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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", "Materials and methods", "Results and discussion" ]	[ "molecular dynamics", "neural networks", "particle physics", "statistics", "rna structure prediction", "neuroscience", "nucleotides", "atoms", "mathematics", "forecasting", "composite particles", "research and analysis methods", "computer and information sciences", "rna structure", "math...	RNA3DCNN: Local and global quality assessments of RNA 3D structures using 3D deep convolutional neural networks	journal.pcbi.1006514	null	[ [ "RNA molecules consist of unbranched chains of ribonucleotides , which have various essential roles in coding , decoding , regulation , expression of genes , and cancer-related networks via the maintenance of stable and specific 3D structures [1–5] .", "Therefore , their 3D structural information would he...	[ "Quality assessment is essential for the computational prediction and design of RNA tertiary structures .", "To date , several knowledge-based statistical potentials have been proposed and proved to be effective in identifying native and near-native RNA structures .", "All these potentials are based on the inve...	[ "RNA is an important and versatile macromolecule participating in various biological processes .", "In addition to experimental approaches , the computational prediction of RNA 3D structures is an alternative and important source of obtaining structural information and insights into their functions .", "An impo...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "chickenpox", "shingles", "viral diseases" ]	Three-Dimensional Normal Human Neural Progenitor Tissue-Like Assemblies: A Model of Persistent Varicella-Zoster Virus Infection	journal.ppat.1003512	null	[ [ "Varicella-zoster virus ( VZV ) is a ubiquitous human herpesvirus , as evidenced by a seroprevalence of more than 95% worldwide [1] .", "Among human herpesviruses , VZV has the smallest genome of approximately 125 kbp , which contains at least 70 open reading frames ( ORFs ) and consists of two unique reg...	[ "Varicella-zoster virus ( VZV ) is a neurotropic human alphaherpesvirus that causes varicella upon primary infection , establishes latency in multiple ganglionic neurons , and can reactivate to cause zoster .", "Live attenuated VZV vaccines are available; however , they can also establish latent infections and re...	[ "Varicella-zoster virus ( VZV ) , the alphaherpesvirus that typically causes childhood chickenpox and shingles in adults , becomes latent in neurons , thus remaining in the body for a lifetime .", "Unfortunately , few models are available to study the establishment of VZV latency since the virus infects only huma...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "humoral immunity", "medicine", "infectious diseases", "viral immune evasion", "immunity", "hiv", "virology", "immunology", "biology", "microbiology", "viral diseases", "viral evolution", "immunoglobulins" ]	Evidence for a Continuous Drift of the HIV-1 Species towards Higher Resistance to Neutralizing Antibodies over the Course of the Epidemic	journal.ppat.1003477	null	[ [ "Thirty years after the discovery of the human immunodeficiency virus ( HIV ) , the development of an effective vaccine remains an elusive goal .", "Experiments of passive immunization and vectored immunoprophylaxis in animal models have shown that human monoclonal ( HuMo ) broadly neutralizing antibodies...	[ "We compared the neutralization sensitivity of early/transmitted HIV-1 variants from patients infected by subtype B viruses at 3 periods of the epidemic ( 1987–1991 , 1996–2000 , 2006–2010 ) .", "Infectious pseudotyped viruses expressing envelope glycoproteins representative of the viral quasi-species infecting e...	[ "Most of the patients develop autologous neutralizing antibodies ( NAbs ) during HIV-1 infection .", "These NAbs drive the viral evolution and lead to the selection of escape variants at the individual level .", "The aim of our study was to check if , subsequently to the selective pressure exerted by the indivi...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cingulate cortex", "control theory", "medicine and health sciences", "decision theory", "diagnostic radiology", "functional magnetic resonance imaging", "decision making", "engineering and technology", "prefrontal cortex", "applied mathematics", "brain", "social sciences", "neuroscience", ...	The neural system of metacognition accompanying decision-making in the prefrontal cortex	journal.pbio.2004037	null	[ [ "Decision-making is a process of evidence accumulation .", "That evidence may come from sensory signals of external stimuli or from mental representations of internal cognitive operations .", "Variations in evidence can create uncertainty in the person rendering a decision .", "The decision maker ...	[ "Decision-making is usually accompanied by metacognition , through which a decision maker monitors uncertainty regarding a decision and may then consequently revise the decision .", "These metacognitive processes can occur prior to or in the absence of feedback .", "However , the neural mechanisms of metacognit...	[ "Decision-making is often accompanied by a sense of uncertainty regarding the outcome .", "In many situations , there is no explicit feedback or cue to indicate whether the decision is correct or not .", "Fortunately , our brain can evaluate decision uncertainty using the internal signals and subsequently make ...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "cell death", "medicine and health sciences", "cell cycle and cell division", "cancer treatment", "cell processes", "biological cultures", "cancers and neoplasms", "epithelial cells", "oncology", "cell cultures", "chromatophores", "melanoma cells", "immunologic techniques", "research and a...	PERK Is a Haploinsufficient Tumor Suppressor: Gene Dose Determines Tumor-Suppressive Versus Tumor Promoting Properties of PERK in Melanoma	journal.pgen.1006518	null	[ [ "Folding and maturation of secreted proteins occurs in the endoplasmic reticulum ( ER ) .", "Cellular stresses that generate mis-folded proteins trigger a stress response termed the unfolded protein response pathway ( UPR ) [1–5] .", "Activation of the UPR is characterized by increased transcription o...	[ "The unfolded protein response ( UPR ) regulates cell fate following exposure of cells to endoplasmic reticulum stresses .", "PERK , a UPR protein kinase , regulates protein synthesis and while linked with cell survival , exhibits activities associated with both tumor progression and tumor suppression .", "For ...	[ "PERK is critical for progression of specific cancers and has provided stimulus for the generation of small molecule PERK inhibitors .", "Paradoxically , the anti-proliferative and pro-death functions of PERK have potential tumor suppressive qualities .", "We demonstrate that PERK can function as either a tumor...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genome-wide association studies", "medicine", "public health and epidemiology", "epidemiology", "genetics", "population genetics", "biology", "human genetics", "public health", "genetics and genomics" ]	A Systematic Mapping Approach of 16q12.2/FTO and BMI in More Than 20,000 African Americans Narrows in on the Underlying Functional Variation: Results from the Population Architecture using Genomics and Epidemiology (PAGE) Study	journal.pgen.1003171	null	[ [ "The association between variants in the fat mass and obesity associated ( FTO ) gene on chromosome 16q12 . 2 and body mass index ( BMI ) is well-established in populations of European descent .", "Genome-wide association studies ( GWAS ) and subsequent replication studies have identified several strongly...	[ "Genetic variants in intron 1 of the fat mass– and obesity-associated ( FTO ) gene have been consistently associated with body mass index ( BMI ) in Europeans .", "However , follow-up studies in African Americans ( AA ) have shown no support for some of the most consistently BMI–associated FTO index single nucleo...	[ "Genetic variants within the fat mass– and obesity-associated ( FTO ) gene are associated with increased risk of obesity .", "To better understand which specific genetic variant ( s ) in this genetic region is associated with obesity risk , we attempt to genotype or impute all known genetic variants in the region...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology/immunodeficiency viruses", "microbiology/medical microbiology", "microbiology/innate immunity" ]	APOBEC3G and APOBEC3F Require an Endogenous Cofactor to Block HIV-1 Replication	journal.ppat.1000095	null	[ [ "Cytidine deaminases are RNA-editing enzymes that target cytosines for conversion to uracils ( C-to-U ) .", "They belong to the apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like ( APOBEC ) family , which includes activation-induced deaminase ( AID ) , APOBEC1 ( A1 ) , APOBEC2 ( A2 ) , a grou...	[ "APOBEC3G ( A3G ) /APOBEC3F ( A3F ) are two members of APOBEC3 cytidine deaminase subfamily .", "Although they potently inhibit the replication of vif-deficient HIV-1 , this mechanism is still poorly understood .", "Initially , A3G/A3F were thought to catalyze C-to-U transitions on the minus-strand viral cDNAs ...	[ "Cytidine deaminases are host enzymes that remove the amino group from the cytidine base on single-stranded DNA or RNA , resulting in a replacement of the cytidine with a uracil .", "Such replacement may alter the amino acid–coding sequence of the gene and change protein function .", "It has been well documente...	2008
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "recreation", "infographics", "taxonomy", "applied mathematics", "population genetics", "social sciences", "data management", "mathematics", "population biology", "computer and information sciences", "games", "behavior", "social psychology", "evolutionary systematics", "approximation met...	Evolutionary Games of Multiplayer Cooperation on Graphs	journal.pcbi.1005059	null	[ [ "Graphs are a natural starting point to assess the role of population structure in the evolution of cooperation .", "Vertices of the graph represent individuals , while links ( edges ) define interaction and dispersal neighborhoods .", "Classical models of population structure , such as island models ...	[ "There has been much interest in studying evolutionary games in structured populations , often modeled as graphs .", "However , most analytical results so far have only been obtained for two-player or linear games , while the study of more complex multiplayer games has been usually tackled by computer simulations...	[ "Cooperation can be defined as the act of providing fitness benefits to other individuals , often at a personal cost .", "When interactions occur mainly with neighbors , assortment of strategies can favor cooperation but local competition can undermine it .", "Previous research has shown that a single coefficie...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "viruses", "infectious diseases", "virology", "evolutionary biology", "molecular biology" ]	Target Cell APOBEC3C Can Induce Limited G-to-A Mutation in HIV-1	journal.ppat.0030153	null	[ [ "The evolutionary success of primate lentiviruses is evident from their prevalence in Old-World primates and their capacity to spread to new host species , frequently leading to the emergence of zoonotic disease [1 , 2] .", "Establishing persistent infection in individual hosts requires high mutation rate...	[ "The evolutionary success of primate lentiviruses reflects their high capacity to mutate and adapt to new host species , immune responses within individual hosts , and , in recent years , antiviral drugs .", "APOBEC3G ( A3G ) and APOBEC3F ( A3F ) are host cell DNA-editing enzymes that induce extensive HIV-1 mutat...	[ "HIV has shown a chameleon-like nature , always changing to adapt to its environment .", "Defining the factors that drive and regulate genetic changes in HIV over time is key to understanding how HIV causes disease and escapes from the body's immune responses and drug treatment .", "The diversity of HIV has imp...	2007
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "gene regulation", "cancer treatment", "cancers and neoplasms", "ethnicities", "oncology", "dna", "small interfering rnas", "chinese people", "lung and intrathoracic tumors", "gene expression", "people and places", "biochemistry", "rna", "carcinogenesis", ...	Genomic Landscape Survey Identifies SRSF1 as a Key Oncodriver in Small Cell Lung Cancer	journal.pgen.1005895	null	[ [ "Small cell lung cancer ( SCLC ) represents 13% of all newly diagnosed cases of lung cancer worldwide with more than 180 , 000 cases per year [1] .", "It is an aggressive neuroendocrine malignancy with a unique natural history of a short doubling time , high growth fraction , and early development of wide...	[ "Small cell lung cancer ( SCLC ) is an aggressive disease with poor survival .", "A few sequencing studies performed on limited number of samples have revealed potential disease-driving genes in SCLC , however , much still remains unknown , particularly in the Asian patient population .", "Here we conducted who...	[ "SCLC patients are initially highly chemo-sensitive with response rates of greater than 80% in both limited and extensive diseases , but suffer uniform disease recurrence or progression in a very short period of time .", "In the absence of well-defined genomic biomarkers and insights into the resistance mechanism...	2016
[ "Introduction", "Results", "Model 1: General Principles of Antibiotic-Target Reaction Kinetics", "Model 2: Onset and End of Antibiotic Action Determine Pharmacodynamic Properties of Ampicillin and Isoniazid", "Model 3: Antibiotic Action below MIC Modifies Pharmacodynamic Properties of Tetracycline", "Disc...	[ "antimicrobials", "medicine and health sciences", "pathology and laboratory medicine", "intracellular pathogens", "pathogens", "drugs", "microbiology", "developmental biology", "antibiotic resistance", "tetracyclines", "antibiotics", "pharmacodynamics", "pharmacology", "microbial growth an...	Using Chemical Reaction Kinetics to Predict Optimal Antibiotic Treatment Strategies	journal.pcbi.1005321	null	[ [ "The rise of antibiotic resistance underlines the need for employing existing antibiotics prudently .", "Although antibiotic dosing regimens have been investigated for more than half a century [1] , we do not yet have a sufficient understanding of the link between drug dosing and bacterial killing to desi...	[ "Identifying optimal dosing of antibiotics has proven challenging—some antibiotics are most effective when they are administered periodically at high doses , while others work best when minimizing concentration fluctuations .", "Mechanistic explanations for why antibiotics differ in their optimal dosing are lacki...	[ "In this era of rising concerns about antibiotic resistance , the rational design of optimal antibiotic treatment regimens remains an important unrealized goal .", "At this time , the characteristics of antibiotic treatment regimens ( e . g . dosing levels , treatment duration , route of administration ) are dete...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/protozoal infections", "immunology/innate immunity" ]	NFATc1 Mediates Toll-Like Receptor-Independent Innate Immune Responses during Trypanosoma cruzi Infection	journal.ppat.1000514	null	[ [ "The host defense against invasion of intracellular pathogens relies on Th1 cell-derived IFN-γ that activates macrophages to kill the engulfed pathogens [1] .", "Toll-like receptor ( TLR ) -mediated recognition of pathogens has been established to induce activation of innate immune cells such as dendritic...	[ "Host defense against the intracellular protozoan parasite Trypanosoma cruzi depends on Toll-like receptor ( TLR ) -dependent innate immune responses .", "Recent studies also suggest the presence of TLR-independent responses to several microorganisms , such as viruses , bacteria , and fungi .", "However , the T...	[ "Trypanosoma cruzi is an intracellular protozoan parasite that causes Chagas diseases in humans .", "Invasion of T . cruzi into the host is sensed by Toll-like receptors ( TLRs ) , which recognize microbial components that are present in microbes but not in the host .", "TLRs are essential for the initiation of...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "neuroscience", "genetics and genomics" ]	Light Activates Output from Evening Neurons and Inhibits Output from Morning Neurons in the Drosophila Circadian Clock	journal.pbio.0050315	In fruit flies, light not only resets the circadian clock to solar time, but also enables the signaling from one oscillator while disabling the signaling from the other.	[ [ "Circadian rhythms are controlled by endogenous clocks that tick with an approximately 24-h period fitted to the rotation of the earth .", "They are synchronized to day–light cycles by environmental cues , the strongest of which is light .", "Since activity must occur at the most favorable time of the...	[ "Animal circadian clocks are based on multiple oscillators whose interactions allow the daily control of complex behaviors .", "The Drosophila brain contains a circadian clock that controls rest–activity rhythms and relies upon different groups of PERIOD ( PER ) –expressing neurons .", "Two distinct oscillators...	[ "Living organisms have evolved circadian clocks that anticipate daily changes in their environment .", "Their clockwork is fully endogenous , but can be reset by external cues .", "( Light is the most efficient cue . )", "The circadian neuronal network of the fruit fly ( Drosophila ) brain perceives light thr...	2007
