires the Rab32...	[ "Lysosome-related organelles represent a diverse collection of intracellular compartments that have important physiological functions .", "In mammals they include melanosomes , key sites of pigment synthesis , and platelet dense granules , which play important roles in blood clotting .", "Defects in the pathway...	2018
[ "Introduction", "Model", "Results/Discussion" ]	[ "mathematics", "biophysics/theory and simulation", "neuroscience/theoretical neuroscience", "computational biology/computational neuroscience" ]	Action Potential Initiation in the Hodgkin-Huxley Model	journal.pcbi.1000265	null	[ [ "In 1952 , Hodgkin and Huxley explained how action potentials are generated through the electrical excitability of neuronal membranes [1] .", "Action potentials arise from the synergistic action of sodium channels and potassium channels , each of which opens and closes in a voltage dependent fashion .", ...	[ "A recent paper of B . Naundorf et al . described an intriguing negative correlation between variability of the onset potential at which an action potential occurs ( the onset span ) and the rapidity of action potential initiation ( the onset rapidity ) .", "This correlation was demonstrated in numerical simulati...	[ "In 1952 , Hodgkin and Huxley described the underlying mechanism for the firing of action potentials through which information is propagated in the nervous system .", "Hodgkin and Huxley's model relies on the opening and closing of channels , selectively allowing ions to move across the membrane .", "In the ori...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine" ]	Mycolactone Diffuses into the Peripheral Blood of Buruli Ulcer Patients - Implications for Diagnosis and Disease Monitoring	journal.pntd.0001237	null	[ [ "Buruli ulcer ( BU ) , caused by Mycobacterium ulcerans , is the third most common mycobacterial disease after tuberculosis and leprosy and represents an emerging threat [1] , [2] .", "Since the late 1980s , the disease has been developing throughout West and Central Africa , prompting the WHO in 1998 to ...	[ "Mycobacterium ulcerans , the causative agent of Buruli ulcer ( BU ) , is unique among human pathogens in its capacity to produce a polyketide-derived macrolide called mycolactone , making this molecule an attractive candidate target for diagnosis and disease monitoring .", "Whether mycolactone diffuses from ulce...	[ "Mycolactone is a diffusible cytotoxin produced by Mycobacterium ulcerans , the causative agent of the skin disease Buruli ulcer .", "In a previous study using animal models , we reported that mycolactone released by cutaneous foci of infection gains access to the peripheral blood .", "Here we investigated whet...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Whole Genome Comparisons Suggest Random Distribution of Mycobacterium ulcerans Genotypes in a Buruli Ulcer Endemic Region of Ghana	journal.pntd.0003681	null	[ [ "Buruli ulcer ( BU ) is a neglected tropical disease caused by infection with Mycobacterium ulcerans .", "Each year 5000–6000 cases are reported from 15 of the 33 countries where BU cases have been reported , predominantly from rural regions across West and Central Africa [1] .", "The disease involves...	[ "Efforts to control the spread of Buruli ulcer – an emerging ulcerative skin infection caused by Mycobacterium ulcerans - have been hampered by our poor understanding of reservoirs and transmission .", "To help address this issue , we compared whole genomes from 18 clinical M . ulcerans isolates from a 30km2 regi...	[ "In this study we use the power of whole genome sequence comparisons to track the spread of Mycobacterium ulcerans , the causative agent of Buruli ulcer , through several villages in the Ashanti region of Ghana , providing new insights on the behaviour of this enigmatic and emerging pathogen ." ]	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunizations", "medicine", "infectious diseases", "immune cells", "aging and immunity", "immunity", "t cells", "immunity to infections", "immunology", "biology", "viral diseases", "cytomegalovirus infection" ]	Immune Senescence: Relative Contributions of Age and Cytomegalovirus Infection	journal.ppat.1002850	null	[ [ "Immune senescence , defined as the age-related alterations of the immune system , is associated with an increased incidence of infections , cancer , autoimmunity and a reduced efficacy of prophylactic vaccines [1]–[3] .", "Although all components of the immune system undergo age-related changes , the T c...	[ "Immune senescence , defined as the age-associated dysregulation and dysfunction of the immune system , is characterised by impaired protective immunity and decreased efficacy of vaccines .", "Recent clinical , epidemiological and immunological studies suggest that Cytomegalovirus ( CMV ) infection may be associa...	[ "Cytomegalovirus ( CMV ) persistently infects 50–90% of the human population .", "After primary infection , constant immune surveillance is required to prevent CMV-related disease .", "During ageing , increasing T cell resources are expended to keep CMV under control .", "Recent human studies have suggested t...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "biology", "neuroscience" ]	Maintaining a Cognitive Map in Darkness: The Need to Fuse Boundary Knowledge with Path Integration	journal.pcbi.1002651	null	[ [ "In 1948 , Tolman employed two analogies to describe the prevailing classes of models used to explain the experimental data on maze navigation and learning obtained from rats [1] .", "Tolman likened the stimulus-response class of models to an old fashioned telephone exchange , where incoming calls are lin...	[ "Spatial navigation requires the processing of complex , disparate and often ambiguous sensory data .", "The neurocomputations underpinning this vital ability remain poorly understood .", "Controversy remains as to whether multimodal sensory information must be combined into a unified representation , consisten...	[ "Do animals need “cognitive maps“ ?", "One of the main difficulties in answering this question is finding a definitive scenario where having and not having a “cognitive map“ result in measurably different outcomes .", "Many key predictions made by models involving some sort of “cognitive map“ can also be replic...	2012
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "neurological disorders/peripheral neuropathies", "developmental biology/neurodevelopment", "genetics and genomics/gene discovery", "genetics and genomics/medical genetics" ]	Mutation in the Gene Encoding Ubiquitin Ligase LRSAM1 in Patients with Charcot-Marie-Tooth Disease	journal.pgen.1001081	null	[ [ "Charcot-Marie-Tooth disease ( CMT ) comprises a set of genetically heterogeneous disorders of the peripheral nervous system , affecting motor and sensory function .", "CMT is the most common inherited neuromuscular disorder , with a wide range of clinical presentations , but as described by OMIM ( 118200...	[ "Charcot-Marie-Tooth disease ( CMT ) represents a family of related sensorimotor neuropathies .", "We studied a large family from a rural eastern Canadian community , with multiple individuals suffering from a condition clinically most similar to autosomal recessive axonal CMT , or AR-CMT2 .", "Homozygosity map...	[ "Sensory motor neuropathies are diseases of the peripheral nervous system , involving primarily the nerves which control our muscles .", "These can result from either genetic or non-genetic causes , with genetic causes usually referred to as Charcot-Marie-Tooth ( CMT ) disease after the three clinicians who first...	2010
