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headings list	keywords list	title stringlengths 20 281	id stringlengths 20 20	toc stringlengths 57 522 ⌀	sections list	abstract list	summary list	year stringclasses 13 values
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "cystic echinococcosis", "invertebrates", "medicine and health sciences", "helminths", "tropical diseases", "fibrosis", "parasitic diseases", "animals", "echinococcus", "developmental biology", "pharmaceutics", "microscopy", "neglected tropical diseases", "sequence motif analysis", "rese...	Metformin exhibits preventive and therapeutic efficacy against experimental cystic echinococcosis	journal.pntd.0005370	null	[ [ "Cystic echinococcosis ( CE ) , also called hydatid disease or hydatidosis , is a neglected zoonotic disease caused by the infection with the larval stage of the cestode Echinococcus granulosus [1] .", "The greatest prevalence of this disease is found in countries of the temperate zones , and it is an end...	[ "Metformin ( Met ) is an anti-hyperglycemic and potential anti-cancer agent which may exert its anti-proliferative effects via the induction of energetic stress .", "In this study we investigated the in vitro and in vivo efficacy of Met against the larval stage of Echinococcus granulosus .", "Metformin showed s...	[ "Cystic echinococcosis is a worldwide zoonosis of public health concern and economic significance caused by infection with the larval stage of the cestode Echinococcus granulosus .", "Chemotherapy treatment for this disease has had limited effectiveness thus far , which is why it is a dire need to find new drugs ...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "learning", "medicine and health sciences", "decision making", "neural networks", "prefrontal cortex", "brain", "social sciences", "vertebrates", "neuroscience", "learning and memory", "animals", "mammals", "primates", "cognitive psychology", "animal behavior", "cognition", "memory",...	Reservoir Computing Properties of Neural Dynamics in Prefrontal Cortex	journal.pcbi.1004967	null	[ [ "One of the properties that sets primates apart in the animal kingdom is their extraordinary adaptation skills which are supported by efficient context-dependent learning mechanisms .", "The ability to reliably encode unanticipated behavioral contexts appears to be crucial to such adaptive capabilities ."...	[ "Primates display a remarkable ability to adapt to novel situations .", "Determining what is most pertinent in these situations is not always possible based only on the current sensory inputs , and often also depends on recent inputs and behavioral outputs that contribute to internal states .", "Thus , one can ...	[ "One of the most noteworthy properties of primate behavior is its diversity and adaptability .", "Human and non-human primates can learn an astonishing variety of novel behaviors that could not have been directly anticipated by evolution .", "How then can the nervous system be prewired to anticipate the ability...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "rheumatology", "medicine and health sciences", "enzyme-linked immunoassays", "toxoplasma gondii", "immunology", "parasitic diseases", "parasitic protozoans", "rheumatoid arthritis", "clinical medicine", "protozoans", "mathematics", "toxoplasma", "statistics (mathematics)", "immunologic te...	Toxoplasmosis seroprevalence in rheumatoid arthritis patients: A systematic review and meta-analysis	journal.pntd.0006545	null	[ [ "Toxoplasmosis is a parasitic disease with worldwide distribution caused by obligate intracellular coccidian protozoan Toxoplasma gondii ( T . gondii ) [1] .", "It is estimated that one-third of the world’s population are infected with this parasite in both developed and developing countries [2 , 3] .", ...	[ "Toxoplasmosis is a cosmopolitan infection caused by an intracellular obligatory protozoan , Toxoplasma gondii .", "Infection to this parasite in immunocompetent patients is usually asymptomatic , but today it is believed that the infection can be a risk factor for a variety of diseases , including rheumatoid art...	[ "Toxoplasma gondii is an intracellular obligatory protozoan , which causes toxoplasmosis .", "T . gondii infection in immunocompetent individuals is mostly asymptomatic , but it may be reactivated as a result of immune disorders inducing serious complications .", "Rheumatoid arthritis ( RA ) , as a complex auto...	2018
[ "Introduction", "Results/Discussion", "Methods" ]	[ "physics", "biology", "biophysics" ]	Collective Dynamics Differentiates Functional Divergence in Protein Evolution	journal.pcbi.1002428	null	[ [ "Proteins are effective and efficient machines that carry out a wide range of essential biochemical functions in the cell .", "Beyond being robust and efficient , the outstanding property of proteins is that they can evolve and they show a remarkable capacity to acquire new functions and structures .", ...	[ "Protein evolution is most commonly studied by analyzing related protein sequences and generating ancestral sequences through Bayesian and Maximum Likelihood methods , and/or by resurrecting ancestral proteins in the lab and performing ligand binding studies to determine function .", "Structural and dynamic evolu...	[ "Proteins are remarkable machines of the living systems that show diverse biochemical functions .", "Biochemical diversity has grown over time via molecular evolution .", "In order to understand how diversity arose , it is fundamental to understand how the earliest proteins evolved and served as templates for t...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "animal genetics", "genetic disorders", "retrotransposons", "neurophysiology", "neurotransmission", "genetic elements", "genetics", "transposable elements", "biology and life sciences", "brain electrophysiology", "mobile genetic elements", "mammalian genetics", "genetics of disease", "neur...	Unraveling Genetic Modifiers in the Gria4 Mouse Model of Absence Epilepsy	journal.pgen.1004454	null	[ [ "Laboratory mouse strains are well known to vary in their susceptibility to convulsive seizures , including acute experimentally induced seizures [1] , [2] , [3] , [4] , [5] , [6] , and spontaneous seizures induced by genetic mutation [7] , [8] , [9] , [10] , [11] , [12] , [13] .", "Most of the known stra...	[ "Absence epilepsy ( AE ) is a common type of genetic generalized epilepsy ( GGE ) , particularly in children .", "AE and GGE are complex genetic diseases with few causal variants identified to date .", "Gria4 deficient mice provide a model of AE , one for which the common laboratory inbred strain C3H/HeJ ( HeJ ...	[ "Absence seizures - also known as “petit-mal” - define a common form of epilepsy most prevalent in children , but also seen at other ages , and in related diseases such as juvenile myoclonic epilepsy .", "Absence seizures cause brief periods of unconsciousness , and are accompanied by characteristic abnormal brai...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunology/genetics of the immune system", "immunology/leukocyte signaling and gene expression", "immunology/innate immunity" ]	Genetic Control of Variegated KIR Gene Expression: Polymorphisms of the Bi-Directional KIR3DL1 Promoter Are Associated with Distinct Frequencies of Gene Expression	journal.pgen.1000254	null	[ [ "Natural killer ( NK ) cells play an important role in the detection and elimination of tumors and virus-infected cells by the innate immune system [1] .", "NK cells can identify stressed cells via cell surface receptors for class I MHC that sense alterations of these molecules on potential target cells [...	[ "Natural killer ( NK ) cells play an important role in the detection and elimination of tumors and virus-infected cells by the innate immune system .", "Human NK cells use cell surface receptors ( KIR ) for class I MHC to sense alterations of class I on potential target cells .", "Individual NK cells only expre...	[ "Natural killer ( NK ) cells represent a specialized blood cell that plays an important role in the detection of virus-infected or cancer cells .", "NK cells recognize and kill diseased cells using receptors for self antigens ( HLA ) that are frequently altered on aberrant cells .", "The HLA receptors are known...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology and life sciences", "plant science" ]	Expression Profiling during Arabidopsis/Downy Mildew Interaction Reveals a Highly-Expressed Effector That Attenuates Responses to Salicylic Acid	journal.ppat.1004443	null	[ [ "During co-evolution with pathogens , plants have evolved multiple immune signaling mechanisms that successful pathogens have evolved to evade or suppress .", "The first layer is based on recognition of broadly conserved pathogen molecules ( pathogen/microbe-associated molecular patterns , PAMP/MAMPs ) by...	