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Perturbation-Expression Analysis Identifies RUNX1 as a Regulator of Human Mammary Stem Cell Differentiation	journal.pcbi.1004161	null	[ [ "Adult stem cells are functionally defined based on their ability to regenerate tissues .", "This unique regenerative ability can be recapitulated in culture models , where single stem cells , but not differentiated cells , form tissue rudiments in three-dimensional extracellular matrices .", "These t...	[ "The search for genes that regulate stem cell self-renewal and differentiation has been hindered by a paucity of markers that uniquely label stem cells and early progenitors .", "To circumvent this difficulty we have developed a method that identifies cell-state regulators without requiring any markers of differe...	[ "The discovery of stem cell regulators is a major goal of biological research , but progress is often limited by a lack of definitive markers capable of distinguishing stem cells from early progenitors .", "Even in cases where markers have been identified , they often only enrich for certain cell states and do no...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "chromosome structure and function", "cell cycle and cell division", "cell processes", "cloning", "telomeres", "mutation", "fungi", "model organisms", "non-homologous end joining", "experimental organism systems", "dna", "molecular biology techniques", "schizosaccharomyces", "research and ...	Telomere-binding proteins Taz1 and Rap1 regulate DSB repair and suppress gross chromosomal rearrangements in fission yeast	journal.pgen.1008335	null	[ [ "The integrity of chromosomal DNA can be compromised by mutations that vary in size , ranging from small perturbations , such as point mutations and short insertions/deletions , to large changes , such as deletions , duplications , inversions , and translocations of long chromosome segments .", "The latte...	[ "Genomic rearrangements ( gross chromosomal rearrangements , GCRs ) threatens genome integrity and cause cell death or tumor formation .", "At the terminus of linear chromosomes , a telomere-binding protein complex , called shelterin , ensures chromosome stability by preventing chromosome end-to-end fusions and r...	[ "Tips of chromosomes , telomeres , are bound and protected by a telomere-binding protein complex called shelterin .", "Most previous studies focused on shelterin’s telomere-specific role , and its general role in genome maintenance has not been explored extensively .", "In this study , we first set up an assay ...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "invertebrates", "insect metamorphosis", "animals", "developmental biology", "animal anatomy", "nymphs", "pupae", "hemimetabolism", "zoology", "wings", "holometabolism", "insects", "arthropoda", "entomology", "metamorphosis", "biology and life sciences", "larvae", "organisms" ]	The Occurrence of the Holometabolous Pupal Stage Requires the Interaction between E93, Krüppel-Homolog 1 and Broad-Complex	journal.pgen.1006020	null	[ [ "Insects are , by far , the most successful and diversified animal group , with more than two million species described ( approximately half of all animal species reported ) .", "One of the reasons of this taxonomic richness lies in the appearance of specific novel phenotypic characters known as “key inno...	[ "Complete metamorphosis ( Holometaboly ) is a key innovation that underlies the spectacular success of holometabolous insects .", "Phylogenetic analyses indicate that Holometabola form a monophyletic group that evolved from ancestors exhibiting hemimetabolous development ( Hemimetaboly ) .", "However , the natu...	[ "Complete metamorphosis is an evolutionary innovation that has been critical for the success of insects .", "Phylogenetic relationships reveal that holometabolous insects evolved from ancestors displaying hemimetabolous development .", "Yet , little is known about the molecular nature of the changes required fo...	2016
[ "Introduction", "Materials and Methods", "Results" ]	[]	Pathways-Driven Sparse Regression Identifies Pathways and Genes Associated with High-Density Lipoprotein Cholesterol in Two Asian Cohorts	journal.pgen.1003939	null	[ [ "Much attention continues to be focused on the problem of identifying SNPs and genes influencing a quantitative or dichotomous trait in genome wide scans [1] .", "Despite this , in many instances gene variants identified in GWAS have so far uncovered only a relatively small part of the known heritability ...	[ "Standard approaches to data analysis in genome-wide association studies ( GWAS ) ignore any potential functional relationships between gene variants .", "In contrast gene pathways analysis uses prior information on functional structure within the genome to identify pathways associated with a trait of interest ."...	[ "Genes do not act in isolation , but interact in complex networks or pathways .", "By accounting for such interactions , pathways analysis methods hope to identify aspects of a disease or trait's genetic architecture that might be missed using more conventional approaches .", "Most existing pathways methods tak...	2013
[ "Results", "Discussion" ]	[ "organismal evolution", "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "applied mathematics", "microbiology", "viral structure", "simulation and modeling", "viruses", "algorithms", "evolutionary computation", "mathematics", "rna viruses", "statistics (mat...	The role of spatial heterogeneity in the evolution of local and global infections of viruses	journal.pcbi.1005952	null	[ [ "For the first step , we checked whether a strain with a certain G value can be endemic or not by using the stability analysis of the disease free equilibrium .", "A similar analysis is done by Hiebeler [18] but the endemic condition was calculated for extreme cases ( G = 0 or G = 1 ) in that study .", ...	[ "Viruses have two modes spread in a host body , one is to release infectious particles from infected cells ( global infection ) and the other is to infect directly from an infected cell to an adjacent cell ( local infection ) .", "Since the mode of spread affects the evolution of life history traits , such as vir...	[ "Viruses such as human immunodeficiency virus and measles virus can spread through physical contact between infected and susceptible cells ( cell-to-cell infection ) , as well as normal cell-free infection through virions .", "Some experimental evidences support the possibility that high ability of cell-to-cell i...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry/chemical biology of the cell", "biochemistry/transcription and translation", "biochemistry/biocatalysis", "infectious diseases/protozoal infections" ]	Regulated Expression of an Essential Allosteric Activator of Polyamine Biosynthesis in African Trypanosomes	journal.ppat.1000183	null	[ [ "Human African trypanosomiasis is a neglected disease of sub-Saharan Africa caused by the protozoan parasite Trypanosoma brucei .", "Current estimates are that more than 50 million people are at risk for infection [1] .", "Without treatment the disease is always fatal and available drug therapy is lim...	[ "Trypanosoma brucei is the causative agent of African sleeping sickness .", "The polyamine biosynthetic pathway has the distinction of being the target of the only clinically proven anti-trypanosomal drug with a known mechanism of action .", "Polyamines are essential for cell growth , and their metabolism is ex...	[ "Human African trypanosomiasis ( HAT ) is an important vector-borne pathogen .", "The World Health Organization estimates that more than 50 million people are at risk for the disease , which occurs focally , in remote regions , and periodically reaches epidemic levels .", "Untreated HAT is always fatal , and th...	2008
[ "Introduction", "Results", "Materials and Methods" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "gene regulation", "pathogens", "microbiology", "dna transcription", "regulator genes", "gene types", "bacterial pathogens", "medical microbiology", "gene expression", "microbial pathogens", "pathogen motility", "listeria...	Systems Level Analyses Reveal Multiple Regulatory Activities of CodY Controlling Metabolism, Motility and Virulence in Listeria monocytogenes	journal.pgen.1005870	null	[ [ "Listeria monocytogenes is a Gram-positive facultative intracellular pathogen transmitted by ingesting contaminated foods .", "L . monocytogenes causes a disease termed listeriosis associated with a mortality rate of up to 30% .", "Listeriosis typically manifests as a mild gastroenteritis in healthy p...	[ "Bacteria sense and respond to many environmental cues , rewiring their regulatory network to facilitate adaptation to new conditions/niches .", "Global transcription factors that co-regulate multiple pathways simultaneously are essential to this regulatory rewiring .", "CodY is one such global regulator , cont...	[ "Bacterial pathogens sense multiple host-related metabolic signals that alert them of host localization and result in induction of virulence traits .", "The Gram-positive foodborne pathogen Listeria monocytogenes activates the transcription of its virulence genes in response to low levels of branch-chained amino ...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "chemistry", "biology", "veterinary science", "agriculture" ]	Sheep Skin Odor Improves Trap Captures of Mosquito Vectors of Rift Valley Fever	journal.pntd.0001879	null	[ [ "Rift Valley fever virus ( RVFV ) is transmitted primarily by mosquitoes and there are periodic outbreaks of this disease in humans and domestic animals in Africa and the Arabian Peninsula [1] , [2] .", "Key mosquito vectors involved in the enzootic transmission include flood water Aedes spp .", "as t...	[ "In recent years , the East African region has seen an increase in arboviral diseases transmitted by blood-feeding arthropods .", "Effective surveillance to monitor and reduce incidence of these infections requires the use of appropriate vector sampling tools .", "Here , trapped skin volatiles on fur from sheep...	[ "The East African region is a major epizootic center for endemic and emerging mosquito borne-arboviruses such as Rift Valley fever virus ( RVFV ) , as evidenced by the increasing frequency and magnitude of this disease .", "The absence of vaccines or prophylactic drugs for most of these diseases emphasizes the ne...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "computational biology/systems biology", "computational biology/genomics" ]	Use of Data-Biased Random Walks on Graphs for the Retrieval of Context-Specific Networks from Genomic Data	journal.pcbi.1000889	null	[ [ "An important challenge in the analyses of high throughput datasets is integration of the data with prior knowledge interactions of the measured molecules for the retrieval of most relevant biomolecular networks [1]–[7] .", "This approach facilitates interpretation of the data within the context of known ...	[ "Extracting network-based functional relationships within genomic datasets is an important challenge in the computational analysis of large-scale data .", "Although many methods , both public and commercial , have been developed , the problem of identifying networks of interactions that are most relevant to the g...	[ "Analysis of high-content genomic data within the context of known networks of interactions of genes can lead to a better understanding of the underlying biological processes .", "However , finding the networks of interactions that are most relevant to the given data is a challenging task .", "We present a rand...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology", "viruses and cancer", "biology", "microbiology" ]	Phosphorylation of the Chromatin Binding Domain of KSHV LANA	journal.ppat.1002972	null	[ [ "The Kaposi sarcoma associated herpesvirus ( KSHV ) LANA protein is essential for establishment of KSHV latency through its role in replicating the KSHV genome , tethering the episomal genomes to cell chromosomes , interfering with induction of the viral lytic program and creating an environment that is permi...	[ "The Kaposi sarcoma associated herpesvirus ( KSHV ) latency associated nuclear antigen ( LANA ) is expressed in all KSHV associated malignancies and is essential for maintenance of KSHV genomes in infected cells .", "To identify kinases that are potentially capable of modifying LANA , in vitro phosphorylation ass...	[ "The Kaposi sarcoma associated herpesvirus ( KSHV ) is associated with cancers that have an increased incidence in individuals with compromised immune systems .", "KSHV expresses a protein , LANA , that is needed to maintain KSHV genomes in infected cells and also promotes the growth of KSHV associated tumors .",...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "chitin", "trophozoites", "parasite groups", "vesicles", "chemical compounds", "cellulose", "organic compounds", "parasitic protozoans", "parasitology", "acanthamoeba", "apicomplexa", "protozoans", "materials science", "macromolecules", "cellular structures and organelles", "polymers",...	The most abundant cyst wall proteins of Acanthamoeba castellanii are lectins that bind cellulose and localize to distinct structures in developing and mature cyst walls	journal.pntd.0007352	null	[ [ "Acanthamoebae , which include the genome project A . castellanii Neff strain , are soil protists named for acanthopods ( spikes ) on the surface of trophozoites [1] .", "In immunocompetent persons , Acanthamoeba is a rare but important cause of corneal inflammation ( keratitis ) , which is difficult to t...	[ "Acanthamoeba castellanii , which causes keratitis and blindness in under-resourced countries , is an emerging pathogen worldwide , because of its association with contact lens use .", "The wall makes cysts resistant to sterilizing reagents in lens solutions and to antibiotics applied to the eye .", "Transmissi...	[ "A half century ago , investigators identified cellulose in the Acanthamoeba cyst wall , which has two layers and conical ostioles that connect them .", "Here we showed cyst walls contain three large sets of cellulose-binding lectins , which localize to the ectocyst layer ( a Jonah lectin ) or to the endocyst lay...	2019
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blastocysts", "vero cells", "medicine and health sciences", "reproductive system", "pathology and laboratory medicine", "pathogens", "animal models of disease", "biological cultures", "microbiology", "animal models", "viruses", "developmental biology", "model organisms", "rna viruses", ...	Zika virus infection in immunocompetent pregnant mice causes fetal damage and placental pathology in the absence of fetal infection	journal.ppat.1006994	null	[ [ "Zika virus ( ZIKV ) is a mosquito-borne virus belonging to the genus Flaviviridae and is closely related to several other arboviruses , including dengue viruses ( DENV ) , yellow fever virus ( YFV ) , West Nile virus ( WNV ) , Japanese encephalitis virus ( JEV ) and tick-borne encephalitis virus ( TBEV ) [1]...	[ "Zika virus ( ZIKV ) infection during human pregnancy may cause diverse and serious congenital defects in the developing fetus .", "Previous efforts to generate animal models of human ZIKV infection and clinical symptoms often involved manipulating mice to impair their Type I interferon ( IFN ) signaling , thereb...	[ "Zika virus ( ZIKV ) infection during human pregnancy may cause severe congenital abnormalities and fetal death .", "There is currently no licensed vaccine or anti-ZIKV therapeutic to prevent or treat infection and/or disease .", "To generate an animal model that mimics human ZIKV infections , others have manip...	2018