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "neonatology", "medicine and health sciences", "ecology and environmental sciences", "water resources", "pathology and laboratory medicine", "maternal health", "cryptosporidium", "parasitic diseases", "parasitic protozoans", "pediatrics", "diarrhea", "protozoans", "mathematics", "statistic...	Risk factors for Cryptosporidium infection in low and middle income countries: A systematic review and meta-analysis	journal.pntd.0006553	null	[ [ "Cryptosporidium is a protozoan parasite with a worldwide distribution infecting humans and animals .", "In high income countries , Cryptosporidium occasionally causes sizable outbreaks due to contaminated water supplies or food sources [1] .", "In Low and Middle Income Countries ( LMICs ) , cryptospo...	[ "Cryptosporidium infection causes gastrointestinal disease and has a worldwide distribution .", "The highest burden is in developing countries .", "We sought to conduct a systematic review and meta-analysis to identify Cryptosporidium risk factors in Low and Middle Income countries ( LMICs ) .", "Medline Ovid...	[ "Cryptosporidium is a parasite that causes diarrhoea and is transmitted through faecal contamination of water and food .", "Though it occurs in developed nations , it is much more prevalent in developing countries and is associated with high mortality in children under 2 years old .", "In this review , we looke...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "functional genomics", "gene regulation", "cell differentiation", "parasitology", "gene function", "germ cells", "developmental biology", "organism development", "stem cells", "molecular development", "neglected tropical diseases", "molecular genetics", "signaling pathways", ...	Whole-Organ Isolation Approach as a Basis for Tissue-Specific Analyses in Schistosoma mansoni	journal.pntd.0002336	null	[ [ "Schistosomes are blood-dwelling digenean trematodes with a complex life-cycle comprising a freshwater intermediate snail host and a mammalian final host .", "Depending on the schistosome species , adults reside in the intestinal or urinary veins , predominantly of mammals [1]–[4] .", "Schistosome fem...	[ "Schistosomiasis is one of the most important parasitic diseases worldwide , second only to malaria .", "Schistosomes exhibit an exceptional reproductive biology since the sexual maturation of the female , which includes the differentiation of the reproductive organs , is controlled by pairing .", "Pathogenicit...	[ "As a neglected disease , schistosomiasis is still an enormous problem in the tropics and subtropics .", "Since the 1980s , Praziquantel ( PZQ ) has been the drug of choice but can be anticipated to lose efficacy in the future due to emerging resistance .", "Alternative drugs or efficient vaccines are still lac...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Early Developmental and Evolutionary Origins of Gene Body DNA Methylation Patterns in Mammalian Placentas	journal.pgen.1005442	null	[ [ "In eutherian mammals the placenta plays a vital role in not only the transfer of nutrients and waste between mother and offspring but also as a protective layer between the maternal and fetal immune systems during fetal development .", "Despite this , the gross morphologies and cellular characteristics o...	[ "Over the last 20-80 million years the mammalian placenta has taken on a variety of morphologies through both divergent and convergent evolution .", "Recently we have shown that the human placenta genome has a unique epigenetic pattern of large partially methylated domains ( PMDs ) and highly methylated domains (...	[ "The placenta is vital for the proper development of the fetus , not only facilitating the exchange of nutrients , oxygen , and waste between the mother and the fetus but also acting as an interface to the maternal immune system and regulating fetal growth by excreting hormones and growth factors .", "DNA methyla...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "neuroscience/behavioral neuroscience", "neuroscience/cognitive neuroscience", "neuroscience/theoretical neuroscience" ]	Attention Increases the Temporal Precision of Conscious Perception: Verifying the Neural-ST2 Model	journal.pcbi.1000576	null	[ [ "An apparent temporal limitation of visual perception is illustrated by the attentional blink ( AB; [6] ) .", "The AB describes a finding that observers often fail to detect a second target stimulus ( T2 ) presented in short succession ( between 100 and 600 ms ) after an identified first target stimulus (...	[ "What role does attention play in ensuring the temporal precision of visual perception ?", "Behavioural studies have investigated feature selection and binding in time using fleeting sequences of stimuli in the Rapid Serial Visual Presentation ( RSVP ) paradigm , and found that temporal accuracy is reduced when a...	[ "Our visual system keeps pace with a rapidly changing stream of information as we view the natural world .", "To do so , it uses a strongly regulated system of attentional filters to constrain which visual stimuli are permitted to be fully processed to the level of conscious awareness .", "This article explores...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Proteomics-Based Characterization of the Humoral Immune Response in Sporotrichosis: Toward Discovery of Potential Diagnostic and Vaccine Antigens	journal.pntd.0004016	null	[ [ "Sporothrix schenckii was originally described in 1898 as the causal agent of a subcutaneous disease in humans in the Mid-Atlantic USA [1] .", "Subsequently , the disease was reported in rats naturally infected in southeastern Brazil [2] and later in a wide range of animals including dogs , cats , horses ...	[ "Sporothrix schenckii and associated species are agents of human and animal sporotrichosis that cause large sapronoses and zoonoses worldwide .", "Epidemiological surveillance has highlighted an overwhelming occurrence of the highly pathogenic fungus Sporothrix brasiliensis during feline outbreaks , leading to ma...	[ "Sporotrichosis is a neglected fungal disease of humans and animals that remains a serious public-health problem .", "Sporothrix infections persist in cats , leading to continued transmission via cat-to-cat and cat-to-human contact .", "Cats are the major source of transmission of Sporothrix brasiliensis to the...