[ "Plants have evolved strong innate immunity mechanisms , but successful pathogens evade or suppress plant immunity via effectors delivered into the plant cell .", "Hyaloperonospora arabidopsidis ( Hpa ) causes downy mildew on Arabidopsis thaliana , and a genome sequence is available for isolate Emoy2 .", "Here ...	[ "A comprehensive understanding of host-pathogen interactions requires knowledge of the dynamics of gene expression changes in both the host and the pathogen during a time course of infection .", "However , expression profiling has often focused on either the host or the pathogen due to limitations of methods that...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunology/innate immunity" ]	Tsetse EP Protein Protects the Fly Midgut from Trypanosome Establishment	journal.ppat.1000793	null	[ [ "African trypanosomes are protozoan parasites that cause sleeping sickness in humans and nagana in domestic livestock in sub-Saharan Africa .", "An epidemic involving several hundred thousand people that spread through Sudan , the Central African Republic , DRC and Angola in the 1990's , demonstrated how ...	[ "African trypanosomes undergo a complex developmental process in their tsetse fly vector before transmission back to a vertebrate host .", "Typically , 90% of fly infections fail , most during initial establishment of the parasite in the fly midgut .", "The specific mechanism ( s ) underpinning this failure are...	[ "In Africa , tsetse flies transmit the trypanosomes causing the devastating diseases sleeping sickness in man and nagana in domesticated animals .", "These diseases are major causes of underdevelopment in Africa .", "Paradoxically , most , but not all , flies are resistant to infection with trypanosomes , but w...	2010
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "horizontal gene transfer", "cloning", "gene transfer", "fungal evolution", "mycoplasma", "genome analysis", "molecular biology techniques", "bacteria", "research and analysis methods", "genome complexity", "mycology", "mollicutes", "comparative genomics", "molecular biology", "genetic l...	Mycoplasmas under experimental antimicrobial selection: The unpredicted contribution of horizontal chromosomal transfer	journal.pgen.1007910	null	[ [ "Over the past decade , advances in metagenomics have uncovered the fascinating richness and diversity of bacterial taxa .", "As free-living cells or as parasites , bacteria colonize an impressive array of ecosystems , from those offering ideal conditions to those too extreme to support most life forms ."...	[ "Horizontal Gene Transfer was long thought to be marginal in Mycoplasma a large group of wall-less bacteria often portrayed as minimal cells because of their reduced genomes ( ca . 0 . 5 to 2 . 0 Mb ) and their limited metabolic pathways .", "This view was recently challenged by the discovery of conjugative excha...	[ "Genome downsizing is often viewed as a degenerative process of evolution .", "Such erosion has left current mycoplasmas with a minimal genome: for some species its size barely exceeds the amount of information needed for sustaining autonomous life .", "Despite such limitations , these simple bacteria showcase ...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "crystallization techniques", "perimeters", "biological cultures", "radii", "geometry", "interface diffusion", "mathematics", "cellular structures and organelles", "thermodynamics", "research and analysis methods", "separation processes", "cho cells", "cell lines", "cell membranes", "fre...	Modeling the Excess Cell Surface Stored in a Complex Morphology of Bleb-Like Protrusions	journal.pcbi.1004841	null	[ [ "Cells maintain their structural integrity while being flexible enough to adopt a variety of shapes .", "In general , it is the cytoskeleton of eukaryotic cells that drives shape transformation leading to cell movement and provides the structural support to the cytoplasm and the means to resist external f...	[ "Cells transition from spread to rounded morphologies in diverse physiological contexts including mitosis and mesenchymal-to-amoeboid transitions .", "When these drastic shape changes occur rapidly , cell volume and surface area are approximately conserved .", "Consequently , the rounded cells are suddenly pres...	[ "Individual cells must have the capability for rapid morphological transformations under various physiological conditions .", "One of the most drastic shape transformations occurs during the transition from spread to rounded morphologies .", "When this transition occurs rapidly , there is insufficient time for ...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "toxoplasma gondii", "microbiology", "host-pathogen interaction", "plasmodium falciparum", "parasitic diseases", "parasitology", "parastic protozoans", "infectious diseases", "microbial pathogens", "biology", "protozoan infections", "pathogenesis", "toxoplasmosis", "protozool...	The Moving Junction Protein RON8 Facilitates Firm Attachment and Host Cell Invasion in Toxoplasma gondii	journal.ppat.1002007	null	[ [ "Host cell invasion by apicomplexan parasites is a highly specialized feature of this phylum that is crucial to their survival in humans ( Toxoplasma gondii , Plasmodium spp . , Cryptosporidium spp . ) and animals ( Neospora caninum , Eimeria spp . ) [1] , [2] .", "Following initial contact with a target ...	[ "The apicomplexan moving junction ( MJ ) is a highly conserved structure formed during host cell entry that anchors the invading parasite to the host cell and serves as a molecular sieve of host membrane proteins that protects the parasitophorous vacuole from host lysosomal destruction .", "While recent work in T...	[ "Apicomplexan parasites actively invade host cells to survive , with an important step being the formation of a tight interface between parasite and host cell membranes called the moving junction ( MJ ) .", "Passing over the length of the invading parasite , the MJ anchors the pathogen to enable propulsion into a...	2011
[ "Introduction", "Results", "Discussion" ]	[ "genetics and genomics/genomics", "genetics and genomics/gene discovery", "genetics and genomics/functional genomics", "genetics and genomics/genetics of disease", "genetics and genomics/gene function", "genetics and genomics", "genetics and genomics/medical genetics", "genetics and genomics/cancer ge...	Common Genetic Variants and Modification of Penetrance of BRCA2-Associated Breast Cancer	journal.pgen.1001183	null	[ [ "After more than a decade of clinical testing for mutations of BRCA1 and BRCA2 , there remains considerable uncertainty regarding cancer risks associated with inherited mutations of these genes .", "This variable penetrance is most striking for BRCA2 [1]–[4] , and it affects medical management [5] .", ...	[ "The considerable uncertainty regarding cancer risks associated with inherited mutations of BRCA2 is due to unknown factors .", "To investigate whether common genetic variants modify penetrance for BRCA2 mutation carriers , we undertook a two-staged genome-wide association study in BRCA2 mutation carriers .", "...	[ "The risk of breast cancer associated with BRCA2 mutations varies widely .", "To determine whether common genetic variants modify the penetrance of BRCA2 mutations , we conducted the first genome-wide association study of breast cancer among women with BRCA2 mutations using a two-stage approach .", "The major f...	2010
[ "I. Introduction and Project Overview", "II. ENCODE Project Data", "III. Accessing ENCODE Data", "IV. Working with ENCODE Data", "V. ENCODE Data Analysis", "VI. Future Plans and Challenges" ]	[ "genomics", "genetics", "biology", "computational biology", "genetics and genomics" ]	A User's Guide to the Encyclopedia of DNA Elements (ENCODE)	journal.pbio.1001046	null	[ [ "Interpreting the human genome sequence is one of the leading challenges of 21st century biology [1] .", "In 2003 , the National Human Genome Research Institute ( NHGRI ) embarked on an ambitious project—the Encyclopedia of DNA Elements ( ENCODE ) —aiming to delineate all of the functional elements encode...	[ "The mission of the Encyclopedia of DNA Elements ( ENCODE ) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health .", "The ENCODE Consortium is integrating multiple technologies and approaches in a collective ...	[ "The Encyclopedia of DNA Elements ( ENCODE ) Project was created to enable the scientific and medical communities to interpret the human genome sequence and to use it to understand human biology and improve health .", "The ENCODE Consortium , a large group of scientists from around the world , uses a variety of e...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "togaviruses", "chikungunya infection", "pathogens", "animal models of disease", "immunology", "tropical diseases", "microbiology", "alphaviruses", "animal models", "viruses", "model organ...	The NLRP3 inflammasome is involved with the pathogenesis of Mayaro virus	journal.ppat.1007934	null	[ [ "Arboviruses are one of the public health authorities major concerns , contributing to an increasing awareness of emerging infections worldwide .", "After the spread of chikungunya virus ( CHIKV ) to new areas of the globe and the emergence of Zika virus ( ZIKV ) , surveillance systems worldwide are focus...	[ "Mayaro virus ( MAYV ) is an arbovirus that circulates in Latin America and is emerging as a potential threat to public health .", "Infected individuals develop Mayaro fever , a severe inflammatory disease characterized by high fever , rash , arthralgia , myalgia and headache .", "The disease is often associate...	[ "Viruses transmitted by mosquitoes have recently received huge attention from the media because the epidemics caused by Zika and chikungunya virus rapidly spread to new areas and infected a large number of individuals .", "Mayaro is a virus transmitted by mosquitoes that circulates in the Caribbean and tropical r...	2019