[ "Introduction", "Materials and Methods", "Results and Discussion" ]	[]	Minimizing the Risk of Disease Transmission in Emergency Settings: Novel In Situ Physico-Chemical Disinfection of Pathogen-Laden Hospital Wastewaters	journal.pntd.0003776	null	[ [ "Outbreaks of specific infectious diseases that may potentially be transmitted by human excreta , including cholera , Ebola and hepatitis A and E present a challenge to existing WASH ( water , sanitation and hygiene ) practices and a greater focus on practical in situ disinfection of human waste may offer an ...	[ "The operation of a health care facility , such as a cholera or Ebola treatment center in an emergency setting , results in the production of pathogen-laden wastewaters that may potentially lead to onward transmission of the disease .", "The research presented here evaluated the design and operation of a novel tr...	[ "When an outbreak of infectious disease occurs in a low-resource setting , the rapid construction of emergency healthcare facilities may significantly reduce mortality .", "The facilities also result in the generation of large volumes of highly contaminated fecal waste that represents a potential basis for furthe...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "genomics", "cell biology", "dna replication", "nucleic acids", "genetics", "biology and life sciences", "dna", "epigenetics", "computational biology", "molecular cell biology" ]	The Spatiotemporal Program of DNA Replication Is Associated with Specific Combinations of Chromatin Marks in Human Cells	journal.pgen.1004282	null	[ [ "The faithful duplication of mammalian genomes at each S phase is under the control of a spatiotemporal program that orchestrates and regulates both the positioning and the timing of firing of replication starting points also called replication origins .", "The molecular mechanisms involved in coordinatin...	[ "The duplication of mammalian genomes is under the control of a spatiotemporal program that orchestrates the positioning and the timing of firing of replication origins .", "The molecular mechanisms coordinating the activation of about predicted origins remain poorly understood , partly due to the intrinsic rarit...	[ "Replication is the mechanism by which genomes are duplicated into two exact copies .", "Genomic stability is under the control of a spatiotemporal program that orchestrates both the positioning and the timing of firing of about 50 , 000 replication starting points , also called replication origins .", "Replica...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "cell differentiation", "biology", "cell fate determination" ]	Dynamic Rewiring of the Drosophila Retinal Determination Network Switches Its Function from Selector to Differentiation	journal.pgen.1003731	null	[ [ "During organogenesis , cells undergo progressive cell fate restriction coupled with a loss of pluripotency .", "This process is hallmarked by the stages of specification , proliferation , and differentiation [1] .", "The transitions between each of these states mark major changes in developmental com...	[ "Organ development is directed by selector gene networks .", "Eye development in the fruit fly Drosophila melanogaster is driven by the highly conserved selector gene network referred to as the “retinal determination gene network , ” composed of approximately 20 factors , whose core comprises twin of eyeless ( to...	[ "Animals develop by using different combinations of simple instructions .", "The highly conserved retinal determination ( RD ) network is an ancient set of instructions that evolved when multicellular animals first developed primitive eyes .", "Evidence suggests that this network is re-used throughout evolution...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	High Prevalence of Skin Disorders among HTLV-1 Infected Individuals Independent of Clinical Status	journal.pntd.0002546	null	[ [ "Adult T-cell leukemia/lymphoma ( ATLL ) , HTLV-1-associated myelopathy/tropical spastic paraparesis ( HAM/TSP ) and infective dermatitis associated with HTLV-1 ( IDH ) are the main diseases caused by human T-cell lymphotropic virus type 1 ( HTLV-1 ) infection [1]–[3] .", "However , several other clinical...	[ "Human T-cell lymphotropic virus type 1 ( HTLV-1 ) infection can increase the risk of developing skin disorders .", "This study evaluated the correlation between HTLV-1 proviral load and CD4+ and CD8+ T cells count among HTLV-1 infected individuals , with or without skin disorders ( SD ) associated with HTLV-1 in...	[ "HTLV-1 infection may increase the risk of developing skin disorders .", "A total of 193 HTLV-1 infected subjects were studied , including asymptomatic carriers and HAM/TSP patients .", "Of the subjects , 76% had an abnormal skin condition , with a high prevalence both among HTLV-1 asymptomatic carriers and HAM...	2013
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "heme", "invertebrates", "medicine and health sciences", "parasitic diseases", "animals", "wolbachia", "parasitology", "invertebrate genomics", "nematode infections", "developmental biology", "brugia", "bacteria", "proteins", "gene expression", "life cycles", "animal genomics", "bioc...	Defining Brugia malayi and Wolbachia symbiosis by stage-specific dual RNA-seq	journal.pntd.0005357	null	[ [ "Human filarial infections are currently a leading cause of morbidity in the developing world .", "Despite the large cost to human health , the chronic and debilitating diseases caused by filarial nematodes remain largely neglected .", "Two of the most prevalent chronic diseases caused by filaria incl...	[ "Filarial nematodes currently infect up to 54 million people worldwide , with millions more at risk for infection , representing the leading cause of disability in the developing world .", "Brugia malayi is one of the causative agents of lymphatic filariasis and remains the only human filarial parasite that can b...	[ "Filarial nematodes currently infect millions of people worldwide and represent a leading cause of disability .", "Currently available medications are insufficient in reaching elimination of these parasites .", "Many filarial nematodes , including Brugia malayi , have an Achilles heel of sorts—that is their obl...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "model organisms", "genetics", "biology", "genomics", "microbiology", "genetics and genomics" ]	Discovery of a Splicing Regulator Required for Cell Cycle Progression	journal.pgen.1003305	null	[ [ "Protozoans belonging to the Apicomplexa were recently combined with two other groups the ciliates and dinoflagellates to form a new monophyletic group called the Alveolata [1] .", "Unicellular Alveolates arose early in the evolution of eukaryotes , and while the placement of this branch before or after t...	[ "In the G1 phase of the cell division cycle , eukaryotic cells prepare many of the resources necessary for a new round of growth including renewal of the transcriptional and protein synthetic capacities and building the machinery for chromosome replication .", "The function of G1 has an early evolutionary origin ...	[ "The study of eukaryotic cell division has overwhelmingly focused on cells from two branches of evolution , fungal and metazoan , with more distant eukaryotes rarely studied .", "One exception is apicomplexan pathogens where in the last two decades development of genetic models has been rapid .", "While not a p...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular biology/dna replication", "cell biology/cellular death and stress responses", "molecular biology/recombination", "genetics and genomics/gene function", "microbiology/microbial growth and development", "molecular biology/dna repair" ]	A Major Role of the RecFOR Pathway in DNA Double-Strand-Break Repair through ESDSA in Deinococcus radiodurans	journal.pgen.1000774	null	[ [ "The bacterium Deinococcus radiodurans is extremely resistant to treatments such as ionizing radiation and desiccation .", "This resistance can be correlated with the ability of D . radiodurans to reconstruct a functional genome from hundreds of radiation or dessication-induced chromosomal fragments , whi...	[ "In Deinococcus radiodurans , the extreme resistance to DNA–shattering treatments such as ionizing radiation or desiccation is correlated with its ability to reconstruct a functional genome from hundreds of chromosomal fragments .", "The rapid reconstitution of an intact genome is thought to occur through an exte...	[ "Deinococcus radiodurans bacterium is among the best-known organisms found to resist extremely high exposures to desiccation and ionizing radiation , both causing extensive DNA double-strand breaks .", "Because a single unrepaired DNA double-strand break is usually lethal , DNA double-strand breaks are considered...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "mycobacteria", "proteins", "protein folding", "medical microbiology", "chaperone proteins", "protein structure", "microbial pathogens", "biology and life sciences", "microbiology", "bacterial pathogens" ]	An Essential Nonredundant Role for Mycobacterial DnaK in Native Protein Folding	journal.pgen.1004516	null	[ [ "Proper protein folding is essential for all organisms and assures that the primary sequence of the polypeptide forms its functional tertiary and quaternary structures .", "Protein chaperones are present in all domains of life and serve multiple functions in protein homeostasis .", "During translation...	[ "Protein chaperones are essential in all domains of life to prevent and resolve protein misfolding during translation and proteotoxic stress .", "HSP70 family chaperones , including E . coli DnaK , function in stress induced protein refolding and degradation , but are dispensable for cellular viability due to red...	[ "All living organisms use protein chaperones to prevent proteins from becoming insoluble either spontaneously or during cellular stress that can damage proteins .", "The HSP70 chaperone DnaK has been well characterized in E . coli and is important for that bacterium to resist protein denaturation from heat , but ...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Latent KSHV Infected Endothelial Cells Are Glutamine Addicted and Require Glutaminolysis for Survival	journal.ppat.1005052	null	[ [ "Kaposi’s Sarcoma-associated Herpesvirus ( KSHV ) is a human γ-herpesvirus and the etiologic agent of several malignancies , including two B-cell lymphomas , primary effusion lymphoma ( PEL ) and Multicentric Castleman’s Disease ( MCD ) , as well as Kaposi’s Sarcoma ( KS ) , an angioproliferative tumor[1 , 2]...	[ "Kaposi’s Sarcoma-associated Herpesvirus ( KSHV ) is the etiologic agent of Kaposi’s Sarcoma ( KS ) .", "KSHV establishes a predominantly latent infection in the main KS tumor cell type , the spindle cell , which is of endothelial cell origin .", "KSHV requires the induction of multiple metabolic pathways , inc...	[ "KSHV is the etiologic agent of KS , the most common tumor of AIDS patients worldwide .", "Currently , there are no therapeutics available to directly treat latent KSHV infection .", "This study reveals that latent KSHV infection induces endothelial cells to become glutamine addicted , similarly to cancer cells...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "vero cells", "medicine and health sciences", "milk", "breast milk", "body fluids", "reproductive system", "pathology and laboratory medicine", "pathogens", "biological cultures", "microbiology", "diet", "viruses", "animal models", "model organisms", "nutrition", "rna viruses", "gast...	Detection of Zika virus in mouse mammary gland and breast milk	journal.pntd.0007080	null	[ [ "Zika virus ( ZIKV ) is an enveloped virus with a positive-sense , single-stranded RNA genome [1] .", "For over half a century , this flavivirus was regarded as an arbovirus leading to self-limiting , febrile disease .", "However , confirmation of or association with new syndromes , including teratoge...	[ "Clinical reports of Zika Virus ( ZIKV ) RNA detection in breast milk have been described , but evidence conflicts as to whether this RNA represents infectious virus .", "We infected post-parturient AG129 murine dams deficient in type I and II interferon receptors with ZIKV .", "ZIKV RNA was detected in pup sto...	[ "Can Zika virus be transmitted from nursing mothers to their children via breast milk ?", "Only 4 years have passed since the Zika virus outbreak in Brazil , and much remains to be understood about the transmission and health consequences of Zika infection .", "To date , some case reports have detected Zika vir...	2019
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	High Prevalence of the Liver Fluke Amphimerus sp. in Domestic Cats and Dogs in an Area for Human Amphimeriasis in Ecuador	journal.pntd.0003526	null	[ [ "Amphimerus Barker , 1911 is a genus of parasitic liver fluke which are flat helminths ( Platyhelminthes ) of the Trematoda class and belong to the Opisthorchiidae family .", "The adult flukes reside within the bile ducts of a definitive host [1] .", "Infection by liver flukes of this family , which i...	[ "Amphimerus sp .", "is a liver fluke which recently has been shown to have a high prevalence of infection among an indigenous group , Chachi , who reside in a tropical rainforest in the northwestern region of Ecuador .", "Since it is unknown which animals can act as a reservoir and/or definitive hosts for Amphi...	[ "Amphimerus sp .", "is a fluke that infects the bile ducts of its definitive hosts .", "Recently , it has been shown that an indigenous Amerindian group , the Chachi , living in a rural and remote tropical area of Ecuador , are infected with this parasite .", "The epidemiology and life cycle of this parasite ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Swimming in Light: A Large-Scale Computational Analysis of the Metabolism of Dinoroseobacter shibae	journal.pcbi.1003224	null	[ [ "The Roseobacter clade is a versatile group of Gram-negative α-proteobacteria , which can be found in all oceans worldwide .", "Especially during phytoplankton blooms they account for a large fraction of the marine bacterial community [1] , [2] .", "Here , we focus on the aerobic anoxygenic phototroph...	[ "The Roseobacter clade is a ubiquitous group of marine α-proteobacteria .", "To gain insight into the versatile metabolism of this clade , we took a constraint-based approach and created a genome-scale metabolic model ( iDsh827 ) of Dinoroseobacter shibae DFL12T .", "Our model is the first accounting for the en...	[ "The oceans are home to a large variety of microorganisms , which interact in several ways with world-wide metabolic cycles .", "A representative of an important group of marine bacteria called the Roseobacter clade is Dinoroseobacter shibae .", "This organism is known to use a variant of photosynthesis to obta...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "innate immune system", "medicine and health sciences", "immune physiology", "cytokines", "chemical compounds", "pathology and laboratory medicine", "viral transmission and infection", "immunology", "microbiology", "carbohydrates", "organic compounds", "glucose", "pulmonology", "diabetes m...	Preexisting chronic conditions for fatal outcome among SFTS patients: An observational Cohort Study	journal.pntd.0007434	null	[ [ "SFTS is an emerging infectious disease that was first reported in 2009 in rural areas in central China .", "SFTSV is principally transmitted to human by tick bites in natural foci , with a possible human-to-human transmission through contacts with infected blood or body fluid [1] .", "After infection...	[ "Severe fever with thrombocytopenia syndrome ( SFTS ) is an emerging infectious disease that is caused by a novel bunyavirus SFTSV .", "Currently our knowledge of the host-related factors that influence the pathogenesis of disease is inadequate to allow prediction of fatal outcome .", "Here we conducted a prosp...	[ "SFTS now brings about a substantial global public health concern .", "Preexisting chronic conditions were thought to increase risk of severe SFTSV infections , however with sparse data mining efforts .", "In this study , we quantified the frequency of chronic comorbidities in SFTS , estimated their contributio...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "biotechnology", "ecology and environmental sciences", "medicine and health sciences", "environmental impacts", "immunology", "microbiology", "technology regulations", "parasitic diseases", "parasitology", "population biology", "zoology", "veterinary science", "public and occupational health...	Wolbachia Enhances West Nile Virus (WNV) Infection in the Mosquito Culex tarsalis	journal.pntd.0002965	null	[ [ "Efforts to control vector-borne pathogens have been hindered by evolution of insecticide resistance and failing drug therapies .", "Evidence suggests bed nets and indoor residual spraying with insecticides are losing efficacy in developing countries [1] , [2] .", "To improve the sustainability and ef...	[ "Novel strategies are required to control mosquitoes and the pathogens they transmit .", "One attractive approach involves maternally inherited endosymbiotic Wolbachia bacteria .", "After artificial infection with Wolbachia , many mosquitoes become refractory to infection and transmission of diverse pathogens ....	[ "Current methods to control mosquitoes and the pathogens they transmit are ineffective , partly due to insecticide and drug resistance .", "One novel control method involves exploiting naturally occurring Wolbachia bacteria in insects .", "Wolbachia are bacterial symbionts that are attractive candidates for mos...	2014