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology/neuronal and glial cell biology", "oncology", "ophthalmology/pediatric ophthalmology", "cell biology/cell signaling", "cell biology/cell growth and division", "developmental biology/cell differentiation", "cell biology/cell adhesion", "ophthalmology/ocular tumors", "cell biology/gene e...	Cdh11 Acts as a Tumor Suppressor in a Murine Retinoblastoma Model by Facilitating Tumor Cell Death	journal.pgen.1000923	null	[ [ "Retinoblastoma is initiated by loss of both RB1 alleles , denoted M1 and M2 mutational events [1] .", "These initiating events are sufficient for the development of the benign tumor , retinoma , but not enough to drive to malignancy; additional mutational events ( M3-Mn ) are required for development to ...	[ "CDH11 gene copy number and expression are frequently lost in human retinoblastomas and in retinoblastomas arising in TAg-RB mice .", "To determine the effect of Cdh11 loss in tumorigenesis , we crossed Cdh11 null mice with TAg-RB mice .", "Loss of Cdh11 had no gross morphological effect on the developing retin...	[ "Despite over two decades since loss of RB1 was implicated in initiating retinoblastoma , the unique tissue specificity of this process remains puzzling .", "Indeed , functional loss of both alleles of the RB1 tumor suppressor gene results in >40 , 000-fold increase in predisposition to retinal cancer during chil...	2010
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "medicine and health sciences", "microbial mutation", "immune cells", "pathology and laboratory medicine", "viral transmission and infection", "pathogens", "immunology", "microbiology", "vertebrates", "animals", "mammals", "genetic mapping", "retroviruses", "primates", "...	In vivo virulence of MHC-adapted AIDS virus serially-passaged through MHC-mismatched hosts	journal.ppat.1006638	null	[ [ "Human immunodeficiency virus ( HIV ) induces persistent viremia leading to AIDS onset in humans .", "Virus-specific CD8+ T-cell responses exert strong suppressive pressure on HIV replication [1–3] but fail to control viremia in most infections .", "Several human leukocyte antigen ( HLA ) or major his...	[ "CD8+ T-cell responses exert strong suppressive pressure on HIV replication and select for viral escape mutations .", "Some of these major histocompatibility complex class I ( MHC-I ) -associated mutations result in reduction of in vitro viral replicative capacity .", "While these mutations can revert after vir...	[ "CD8+ T-cell responses exert considerable control over replication of HIV and select for viral escape mutations .", "Recent studies have suggested that these major histocompatibility complex class I ( MHC-I ) -associated mutations accumulate in populations and make viruses less pathogenic in vitro .", "Other st...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology/virion structure, assembly, and egress", "virology/viral replication and gene regulation", "virology" ]	Production of Infectious Genotype 1b Virus Particles in Cell Culture and Impairment by Replication Enhancing Mutations	journal.ppat.1000475	null	[ [ "HCV is a positive strand RNA virus which belongs to the family Flaviviridae [1] .", "Its genome of about 9 . 6 kb is composed of the 5′non-translated region ( NTR ) , an open reading frame encoding a large polyprotein , and the 3′NTR [2] ( Fig . 1A ) .", "In the N-terminal region , the polyprotein is...	[ "With the advent of subgenomic hepatitis C virus ( HCV ) replicons , studies of the intracellular steps of the viral replication cycle became possible .", "These RNAs are capable of self-amplification in cultured human hepatoma cells , but save for the genotype 2a isolate JFH-1 , efficient replication of these HC...	[ "The hepatitis C virus ( HCV ) is a major cause of acute and chronic liver disease .", "Unusual for a positive strand RNA virus , HCV has the high propensity to establish persistent infection , which increases the risk for liver cirrhosis and hepatocellular carcinoma .", "No selective therapy is available thus ...	2009
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Detailed Per-residue Energetic Analysis Explains the Driving Force for Microtubule Disassembly	journal.pcbi.1004313	null	[ [ "Microtubules ( MTs ) are cellular organelles that participate in major cellular processes such as mitosis , cell shape maintenance , cell motility and motor protein transport and constitute a major target for a wide range of drugs , most notably anti-mitotic chemotherapy agents such as paclitaxel .", "Du...	[ "Microtubules are long filamentous hollow cylinders whose surfaces form lattice structures of αβ-tubulin heterodimers .", "They perform multiple physiological roles in eukaryotic cells and are targets for therapeutic interventions .", "In our study , we carried out all-atom molecular dynamics simulations for ar...	[ "The molecular machinery of chromosome segregation during cell division is one of the most sophisticated molecular biology mechanisms employing the interplay of different proteins and forces .", "The long filamentous tube-shaped microtubule structure is a central player in chromosome segregation and cell division...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "hiv infections", "medicine and health sciences", "pathology and laboratory medicine", "viral transmission and infection", "pathogens", "microbiology", "vertebrates", "cancers and neoplasms", "animals", "mammals", "retroviruses", "viruses", "primates", "oncology", "hematologic cancers an...	Gammaherpesvirus infection and malignant disease in rhesus macaques experimentally infected with SIV or SHIV	journal.ppat.1007130	null	[ [ "The lymphotropic human gammaherpesviruses Epstein Barr Virus ( EBV ) and Kaposi’s Sarcoma-Associated Herpesvirus ( KSHV ) are associated with malignancies in the setting of HIV infection[1] .", "EBV is associated with aggressive B cell Non-Hodgkin’s lymphomas such as diffuse large B cell lymphoma ( DLBCL...	[ "Human gammaherpesviruses are associated with malignancies in HIV infected individuals; in macaques used in non-human primate models of HIV infection , gammaherpesvirus infections also occur .", "Limited data on prevalence and tumorigenicity of macaque gammaherpesviruses , mostly cross-sectional analyses of small...	[ "Human gammaherpesviruses cause malignancies in HIV infected persons; in SIV infected macaques , gammaherpesvirus infections also occur .", "To understand the potential role of the rhesus gammaherpesviruses , RRV , RFHV and RLCV in cancers occurring in monkeys during SIV and SHIV studies spanning the last 15 year...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "plant biology/plant-biotic interactions", "plant biology/agricultural biotechnology", "plant biology" ]	A Novel High-Affinity Sucrose Transporter Is Required for Virulence of the Plant Pathogen Ustilago maydis	journal.pbio.1000303	A novel, high-affinity sucrose transporter identified in the plasma membrane of the plant pathogen Ustilago maydis is essential for fungal virulence and successful infection of maize.	