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "urology", "medicine and health sciences", "vesicles", "immune physiology", "cell cycle and cell division", "cell processes", "immunology", "microbiology", "mitosis", "viral genome", "sexually transmitted diseases", "cell enumeration techniques", "cell nucleus", "nuclear bodies", "antibo...	PML nuclear body-residing proteins sequentially associate with HPV genome after infectious nuclear delivery	journal.ppat.1007590	null	[ [ "Promyelocytic leukemia ( PML ) nuclear bodies ( NBs ) are highly dynamic nuclear structures that have been associated with numerous cellular processes , including apoptosis , transcriptional regulation , and innate and intrinsic immune responses [1] .", "While their size and number of residing proteins v...	[ "Subnuclear promyelocytic leukemia ( PML ) nuclear bodies ( NBs ) are targeted by many DNA viruses after nuclear delivery .", "PML protein is essential for formation of PML NBs .", "Sp100 and Small Ubiquitin-Like Modifier ( SUMO ) are also permanently residing within PML NBs .", "Often , large DNA viruses dis...	[ "Promyelocytic leukemia ( PML ) nuclear bodies ( NBs ) are often targeted and reorganized by DNA viruses to counteract their antiviral activity .", "Human papillomavirus ( HPV ) also associates with PML NBs after infectious entry .", "While PML protein is required for nuclear retention and efficient transcripti...	2019
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "flow cytometry", "innate immune system", "antigen presentation", "medicine and health sciences", "293t cells", "immunology", "biological cultures", "membrane proteins", "immunoprecipitation", "genome analysis", "cellular structures and organelles", "research and analysis methods", "genomics...	Molluscum contagiosum virus MC80 sabotages MHC-I antigen presentation by targeting tapasin for ER-associated degradation	journal.ppat.1007711	null	[ [ "Molluscum contagiosum virus ( MCV ) is a phylogenetically distinct poxvirus with a significant global disease burden [1 , 2] .", "MCV infections are thought to be restricted to humans , producing cutaneous lesions which often lack signs of an inflammatory response and persist for months to years in other...	[ "The human specific poxvirus molluscum contagiosum virus ( MCV ) produces skin lesions that can persist with minimal inflammation , suggesting that the virus has developed robust immune evasion strategies .", "However , investigations into the underlying mechanisms of MCV pathogenesis have been hindered by the la...	[ "The presentation of antigenic peptides by classical MHC-I to cytotoxic T-cells is a cornerstone of antiviral immunity .", "As such , viruses have devised a plethora of strategies to target MHC-I or cellular components involved in MHC-I antigen presentation in order to block effective T-cell surveillance .", "M...	2019
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "blood cells", "viral vaccines", "medicine and health sciences", "immune cells", "immune physiology", "pathology and laboratory medicine", "pathogens", "immunology", "cell-mediated immunity", "microbiology", "viruses", "preventive medicine", "vaccines", "rna viruses", "cytotoxic t cells"...	Replication-incompetent rabies virus vector harboring glycoprotein gene of lymphocytic choriomeningitis virus (LCMV) protects mice from LCMV challenge	journal.pntd.0006398	null	[ [ "Arenaviruses ( Genus Arenavirus , Family Arenaviridae ) are enveloped , ambisense RNA viruses containing small ( S ) and large ( L ) RNA segments [1] .", "The S-segment encodes a nucleoprotein ( NP ) and a glycoprotein precursor ( GPC ) .", "The L-segment encodes an RNA-dependent RNA polymerase and a...	[ "Lymphocytic choriomeningitis virus ( LCMV ) causes a variety of diseases , including asymptomatic infections , meningitis , and congenital infections in the fetus of infected mother .", "The development of a safe and effective vaccine against LCMV is imperative .", "This study aims to develop a new candidate v...	[ "Lymphocytic choriomeningitis virus ( LCMV ) causes infections that are often asymptomatic but can be fatal in immunocompromized persons .", "In addition , LCMV infection during pregnancy can cause spontaneous abortion or severe birth defects .", "Humans are exposed to LCMV by direct or indirect contact with wi...	2018
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "blood cells", "medicine and health sciences", "immune cells", "immune physiology", "immunology", "tropical diseases", "parasitic diseases", "bacterial diseases", "memory b cells", "antibodies", "bacteria", "immune system proteins", "infectious diseases", "white blood cells", "animal cel...	Modulation of Mycobacterium tuberculosis-specific humoral immune responses is associated with Strongyloides stercoralis co-infection	journal.pntd.0005569	null	[ [ "Helminth infections are powerful modulators of the immune response and typically elicit both Type 2 and regulatory cytokine responses [1 , 2] .", "Helminths can influence the host immune response to co-existent infections because of their propensity to establish longstanding , persistent infections that ...	[ "Helminth infections are known to influence T cell responses in latent tuberculosis ( LTBI ) .", "Whether helminth infections also modulate B cell responses in helminth-tuberculosis co-infection is not known .", "We assessed Mycobacterium tuberculosis ( Mtb ) –antigen specific IgM and IgG levels , circulating l...	[ "Helminth infections and tuberculosis are two of the major health care problems worldwide and share a great deal of geographical overlap .", "Moreover , helminth infections are known to induce immune responses that are antagonistic to the protective immune responses elicited by Mycobacterium tuberculosis .", "H...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "public health and epidemiology/epidemiology", "diabetes and endocrinology/obesity", "genetics and genomics/complex traits", "genetics and genomics/population genetics" ]	Admixture Mapping of 15,280 African Americans Identifies Obesity Susceptibility Loci on Chromosomes 5 and X	journal.pgen.1000490	null	[ [ "Obesity is a highly prevalent condition that increases the risk of many illnesses such as cardiovascular disease , diabetes , and some cancers .", "Familial aggregation studies have shown that both genetic and environmental factors are involved in the development of common forms of obesity , and heritabi...	[ "The prevalence of obesity ( body mass index ( BMI ) ≥30 kg/m2 ) is higher in African Americans than in European Americans , even after adjustment for socioeconomic factors , suggesting that genetic factors may explain some of the difference .", "To identify genetic loci influencing BMI , we carried out a pooled ...	[ "Obesity is about 1 . 5-fold more prevalent in African Americans than European Americans .", "To determine whether genetic background may contribute to this observed disparity , we scanned the genomes of African Americans , searching for genomic regions where obese individuals have a difference from the average p...	2009