[ "Introduction", "Methods", "Results", "Sensitivity analysis and model limitations", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma mansoni", "medicine and health sciences", "helminths", "immunology", "vertebrates", "parasitic diseases", "animals", "mammals", "health care", "vaccines", "preventive medicine", "age groups", "primates", "infectious disease control", "vacc...	Modelling the impact of a Schistosoma mansoni vaccine and mass drug administration to achieve morbidity control and transmission elimination	journal.pntd.0007349	null	[ [ "Schistosomiasis inflicts significant levels of human morbidity and mortality in regions of the world with endemic infection .", "It is estimated that nearly 258 million people are infected worldwide with up to 700 million at risk of being infected , leading to an estimated 280000 deaths annually [1–3] ."...	[ "Mass drug administration ( MDA ) is , and has been , the principal method for the control of the schistosome helminths .", "Using MDA only is unlikely to eliminate the infection in areas of high transmission and the implementation of other measures such as reduced water contact improved hygiene and sanitation ar...	[ "Nearly 258 million people are infected worldwide by schistosome parasites .", "The World Health Organization ( WHO ) has set control guidelines to combat the morbidity and mortality induced by infection , defined by reaching ≤5% and ≤1% prevalence of heavy-intensity infections in school-aged children ( SAC ) , r...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genome expression analysis", "invertebrates", "innate immune system", "medicine and health sciences", "pathology and laboratory medicine", "viral transmission and infection", "caenorhabditis", "immunology", "microbiology", "animals", "parasitology", "animal models", "caenorhabditis elegans"...	Ubiquitin-Mediated Response to Microsporidia and Virus Infection in C. elegans	journal.ppat.1004200	null	[ [ "The Microsporidia phylum contains over 1400 species of obligate intracellular pathogens most closely related to fungi [1] .", "These pathogens can infect a wide variety of animal hosts including humans , where they can cause significant disease .", "Infections in humans can cause lethal diarrhea in i...	[ "Microsporidia comprise a phylum of over 1400 species of obligate intracellular pathogens that can infect almost all animals , but little is known about the host response to these parasites .", "Here we use the whole-animal host C . elegans to show an in vivo role for ubiquitin-mediated response to the microspori...	[ "Microbial pathogens have two distinct lifestyles: some pathogens live outside of host cells , and others live inside of host cells and are called intracellular pathogens .", "Microsporidia are fungal-related intracellular pathogens that can infect all animals , but are poorly understood .", "We used the roundw...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "mosquitoes", "vector biology", "neglected tropical diseases", "biology", "microbiology", "vectors and hosts", "viral diseases" ]	Oral Susceptibility of Singapore Aedes (Stegomyia) aegypti (Linnaeus) to Zika Virus	journal.pntd.0001792	null	[ [ "Zika virus ( ZIKV ) is an emerging mosquito-borne pathogen belonging to the genus Flavivirus of the Family Flaviviridae [1] .", "It is a positive single stranded RNA virus with a 10 , 794 nucleotide genome that is closely related to the Spondweni virus ( Flavivirus , Family Flaviviridae ) [2] , [3] .", ...	[ "Zika virus ( ZIKV ) is a little known flavivirus that caused a major outbreak in 2007 , in the South-western Pacific Island of Yap .", "It causes dengue-like syndromes but with milder symptoms .", "In Africa , where it was first isolated , ZIKV is mainly transmitted by sylvatic Aedes mosquitoes .", "The viru...	[ "Zika virus ( ZIKV ) is an emerging mosquito-borne zoonotic pathogen that causes dengue-like syndromes .", "Despite its high epidemic potential , little is known about the virus .", "Although the isolation of the virus was confined to the African continent , serological evidences have shown the widespread distr...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "statistical noise", "diagnostic radiology", "functional magnetic resonance imaging", "data acquisition", "statistics", "random variables", "neuroscience", "covariance", "magnetic resonance imaging", "simulation and modeling", "mathematics", "brain mapping", ...	Methods for computing the maximum performance of computational models of fMRI responses	journal.pcbi.1006397	null	[ [ "Computational modelling approaches applied to functional magnetic resonance imaging ( fMRI ) measurements aim to explain and predict the brain responses by expressing them as a function of model features that describe the sensory ( or cognitive ) stimuli [1–5] .", "By doing so , computational neuroimagin...	[ "Computational neuroimaging methods aim to predict brain responses ( measured e . g . with functional magnetic resonance imaging [fMRI] ) on the basis of stimulus features obtained through computational models .", "The accuracy of such prediction is used as an indicator of how well the model describes the computa...	[ "Encoding computational models in brain responses measured with fMRI allows testing the algorithmic representations carried out by the neural population within voxels .", "The accuracy of a model in predicting new responses is used as a measure of the brain validity of the computational model being tested , but t...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "neonatology", "children", "medicine and health sciences", "ecology and environmental sciences", "water resources", "surface water", "pathology and laboratory medicine", "maternal health", "geographical locations", "cryptosporidium", "parasitic protozoans", "pediatrics", "health care", "di...	Clinical, environmental, and behavioral characteristics associated with Cryptosporidium infection among children with moderate-to-severe diarrhea in rural western Kenya, 2008–2012: The Global Enteric Multicenter Study (GEMS)	journal.pntd.0006640	null	[ [ "The Global Enteric Multicenter Study ( GEMS ) was undertaken to assess the burden and etiology of moderate-to-severe diarrhea ( MSD ) in seven countries , three in South Asia and four in sub-Saharan Africa .", "In all African sites , Cryptosporidium was the second-highest enteric pathogen attributable to...	[ "Cryptosporidium is a leading cause of moderate-to-severe diarrhea ( MSD ) in young children in Africa .", "We examined factors associated with Cryptosporidium infection in MSD cases enrolled at the rural western Kenya Global Enteric Multicenter Study ( GEMS ) site from 2008-2012 .", "At health facility enrollm...	[ "Cryptosporidium is an important cause of childhood diarrhea .", "Research on cryptosporidiosis in countries where it is endemic remains limited; few studies have comprehensively examined risk factors for children in Kenya and similar settings .", "We examined characteristics associated with Cryptosporidium in ...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "neuroscience/cognitive neuroscience", "radiology and medical imaging/magnetic resonance imaging", "computational biology/computational neuroscience" ]	Brain Anatomical Network and Intelligence	journal.pcbi.1000395	null	[ [ "Researchers have long studied the biological basis for intelligence and have found increasing evidence relating high performance on intelligence quotient ( IQ ) tests to the coordination of multiple brain regions , utilizing both structural and functional brain imaging techniques [1]–[11] .", "Our hypoth...	[ "Intuitively , higher intelligence might be assumed to correspond to more efficient information transfer in the brain , but no direct evidence has been reported from the perspective of brain networks .", "In this study , we performed extensive analyses to test the hypothesis that individual differences in intelli...	[ "Networks of interconnected brain regions coordinate brain activities .", "Information is processed in the grey matter ( cortex and subcortical structures ) and passed along the network via whitish , fatty-coated fiber bundles , the white matter .", "Using maps of these white matter tracks , we provided evidenc...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "genome-wide association studies", "medicine", "public health and epidemiology", "diabetes mellitus type 2", "diabetic endocrinology", "genetic epidemiology", "molecular epidemiology", "epidemiology", "endocrinology", "diabetes and endocrinology", "biology", "phenotypes", "heredity", "gene...	Stratifying Type 2 Diabetes Cases by BMI Identifies Genetic Risk Variants in LAMA1 and Enrichment for Risk Variants in Lean Compared to Obese Cases	journal.pgen.1002741	null	[ [ "Common diseases such as type 2 diabetes are highly phenotypically heterogeneous .", "Few studies have performed genome wide association studies in subsets of patients defined by more stringent phenotypic characteristics .", "It is possible that reducing the heterogeneity of disease cases may increase...	[ "Common diseases such as type 2 diabetes are phenotypically heterogeneous .", "Obesity is a major risk factor for type 2 diabetes , but patients vary appreciably in body mass index .", "We hypothesized that the genetic predisposition to the disease may be different in lean ( BMI<25 Kg/m2 ) compared to obese cas...	[ "Individuals with Type 2 diabetes ( T2D ) can present with variable clinical characteristics .", "It is well known that obesity is a major risk factor for type 2 diabetes , yet patients can vary considerably—there are many lean diabetes patients and many overweight people without diabetes .", "We hypothesized t...	2012
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "cell biology/gene expression", "genetics and genomics/gene expression", "molecular biology/bioinformatics", "computational biology/signaling networks", "computational biology", "computational biology/systems biology" ]	Identifying Tightly Regulated and Variably Expressed Networks by Differential Rank Conservation (DIRAC)	journal.pcbi.1000792	null	[ [ "Molecular signatures based on the measured abundance of biomolecules ( e . g . , mRNA , proteins , metabolites ) have the potential to discriminate among disease subtypes , to predict clinical outcomes , or to provide insights into the mechanistic underpinnings of disease progression .", "Moreover , with...	[ "A powerful way to separate signal from noise in biology is to convert the molecular data from individual genes or proteins into an analysis of comparative biological network behaviors .", "One of the limitations of previous network analyses is that they do not take into account the combinatorial nature of gene i...	[ "The systems approach to medicine derives from the idea that diseased cells arise from one or more perturbed biological networks due to the net effect of interactions among multiple molecular agents; by measuring differences in the abundance of biomolecules ( e . g . , mRNA , proteins , metabolites ) we can identif...	2010
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "tibia", "medicine and health sciences", "chemical compounds", "salts", "osteoblast differentiation", "fibroblasts", "collagens", "cell differentiation", "animal models", "developmental biology", "model organisms", "osteoblasts", "proteoglycans", "connective tissue cells", "experimental ...	Impaired proteoglycan glycosylation, elevated TGF-β signaling, and abnormal osteoblast differentiation as the basis for bone fragility in a mouse model for gerodermia osteodysplastica	journal.pgen.1007242	null	[ [ "Bone mass is highly heritable and largely determined by bone growth during childhood and adolescence leading to the so-called peak bone mass , and the rate of subsequent bone loss at older ages [1] .", "Gerodermia osteodysplastica ( GO; OMIM #231070 ) belongs to the group of autosomal recessive cutis lax...	[ "Gerodermia osteodysplastica ( GO ) is characterized by skin laxity and early-onset osteoporosis .", "GORAB , the responsible disease gene , encodes a small Golgi protein of poorly characterized function .", "To circumvent neonatal lethality of the GorabNull full knockout , Gorab was conditionally inactivated i...	[ "Gerodermia osteodysplastica ( GO ) is segmental progeroid disorder affecting connective tissues and bone , leading to extreme bone fragility .", "The cause are loss-of-function mutations in the Golgi protein GORAB , whose function has been only partially unravelled .", "Using several mouse models and patient-d...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "enzyme-linked immunoassays", "immune physiology", "pathology and laboratory medicine", "body fluids", "pathogens", "immunology", "sociology", "microbiology", "social sciences", "vertebrates", "animals", "mammals", "viruses", "social systems", "primates"...	Serological analysis of Ebola virus survivors and close contacts in Sierra Leone: A cross-sectional study	journal.pntd.0007654	null	[ [ "There are six antigenically distinct species in the genus Ebolavirus that vary in viral pathogenesis .", "Infections caused by Zaire ebolavirus result in the highest lethality in humans with case fatality rates during outbreaks ranging from 41% to 90% ( average rate , 78% ) .", "Ebola virus ( EBOV ) ...	[ "The 2013–2016 Ebola virus outbreak in West Africa was the largest and deadliest outbreak to date .", "Here we conducted a serological study to examine the antibody levels in survivors and the seroconversion in close contacts who took care of Ebola-infected individuals , but did not develop symptoms of Ebola viru...	[ "As the causative agent of an often lethal hemorrhagic fever disease in humans and nonhuman primates , Zaire ebolavirus typically causes high fever , severe diarrhea , and vomiting which results in case fatality rates as high as 90% .", "The 2013–2016 outbreak in West Africa was the largest and most devastating E...	2019