[ [ "Plant pathogenic fungi cause major yield losses and affect the quality and safety of food and feed produced from infected plant material .", "Different fungi have developed different strategies to deal with their hosts .", "Infected plants are either kept alive to ensure a prolonged supply of organic...	[ "Plant pathogenic fungi cause massive yield losses and affect both quality and safety of food and feed produced from infected plants .", "The main objective of plant pathogenic fungi is to get access to the organic carbon sources of their carbon-autotrophic hosts .", "However , the chemical nature of the carbon...	[ "The plant parasitic fungus Ustilago maydis is a biotrophic pathogen that depends on live plant tissue for development .", "It is highly adapted to maize ( Zea mays ) , where it causes the corn smut disease .", "Fungal cells growing within the plant apoplast are surrounded by the host plasma membrane at all gro...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "systems biology", "genetics", "biology", "genomics", "molecular cell biology", "genetics and genomics" ]	Patterns and Mechanisms of Ancestral Histone Protein Inheritance in Budding Yeast	journal.pbio.1001075	Tracking of ancestral histone proteins over multiple generations of genome replication in yeast reveals that old histones move along genes from 3′ toward 5′ over time, and that maternal histones move up to around 400 bp during genomic replication.	[ [ "In addition to the information encoded in DNA sequence , replicating cells can inherit", "epigenetic information , which refers to variable phenotypes that are heritable", "without an underlying change in DNA sequence .", "It is widely accepted that chromatin ,", "the nucleoprotein packaging ...	[ "Replicating chromatin involves disruption of histone-DNA contacts and subsequent", "reassembly of maternal histones on the new daughter genomes .", "In bulk , maternal", "histones are randomly segregated to the two daughters , but little is known about", "the fine details of this process: do maternal histo...	[ "It is widely believed that chromatin , the nucleoprotein packaged state of", "eukaryotic genomes , can carry epigenetic information and thus transmit gene", "expression patterns to replicating cells .", "However , the inheritance of genomic", "packaging status is subject to mechanistic challenges that do n...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "geomorphology", "medicine and health sciences", "landforms", "dose prediction methods", "topography", "tropical diseases", "geographical locations", "bacterial diseases", "pharmaceutics", "kiribati", "neglected tropical diseases", "islands", "bangladesh", "infectious diseases", "compute...	Predicting the impact of household contact and mass chemoprophylaxis on future new leprosy cases in South Tarawa, Kiribati: A modelling study	journal.pntd.0007646	null	[ [ "Despite being one of the most ancient diseases , there are annually still around 200 , 000 newly diagnosed leprosy cases worldwide [1] .", "Leprosy is one of the neglected tropical diseases , affecting the poorest and least-developed countries [2] .", "Most cases are in India , Brazil , and Indonesia...	[ "The country of Kiribati is a small Pacific island nation which had a new case detection rate of 191 per 100 , 000 in 2016 , and is one of the few countries yet to reach the WHO leprosy elimination goal .", "Chemoprophylaxis of household contacts of new cases , or to the whole population in a highly endemic areas...	[ "Leprosy rates in Kiribati are some of the highest in the world and it is one of the few countries yet to reach the World Health Organization leprosy elimination goal of a prevalence of less than one case per 10 , 000 population .", "The greatest burden is in the capital South Tarawa and the connected islet of Be...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "psychology", "animal behavior", "zoology", "ecology", "cognition", "decision making", "behavior", "biology and life sciences", "cognitive science", "neuroscience", "behavioral ecology" ]	An Extra Dimension to Decision-Making in Animals: The Three-way Trade-off between Speed, Effort per-Unit-Time and Accuracy	journal.pcbi.1003937	null	[ [ "In order to study this three-way tradeoff , we distinguish between the “baseline” cost of time , and the additional cost of the effort that is invested within each unit of time .", "The “baseline” cost of each unit of time encompasses all those costs that accumulate at a fixed rate when an individual spe...	[ "The standard view in biology is that all animals , from bumblebees to human beings , face a trade-off between speed and accuracy as they search for resources and mates , and attempt to avoid predators .", "For example , the more time a forager spends out of cover gathering information about potential food source...	[ "Efficient decision-making is vital to the lives of all animals , but the underlying principles of how they achieve this are not yet fully understood .", "Researchers studying decision-making have generally assumed that animals balance a two-way trade-off between speed and accuracy: the more time they spend gathe...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "genome-wide association studies", "medicine and health sciences", "variant genotypes", "carcinomas", "cancers and neoplasms", "gastrointestinal tumors", "liver diseases", "genetic mapping", "epidemiological methods and statistics", "oncology", "research design", "mathematics", "statistics (...	A Powerful Procedure for Pathway-Based Meta-analysis Using Summary Statistics Identifies 43 Pathways Associated with Type II Diabetes in European Populations	journal.pgen.1006122	null	[ [ "Genome-wide association study ( GWAS ) has become a very effective way to identify common genetic variants underlying various complex traits [1] .", "The most commonly used approach to analyze GWAS data is the single-locus test , which evaluates one single nucleotide polymorphism ( SNP ) at a time .", ...	[ "Meta-analysis of multiple genome-wide association studies ( GWAS ) has become an effective approach for detecting single nucleotide polymorphism ( SNP ) associations with complex traits .", "However , it is difficult to integrate the readily accessible SNP-level summary statistics from a meta-analysis into more ...	[ "As GWAS continue to grow in sample size , it is evident that these studies need to be utilized more effectively for detecting individual susceptibility variants , and more importantly , to provide insight into global genetic architecture of complex traits .", "Towards this goal , identifying association with res...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular cell biology", "gene expression", "genetics", "biology", "molecular biology", "genetics and genomics", "dna transcription", "gene function" ]	Transcription Factor Oct1 Is a Somatic and Cancer Stem Cell Determinant	journal.pgen.1003048	null	[ [ "Mammalian somatic stem cells have been identified in blood , lung , intestine , breast , epidermis and other tissues [1]–[6] .", "Cancer stem cells ( or cancer-initiating cells ) have been defined in a variety of developmentally heterogeneous neoplasms [7]–[11] .", "Two functional properties are cons...	[ "Defining master transcription factors governing somatic and cancer stem cell identity is an important goal .", "Here we show that the Oct4 paralog Oct1 , a transcription factor implicated in stress responses , metabolic control , and poised transcription states , regulates normal and pathologic stem cell functio...	[ "Understanding the mechanisms that control stem cell function is a fundamental prerequisite both for the full application of stem cells to regenerative medicine and for a full understanding of the relationship between stem cells and cancer .", "In this study we show that a transcription factor known as Oct1 is a ...	2012