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "split-decomposition method", "pathogens", "microbiology", "viruses", "multiple alignment calculation", "genomic databases", "rna viruses", "viral genome", "dna viruses", "genome analysis", "herpesviruses", "microbial gen...	G-quadruplex forming sequences in the genome of all known human viruses: A comprehensive guide	journal.pcbi.1006675	null	[ [ "G-quadruplexes ( G4s ) are nucleic-acid secondary structures that may form in single-stranded DNA and RNA G-rich sequences under physiological conditions [1] .", "Four Gs bind via Hoogsteen-type base-pairing to yield G-quartets: stacking of at least two G-quartets leads to G4 formation , through π-π inte...	[ "G-quadruplexes are non-canonical nucleic-acid structures that control transcription , replication , and recombination in organisms .", "G-quadruplexes are present in eukaryotes , prokaryotes , and viruses .", "In the latter , mounting evidence indicates their key biological activity .", "Since data on viruse...	[ "G-quadruplexes are nucleic acid non-canonical structures that have been implicated in the regulation of different biological processes of many organisms .", "Their presence has been demonstrated also in several viral pathogens , providing new insights into viruses’ biology and potentially serving as drug targets...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biotechnology", "physics", "developmental biology", "infectious diseases", "cell biology", "microbiology", "computational biology", "biophysics" ]	Self-Organization in High-Density Bacterial Colonies: Efficient Crowd Control	journal.pbio.0050302	In nature, bacteria often found themselves in high-density colonies. The combination of a novel microfluidic device and computational analysis reveals an unexpected self-organization behavior of tightly packed bacterial cells.	[ [ "The past few decades witnessed an emergence of the realization that bacterial cells in their natural environments are not asocial , but can exist as colonies with complex organization and exhibit sophisticated and highly regulated collective behaviors [1–5] .", "Consequently , significant efforts have be...	[ "Colonies of bacterial cells can display complex collective dynamics , frequently culminating in the formation of biofilms and other ordered super-structures .", "Recent studies suggest that to cope with local environmental challenges , bacterial cells can actively seek out small chambers or cavities and assemble...	[ "Bacterial cells form colonies with complex organization ( aka biofilms ) , particularly in response to hostile environmental conditions .", "Recent studies have shown that biofilm development occurs when bacterial cells seek out small cavities and populate them at high densities .", "However , bacteria in cavi...	2007
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Prognostic Analysis of Patients with Ebola Virus Disease	journal.pntd.0004113	null	[ [ "In the year of 2014 , Ebola virus disease ( EVD ) was quickly widespread and caused the whole world to pay attention [1 , 2] .", "By the end of 2014 , more than eleven thousand cases were reported from West African countries such as Guinea , Sierra Leone , Liberia , Senegal , Nigeria , and Mali [1 , 2] ....	[ "The Ebola virus causes an acute , serious illness which is often fatal if untreated .", "However , factors affecting the survival of the disease remain unclear .", "Here , we investigated the prognostic factors of Ebola virus disease ( EVD ) through various statistical models .", "Sixty three laboratory-conf...	[ "The current outbreak of Ebola virus disease ( EVD ) in West Africa is the largest and most complex Ebola outbreak since the virus was first discovered in 1976 .", "Factors affecting the survival of the disease remain unclear .", "Here , we investigated the prognostic factors of EBV from 63 cases with relativel...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "circuit models", "cognitive neuroscience", "cognition", "computational neuroscience", "decision making", "neural networks", "biology", "computational biology", "neuroscience", "learning and memory" ]	Spatial Learning and Action Planning in a Prefrontal Cortical Network Model	journal.pcbi.1002045	null	[ [ "Spatial cognition requires long-term neural representations of the spatiotemporal", "properties of the environment [1] .", "These representations are encoded in terms of multimodal", "descriptions of the animal-environment interaction during active exploration .", "Exploiting these contextual...	[ "The interplay between hippocampus and prefrontal cortex ( PFC ) is fundamental to", "spatial cognition .", "Complementing hippocampal place coding , prefrontal", "representations provide more abstract and hierarchically organized memories", "suitable for decision making .", "We model a prefrontal network...	[ "We study spatial cognition , a high-level brain function based upon the ability to", "elaborate mental representations of the environment supporting goal-oriented", "navigation .", "Spatial cognition involves parallel information processing across a", "distributed network of interrelated brain regions .", ...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "antimicrobials", "cell physiology", "medicine and health sciences", "toxins", "protein interactions", "pathology and laboratory medicine", "cell cycle and cell division", "pathogens", "cell processes", "bacillus", "microbiology", "drugs", "plasmid construction", "toxic agents", "toxicol...	CbtA toxin of Escherichia coli inhibits cell division and cell elongation via direct and independent interactions with FtsZ and MreB	journal.pgen.1007007	null	[ [ "In E . coli , as in most other bacteria , cell shape is defined by the peptidoglycan sacculus [1] , which is built by the coordinated efforts of two major protein complexes , the cell elongation complex and the cell division complex ( reviewed in [2–4] ) .", "The cell elongation complex directs the inser...	[ "The toxin components of toxin-antitoxin modules , found in bacterial plasmids , phages , and chromosomes , typically target a single macromolecule to interfere with an essential cellular process .", "An apparent exception is the chromosomally encoded toxin component of the E . coli CbtA/CbeA toxin-antitoxin modu...	[ "Bacterially encoded toxin-antitoxin systems , which consist of a small toxin protein that is co-produced with a neutralizing antitoxin , are a potential avenue for the identification of novel antibiotic targets .", "These toxins typically target essential cellular processes , causing growth arrest or cell death ...	2017
[ "Introduction", "Methods", "Results", "Discussion", "Lessons Learned" ]	[]	Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models	journal.pcbi.1004096	null	[ [ "Mechanistic modeling is a powerful tool for understanding and engineering biological behavior at the molecular level .", "Davidson et al . have used Boolean modeling to understand Drosophila developmental patterning [1]; Orth et al . have used flux-balance analysis ( FBA ) to predict Escherichia coli met...	[ "Whole-cell models that explicitly represent all cellular components at the molecular level have the potential to predict phenotype from genotype .", "However , even for simple bacteria , whole-cell models will contain thousands of parameters , many of which are poorly characterized or unknown .", "New algorith...	[ "Whole-cell models promise to enable rational bioengineering by predicting how cells behave .", "Even for simple bacteria , whole-cell models require thousands of parameters , many of which are poorly characterized or unknown .", "New approaches are needed to estimate these parameters .", "We organized the Di...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "white blood cells", "immune cells", "mucosal immunity", "cell biology", "animal cells", "clinical immunology", "hiv immunopathogenesis", "immunity", "immune activation", "t cells", "biology and life sciences", "cellular types", "immunology", "cell-mediated immunity" ]	Initiation of ART during Early Acute HIV Infection Preserves Mucosal Th17 Function and Reverses HIV-Related Immune Activation	journal.ppat.1004543	null	[ [ "Eradication of HIV infection has not been achieved except under unique circumstances [1] , [2] .", "Given the limitations of antiretroviral therapy ( ART ) and recent advances in our understanding of HIV persistence with current treatment regimens , there is a growing recognition that a functional cure f...	[ "Mucosal Th17 cells play an important role in maintaining gut epithelium integrity and thus prevent microbial translocation .", "Chronic HIV infection is characterized by mucosal Th17 cell depletion , microbial translocation and subsequent immune-activation , which remain elevated despite antiretroviral therapy (...	[ "Persistent systemic immune activation is a hallmark of chronic HIV infection and an independent predictor of disease progression .", "The underlying mechanism is not yet completely understood but thought to be associated with the loss of Th17 cells leading to the disruption of the mucosal barrier and subsequent ...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "cell biology", "neurological disorders", "eukaryotes", "drosophila", "neuroscience", "animals", "genetics and genomics", "insects" ]	Genome-Wide Screen for Modifiers of Ataxin-3 Neurodegeneration in Drosophila	journal.pgen.0030177	null	[ [ "Spinocerebellar ataxia type 3 ( SCA3 ) is the most common dominantly inherited ataxia worldwide and is caused by a CAG repeat expansion encoding glutamine within the ATXN3 gene [1 , 2] .", "The expanded polyglutamine ( polyQ ) is thought to confer toxicity on the protein Ataxin-3 , leading to neural dysf...	[ "Spinocerebellar ataxia type-3 ( SCA3 ) is among the most common dominantly inherited ataxias , and is one of nine devastating human neurodegenerative diseases caused by the expansion of a CAG repeat encoding glutamine within the gene .", "The polyglutamine domain confers toxicity on the protein Ataxin-3 leading ...	[ "Spinocerebellar ataxia type-3 is the most common dominantly inherited movement disorder and is caused by a CAG repeat expansion within the gene ATXN3 , encoding the Ataxin-3 protein .", "This leads to a protein with an expanded polyglutamine domain , which confers a dominant toxicity on the protein , leading to ...	2007