[ "Introduction", "Materials and Methods", "Results/Discussion" ]	[ "physics", "computer science", "computer animation", "biophysic al simulations", "computing methods", "biology", "computational biology", "biophysics simulations", "biophysics" ]	In Silico Single-Molecule Manipulation of DNA with Rigid Body Dynamics	journal.pcbi.1003456	null	[ [ "The mechanical and topological properties of DNA and protein-DNA assemblies are of primary importance in many biological processes , including transcription , replication , chromatin organization and remodeling .", "Since techniques have become available enabling the manipulation of single-molecules [1] ...	[ "We develop a new powerful method to reproduce in silico single-molecule manipulation experiments .", "We demonstrate that flexible polymers such as DNA can be simulated using rigid body dynamics thanks to an original implementation of Langevin dynamics in an open source library called Open Dynamics Engine .", ...	[ "Video game techniques are designed to simulate rigid body dynamics of macroscopic bodies , e . g . characters or vehicles , in a realistic manner .", "However they are not able to deal with temperature effects , hence they are not able to deal with molecules .", "In order to extend these powerful techniques to...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "public health and epidemiology", "haplotypes", "genetic mutation", "genetic polymorphism", "epidemiology", "genetics", "population genetics", "biology", "population biology", "genetics and genomics" ]	Trypanosoma brucei gambiense Group 1 Is Distinguished by a Unique Amino Acid Substitution in the HpHb Receptor Implicated in Human Serum Resistance	journal.pntd.0001728	null	[ [ "Trypanosomiasis , a deadly disease of humans and livestock in sub-Saharan Africa , is caused by protozoan parasites of the genus Trypanosoma , which are transmitted between mammalian hosts by insect vectors of the genus Glossina ( tsetse ) .", "Human-infective members of the Trypanosoma brucei complex ca...	[ "Trypanosoma brucei rhodesiense ( Tbr ) and T . b .", "gambiense ( Tbg ) , causative agents of Human African Trypanosomiasis ( sleeping sickness ) in Africa , have evolved alternative mechanisms of resisting the activity of trypanosome lytic factors ( TLFs ) , components of innate immunity in human serum that pro...	[ "Human African Trypanosomiasis , or sleeping sickness , is caused by two different parasites: Trypanosoma brucei gambiense ( Tbg ) and T . b .", "rhodesiense ( Tbr ) .", "Each parasite employs a different mechanism to resist trypanosome lytic factor ( TLF ) , the active innate immune component of human serum ."...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "developmental biology/germ cells", "genetics and genomics/animal genetics", "cell biology/cellular death and stress responses", "developmental biology/aging", "developmental biology/developmental molecular mechanisms" ]	Apoptosis Maintains Oocyte Quality in Aging Caenorhabditis elegans Females	journal.pgen.1000295	null	[ [ "As women age , the quality and quantity of their oocytes decline , resulting in a decreased chance of becoming pregnant and an increased chance of having a child with birth defects [1] , [2] .", "A major cause of this decline is the increasing fraction of oocytes with chromosomal abnormalities , such as ...	[ "In women , oocytes arrest development at the end of prophase of meiosis I and remain quiescent for years .", "Over time , the quality and quantity of these oocytes decreases , resulting in fewer pregnancies and an increased occurrence of birth defects .", "We used the nematode Caenorhabditis elegans to study h...	[ "As women age , the quality of their oocytes declines , causing the eggs they make to have a higher chance of producing a miscarriage or a child with birth defects .", "We used the roundworm C . elegans to study this problem .", "We show that oocyte quality declines in these small animals during aging , much as...	2008
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "chemical compounds", "oxides", "oxidative stress", "enzymes", "pathogens", "immunology", "microbiology", "enzymology", "animal models", "fungi", "model organisms", "experimental organis...	Elevated catalase expression in a fungal pathogen is a double-edged sword of iron	journal.ppat.1006405	null	[ [ "Of the circa three million fungal species that are thought to inhabit our planet [1] , only a relatively small number have been reported to cause infections in humans .", "( About 400 species are described in the Atlas of Clinical Fungi [2] . )", "Nevertheless , there is an increasing awareness that ...	[ "Most fungal pathogens of humans display robust protective oxidative stress responses that contribute to their pathogenicity .", "The induction of enzymes that detoxify reactive oxygen species ( ROS ) is an essential component of these responses .", "We showed previously that ectopic expression of the heme-cont...	[ "The pathogenic yeast Candida albicans faces multiple challenges within its human host .", "These include the need to protect itself against the toxic oxidants used by the host to kill invading microbes , and the need to scavenge iron , an essential micronutrient that is limiting in certain tissues .", "The iro...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "public and occupational health", "infectious diseases", "medicine and health sciences", "global health", "epidemiology" ]	Risk Factors for Active Trachoma and Ocular Chlamydia trachomatis Infection in Treatment-Naïve Trachoma-Hyperendemic Communities of the Bijagós Archipelago, Guinea Bissau	journal.pntd.0002900	null	[ [ "Trachoma is caused by ocular infection with Chlamydia trachomatis and is the leading infectious cause of blindness worldwide .", "It manifests as distinct clinical syndromes beginning with an acute self-limiting keratoconjunctivitis , which following repeated episodes may progress to a more chronic infla...	[ "Trachoma , caused by ocular infection with Chlamydia trachomatis , is hyperendemic on the Bijagós Archipelago of Guinea Bissau .", "An understanding of the risk factors associated with active trachoma and infection on these remote and isolated islands , which are atypical of trachoma-endemic environments describ...	[ "Trachoma , caused by ocular infection with Chlamydia trachomatis , is the leading infectious cause of blindness worldwide .", "The World Health Organization elimination strategy includes community mass treatment with oral antibiotics , education regarding hygiene and facial cleanliness and environmental improvem...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "plant breeding", "mobile genetic elements", "plant science", "agronomy", "cell biology", "genetic elements", "genetics", "transposable elements", "biology and life sciences", "dna transposons", "plant genetics", "molecular cell biology", "agriculture" ]	Early Embryogenesis-Specific Expression of the Rice Transposon Ping Enhances Amplification of the MITE mPing	journal.pgen.1004396	null	[ [ "Transposable elements ( TEs ) are DNA sequences that are capable of jumping from one genomic locus to another and make up a large fraction of eukaryotic genomes .", "More than 80% of the maize ( Zea mays ) and barley ( Hordeum vulgare ) genomes are composed of TEs [1] , [2] , and they constitute 35% and ...	[ "Miniature inverted-repeat transposable elements ( MITEs ) are numerically predominant transposable elements in the rice genome , and their activities have influenced the evolution of genes .", "Very little is known about how MITEs can rapidly amplify to thousands in the genome .", "The rice MITE mPing is quies...	[ "Transposable elements are major components of eukaryotic genomes , comprising a large portion of the genome in some species .", "Miniature inverted-repeat transposable elements ( MITEs ) , which belong to the class II DNA transposable elements , are abundant in gene-rich regions , and their copy numbers are very...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Functional Activation of the Flagellar Type III Secretion Export Apparatus	journal.pgen.1005443	null	[ [ "Some bacteria swim through liquid and swarm over surfaces by synthesizing trans-envelope nanomachines called flagella .", "Flagella spontaneously self-assemble from over twenty separate proteins thought to be organized into three structural domains called the basal body , the hook and the filament [1–3] ...	[ "Flagella are assembled sequentially from the inside-out with morphogenetic checkpoints that enforce the temporal order of subunit addition .", "Here we show that flagellar basal bodies fail to proceed to hook assembly at high frequency in the absence of the monotopic protein SwrB of Bacillus subtilis .", "Gene...	[ "Bacteria build needle-like injectsomes to secrete toxins into host cells and build propeller-like flagella to swim through their environment using a molecular machine called the type III secretion system ( T3SS ) .", "Both the injectisome and the flagellum are large self-assembling complexes and regulation of th...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing techniques", "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "microbiology", "plasmid construction", "viruses", "next-generation sequencing", "rna viruses", "genome analysis", "dna construction", "molecular biology techniques", "microbial genetic...	Development of reverse genetics systems and investigation of host response antagonism and reassortment potential for Cache Valley and Kairi viruses, two emerging orthobunyaviruses of the Americas	journal.pntd.0006884	null	[ [ "The bunyaviruses are a large grouping of animal and plant-infecting viruses with a segmented , negative-stranded genome .", "The order Bunyavirales was recently proposed to include ‘bunyavirus like’ viruses that could not be assigned to the previous 5 genera ( https://talk . ictvonline . org/taxonomy/ ) ...	[ "Orthobunyaviruses such as Cache Valley virus ( CVV ) and Kairi virus ( KRIV ) are important animal pathogens .", "Periodic outbreaks of CVV have resulted in the significant loss of lambs on North American farms , whilst KRIV has mainly been detected in South and Central America with little overlap in geographica...	[ "Cache Valley and Kairi viruses ( CVV and KRIV; Peribunyaviridae , Orthobunyavirus ) are important animal pathogens of the Americas .", "In this study we developed reverse genetics systems to study and manipulate viral genomes of both viruses .", "Viral genomes were mutated to prevent the expression of the NSs ...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biotechnology", "genomics", "genome analysis", "gene expression", "transcriptome analysis", "genetics", "biology and life sciences", "computational biology", "genetic engineering" ]	Transcriptome Sequencing from Diverse Human Populations Reveals Differentiated Regulatory Architecture	journal.pgen.1004549	null	[ [ "A central challenge in modern medical and population genomics is identifying trait-disposing genetic variants , interpreting their molecular consequences , and determining the transferability of their functional roles across individuals and populations .", "While genome-wide association studies ( GWAS ) ...	[ "Large-scale sequencing efforts have documented extensive genetic variation within the human genome .", "However , our understanding of the origins , global distribution , and functional consequences of this variation is far from complete .", "While regulatory variation influencing gene expression has been stud...	[ "Previous gene expression studies have identified factors influencing population-level variation in gene regulation .", "However , these efforts have been limited to a small set of well-studied populations .", "By leveraging the high resolution of RNA sequencing and broad population sampling , we survey the lan...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "molecular biology", "developmental biology", "homo (human)" ]	Genome-Wide Profiling of DNA Methylation Reveals a Class of Normally Methylated CpG Island Promoters	journal.pgen.0030181	null	[ [ "CpG islands ( CGIs ) are discrete CpG-rich regions present in the promoters of 50%–70% of human genes [1] .", "DNA methylation within CGIs is associated with mitotically stable gene silencing ( an epigenetic process ) .", "Such CGI methylation is involved physiologically in genomic imprinting [2] and...	[ "The role of CpG island methylation in normal development and cell differentiation is of keen interest , but remains poorly understood .", "We performed comprehensive DNA methylation profiling of promoter regions in normal peripheral blood by methylated CpG island amplification in combination with microarrays .",...	[ "About half of all human genes contain a CpG-rich region called a “CpG island” in the 5′ area , often encompassing the promoter and transcription start site of the associated gene .", "DNA methylation was initially suggested to control tissue-specific gene expression in mammalian cells , but most promoter region ...	2007
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "blood cells", "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "immunology", "microbiology", "parasitic diseases", "protozoan life cycles", "parasitic protozoans", "developmental biology", "protozoans", "leishmania", "sequence motif analysis", "molecula...	A putative ATP/GTP binding protein affects Leishmania mexicana growth in insect vectors and vertebrate hosts	journal.pntd.0005782	null	[ [ "The genus Leishmania unites parasitic protozoa of the family Trypanosomatidae causing leishmaniases , diseases affecting human and animal populations mainly in tropical and subtropical regions .", "Clinical manifestations vary from spontaneously healing skin lesions to potentially fatal visceral organ fa...	[ "Leishmania virulence factors responsible for the complicated epidemiology of the various leishmaniases remain mainly unidentified .", "This study is a characterization of a gene previously identified as upregulated in two of three overlapping datasets containing putative factors important for Leishmania’s abilit...	[ "Leishmaniases are human parasitic diseases caused by several species of insect-transmitted Leishmania .", "The pathogenic genus Leishmania has close relatives that also colonize the guts of insects but are not able to infect mammalian cells .", "When the genes and gene expression profiles of pathogenic Leishma...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "meiosis", "retrotransposons", "gene regulation", "cell cycle and cell division", "cell processes", "germ cells", "zygotes", "developmental biology", "oocytes", "genetic elements", "embryos", "small interfering rnas", "embryology", "mobile genetic elements", "animal cells", "chromosome...	Maternal Setdb1 Is Required for Meiotic Progression and Preimplantation Development in Mouse	journal.pgen.1005970	null	[ [ "Mammalian development begins with fertilization , when the haploid sperm and egg fuse to form the diploid zygote .", "Although both gametes have equal genetic contributions to the offspring , the early embryo is almost entirely dependent on the egg for the supply of subcellular organelles and macromolecu...	[ "Oocyte meiotic progression and maternal-to-zygote transition are accompanied by dynamic epigenetic changes .", "The functional significance of these changes and the key epigenetic regulators involved are largely unknown .", "Here we show that Setdb1 , a lysine methyltransferase , controls the global level of h...	[ "During oogenesis , oocytes accumulate transcripts and proteins that support meiotic maturation and early embryogenesis .", "Although a number of such maternal-effect factors have been identified , our knowledge about the molecular machinery that drives meiotic progression and maternal-to-zygotic transition is st...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "neurological disorders", "neurology", "neurodegenerative diseases" ]	Macroautophagy Is Regulated by the UPR–Mediator CHOP and Accentuates the Phenotype of SBMA Mice	journal.pgen.1002321	null	[ [ "Many adult onset neurodegenerative disorders are characterized by the accumulation of abnormally folded proteins that self-associate into soluble oligomeric species or coalesce into insoluble protein aggregates .", "Among these disorders are ones caused by expansions of CAG/glutamine tracts [1] , [2] .",...	[ "Altered protein homeostasis underlies degenerative diseases triggered by misfolded proteins , including spinal and bulbar muscular atrophy ( SBMA ) , a neuromuscular disorder caused by a CAG/glutamine expansion in the androgen receptor .", "Here we show that the unfolded protein response ( UPR ) , an ER protein ...	[ "In many age-dependent neurodegenerative diseases , the accumulation of misfolded or mutant proteins drives pathogenesis .", "Several protein quality control pathways have emerged as central regulators of the turnover of these toxic proteins and therefore impact phenotypic severity .", "In spinal and bulbar mus...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The GATA Factor elt-1 Regulates C. elegans Developmental Timing by Promoting Expression of the let-7 Family MicroRNAs	journal.pgen.1005099	null	[ [ "Extensive study of postembryonic development in the nematode Caenorhabditis elegans has advanced our understanding of the temporal regulation of development and the roles of microRNAs ( miRNAs ) in controlling gene expression [1–5] .", "In C . elegans , developmental timing is regulated by the heterochro...	[ "Postembryonic development in Caenorhabditis elegans is a powerful model for the study of the temporal regulation of development and for the roles of microRNAs in controlling gene expression .", "Stable switch-like changes in gene expression occur during development as stage-specific microRNAs are expressed and s...	[ "In the nematode roundworm C . elegans , seam cells , a type of adult stem cell , divide in a completely predictable manner throughout post-embryonic development .", "Study of the control of the timing of these cells’ division and differentiation led to the discovery of the first microRNAs , which are small non-c...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "bacteriology", "emerging infectious diseases", "immunity", "medical microbiology", "innate immunity", "immunology", "biology", "microbiology", "host-pathogen interaction", "immune response", "pathogenesis" ]	Signal Transduction through CsrRS Confers an Invasive Phenotype in Group A Streptococcus	journal.ppat.1002361	null	[ [ "Human beings are thought to be the principal if not exclusive host for group A Streptococcus ( S . pyogenes , GAS ) .", "The organism's primary environmental niche is the human pharynx where GAS can colonize the epithelium without evoking any clinical symptoms , or it can produce local inflammation and s...	[ "The CsrRS ( or CovRS ) two component system controls expression of up to 15% of the genome of group A Streptococcus ( GAS ) .", "While some studies have suggested that the sensor histidine kinase CsrS responds to membrane perturbations as a result of various environmental stresses , other data have implicated th...	[ "Group A Streptococcus ( S . pyogenes or GAS ) is exclusively a human pathogen that can inhabit the human throat as a harmless commensal , cause localized , self-limited infection in the form of pharyngitis or strep throat , or invade local tissues or the bloodstream to produce life-threatening disease states such ...	2011