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "medicine and health sciences", "nervous system", "pervasive developmental disorders", "autism", "social sciences", "neuroscience", "animals", "developmental psychology", "animal models", "membrane proteins", "developmental biology", "drosophila melanogaster", "model organ...	The WAGR syndrome gene PRRG4 is a functional homologue of the commissureless axon guidance gene	journal.pgen.1006865	null	[ [ "The Commissureless protein ( Comm ) in Drosophila regulates the cell surface expression of Roundabout ( Robo ) axon guidance receptors by targeting Robos for degradation during secretion through the ER/Golgi network [1] , reviewed in [2] .", "Failure to down-regulate Robo leads to a dramatic phenotype in...	[ "WAGR syndrome is characterized by Wilm’s tumor , aniridia , genitourinary abnormalities and intellectual disabilities .", "WAGR is caused by a chromosomal deletion that includes the PAX6 , WT1 and PRRG4 genes .", "PRRG4 is proposed to contribute to the autistic symptoms of WAGR syndrome , but the molecular fun...	[ "Mutants for the fruit fly commmissureless gene ( comm ) dramatically lack connections between the left and right hand sides of the nervous system .", "This is due to a failure to prevent Robo receptors from reaching the cell surface , where they guide growing axons away from the CNS midline .", "Comm proteins ...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "model organisms", "genetics", "biology", "genomics", "genetics and genomics" ]	Phenotypic Plasticity of the Drosophila Transcriptome	journal.pgen.1002593	null	[ [ "Phenotypic plasticity is the ability of a single genotype to give rise to different phenotypes in different environments [1] .", "Phenotypic plasticity is the counterpoint to environmental canalization [2]–[3] , whereby genotypes produce the same phenotype in different environments .", "Phenotypic pl...	[ "Phenotypic plasticity is the ability of a single genotype to produce different phenotypes in response to changing environments .", "We assessed variation in genome-wide gene expression and four fitness-related phenotypes of an outbred Drosophila melanogaster population under 20 different physiological , social ,...	[ "Unlike Mendelian traits , where the genotype allows a direct prediction of the phenotype , predicting phenotypic values is not straightforward for complex traits , which arise from multiple segregating genes and their interactions with the environment .", "Here , a single genotype can often express different phe...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "mathematics/statistics", "neuroscience/theoretical neuroscience", "neuroscience/sensory systems" ]	Neural Coding of Natural Stimuli: Information at Sub-Millisecond Resolution	journal.pcbi.1000025	null	[ [ "Throughout the brain , information is represented by discrete electrical pulses termed action potentials or ‘spikes’ [1] .", "For decades there has been controversy about the extent to which the precise timing of these spikes is significant: Should we think of each spike arrival time as having meaning do...	[ "Sensory information about the outside world is encoded by neurons in sequences of discrete , identical pulses termed action potentials or spikes .", "There is persistent controversy about the extent to which the precise timing of these spikes is relevant to the function of the brain .", "We revisit this issue ...	[ "Neurons communicate by means of stereotyped pulses , called action potentials or spikes , and a central issue in systems neuroscience is to understand this neural coding .", "Here we study how sensory information is encoded in sequences of spikes , using a combination of novel theoretical and experimental techni...	2008
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "sequencing techniques", "messenger rna", "mathematics", "forecasting", "statistics (mathematics)", "untranslated regions", "molecular biology techniques", "cellular structures and organelles", "research and analysis methods", "translation initiation", "sequence analysis", "sequence alignment"...	PreTIS: A Tool to Predict Non-canonical 5’ UTR Translational Initiation Sites in Human and Mouse	journal.pcbi.1005170	null	[ [ "Translational initiation is a more complex process than reported in common textbooks .", "Experimental work showed that the canonical AUG–Methionine translational start is not always used to initiate eukaryotic translation [1–5] .", "Further alternative codons located upstream of the annotated AUG st...	[ "Translation of mRNA sequences into proteins typically starts at an AUG triplet .", "In rare cases , translation may also start at alternative non–AUG codons located in the annotated 5’ UTR which leads to an increased regulatory complexity .", "Since ribosome profiling detects translational start sites at the n...	[ "Ribosome profiling data and mRNA sequence features can be used to build reliable classification models with accuracies of about 80% for start codon and open reading frame prediction in human .", "All predicted start sites of one transcript are postulated to have the potential to initiate translation .", "They ...	2016
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "blood cells", "biliary system", "invertebrates", "cell motility", "innate immune system", "medicine and health sciences", "liver", "immune cells", "immune physiology", "cytokines", "helminths", "immunology", "fibrosis", "parasitic diseases", "animals", "trematodes", "clonorchis sine...	Clonorchis sinensis antigens alter hepatic macrophage polarization in vitro and in vivo	journal.pntd.0005614	null	[ [ "Clonorchis sinensis infection represents a major public health problem in Asia , with approximately 30 million people infected , of which 1 . 3 million reside in Korea [1 , 2] .", "C . sinensis infection causes several pathological alterations in the bile ducts , including hyperplasia of the mucosa , dil...	[ "Clonorchis sinensis infection elicits hepatic inflammation , which can lead to cholangitis , periductal hepatic fibrosis , liver cirrhosis , and even cholangiocarcinoma .", "Hepatic macrophages are an intrinsic element of both innate and acquired immunity .", "This study was conducted to demonstrate the dynami...	