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases", "medicine and health sciences", "chagas disease", "parasite evolution", "biology and life sciences", "microbiology", "protozoan infections", "parasitic diseases", "parasitology" ]	Optimized Multilocus Sequence Typing (MLST) Scheme for Trypanosoma cruzi	journal.pntd.0003117	null	[ [ "Trypanosoma cruzi , the protozoan causative agent of Chagas disease , is a monophyletic and genetically heterogeneous taxon , with at least six phylogenetic lineages formally recognised as Discrete Typing Units ( DTUs ) , TcI–TcVI [1] , or near-clades ( clades that are blurred by infrequent inter-lineage gen...	[ "Trypanosoma cruzi , the aetiological agent of Chagas disease possess extensive genetic diversity .", "This has led to the development of a plethora of molecular typing methods for the identification of both the known major genetic lineages and for more fine scale characterization of different multilocus genotype...	[ "The single-celled parasite Trypanosoma cruzi occurs in mammals and insect vectors in the Americas .", "When transmitted to humans it causes Chagas disease ( American trypanosomiasis ) a major public health problem .", "T . cruzi is genetically diverse and currently split into six groups , known as TcI to TcVI ...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Effect of Antenatal Parasitic Infections on Anti-vaccine IgG Levels in Children: A Prospective Birth Cohort Study in Kenya	journal.pntd.0003466	null	[ [ "Vaccine-preventable diseases ( VPD ) continue to kill an estimated one to two million children each year , comprising about 14% of global mortality in children under 5 years of age [1 , 2] .", "Vaccination studies have repeatedly shown that children in developing nations are less responsive to vaccines t...	[ "Parasitic infections are prevalent among pregnant women in sub-Saharan Africa .", "We investigated whether prenatal exposure to malaria and/or helminths affects the pattern of infant immune responses to standard vaccinations against Haemophilus influenzae ( Hib ) , diphtheria ( DT ) , hepatitis B ( Hep B ) and t...	[ "Parasitic infections are prevalent among pregnant women in sub-Saharan Africa .", "Prenatal exposure to parasitic infections can generate several potential effects on fetal immune responses and affect functional antibody generation during subsequent vaccination .", "There is a paucity of data on the detrimenta...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics", "biology", "molecular cell biology", "genetics and genomics" ]	Phosphorylation of Chromosome Core Components May Serve as Axis Marks for the Status of Chromosomal Events during Mammalian Meiosis	journal.pgen.1002485	null	[ [ "Meiosis is a special type of cell division that gives rise to haploid gametes required for sexual reproduction .", "To halve the chromosome number , two successive chromosome segregation events follow a single round of DNA replication .", "At the first stage of meiosis , the leptotene stage of propha...	[ "Meiotic recombination and chromosome synapsis between homologous chromosomes are essential for proper chromosome segregation at the first meiotic division .", "While recombination and synapsis , as well as checkpoints that monitor these two events , take place in the context of a prophase I-specific axial chromo...	[ "Meiosis is a specialized cell division to generate haploid sperm and eggs .", "For accurate segregation of homologous chromosomes during the first meiotic division , chromosome synapsis and recombination should be properly established between them during the prophase I stage .", "Chromosome synapsis and recomb...	2012
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "invertebrates", "rna interference", "helminths", "gene regulation", "enzymes", "messenger rna", "enzymology", "dismutases", "animals", "organisms", "trematodes", "epigenetics", "molecular biology techniques", "research and analysis methods", "small interfering rnas", "specimen prepara...	RNA interference in Fasciola gigantica: Establishing and optimization of experimental RNAi in the newly excysted juveniles of the fluke	journal.pntd.0006109	null	[ [ "Fasciola gigantica ( tropical liver fluke ) and F . hepatica ( temperate liver fluke ) are the two causative agents of fasciolosis in livestock and are economically important veterinary parasites due to the substantial production and monetary losses that these parasites cause to the livestock industry .", ...	[ "Fasciolosis caused by Fasciola gigantica is a neglected tropical disease but a constraint on the growth and productivity of cattle , buffaloes and sheep in the tropical countries of Asia and Africa .", "Resistance to commonly used anthelmintics in Fasciola has increased the need to search for alternative therape...	[ "RNA interference ( RNAi ) is a powerful method for selectively silencing genes for the validation of potential targets for drug and vaccine development .", "The susceptibility of juvenile Fasciola hepatica to double stranded ( ds ) RNA induced RNAi has been established but in F . gigantica a single report of a p...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "oncology", "homo (human)", "genetics and genomics", "computational biology" ]	Elucidating the Altered Transcriptional Programs in Breast Cancer using Independent Component Analysis	journal.pcbi.0030161	null	[ [ "Microarray technology is enabling genetic diseases like cancer to be studied in unprecedented detail , at both transcriptomic and genomic levels .", "A significant challenge that needs to be overcome to further our understanding of the relation between the quantitative transcriptome of a sample/cell and ...	[ "The quantity of mRNA transcripts in a cell is determined by a complex interplay of cooperative and counteracting biological processes .", "Independent Component Analysis ( ICA ) is one of a few number of unsupervised algorithms that have been applied to microarray gene expression data in an attempt to understand...	[ "The amount of a given transcript or protein in a cell is determined by a balance of expression and repression in a complex network of biological processes .", "This delicate balance is compromised in complex genetic diseases such as cancer by alterations in the activation patterns of functionally important biolo...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "molecular cell biology", "mathematics", "statistics", "genetics", "immunology", "biology", "genomics", "microbiology", "population biology", "genetics and genomics" ]	Attenuated Salmonella Typhimurium Lacking the Pathogenicity Island-2 Type 3 Secretion System Grow to High Bacterial Numbers inside Phagocytes in Mice	journal.ppat.1003070	null	[ [ "Infection of a host by a bacterium is a dynamic process that can be measured and analyzed at different scales .", "Many experimental systems for understanding infection measure the overall increase or decrease in numbers of bacteria in different organs in the host over time .", "Often , fine-structur...	[ "Intracellular replication within specialized vacuoles and cell-to-cell spread in the tissue are essential for the virulence of Salmonella enterica .", "By observing infection dynamics at the single-cell level in vivo , we have discovered that the Salmonella pathogenicity island 2 ( SPI-2 ) type 3 secretory syste...	[ "High quality science has been published concerning the dynamics of infectious disease spread through communities of people or animals , but less work has been done to understand infectious disease dynamics within the host .", "Many conclusions about how infectious agents work are based on experiments in isolated...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "blood cells", "innate immune system", "medicine and health sciences", "immune cells", "immune physiology", "pathology and laboratory medicine", "cytokines", "spleen", "immunology", "bone marrow cells", "developmental biology", "signs and symptoms", "molecular development", "research and a...	Bacterial Manipulation of NK Cell Regulatory Activity Increases Susceptibility to Listeria monocytogenes Infection	journal.ppat.1005708	null	[ [ "Immune defense against diverse pathogens requires timely recruitment of monocytes to sites of infection and activation of their antimicrobial functions [1] .", "IFNγ promotes antimicrobial activation of myeloid cells and is required for innate resistance to numerous pathogenic bacteria , including Lm [2 ...	[ "Natural killer ( NK ) cells produce interferon ( IFN ) -γ and thus have been suggested to promote type I immunity during bacterial infections .", "Yet , Listeria monocytogenes ( Lm ) and some other pathogens encode proteins that cause increased NK cell activation .", "Here , we show that stimulation of NK cell...	[ "Natural killer ( NK ) cells are an innate immune cell population known to promote antiviral immunity through cytolysis and production of cytokines .", "Yet , some pathogens encode proteins that cause increased NK cell activation .", "Here , using a model of systemic infection by the bacterial pathogen Listeria...	2016