[ "Introduction", "HTCondor", "Materials and methods", "Sandbox code", "Examples", "When not to use HTC", "Additional resources", "Conclusion" ]	[ "employment", "ecology and environmental sciences", "education", "social sciences", "computers", "neuroscience", "learning and memory", "scientists", "cognition", "memory", "information technology", "data processing", "science and technology workforce", "computer and information sciences",...	Wrangling distributed computing for high-throughput environmental science: An introduction to HTCondor	journal.pcbi.1006468	null	[ [ "The life and environmental sciences are becoming computationally intense disciplines [1] .", "Individual studies can generate gigabytes and even petabytes of data [2 , 3] .", "Examples include -omics data [2 , 4] , high-resolution imagery [5] , lidar [6] , and real-time monitoring data [3] .", "A...	[ "Biologists and environmental scientists now routinely solve computational problems that were unimaginable a generation ago .", "Examples include processing geospatial data , analyzing -omics data , and running large-scale simulations .", "Conventional desktop computing cannot handle these tasks when they are l...	[ "Computational biology often requires processing large amounts of data , running many simulations , or other computationally intensive tasks .", "In this hybrid primer/tutorial , we describe how high-throughput computing ( HTC ) can be used to solve these problems .", "First , we present an overview of high-thr...	2018
[ "Introduction", "Materials & methods", "Results", "Discussion" ]	[ "geographical locations", "parasitic protozoans", "genetic mapping", "north america", "protozoans", "research and analysis methods", "central america", "sequence analysis", "south america", "bioinformatics", "sequence alignment", "people and places", "trypanosoma cruzi", "mexico", "haplo...	The diversity of the Chagas parasite, Trypanosoma cruzi, infecting the main Central American vector, Triatoma dimidiata, from Mexico to Colombia	journal.pntd.0005878	null	[ [ "Trypanosoma cruzi is the causative agent of Chagas disease and infects approximately six million people in Latin America [1] as well as many other mammals .", "Although initially considered largely clonal with only rare genetic mixing during its evolution [2] , studies of the population structure and inc...	[ "Little is known about the strains of Trypanosoma cruzi circulating in Central America and specifically in the most important vector in this region , Triatoma dimidiata .", "Approximately six million people are infected with T . cruzi , the causative agent of Chagas disease , which has the greatest negative econo...	[ "Little is known about the strains of the Chagas parasite circulating in Central America .", "This parasite is responsible for the most serious parasitic disease in Latin America and is presently divided into seven different strains .", "In Central America , the Chagas parasite is spread mainly by one species o...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "computational biology/metabolic networks", "computational biology/systems biology", "physics/interdisciplinary physics" ]	Signatures of Arithmetic Simplicity in Metabolic Network Architecture	journal.pcbi.1000725	null	[ [ "The prominent role of metabolism in any biological process and the fact that a large portion of the environmental factors shaping living systems are ultimately metabolic in nature , suggest that strong selective forces have been acting on metabolic networks throughout the history of life .", "In laborato...	[ "Metabolic networks perform some of the most fundamental functions in living cells , including energy transduction and building block biosynthesis .", "While these are the best characterized networks in living systems , understanding their evolutionary history and complex wiring constitutes one of the most fascin...	[ "Metabolism is the network of biochemical reactions that transforms available resources ( “inputs” ) into energy currency and building blocks ( “outputs” ) .", "Different organisms have different assortments of metabolic pathways and input/output requirements , reflecting their adaptation to specific environments...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "immune physiology", "pathology and laboratory medicine", "enzyme-linked immunoassays", "pathogens", "immunology", "microbiology", "retroviruses", "viruses", "preventive medicine", "immunodeficiency viruses", "rna viruses", "...	Persistent Low-Level Replication of SIVΔnef Drives Maturation of Antibody and CD8 T Cell Responses to Induce Protective Immunity against Vaginal SIV Infection	journal.ppat.1006104	null	[ [ "Despite the considerable resources committed to developing an effective HIV vaccine over the past three decades , this objective remains elusive .", "Recent failures of HIV vaccine trials to demonstrate protection against infection [1 , 2] and the only marginal apparent efficacy demonstrated in another ,...	[ "Defining the correlates of immune protection conferred by SIVΔnef , the most effective vaccine against SIV challenge , could enable the design of a protective vaccine against HIV infection .", "Here we provide a comprehensive assessment of immune responses that protect against SIV infection through detailed anal...	[ "Annually , more than two million people worldwide are infected with HIV , the virus that causes AIDS .", "Rhesus macaques can be infected with SIV , a close relative and ancestor of HIV , resulting in simian AIDS , recapitulating key aspects of human HIV infection .", "SIVΔnef , a live attenuated form of SIV ,...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "stiffness", "cell motility", "mechanical properties", "actin filaments", "classical mechanics", "molecular motors", "actin motors", "materials science", "damage mechanics", "motor proteins", "dynamic actin filaments", "buckling", "polymer chemistry", "proteins", "deformation", "chemis...	Morphological Transformation and Force Generation of Active Cytoskeletal Networks	journal.pcbi.1005277	null	[ [ "The actin cytoskeleton plays an important role in various cellular processes , such as changes in cell shape , cytokinesis , and cell migration [1] .", "Much of the mechanical forces required for these processes are generated by interactions between actin filaments ( F-actin ) and myosin II motors [2] ."...	[ "Cells assemble numerous types of actomyosin bundles that generate contractile forces for biological processes , such as cytokinesis and cell migration .", "One example of contractile bundles is a transverse arc that forms via actomyosin-driven condensation of actin filaments in the lamellipodia of migrating cell...	[ "Contractile networks and bundles generate mechanical forces required for various cellular processes , particularly cell division and migration .", "In many of these processes , networks are structurally reorganized into bundles by the activity of molecular motors .", "During this morphological transformation ,...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology", "microbiology", "bacterial pathogens" ]	Differential Function of Lip Residues in the Mechanism and Biology of an Anthrax Hemophore	journal.ppat.1002559	null	[ [ "An important determinant in the outcome of a bacterial infection is how well the invading pathogen can acquire host iron .", "Hosts with high levels of free iron are more susceptible to infection , and deletion of iron acquisition systems in a wide range of bacterial species generally attenuates virulenc...	[ "To replicate in mammalian hosts , bacterial pathogens must acquire iron .", "The majority of iron is coordinated to the protoporphyrin ring of heme , which is further bound to hemoglobin .", "Pathogenic bacteria utilize secreted hemophores to acquire heme from heme sources such as hemoglobin .", "Bacillus an...	[ "Pathogenic bacteria need to acquire host iron to replicate during infection .", "Approximately 80% of mammalian iron is associated with a small molecule termed heme , most of which is bound to circulating hemoglobin and involved in O2 transport in red cells .", "Bacteria secrete proteins , termed hemophores , ...	2012
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "biogeography", "taxonomy", "ecology and environmental sciences", "mitochondrial dna", "atmospheric science", "population genetics", "species delimitation", "data management", "speciation", "paleontology", "forms of dna", "dna", "population biology", "ecological metrics", "geography", ...	A latitudinal phylogeographic diversity gradient in birds	journal.pbio.2001073	null	[ [ "Phylogeographic studies leverage spatial and genetic data to examine the earliest stages of speciation , illuminating how populations differentiate across a landscape [1] .", "Comparisons across species show that the level of genetic structuring varies from deep phylogeographic breaks to unstructured pan...	[ "High tropical species diversity is often attributed to evolutionary dynamics over long timescales .", "It is possible , however , that latitudinal variation in diversification begins when divergence occurs within species .", "Phylogeographic data capture this initial stage of diversification in which populatio...	[ "The causes of high tropical species diversity remain contentious and disputed .", "Recent studies have shown that latitudinal differences in speciation and extinction rates give rise to high tropical diversity .", "However , it is unclear if this gradient is the product of population-level , species-level , or...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "epistasis", "physics", "sound waves", "mutation", "substitution mutation", "point mutation", "fitness epistasis", "acoustics", "mathematics", "statistics (mathematics)", "confidence intervals", "heredity", "genetics", "biology and life sciences", "physical sciences", "evolutionary bio...	High-order epistasis shapes evolutionary trajectories	journal.pcbi.1005541	null	[ [ "Epistasis creates historical contingency , as it means that the effect of a mutation depends on previous substitutions [1–6] .", "Interactions between pairs of mutations can cause mutations to accumulate in a specific order [1 , 4] , stochastically open and close pathways [3 , 6] , and make evolution irr...	[ "High-order epistasis—where the effect of a mutation is determined by interactions with two or more other mutations—makes small , but detectable , contributions to genotype-fitness maps .", "While epistasis between pairs of mutations is known to be an important determinant of evolutionary trajectories , the evolu...	[ "A key goal for evolutionary biologists is understanding why one evolutionary trajectory is taken rather than others .", "This requires understanding how individual mutations , as well as interactions between them , determine the accessibility of evolutionary pathways .", "We used a robust statistical analysis ...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "biology" ]	Loss of Catalytically Inactive Lipid Phosphatase Myotubularin-related Protein 12 Impairs Myotubularin Stability and Promotes Centronuclear Myopathy in Zebrafish	journal.pgen.1003583	null	[ [ "X-linked myotubular myopathy ( XLMTM ) is a congenital disorder caused by mutations of the MTM1 gene that encodes myotubularin [1] , [2] .", "Affected males are born with severe generalized hypotonia and weakness of skeletal muscles with respiratory insufficiency .", "In majority of cases the disease...	[ "X-linked myotubular myopathy ( XLMTM ) is a congenital disorder caused by mutations of the myotubularin gene , MTM1 .", "Myotubularin belongs to a large family of conserved lipid phosphatases that include both catalytically active and inactive myotubularin-related proteins ( i . e . , “MTMRs” ) .", "Biochemica...	[ "Congenital myopathies are a group of heredity diseases characterized by muscle weakness and impaired locomotion that manifest in both children and adults .", "X-linked myotubular myopathy ( XLMTM ) is a subtype of congenital myopathy that predominantly affects males and is caused by mutations in the myotubularin...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "blood cells", "genome-wide association studies", "medicine and health sciences", "functional genomics", "immune cells", "neurodegenerative diseases", "immunology", "human genomics", "genome analysis", "genome annotation", "alzheimer disease", "white blood cells", "animal cells", "dementia...	Systematic tissue-specific functional annotation of the human genome highlights immune-related DNA elements for late-onset Alzheimer’s disease	journal.pgen.1006933	null	[ [ "Large consortia such as ENCODE [1] and Epigenomics Roadmap Project [2] have generated a rich collection of high-throughput genomic and epigenomic data , providing unprecedented opportunities to delineate functional structures in the human genome .", "As complex disease research rapidly advances , evidenc...	[ "Continuing efforts from large international consortia have made genome-wide epigenomic and transcriptomic annotation data publicly available for a variety of cell and tissue types .", "However , synthesis of these datasets into effective summary metrics to characterize the functional non-coding genome remains a ...	[ "After years of community efforts , many experimental and computational approaches have been developed and applied for functional annotation of the human genome , yet proper annotation still remains challenging , especially in non-coding regions .", "As complex disease research rapidly advances , increasing evide...	2017