[ "Infection with Clonorchis sinensis is a major public health problem in Asia , resulting in loss of liver function and chronic liver diseases , including cancers .", "However , to the best of our knowledge , the immune response to fluke infection in the liver has not been systematically investigated .", "Here ,...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunodeficiency viruses", "viral preintegration complex", "mechanisms of resistance and susceptibility", "viral immune evasion", "virology", "biology", "microbiology", "viral replication", "viral evolution" ]	In Vivo Functions of CPSF6 for HIV-1 as Revealed by HIV-1 Capsid Evolution in HLA-B27-Positive Subjects	journal.ppat.1003868	null	[ [ "An essential part of the HIV-1 lifecycle is the transfer of its genetic material from the cytoplasm into the nucleus for subsequent integration into the host genome .", "In actively proliferating cells , breakdown of the nuclear membrane during mitosis ensures viral access to the host chromosomes .", ...	[ "The host protein CPSF6 possesses a domain that can interact with the HIV-1 capsid ( CA ) protein .", "CPSF6 has been implicated in regulating HIV-1 nuclear entry .", "However , its functional significance for HIV-1 replication has yet to be firmly established .", "Here we provide evidence for two divergent f...	[ "The viral capsid ( CA ) protein of HIV-1 determines both the ability to infect non-dividing cells and the utilization of host factors implicated in nuclear entry .", "Understanding how CA controls these two properties is critical .", "CPSF6 , a CA-interacting host protein , may be important for these propertie...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "neuroinvasiveness", "viral transmission and infection", "microbiology", "immunodeficiency viruses", "neurovirulence", "infectious diseases", "infectious diseases of the nervous system", "viral entry", "biology", "pathogenesis", "viral evolution", "virology" ]	Central Nervous System Compartmentalization of HIV-1 Subtype C Variants Early and Late in Infection in Young Children	journal.ppat.1003094	null	[ [ "Human immunodeficiency virus type 1 ( HIV-1 ) infection of the central nervous system ( CNS ) can occur shortly after transmission , and compartmentalized HIV-1 variants , genetically distinct from the virus in the blood , can be detected in the cerebrospinal fluid ( CSF ) in some individuals throughout the ...	[ "HIV-1 subtype B replication in the CNS can occur in CD4+ T cells or macrophages/microglia in adults .", "However , little is known about CNS infection in children or the ability of subtype C HIV-1 to evolve macrophage-tropic variants .", "In this study , we examined HIV-1 variants in ART-naïve children aged th...	[ "Genetically compartmentalized human immunodeficiency virus type 1 ( HIV-1 ) subtype B populations can be variably detected in the cerebrospinal fluid ( CSF ) of adults .", "Compartmentalization is indicative of local CNS replication , and late in disease is linked to HIV-associated dementia ( HAD ) .", "Compar...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "viral vaccines", "viral entry", "rift valley fever", "zoonoses", "veterinary diseases", "viral transmission and infection", "zoonotic diseases", "virology", "biology", "microbiology", "viral diseases", "viral replication", "veterinary science" ]	Development of a Novel, Single-Cycle Replicable Rift Valley Fever Vaccine	journal.pntd.0002746	null	[ [ "Rift Valley fever virus ( RVFV ) , a member of the genus Phlebovirus within the family Bunyaviridae , carries a tripartite , single-stranded and negative–sense RNA genome [1]–[3] .", "The L RNA encodes the L protein , a viral RNA-dependent RNA polymerase; the M RNA encodes four proteins , including two a...	[ "Rift Valley fever virus ( RVFV ) ( genus Phlebovirus , family Bunyaviridae ) is an arbovirus that causes severe disease in humans and livestock in sub-Saharan African countries .", "Although the MP-12 strain of RVFV is a live attenuated vaccine candidate , neuroinvasiveness and neurovirulence of MP-12 in mice ma...	[ "Rift Valley fever virus ( RVFV ) is a mosquito-borne zoonotic pathogen , which causes febrile illness , encephalitis and fatal hemorrhagic fever in humans and severe hepatic disease with high mortality and spontaneous abortion rates in ruminants .", "RVFV is endemic to the African continent .", "Because many d...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Global Rescue of Defects in HIV-1 Envelope Glycoprotein Incorporation: Implications for Matrix Structure	journal.ppat.1003739	null	[ [ "Human immunodeficiency virus type 1 ( HIV-1 ) , like all replication-competent orthoretroviruses , encodes three main polyproteins – Gag , Pol and Env – which contain determinants necessary for particle assembly , enzymatic functions , and virus entry , respectively .", "HIV-1 assembly occurs in a series...	[ "The matrix ( MA ) domain of HIV-1 Gag plays key roles in membrane targeting of Gag , and envelope ( Env ) glycoprotein incorporation into virions .", "Although a trimeric MA structure has been available since 1996 , evidence for functional MA trimers has been elusive .", "The mechanism of HIV-1 Env recruitment...	[ "One of the enduring problems in HIV-1 research is the mechanism of incorporation of the viral envelope ( Env ) glycoprotein into viral particles .", "Several models have been proposed ranging from an entirely passive process to a requirement for binding of Env by the matrix ( MA ) domain of the Gag precursor pol...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "public health and epidemiology", "soil-transmitted helminths", "epidemiology", "environmental epidemiology", "infectious disease epidemiology", "neglected tropical diseases", "parasitic diseases", "helminth infection" ]	Calodium hepaticum: Household Clustering Transmission and the Finding of a Source of Human Spurious Infection in a Community of the Amazon Region	journal.pntd.0001943	null	[ [ "Calodium hepaticum ( syn . Capillaria hepatica ) is a zoonotic nematode of the Trichinellidae family found worldwide .", "This helminth infects the hepatic parenchyma of rodents ( principle hosts ) and various other mammals ( e . g . carnivores , humans ) of different families [1] .", "In humans infe...	[ "Background: Calodium hepaticum ( syn . Capillaria hepatica ) is a worldwide helminth parasite of which several aspects of transmission still remain unclear .", "In the Amazon region , the mechanism of transmission based on the ingestion of eggs present in the liver of wild mammals has been suggested as the cause...	[ "The zoonotic parasite Calodium hepaticum is the causative agent of rarely reported liver disease ( hepatic calodiasis ) and spurious infections in humans .", "In spurious infections eggs of this parasite are excreted in the stools without causing disease .", "It has been suggested that the cause of this type o...