[ "Introduction", "Results", "Discussion", "Material and methods" ]	[ "ecology and environmental sciences", "medicine and health sciences", "pathology and laboratory medicine", "cell cycle and cell division", "pathogens", "cell processes", "dna-binding proteins", "microbiology", "aquatic hypoxia", "viruses", "dna replication", "dna viruses", "hypoxia", "dna"...	KSHV-encoded LANA protects the cellular replication machinery from hypoxia induced degradation	journal.ppat.1008025	null	[ [ "Kaposi Sarcoma associated herpesvirus ( KSHV ) or Human herpesvirus 8 ( HHV8 ) infects human endothelial cells and B-lymphocytes and is strongly associated with Kaposi sarcoma ( KS ) , Pleural Effusion Lymphoma ( PEL ) and Multicentric Castleman’s Disease ( MCD ) [1–4] .", "Like other herpesviruses , KSH...	[ "Kaposi’s sarcoma associated herpesvirus ( KSHV ) , like all herpesviruses maintains lifelong persistence with its host genome in latently infected cells with only a small fraction of cells showing signatures of productive lytic replication .", "Modulation of cellular signaling pathways by KSHV-encoded latent ant...	[ "Hypoxia induces cell cycle arrest and DNA replication to minimize energy and macromolecular demands on the ATP stores of cells in this microenvironment .", "A select set of proteins functions as transcriptional activators in hypoxia .", "However , transcriptional and translational pathways are negatively regul...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "immunology/cellular microbiology and pathogenesis", "immunology/immunomodulation", "infectious diseases/neglected tropical diseases", "infectious diseases/bacterial infections", "immunology/immunity to infections" ]	Role of Secreted Conjunctival Mucosal Cytokine and Chemokine Proteins in Different Stages of Trachomatous Disease	journal.pntd.0000264	null	[ [ "Trachoma , the leading global cause of preventable blindness , has plagued populations for thousands of years [1] .", "There are over 360 million trachoma cases of whom ∼6 million are blind [2] , [3] .", "Limited access to clean water and inadequate sanitary conditions provides ideal conditions for t...	[ "Chlamydia trachomatis is responsible for trachoma , the primary cause of preventable blindness worldwide .", "Plans to eradicate trachoma using the World Health Organization's SAFE program ( Surgery , Antibiotics , Facial Cleanliness and Environment Improvement ) have resulted in recurrence of infection and dise...	[ "Trachoma , a disease of antiquity dating back to the 16th century B . C . E . , predominates among developing countries , where it remains the primary cause of preventable blindness worldwide .", "In trachoma , recurrent Chlamydia trachomatis bacterial infections during childhood are thought to result in inflamm...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics of the immune system", "genetics", "molecular genetics", "population genetics", "biology", "human genetics", "immunology", "genetics of disease" ]	Trans-Ancestral Studies Fine Map the SLE-Susceptibility Locus TNFSF4	journal.pgen.1003554	null	[ [ "Tumour Necrosis Factor Superfamily ( TNFS ) members control wide-ranging facets of immunity when they interact with their complimentary TNF Receptors [1] .", "One of these , TNFSF4 ( OX40L ) , uniquely binds its receptor , monomeric TNFRSF4 ( OX40 ) , on T lymphocytes to strongly activate NF-κB [2] .", ...	[ "We previously established an 80 kb haplotype upstream of TNFSF4 as a susceptibility locus in the autoimmune disease SLE .", "SLE-associated alleles at this locus are associated with inflammatory disorders , including atherosclerosis and ischaemic stroke .", "In Europeans , the TNFSF4 causal variants have remai...	[ "Systemic lupus erythematosus ( SLE/lupus ) is a complex disease in which the body's immune cells cause inflammation in one or more systems to cause the associated morbidity .", "Hormones , the environment and genes are all causal contributors to SLE and over the past several years the genetic component of SLE ha...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "invertebrates", "animal types", "medicine and health sciences", "respiratory infections", "pathology and laboratory medicine", "pathogens", "domestic animals", "microbiology", "animals", "pulmonology", "parasitology", "rickettsia", "fleas", "zoology", "bacteria", "bacterial pathogens"...	Rickettsial Disease in the Peruvian Amazon Basin	journal.pntd.0004843	null	[ [ "Rickettsiae and rickettsia-like organisms are a diverse group of obligate intracellular bacteria within the order Rickettsiales that include members of the genera Rickettsia , Orientia , Ehrlichia , Anaplasma , Neorickettsia and Wolbachia .", "Based on whole-genome analysis , species within the genus Ric...	[ "Using a large , passive , clinic-based surveillance program in Iquitos , Peru , we characterized the prevalence of rickettsial infections among undifferentiated febrile cases and obtained evidence of pathogen transmission in potential domestic reservoir contacts and their ectoparasites .", "Blood specimens from ...	[ "Rickettsial infection remains relatively unexplored in South America compared to other regions of the world .", "For most regions of Peru ( including the Amazon Basin ) , nothing more than broad serological characterization is available about circulating rickettsiae .", "Even less is known about the animal res...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "engineering" ]	Bistability versus Bimodal Distributions in Gene Regulatory Processes from Population Balance	journal.pcbi.1002140	null	[ [ "In the study of cell populations , with vastly improved flow cytometry , access to multivariate distribution measures of cell populations has advanced considerably , calling for a concomitant application of theory sensitive to population heterogeneity .", "In this regard , the population balance framewor...	[ "In recent times , stochastic treatments of gene regulatory processes have appeared in the literature in which a cell exposed to a signaling molecule in its environment triggers the synthesis of a specific protein through a network of intracellular reactions .", "The stochastic nature of this process leads to a d...	[ "Traditionally cells in a population have been assumed to behave identically by using deterministic mathematical equations describing average cell behavior , thus ignoring its inherent randomness .", "A single cell stochastic model has therefore evolved in the literature to overcome this drawback .", "However ,...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology/host antiviral responses", "virology/animal models of infection", "virology" ]	Viral Capsid Is a Pathogen-Associated Molecular Pattern in Adenovirus Keratitis	journal.ppat.1000841	null	[ [ "Human adenoviruses ( HAdV ) are major mucosal pathogens of the ocular , respiratory , and gastrointestinal tracts [1] .", "HAdV are also a source of disseminated infections involving multiple organs in immunocompromised patients [2] , [3] .", "Epidemic keratoconjunctivitis ( EKC ) is a highly contagi...	[ "Human adenovirus ( HAdV ) infection of the human eye , in particular serotypes 8 , 19 and 37 , induces the formation of corneal subepithelial leukocytic infiltrates .", "Using a unique mouse model of adenovirus keratitis , we studied the role of various virus-associated molecular patterns in subsequent innate im...	[ "Adenoviruses are nonenveloped DNA viruses that infect mucosal tissues , causing a wide array of diseases .", "Adenovirus infection of the cornea induces inflammation in the form of multifocal leukocytic infiltrates .", "Although studied extensively in tissue culture models , how adenoviruses induce inflammatio...