[ "Introduction", "Results and Discussion", "Materials and Methods" ]	[]	Retinoic Acid Receptors Control Spermatogonia Cell-Fate and Induce Expression of the SALL4A Transcription Factor	journal.pgen.1005501	null	[ [ "Spermatogenesis is a tightly regulated , cyclical , cell differentiation process , taking place in the seminiferous epithelium of the testis and yielding mature spermatozoa from stem cells .", "Spermatogonia in the single cell state , known as A single ( As ) spermatogonia , have traditionally be conside...	[ "All-trans retinoic acid ( ATRA ) is instrumental to male germ cell differentiation , but its mechanism of action remains elusive .", "To address this question , we have analyzed the phenotypes of mice lacking , in spermatogonia , all rexinoid receptors ( RXRA , RXRB and RXRG ) or all ATRA receptors ( RARA , RARB...	[ "Differentiation of spermatozoa from immature germ cells , called spermatogonia , critically depends on retinoic acid ( ATRA ) , the active metabolite of vitamin A that acts though binding to nuclear receptors called RXR and RAR .", "To understand the mechanism by which ATRA control germ cell differentiation , we...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "public health and epidemiology/epidemiology", "genetics and genomics", "diabetes and endocrinology/type 2 diabetes" ]	Consistent Association of Type 2 Diabetes Risk Variants Found in Europeans in Diverse Racial and Ethnic Groups	journal.pgen.1001078	null	[ [ "Multiple common risk alleles have been identified as reproducibly associated with risk of type 2 diabetes ( T2D ) [1]–[13] .", "With the exception of the KCNQ1 locus which was identified in the Japanese population [1] , [2] , all of the well-replicated risk variants were first identified in populations o...	[ "It has been recently hypothesized that many of the signals detected in genome-wide association studies ( GWAS ) to T2D and other diseases , despite being observed to common variants , might in fact result from causal mutations that are rare .", "One prediction of this hypothesis is that the allelic associations ...	[ "Single rare causal alleles and/or collections of multiple rare alleles have been suggested to create “synthetic associations” with common variants in genome-wide association studies ( GWAS ) .", "This model predicts that associations with common variants will not be consistent across populations .", "In this s...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell physiology", "animal genetics", "vertebrates", "animals", "osteichthyes", "animal models", "developmental biology", "model organisms", "organism development", "molecular genetics", "research and analysis methods", "fishes", "organogenesis", "membrane trafficking", "zebrafish", "c...	Souffle/Spastizin Controls Secretory Vesicle Maturation during Zebrafish Oogenesis	journal.pgen.1004449	null	[ [ "Oogenesis prepares the egg to start the development of a new organism .", "During their development , oocytes actively import and secrete proteins using the basic cellular mechanism of vesicle transport [1]–[3] .", "As a consequence , oocytes contributed substantially to our understanding of vesicle ...	[ "During oogenesis , the egg prepares for fertilization and early embryogenesis .", "As a consequence , vesicle transport is very active during vitellogenesis , and oocytes are an outstanding system to study regulators of membrane trafficking .", "Here , we combine zebrafish genetics and the oocyte model to iden...	[ "Oocytes of egg laying animals frequently represent the biggest cell type of a species .", "The size of the egg is a consequence of active transport processes , e . g . the import of yolk proteins , which results in the massive storage of vesicles .", "In addition , secretory vesicles termed cortical granules a...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "mathematics", "tropical diseases (non-neglected)", "infectious disease epidemiology", "epidemiology", "plasmodium malariae", "applied mathematics", "population biology", "biology", "malaria", "parasitic diseases" ]	Malaria's Missing Number: Calculating the Human Component of R0 by a Within-Host Mechanistic Model of Plasmodium falciparum Infection and Transmission	journal.pcbi.1003025	null	[ [ "Approximately 2 . 5 billion people live in areas whose local epidemiology permits transmission of Plasmodium falciparum , the parasite that causes the most life-threatening form of malaria [1] .", "Malaria has inflicted a severe toll in morbidity and mortality over the course of human history .", "No...	[ "Human infection by malarial parasites of the genus Plasmodium begins with the bite of an infected Anopheles mosquito .", "Current estimates place malaria mortality at over 650 , 000 individuals each year , mostly in African children .", "Efforts to reduce disease burden can benefit from the development of math...	[ "We report a new mathematical model of the progression , within a human host , of a malaria infection caused by the parasite Plasmodium falciparum .", "This model incorporates probability distributions for the key parameters of infection and transmission so that model outputs match the entire range of observed re...	2013
[ "Introduction", "Results", "Estimating triplet interactions requires an accurate null model", "Discussion", "Methods" ]	[ "antimicrobials", "deletion mutation", "medicine and health sciences", "microbial mutation", "statistical noise", "statistics", "drugs", "microbiology", "mathematical models", "mutation", "antibiotic resistance", "mathematics", "antibiotics", "artificial intelligence", "pharmacology", ...	Noise-precision tradeoff in predicting combinations of mutations and drugs	journal.pcbi.1006956	null	[ [ "Different fields of biology ask how multiple perturbations affect a biological system .", "For example , to understand the function of DNA sequences such as promoters or coding regions , or to design new ones , it is important to understand how mutations combine to affect function [1–4] .", "Another ...	[ "Many biological problems involve the response to multiple perturbations .", "Examples include response to combinations of many drugs , and the effects of combinations of many mutations .", "Such problems have an exponentially large space of combinations , which makes it infeasible to cover the entire space exp...	[ "Sometimes a combination of drugs works much better than each drug alone .", "Finding such drug cocktails is a pressing challenge in order to combat drug resistance and to improve drug effects .", "However , it is impossible to test all combinations of multiple drug experimentally .", "Therefore , researchers...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Task-Driven Activity Reduces the Cortical Activity Space of the Brain: Experiment and Whole-Brain Modeling	journal.pcbi.1004445	null	[ [ "How spontaneous brain dynamics are altered under stimulation or task conditions remains an important open question in neuroscience .", "Empirically , one of the most robust hallmarks of task-driven brain activity is the decrease of variability following an external stimulus input , a phenomenon observed ...	[ "How a stimulus or a task alters the spontaneous dynamics of the brain remains a fundamental open question in neuroscience .", "One of the most robust hallmarks of task/stimulus-driven brain dynamics is the decrease of variability with respect to the spontaneous level , an effect seen across multiple experimental...	[ "Task- or stimulus-related changes of brain dynamics have been the subject of intense investigation during the last years .", "One of the most robust hallmarks of task/stimulus-driven brain dynamics , as measured using diverse recording techniques , is the decrease of variability with respect to the spontaneous l...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell binding", "cell physiology", "medicine and health sciences", "pathology and laboratory medicine", "molecular probe techniques", "hepacivirus", "pathogens", "gene regulation", "vector-borne diseases", "microbiology", "immunoblotting", "viruses", "lipoprotein receptors", "rna viruses",...	Lipoprotein Receptors Redundantly Participate in Entry of Hepatitis C Virus	journal.ppat.1005610	null	[ [ "More than 160 million individuals worldwide are infected with hepatitis C virus ( HCV ) , which is especially troubling because HCV-induced cirrhosis and hepatocellular carcinoma are life-threatening diseases [1] .", "Current standard therapy combining peg-interferon ( IFN ) , ribavirin ( RBV ) and a pro...	[ "Scavenger receptor class B type 1 ( SR-B1 ) and low-density lipoprotein receptor ( LDLR ) are known to be involved in entry of hepatitis C virus ( HCV ) , but their precise roles and their interplay are not fully understood .", "In this study , deficiency of both SR-B1 and LDLR in Huh7 cells was shown to impair ...	[ "Hepatitis C virus ( HCV ) utilizes several receptors to enter hepatocytes , including scavenger receptor class B type 1 ( SR-B1 ) receptor and low-density lipoprotein receptor ( LDLR ) .", "HCV particles interact with lipoprotein and apolipoproteins to form complexes termed lipoviroparticles .", "Several repor...	2016
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "dengue virus", "invertebrates", "medicine and health sciences", "immune physiology", "enzyme-linked immunoassays", "pathology and laboratory medicine", "pathogens", "immunology", "geographical locations", "microbiology", "tropical diseases", "animals", "viruses", "multivariate analysis", ...	A serologic study of dengue in northwest Ethiopia: Suggesting preventive and control measures	journal.pntd.0006430	null	[ [ "Dengue is one of the most important mosquito-borne viral diseases and can be caused by any one of the four dengue virus serotypes ( DENV1-4 ) of the genus Flavivirus [1] .", "Dengue virus is a non-segmented , positive-sense , single-stranded , enveloped RNA virus; transmitted mainly by the bite of Aedes ...	[ "Dengue is one of the most serious and rapidly spreading arboviral diseases in the world .", "Despite many acute febrile illnesses in Ethiopia , the burden of illness due to dengue in the country is largely unknown .", "Thus , the present study aimed to provide the first baseline data on seroprevalence and asso...	[ "Despite dengue is currently one of the leading causes of arboviral diseases in the globe , it is unrecognized and underreported in Africa , particularly in Ethiopia .", "Thus , we conducted a cross-sectional study among febrile patients who were attending health institutions to document seroprevalence and associ...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Ataxin-2 Regulates RGS8 Translation in a New BAC-SCA2 Transgenic Mouse Model	journal.pgen.1005182	null	[ [ "Spinocerebellar ataxia type 2 ( SCA2 ) belongs to the group of neurodegenerative diseases caused by polyglutamine ( polyQ ) expansion .", "This group includes SCA1 , Machado-Joseph disease ( SCA3 or MJD ) , SCA6 , SCA7 , SCA17 , Huntington's disease , spinal bulbar muscular atrophy ( SBMA ) and dentatoru...	[ "Spinocerebellar ataxia type 2 ( SCA2 ) is an autosomal dominant disorder with progressive degeneration of cerebellar Purkinje cells ( PCs ) and other neurons caused by expansion of a glutamine ( Q ) tract in the ATXN2 protein .", "We generated BAC transgenic lines in which the full-length human ATXN2 gene was tr...	[ "Spinocerebellar ataxia type 2 ( SCA2 ) is an inherited neurodegenerative disorder leading to predominant loss of Purkinje cells in the cerebellum and impairment of motor coordination .", "The mutation is expansion of a protein domain consisting of a stretch of glutamine amino acids .", "We generated a mouse mo...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Lyn Delivers Bacteria to Lysosomes for Eradication through TLR2-Initiated Autophagy Related Phagocytosis	journal.ppat.1005363	null	[ [ "Gram-negative bacteria , such as Pseudomonas aeruginosa ( hereafter Pa ) and Klebsiella pneumoniae ( Kp ) are formidable threats to human health , imposing huge healthcare costs worldwide .", "Pa is the fourth most commonly isolated nosocomial pathogen , accounting for 10% of all hospital-acquired infect...	[ "Extracellular bacteria , such as Pseudomonas aeruginosa and Klebsiella pneumoniae , have been reported to induce autophagy; however , the role and machinery of infection-induced autophagy remain elusive .", "We show that the pleiotropic Src kinase Lyn mediates phagocytosis and autophagosome maturation in alveola...	[ "It is vital to establish the mechanistic basis for initiation of host defenses and immune responses that are required to eliminate bacterial infection .", "This line of inquiry will increase knowledge of bacterial pathogenesis and uncover new insights that can enhance design and effectiveness of novel therapeuti...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "physicians", "medical doctors", "pathology and laboratory medicine", "medical personnel", "tropical diseases", "geographical locations", "health care", "throat", "health care providers", "signs and symptoms", "neglected tropical diseases", "infectious disease...	Evaluation of the WHO 2009 classification for diagnosis of acute dengue in a large cohort of adults and children in Sri Lanka during a dengue-1 epidemic	journal.pntd.0006258	null	[ [ "Dengue is an important cause of morbidity and mortality worldwide in the tropics and mimics other causes of acute febrile illness ( AFI ) [1–3] .", "Early recognition of severe dengue could improve outcomes [4] .", "The 1997 World Health Organization ( WHO ) dengue clinical classification criteria we...	[ "Dengue is a leading cause of fever and mimics other acute febrile illnesses ( AFI ) .", "In 2009 , the World Health Organization ( WHO ) revised criteria for clinical diagnosis of dengue .", "The new WHO 2009 classification of dengue divides suspected cases into three categories: dengue without warning signs ,...	[ "Dengue is an important cause of acute fever in the tropics that is difficult to distinguish from other common etiologies of fever .", "The World Health Organization ( WHO ) revised criteria for the clinical diagnosis and classification of acute dengue in 2009 .", "The performance of these criteria has not been...	2018
[ "Introduction", "Material and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "public health and epidemiology", "epidemiology", "infectious disease epidemiology", "global health", "infectious disease control", "epidemiological methods", "infectious disease modeling" ]	Transmission Characteristics of the 2009 H1N1 Influenza Pandemic: Comparison of 8 Southern Hemisphere Countries	journal.ppat.1002225	null	[ [ "In late April 2009 , the first cases of the novel swine-derived H1N1pdm influenza A virus were detected in Mexico and the United States , prompting the World Health Organization ( WHO ) to raise the level of influenza pandemic alert to phase 5 [1] .", "By the end of 2009 , the H1N1pdm virus had spread to...	[ "While in Northern hemisphere countries , the pandemic H1N1 virus ( H1N1pdm ) was introduced outside of the typical influenza season , Southern hemisphere countries experienced a single wave of transmission during their 2009 winter season .", "This provides a unique opportunity to compare the spread of a single v...	[ "Although relatively mild , the 2009 H1N1 pandemic reminded us once again of the on-going threat posed by novel respiratory viruses and the need for understanding better how such pathogens emerge and spread .", "From April to September 2009 , countries in temperate regions of the Southern hemisphere experienced l...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Fragile Site Instability in Saccharomyces cerevisiae Causes Loss of Heterozygosity by Mitotic Crossovers and Break-Induced Replication	journal.pgen.1003817	null	[ [ "Cancer cells contain a variety of genomic changes that result in altered gene expression affecting cell growth .", "Amplification or over-expression of oncogenes and loss of heterozygosity ( LOH ) at tumor-suppressor genes are both significant contributors to tumorogenesis .", "Human common fragile s...	[ "Loss of heterozygosity ( LOH ) at tumor suppressor loci is a major contributor to cancer initiation and progression .", "Both deletions and mitotic recombination can lead to LOH .", "Certain chromosomal loci known as common fragile sites are susceptible to DNA lesions under replication stress , and replication...	[ "Loss of heterozygosity ( LOH ) at tumor-suppressor genes contributes to cancer , and deletions resulting in LOH are frequently observed in tumor cells at certain chromosomal regions known as common fragile sites .", "LOH can also result from repair of DNA damage by mitotic recombination , if the homologous chrom...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases/neglected tropical diseases" ]	A History of Chagas Disease Transmission, Control, and Re-Emergence in Peri-Rural La Joya, Peru	journal.pntd.0000970	null	[ [ "An estimated 8 million people in Latin America are infected by the protozoan parasite Trypanosoma cruzi , the causative agent of Chagas disease [1] .", "Trypanosoma cruzi is typically transmitted to humans and other mammals through contact with feces of an infected blood-feeding triatomine insect .", ...	[ "The history of Chagas disease control in Peru and many other nations is marked by scattered and poorly documented vector control campaigns .", "The complexities of human migration and sporadic control campaigns complicate evaluation of the burden of Chagas disease and dynamics of Trypanosoma cruzi transmission ....	