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "obstetrics and gynecology", "pregnancy", "obstetrics", "biology", "microbiology", "host-pathogen interaction", "parasitic diseases", "malaria", "pathogenesis" ]	Plasmodium falciparum Malaria Elicits Inflammatory Responses that Dysregulate Placental Amino Acid Transport	journal.ppat.1003153	null	[ [ "Pregnant women living in malaria endemic regions are highly susceptible to malaria , especially in first pregnancies [1] , [2] .", "Malaria in pregnancy is characterized by placental malaria ( PM ) , the selective accumulation of Plasmodium-falciparum infected erythrocytes ( IE ) in the maternal intervil...	[ "Placental malaria ( PM ) can lead to poor neonatal outcomes , including low birthweight due to fetal growth restriction ( FGR ) , especially when associated with local inflammation ( intervillositis or IV ) .", "The pathogenesis of PM-associated FGR is largely unknown , but in idiopathic FGR , impaired transplac...	[ "Malaria infection during pregnancy can cause fetal growth restriction and low birthweight associated with high infant mortality and morbidity rates .", "The pathogenesis of fetal growth restriction in placental malaria is largely unknown , but in other pathological pregnancies , impaired transplacental amino aci...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "cell biology", "molecular biology", "caenorhabditis", "homo (human)" ]	Conserved Regulation of MAP Kinase Expression by PUF RNA-Binding Proteins	journal.pgen.0030233	null	[ [ "Mitogen-activated protein ( MAP ) kinases ( MAPKs ) control many aspects of animal development , including cell proliferation , differentiation , and survival [1] .", "Most relevant to this work are MPK-1 , the primary Caenorhabditis elegans MAPK/ERK homolog [2 , 3] , as well as ERK2 and p38α , two human...	[ "Mitogen-activated protein kinase ( MAPK ) and PUF ( for Pumilio and FBF [fem-3 binding factor] ) RNA-binding proteins control many cellular processes critical for animal development and tissue homeostasis .", "In the present work , we report that PUF proteins act directly on MAPK/ERK-encoding mRNAs to downregula...	[ "The mitogen-activated protein ( MAP ) kinase ( MAPK ) enzyme is crucial for regulation of both stem cell maintenance and tumorigenesis .", "Two conserved controls of MAPK include its activation by RAS signaling and a kinase cascade as well as its inactivation by MAPK phosphatases ( MKPs ) .", "We identify a th...	2007
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "immune physiology", "enzyme-linked immunoassays", "chemical compounds", "immunology", "tropical diseases", "microbiology", "carbohydrates", "parasitic diseases", "organic compounds", "parasitic protozoans", "protozoan life cycles", "developmental biology", ...	Systematic review on antigens for serodiagnosis of visceral leishmaniasis, with a focus on East Africa	journal.pntd.0007658	null	[ [ "Leishmaniasis comprises a group of diseases caused by protozoan parasites of the genus Leishmania that are transmitted between human or other mammalian hosts by phlebotomine sand flies [1] .", "Visceral leishmaniasis ( VL ) is the most severe form of the disease , for it is almost always fatal if left un...	[ "Accurate and accessible diagnosis is key for the control of visceral leishmaniasis ( VL ) .", "Yet , current diagnostic tests for VL have severe limitations: they are invasive or not suitable as point of care ( POC ) test or their performance is suboptimal in East Africa .", "We analysed the antigens in the VL...	[ "Visceral leishmaniasis is a potentially fatal disease that affects more than 20 000 people every year .", "Its diagnosis is difficult since the clinical symptoms are not specific and the existing diagnostic tests are not useful in limited resource countries or they a not accurate enough in East Africa .", "In ...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Three Gorges Dam: Impact of Water Level Changes on the Density of Schistosome-Transmitting Snail Oncomelania hupensis in Dongting Lake Area, China	journal.pntd.0003882	null	[ [ "Schistosomiasis remains a serious public health problem worldwide , affecting more than 200 million people in approximately 76 countries with a loss of 1 . 53 million disability-adjusted life years ( DALYs ) [1] .", "Schistosomiasis japonica ( S . japonica ) is distributed in 12 provinces in China and 11...	[ "Schistosomiasis remains an important public health issue in China and worldwide .", "Oncomelania hupensis is the unique intermediate host of schistosoma japonicum , and its change influences the distribution of S . japonica .", "The Three Gorges Dam ( TGD ) has substantially changed the ecology and environment...	[ "Oncomelania hupensis , an amphibious animal , is the unique intermediate host of schistosoma japonicum .", "Three Gorges Dam ( TGD ) is a tremendous hydrological project , and it influences the survival of animals downstream .", "It is studied for several reasons .", "First , schistosomiasis is still a world...	2015
[ "Introduction", "Results and Discussion", "Materials and Methods" ]	[ "nuclear staining", "brassica", "dna transcription", "model organisms", "genetic elements", "epigenetics", "dna", "plants", "dna methylation", "chromatin", "arabidopsis thaliana", "research and analysis methods", "specimen preparation and treatment", "staining", "chromosome biology", "...	Arabidopsis AtMORC4 and AtMORC7 Form Nuclear Bodies and Repress a Large Number of Protein-Coding Genes	journal.pgen.1005998	null	[ [ "Maintaining regulatory access to genes while repressing the expression of potentially deleterious transposable elements is a fundamental challenge for living organisms .", "Eukaryotes achieve this in part by parsing their genomes into functional units characterized by distinct chromatin features [1 , 2] ...	[ "The MORC family of GHKL ATPases are an enigmatic class of proteins with diverse chromatin related functions .", "In Arabidopsis , AtMORC1 , AtMORC2 , and AtMORC6 act together in heterodimeric complexes to mediate transcriptional silencing of methylated DNA elements .", "Here , we studied Arabidopsis AtMORC4 an...	[ "Keeping selfish genetic elements–such as transposons–silent , while maintaining access to genes , is a fundamental challenge for eukaryotes .", "Different pathways frequently converge in order to identify transposons and maintain their repression , and in Arabidopsis thaliana , transposons are marked with DNA me...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetic disorders", "gene expression", "genetics", "biology and life sciences", "genetics of disease", "dna transcription" ]	Dynamic Partnership between TFIIH, PGC-1α and SIRT1 Is Impaired in Trichothiodystrophy	journal.pgen.1004732	null	[ [ "In response to various physiological signals , selective and combined actions of a number of transcription factors modulate the expression of protein-coding genes [1] .", "In eukaryotes , the combinatorial use of hundreds of proteins is required for the synthesis of a single messenger RNA by the RNA Poly...	[ "The expression of protein-coding genes requires the selective role of many transcription factors , whose coordinated actions remain poorly understood .", "To further grasp the molecular mechanisms that govern transcription , we focused our attention on the general transcription factor TFIIH , which gives rise , ...	