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell death", "autophagic cell death", "lysosomes", "ecology and environmental sciences", "vesicles", "molecular probe techniques", "cell processes", "immunoblotting", "animal models", "model organisms", "immunoprecipitation", "molecular biology techniques", "cellular structures and organell...	Loss of C9orf72 Enhances Autophagic Activity via Deregulated mTOR and TFEB Signaling	journal.pgen.1006443	null	[ [ "Amyotrophic lateral sclerosis ( ALS ) is a fatal neurodegenerative disease characterized by the progressive degeneration of motor neurons .", "Frontotemporal dementia ( FTD ) is the second most common type of dementia in people younger than 65 and is characterized by degeneration of the frontal and tempo...	[ "The most common cause of the neurodegenerative diseases amyotrophic lateral sclerosis and frontotemporal dementia is a hexanucleotide repeat expansion in C9orf72 .", "Here we report a study of the C9orf72 protein by examining the consequences of loss of C9orf72 functions .", "Deletion of one or both alleles of...	[ "C9orf72 is one of many uncharacterized genes in the human genome .", "The presence of repeated nucleotides in the non-coding region of the C9orf72 gene ( GGGGCC ) has been linked to the neurodegenerative diseases Amyotrophic Lateral Sclerosis ( ALS ) and Frontotemporal dementia ( FTD ) .", "However , how the p...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "reverse transcriptase-polymerase chain reaction", "plant anatomy", "brassica", "endosperm", "developmental biology", "plant science", "model organisms", "experimental organism systems", "mitochondria", "sequence motif analysis", "bioenergetics", "embryos", "molecular biology techniques", ...	Empty Pericarp21 encodes a novel PPR-DYW protein that is required for mitochondrial RNA editing at multiple sites, complexes I and V biogenesis, and seed development in maize	journal.pgen.1008305	null	[ [ "Plant mitochondrion possesses its own genome which retains ~5% genes from its prokaryotic ancestor .", "These genes encode proteins , ribosomal RNAs and transfer RNAs for oxidative phosphorylation , and protein translation .", "Plant mitochondria have acquired characteristic and complex RNA metabolis...	[ "C-to-U editing is an important event in post-transcriptional RNA processing , which converts a specific cytidine ( C ) -to-uridine ( U ) in transcripts of mitochondria and plastids .", "Typically , the pentatricopeptide repeat ( PPR ) protein , which specifies the target C residue by binding to its upstream sequ...	[ "Plant mitochondrial transcripts harbor hundreds of cytidine ( C ) that need to be converted to uridine ( U ) prior to translation .", "Typically , PPR proteins are recruited to specify the target Cs by binding to the upstream sequences of the edited site , and a given PPR is responsible for the editing of just o...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "cytokines", "emerging viral diseases", "immunity to infections", "immunology", "microbiology", "host-pathogen interaction", "mechanisms of resistance and susceptibility", "emerging infectious diseases", "animal models of infection", "inflammation", "biology", "immune response", "immune syst...	A Model of DENV-3 Infection That Recapitulates Severe Disease and Highlights the Importance of IFN-γ in Host Resistance to Infection	journal.pntd.0001663	null	[ [ "Dengue viruses ( DENV ) are the most prevalent mosquito-borne RNA viruses worldwide , classified serologically into four antigenically distinct types ( DENV-1–4 ) .", "They are transmitted to humans by the mosquitoes Aedes aegypti and Aedes albopictus [1]–[3] .", "According to the World Health Organi...	[ "There are few animal models of dengue infection , especially in immunocompetent mice .", "Here , we describe alterations found in adult immunocompetent mice inoculated with an adapted Dengue virus ( DENV-3 ) strain .", "Infection of mice with the adapted DENV-3 caused inoculum-dependent lethality that was prec...	[ "Dengue is a mosquito-borne disease caused by one of four serotypes of Dengue virus ( DENV-1-4 ) .", "Dengue has escalated in geographic distribution and disease severity to become the most common arboviral infection of humans .", "There are no vaccines or specific therapies for dengue and the treatment is supp...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	The Effects of Socioeconomic and Environmental Factors on the Incidence of Dengue Fever in the Pearl River Delta, China, 2013	journal.pntd.0004159	null	[ [ "Dengue fever ( DF ) is an infectious epidemic disease that is principally transmitted by the vector Aedes albopictus and Aedes aegypti . [1]", "Dengue virus infection in humans is often asymptomatic but can lead to different clinical manifestations . [2]", "In the past 50 years , the incidence of DF ...	[ "An outbreak of dengue fever ( DF ) occurred in Guangdong Province , China in 2013 with the highest number of cases observed within the preceding ten years .", "DF cases were clustered in the Pearl River Delta economic zone ( PRD ) in Guangdong Province , which accounted for 99 . 6% of all cases in Guangdong prov...	[ "Dengue fever is an infectious disease transmitted by mosquitoes .", "It is a major public health problem in tropical and subtropical regions around the world .", "Dengue fever is of great interest in the Pearl River Delta economic zone ( PRD ) of Guangdong province , China because the outbreak in 2013 was the ...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases/bacterial infections", "infectious diseases/neglected tropical diseases", "microbiology/immunity to infections" ]	Susceptibility to Vibrio cholerae Infection in a Cohort of Household Contacts of Patients with Cholera in Bangladesh	journal.pntd.0000221	null	[ [ "Vibrio cholerae causes a spectrum of infection in humans ranging from asymptomatic colonization to severe secretory diarrhea .", "V . cholerae is differentiated serologically by the O antigen of its lipopolysaccharide ( LPS ) ; the vast majority of human cholera is caused by the O1 and O139 serogroups ."...	[ "Despite recent progress in understanding the molecular basis of Vibrio cholerae pathogenesis , there is relatively little knowledge of the factors that determine the variability in human susceptibility to V . cholerae infection .", "We performed an observational study of a cohort of household contacts of cholera...	[ "Vibrio cholerae is the bacterium that causes cholera , a severe form of diarrhea that leads to rapid and potentially fatal dehydration when the infection is not treated promptly .", "Cholera remains an important cause of diarrhea globally , and V . cholerae continues to cause major epidemics in the most vulnerab...	2008
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "biotechnology", "sustainable agriculture", "high-input farming", "environmental impacts", "plant biology", "applied mathematics", "crop management", "population genetics", "crop genetics", "mathematics", "crops", "agricultural production", "agrochemicals", "evolutionary modeling", "plan...	Durable Resistance to Crop Pathogens: An Epidemiological Framework to Predict Risk under Uncertainty	journal.pcbi.1002870	null	[ [ "There is increasing social pressure to integrate science , policy and regulation in order to assess and minimize the risks associated with agricultural practices .", "Major risks and uncertainties persist whereby pests and pathogens rapidly overcome disease control methods using resistant cultivars and f...	[ "Increasing the durability of crop resistance to plant pathogens is one of the key goals of virulence management .", "Despite the recognition of the importance of demographic and environmental stochasticity on the dynamics of an epidemic , their effects on the evolution of the pathogen and durability of resistanc...	[ "We want to understand if , and how , the evolution of a pathogen can be delayed/accelerated by random fluctuations always occurring in epidemics .", "We studied a simple biological system relevant to agriculture: a resistant crop immune to the disease , and a plant pathogen that defeats the resistance after a si...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Interaction of the Antimicrobial Peptide Polymyxin B1 with Both Membranes of E. coli: A Molecular Dynamics Study	journal.pcbi.1004180	null	[ [ "Antimicrobial peptides ( AMPs ) are small cationic membrane-active peptides; they can be found in most living organisms and play an essential part in innate immunity [1–3] .", "These peptides exhibit broad-spectrum antimicrobial activity against bacteria , fungi and viruses , making them of great biomedi...	[ "Antimicrobial peptides are small , cationic proteins that can induce lysis of bacterial cells through interaction with their membranes .", "Different mechanisms for cell lysis have been proposed , but these models tend to neglect the role of the chemical composition of the membrane , which differs between bacter...	[ "Antimicrobial peptides have the ability to kill harmful bacteria through interaction with bacterial membranes .", "This manuscript describes the first reported computational study of antimicrobial peptide interaction with both membranes of a Gram-negative bacterium .", "While antimicrobial peptides have been t...	2015