[ "The historically rural problem of Chagas disease is increasing in urban areas in Latin America .", "Peri-rural development may play a critical role in the urbanization of Chagas disease and other parasitic infections .", "We conducted a cross-sectional study in an urbanizing rural area in southern Peru , and w...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "gram negative", "immunity", "innate immunity", "microbial pathogens", "host-pathogen interaction", "biology", "microbiology", "bacterial pathogens" ]	Vibrio cholerae Evades Neutrophil Extracellular Traps by the Activity of Two Extracellular Nucleases	journal.ppat.1003614	null	[ [ "The Gram negative facultative human pathogen Vibrio cholerae is the causative agent of cholera , which is defined as an acute , secretory diarrheal disease .", "Today , the global burden of cholera is estimated to reach several million cases per year , with the majority located in the endemic areas of Af...	[ "The Gram negative bacterium Vibrio cholerae is the causative agent of the secretory diarrheal disease cholera , which has traditionally been classified as a noninflammatory disease .", "However , several recent reports suggest that a V . cholerae infection induces an inflammatory response in the gastrointestinal...	[ "Although several reports describe an inflammatory component of the diarrheal disease cholera , the innate immune response to V . cholerae and its impact on the pathogenesis of the disease is poorly understood .", "In the present study we can link the presence of host neutrophils with a colonization defect of a V...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases", "medicine and health sciences", "emerging infectious diseases", "epidemiology", "biology and life sciences", "microbiology", "viral diseases" ]	Monitoring Antigenic Variations of Enterovirus 71: Implications for Virus Surveillance and Vaccine Development	journal.pntd.0003044	null	[ [ "Enterovirus 71 ( EV71 ) is a non-enveloped RNA virus of the family Picornaviridae and contains a positive sense ssRNA with a single open reading frame ( ORF ) .", "The ORF is expressed as a large polyprotein that can be cleaved into P1 , P2 and P3 regions .", "The P1 gene encodes four structural prot...	[ "Enterovirus 71 ( EV71 ) causes life-threatening epidemics in Asia and can be phylogenetically classified into three major genogroups ( A∼C ) including 11 genotypes ( A , B1∼B5 , and C1∼C5 ) .", "Recently , EV71 epidemics occurred cyclically in Taiwan with different genotypes .", "In recent years , human studie...	[ "Enterovirus 71 ( EV71 ) has caused several life-threatening epidemics in children in the Asia-Pacific region since 1997 .", "EV71 has one single serotype as measured using hyper-immune animal antisera but can be phylogenetically classified into three major genogroups ( A , B and C ) and eleven genotypes ( A , B1...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "chemical compounds", "immunology", "nucleotides", "organic compounds", "dna transcription", "germ cells", "pyrimidines", "epigenetics", "dna", "dna methylation", "chromatin", "sperm", "white blood cells", "chromosome bio...	Developmental regulation of DNA cytosine methylation at the immunoglobulin heavy chain constant locus	journal.pgen.1007930	null	[ [ "DNA methylation is a common epigenetic regulation mechanism in vertebrates and is involved in gene expression regulation during development and differentiation as well as in defense of the genome against transposable elements .", "DNA methylation provides a robust epigenetic mechanism for cell fate decis...	[ "DNA cytosine methylation is involved in the regulation of gene expression during development and its deregulation is often associated with disease .", "Mammalian genomes are predominantly methylated at CpG dinucleotides .", "Unmethylated CpGs are often associated with active regulatory sequences while methylat...	[ "DNA methylation mainly occurs at CpG dinucleotides and strongly influences gene expression during development .", "Deregulation of DNA methylation is often associated with disease .", "In mammalian genomes , unmethylated CpG dinucleotides are generally associated with active regulatory sequences , while methyl...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "mosquitoes", "soil-transmitted helminths", "filariasis", "elephantiasis", "tropical diseases (non-neglected)", "global health", "neglected tropical diseases", "loiasis", "onchocerciasis", "parasitic diseases", "malaria", "lymphatic filariasis", "vector...	Lymphatic Filariasis in Nigeria; Micro-stratification Overlap Mapping (MOM) as a Prerequisite for Cost-Effective Resource Utilization in Control and Surveillance	journal.pntd.0002416	null	[ [ "Lymphatic filariasis ( LF ) is one of the most debilitating neglected tropical diseases ( NTD ) in the world [1] .", "It is caused by the parasitic worms Wuchereria bancrofti , Brugia malayi and B . timori and is transmitted by Anopheles , Culex , Aedes , Ochlerotatus and Mansoni mosquitoes [1] .", "...	[ "Nigeria has a significant burden of lymphatic filariasis ( LF ) caused by the parasite Wuchereria bancrofti .", "A major concern to the expansion of the LF elimination programme is the risk of serious adverse events ( SAEs ) associated with the use of ivermectin in areas co-endemic with Loa filariasis .", "To ...	[ "Nigeria is estimated to have the highest burden of lymphatic filariasis ( LF ) , a disease also known as elephantiasis , which is transmitted by mosquitoes and caused by the parasite Wuchereria bancrofti .", "The National LF Elimination Programme is planning to scale up the elimination programme through mass dru...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases", "immunology/immunomodulation", "immunology/immune response", "public health and epidemiology/global health", "public health and epidemiology/infectious diseases", "immunology", "infectious diseases/protozoal infections", "infectious diseases/tropical and travel-associated diseas...	The Plasmodium falciparum-Specific Human Memory B Cell Compartment Expands Gradually with Repeated Malaria Infections	journal.ppat.1000912	null	[ [ "To date , most successful vaccines have targeted pathogens that induce long-lived protective antibodies after a single infection , such as the viruses that cause smallpox , measles and yellow fever [1] .", "It has proved more difficult to develop highly effective vaccines against pathogens that do not in...	[ "Immunity to Plasmodium falciparum ( Pf ) malaria is only acquired after years of repeated infections and wanes rapidly without ongoing parasite exposure .", "Antibodies are central to malaria immunity , yet little is known about the B-cell biology that underlies the inefficient acquisition of Pf-specific humoral...	[ "Plasmodium falciparum ( Pf ) is a mosquito-borne parasite that causes over 500 million cases of malaria annually , one million of which result in death , primarily among African children .", "The development of an effective malaria vaccine would be a critical step toward the control and eventual elimination of t...	2010
[ "Introduction", "Methods and Materials", "Discussion" ]	[ "physics/interdisciplinary physics", "neuroscience/theoretical neuroscience", "computational biology/computational neuroscience" ]	Broadband Criticality of Human Brain Network Synchronization	journal.pcbi.1000314	null	[ [ "Critical dynamics are recognized as typical of many different physical systems including piles of rice or sand , earthquakes and mountain avalanches .", "Dynamic systems in a critical state will generally demonstrate scale-invariant organization in space and/or time , meaning that there will be similar f...	[ "Self-organized criticality is an attractive model for human brain dynamics , but there has been little direct evidence for its existence in large-scale systems measured by neuroimaging .", "In general , critical systems are associated with fractal or power law scaling , long-range correlations in space and time ...	[ "Systems in a critical state are poised on the cusp of a transition between ordered and random behavior .", "At this point , they demonstrate complex patterning of fluctuations at all scales of space and time .", "Criticality is an attractive model for brain dynamics because it optimizes information transfer , ...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	A trans-acting Variant within the Transcription Factor RIM101 Interacts with Genetic Background to Determine its Regulatory Capacity	journal.pgen.1005746	null	[ [ "Incorporating genomic information into clinical practice is a major focus of personalized medicine .", "Despite the discovery of a large number of disease-associated genetic variants [1 , 2] , few clinical treatments have been developed that take into account such information [3] .", "Furthermore , m...	[ "Most genetic variants associated with disease occur within regulatory regions of the genome , underscoring the importance of defining the mechanisms underlying differences in regulation of gene expression between individuals .", "We discovered a pair of co-regulated , divergently oriented transcripts , AQY2 and ...	[ "Large-scale genome profiling studies have revealed that disease-associated variants occur most frequently within regulatory regions of DNA .", "In order to connect variants ( genotypes ) to expression profiles ( phenotypes ) , it is necessary to have a thorough understanding of the mechanisms underlying transcri...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "model organisms", "genetics", "biology", "molecular cell biology", "genetics and genomics" ]	The Major Roles of DNA Polymerases Epsilon and Delta at the Eukaryotic Replication Fork Are Evolutionarily Conserved	journal.pgen.1002407	null	[ [ "Three DNA polymerases , Polα , Polδ , and Polε , are required for efficient genome replication in eukaryotes [1] , [2] .", "The Polα holoenzyme complex has both primase activity and DNA polymerase activity and is required to initiate each DNA synthesis reaction .", "The primase subunit first synthesi...	[ "Coordinated replication of eukaryotic genomes is intrinsically asymmetric , with continuous leading strand synthesis preceding discontinuous lagging strand synthesis .", "Here we provide two types of evidence indicating that , in fission yeast , these two biosynthetic tasks are performed by two different replica...	[ "It is important to understand the architecture of the DNA replication machinery and whether this is common to all organisms .", "Recent work in Saccharomyces cerevisiae has genetically assigned specific DNA polymerases to leading and lagging strand DNA synthesis , Polε and Polε respectively .", "In this manusc...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience/cognitive neuroscience", "neurological disorders/cognitive neurology and dementia", "neurological disorders/neuroimaging", "computational biology/computational neuroscience", "neurological disorders/neuropsychiatric disorders", "neuroscience/psychology", "neuroscience", "neuroscience/the...	The Organization of Local and Distant Functional Connectivity in the Human Brain	journal.pcbi.1000808	null	[ [ "The human brain is a complex biological structure with specializations for local , modular processing that are distinct from anatomical properties that facilitate integrative processing .", "Specifically , anatomic projection patterns suggest a division between areas that form domain-specific hierarchica...	[ "Information processing in the human brain arises from both interactions between adjacent areas and from distant projections that form distributed brain systems .", "Here we map interactions across different spatial scales by estimating the degree of intrinsic functional connectivity for the local ( ≤14 mm ) neig...	[ "Information processing in the human brain arises from both interactions between adjacent brain areas and from distant projections that form distributed systems .", "Here we estimated functional connectivity profiles in the human brain using a novel approach to map the regional balance between local and distant f...	2010
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "plant anatomy", "plant growth and development", "plant embryo anatomy", "ovules", "brassica", "endosperm", "developmental biology", "plant science", "model organisms", "experimental organism systems", "mitochondria", "bioenergetics", "embryos", "plants", "cellular structures and organel...	A Novel Imprinted Gene NUWA Controls Mitochondrial Function in Early Seed Development in Arabidopsis	journal.pgen.1006553	null	[ [ "Genomic imprinting is a phenomenon in which somatic cells express some genes only from the maternal or paternal chromosome [1] .", "Genes with parent-of-origin-specific allele-biased expression patterns are called imprinted genes [2 , 3] .", "Imprinted genes have only been discovered and confirmed in...	[ "Imprinted genes display biased expression of paternal and maternal alleles and are only found in mammals and flowering plants .", "Compared to several hundred imprinted genes that are functionally characterized in mammals , very few imprinted genes were confirmed in plants and even fewer of them have been functi...	[ "Imprinted genes are only found in mammals and flowering plants , and they express with parent-of-origin-specific patterns .", "Unlike in mammals , only a few imprinted genes was identified and functionally characterized in plants , and almost all of them encode nuclear proteins .", "Here , we identified NUWA a...	2017
[ "Introduction", "Material and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "immunology", "brain", "developmental biology", "metabolites", "signs and symptoms", "cerebellum", "lipids", "inflammation", "lipid mediators", "cerebrum", "metabolic pathways", "life cycles", "immune response", "bioc...	Multiplex profiling of inflammation-related bioactive lipid mediators in Toxocara canis- and Toxocara cati-induced neurotoxocarosis	journal.pntd.0007706	null	[ [ "Toxocara canis ( Werner , 1782 ) and T . cati ( Schrank , 1788 ) are globally distributed , intestinal helminth parasites with canids and felids as definitive hosts [1] .", "Humans and a wide range of other species can act as paratenic hosts after accidental ingestion of infective stages ( L3 ) of Toxoca...	[ "Somatic migration of Toxocara canis- and T . cati-larvae in humans may cause neurotoxocarosis ( NT ) when larvae accumulate and persist in the central nervous system ( CNS ) .", "Host- or parasite-induced immunoregulatory processes contribute to the pathogenesis; however , detailed data on involvement of bioacti...	[ "Neurotoxocarosis ( NT ) is induced by larvae of the zoonotic roundworms Toxocara canis and T . cati migrating and persisting in the central nervous system of paratenic hosts , and may be accompanied by severe neurological symptoms .", "Toxocara spp .", "are known to modulate the hosts’ immune response , but da...	2019
[ "Introduction", "Materials and methods", "Results", "Discussion", "Conclusion" ]	[ "body weight", "medicine and health sciences", "tropical diseases", "database searching", "pediatrics", "physiological parameters", "nutrition", "mathematics", "statistics (mathematics)", "obesity", "neglected tropical diseases", "pediatric infections", "research and analysis methods", "in...	The association between obesity and dengue severity among pediatric patients: A systematic review and meta-analysis	journal.pntd.0006263	null	[ [ "Dengue is an acute systemic viral infection caused by the dengue virus .", "Currently , there are four known dengue virus subtypes ( DEN-1 , DEN-2 , DEN-3 , DEN-4 ) with Aedes aegypti and Aedes albopictus as the principal vectors .", "The burdens of dengue infection were concentrated in the tropical ...	[ "Severe dengue infection often has unpredictable clinical progressions and outcomes .", "Obesity may play a role in the deterioration of dengue infection due to stronger body immune responses .", "Several studies found that obese dengue patients have a more severe presentation with a poorer prognosis .", "How...	[ "Dengue fever , an Aedes mosquito-borne viral infection , is a self-limiting or asymptomatic viral infection .", "In its severe form , severe dengue , the symptoms include organ failure , life-threatening bleeding , and shock .", "Patients with obesity were found to be at higher risks of developing complication...	2018

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