[ "In eukaryotes , the expression of genes encoding proteins requires the action of hundreds of factors , together with the RNA polymerase II .", "While these factors are timely and selectively required for the expression of a given gene , little is known about their partnership upon gene expression .", "Our resu...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "genome-wide association studies", "medicine and health sciences", "genetic networks", "cardiovascular medicine", "animal models", "diabetes mellitus", "model organisms", "endocrine disorders", "network analysis", "genome analysis", "experimental organism systems", "molecular biology technique...	Shared genetic regulatory networks for cardiovascular disease and type 2 diabetes in multiple populations of diverse ethnicities in the United States	journal.pgen.1007040	null	[ [ "Cardiovascular disease ( CVD ) and type 2 diabetes ( T2D ) are two leading causes of death in the United States [1] .", "Patients with T2D are at two to six times higher risk of developing CVD compared to those without T2D [2] , indicating the importance of targeting common pathogenic pathways to improve...	[ "Cardiovascular diseases ( CVD ) and type 2 diabetes ( T2D ) are closely interrelated complex diseases likely sharing overlapping pathogenesis driven by aberrant activities in gene networks .", "However , the molecular circuitries underlying the pathogenic commonalities remain poorly understood .", "We sought t...	[ "Cardiovascular disease ( CVD ) and type 2 diabetes ( T2D ) are two tightly interrelated diseases that are leading epidemics and causes of deaths around the world .", "Elucidating the mechanistic connections between the two diseases will offer critical insights for the development of novel therapeutic avenues to ...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology", "biology", "microbiology", "viral replication", "viral structure" ]	Virion Assembly Factories in the Nucleus of Polyomavirus-Infected Cells	journal.ppat.1002630	null	[ [ "Increasing evidence suggests that the assembly of many viruses occurs at specific intracellular sites , which have been termed “virus factories” [1] , [2] .", "These subcellular domains are gathering points for coordinating genome replication and capsid protein assembly into virions .", "The ultrastr...	[ "Most DNA viruses replicate in the cell nucleus , although the specific sites of virion assembly are as yet poorly defined .", "Electron microscopy on freeze-substituted , plastic-embedded sections of murine polyomavirus ( PyV ) -infected 3T3 mouse fibroblasts or mouse embryonic fibroblasts ( MEFs ) revealed tubu...	[ "Polyomaviruses are infectious pathogens of mammals and birds that have been linked to the development of cancers in their hosts .", "Members of the polyomavirus family are associated with human disease , such as JCV and BKV , and over the past few years , several more human polyomaviruses ( WUV , KIV and MCV ) h...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/comparative genomics", "evolutionary biology/evolutionary and comparative genetics", "developmental biology/developmental evolution", "developmental biology/pattern formation", "genetics and genomics/gene function", "computational biology/genomics", "developmental biology/molecula...	Consequences of Lineage-Specific Gene Loss on Functional Evolution of Surviving Paralogs: ALDH1A and Retinoic Acid Signaling in Vertebrate Genomes	journal.pgen.1000496	null	[ [ "Understanding the evolution of gene functions during vertebrate evolution is important for the proper interpretation of comparative analyses , especially when using model organisms to understand human gene functions .", "Gene duplication has been proposed to facilitate the evolution of gene functions [1]...	[ "Genome duplications increase genetic diversity and may facilitate the evolution of gene subfunctions .", "Little attention , however , has focused on the evolutionary impact of lineage-specific gene loss .", "Here , we show that identifying lineage-specific gene loss after genome duplication is important for u...	[ "Gene duplication may facilitate the acquisition of genetic diversity .", "Little is known , however , about the impact of gene loss on the functions of surviving genes .", "When a gene is lost , can other closely related genes evolve to perform the functions of the lost gene ?", "Answering this question can ...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	A combination of incidence data and mobility proxies from social media predicts the intra-urban spread of dengue in Yogyakarta, Indonesia	journal.pntd.0007298	null	[ [ "Dengue has become a major concern for public health authorities in tropical and sub-tropical developing countries [1]; the frequency and magnitude of epidemics , the incidence of severe disease , and the rate of hospitalizations have increased in the past few decades [2] .", "Asia-Pacific countries bear ...	[ "Only a few studies have investigated the potential of using geotagged social media data for predicting the patterns of spatio-temporal spread of vector-borne diseases .", "We herein demonstrated the role of human mobility in the intra-urban spread of dengue by weighting local incidence data with geo-tagged Twitt...	[ "Recent studies have shown that Twitter can be utilized as a tool for health research , and aggregated large-scale social media data can indicate the risk of infectious disease in real-time with high accuracy and at low cost .", "However , most of these studies relied primarily on content analysis or text mining ...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "public health and epidemiology", "mathematics", "epidemiology", "statistics", "infectious disease epidemiology", "global health", "dengue", "viral diseases", "neglected tropical diseases", "public health", "statistical methods" ]	Prediction of Dengue Incidence Using Search Query Surveillance	journal.pntd.0001258	null	[ [ "Google has reported success in using terms entered into its search engine ( www . google . com ) to predict trends in Influenza-Like Illness ( ILI ) cases one to two weeks ahead of the US CDC Morbidity and Mortality Weekly Report [1] .", "Several studies have reported similar results for influenza survei...	[ "The use of internet search data has been demonstrated to be effective at predicting influenza incidence .", "This approach may be more successful for dengue which has large variation in annual incidence and a more distinctive clinical presentation and mode of transmission .", "We gathered freely-available deng...	[ "Improvements in surveillance , prediction of outbreaks and the monitoring of the epidemiology of dengue virus in countries with underdeveloped surveillance systems are of great importance to ministries of health and other public health decision makers who are often constrained by budget or man-power .", "Google ...	2011

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