[ "Introduction", "Methods", "Results and discussion" ]	[ "chemical compounds", "aliphatic amino acids", "organic compounds", "simulation and modeling", "membrane proteins", "leucine", "amino acids", "cellular structures and organelles", "thermodynamics", "research and analysis methods", "lipids", "proteins", "chemistry", "biophysics", "cell me...	Structurally detailed coarse-grained model for Sec-facilitated co-translational protein translocation and membrane integration	journal.pcbi.1005427	null	[ [ "Most integral membrane proteins ( IMPs ) are co-translationally inserted into the membrane during biosynthesis via the Sec translocon , a multiprotein complex [1–4] .", "In this process , a ribosome docks to the cytosolic opening of the Sec translocon and feeds a nascent polypeptide chain ( NC ) into the...	[ "We present a coarse-grained simulation model that is capable of simulating the minute-timescale dynamics of protein translocation and membrane integration via the Sec translocon , while retaining sufficient chemical and structural detail to capture many of the sequence-specific interactions that drive these proces...	[ "Ubiquitous across all kingdoms of life , the Sec translocon is an essential piece of molecular machinery for protein biosynthesis .", "The translocon is a transmembrane channel that enables the secretion of newly synthesized proteins across the lipid membrane , as well as the integration of protein domains into ...	2017
[ "Introduction", "Materials and Methods", "Results and Discussion" ]	[ "systems biology", "biochemistry", "phytochemistry", "chemistry", "biology", "computational chemistry", "chemical biology" ]	Computational Studies on Sirtuins from Trypanosoma cruzi: Structures, Conformations and Interactions with Phytochemicals	journal.pntd.0002689	null	[ [ "Chagas disease is caused by a flagellated protozoan belonging to the Trypanosomatidae family of the kinetoplastida order .", "This disease which is mainly localized in Central and South America , affects approximately 8 million people , causing near 14 , 000 deaths worldwide [1] and leading to serious me...	[ "The silent-information regulator 2 proteins , otherwise called sirtuins , are currently considered as emerging anti-parasitic targets .", "Nicotinamide , a pan-sirtuin inhibitor , is known to cause kinetoplast alterations and the arrested growth of T . cruzi , the protozoan responsible for Chagas disease .", "...	[ "T . cruzi is a protozoan pathogen responsible for Chagas disease .", "Current therapies rely only on a very small number of drugs , most of which are inadequate because of their severe host toxicity or because of their susceptibility to drug-resistance mechanisms .", "To determine efficient therapeutic alterna...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genome-wide association studies", "dna modification", "gene regulation", "genetics", "gene expression", "epigenetics", "molecular genetics", "biology", "human genetics", "gene function" ]	Genome-Wide Meta-Analysis of Homocysteine and Methionine Metabolism Identifies Five One Carbon Metabolism Loci and a Novel Association of ALDH1L1 with Ischemic Stroke	journal.pgen.1004214	null	[ [ "As the fourth leading cause of death and the leading cause of disability in American adults , stroke constitutes a major public health burden .", "Epidemiological data consistently demonstrate an association between elevated plasma homocysteine ( tHcy ) and increased risk for stroke [1] , cardiovascular ...	[ "Circulating homocysteine levels ( tHcy ) , a product of the folate one carbon metabolism pathway ( FOCM ) through the demethylation of methionine , are heritable and are associated with an increased risk of common diseases such as stroke , cardiovascular disease ( CVD ) , cancer and dementia .", "The FOCM is the...	[ "Elevated homocysteine ( tHcy ) is strongly associated with risk for common disorders such as stroke , cardiovascular disease and Alzheimer disease .", "Lowering tHcy levels has proven to have variable success in reducing clinical risk , so the question remains , “Are we correctly targeting these disorders by low...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Unsaturation of Very-Long-Chain Ceramides Protects Plant from Hypoxia-Induced Damages by Modulating Ethylene Signaling in Arabidopsis	journal.pgen.1005143	null	[ [ "Lipids are essential constituents of plant cells that provide both the structural basis for cell membranes and an energy source for cellular metabolism [1 , 2] .", "Recently , considerable attention has been given to the function of lipids as mediators of various biological activities including growth , ...	[ "Lipid remodeling is crucial for hypoxic tolerance in animals , whilst little is known about the hypoxia-induced lipid dynamics in plants .", "Here we performed a mass spectrometry-based analysis to survey the lipid profiles of Arabidopsis rosettes under various hypoxic conditions .", "We observed that hypoxia ...	[ "Hypoxia is one of the most important abiotic stresses of worldwide concern that determines the crop productivity and the natural distribution of plant species .", "Flooding events such as root waterlogging and submergence strongly affect diffusion of gasses into plant cells , which eventually leads to hypoxia an...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "leptospira", "pathology and laboratory medicine", "ruminants", "pathogens", "tropical diseases", "microbiology", "vertebrates", "animals", "mammals", "bacterial diseases", "farms", "neglected tropical diseases", "bacteria", "bacterial pathogens", "infec...	The prevalence of Leptospira among invasive small mammals on Puerto Rican cattle farms	journal.pntd.0007236	null	[ [ "Along with increasing globalization , climate change , and urban expansion , the rising number of emerging infectious diseases is a major concern .", "Among emerging infectious diseases , over 60% are multi-host zoonoses many of which are classified as “neglected” owing to a general lack of knowledge abo...	[ "Leptospirosis , an emerging infectious disease caused by bacteria of the genus Leptospira , is thought to be the most widespread zoonotic disease in the world .", "A first step in preventing the spread of Leptospira is delineating the animal reservoirs that maintain and disperse the bacteria .", "Quantitative ...	[ "Leptospirosis is a global zoonotic disease that recently has shown an increase of human cases in many regions , Puerto Rico being one of them .", "To decrease human Leptospira infections it is necessary to ascertain the role of animal reservoirs to maintain the pathogen in the environment .", "However , no stu...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "computer science/natural and synthetic vision", "computational biology/computational neuroscience", "computer science/numerical analysis and theoretical computing", "neuroscience/natural and synthetic vision", "mathematics/statistics", "neuroscience/theoretical neuroscience" ]	“I Look in Your Eyes, Honey”: Internal Face Features Induce Spatial Frequency Preference for Human Face Processing	journal.pcbi.1000329	null	[ [ "In the brain , the structure of neuronal circuits for processing sensory information", "matches the statistical properties of the sensory signals [1] .", "Taking advantage of", "these statistical regularities contributes to an “optimal”", "encoding of sensory signals in neuronal responses , i...	[ "Numerous psychophysical experiments found that humans preferably rely on a narrow", "band of spatial frequencies for recognition of face identity .", "A recently", "conducted theoretical study by the author suggests that this frequency", "preference reflects an adaptation of the brain's face processing", ...	[ "Imagine a photograph showing your friend's face .", "Although you might", "think that every single detail in his face matters for recognizing him , numerous", "experiments have shown that the brain prefers a rather coarse resolution", "instead .", "This means that a small rectangular photograph of about ...	2009
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "developmental biology", "histology", "infectious diseases", "veterinary microbiology", "biology", "microbiology", "veterinary science" ]	Tissue and Stage-Specific Distribution of Wolbachia in Brugia malayi	journal.pntd.0001174	null	[ [ "Filarial parasites infect more than 150 million people in tropical and subtropical countries and are responsible for important tropical diseases such as lymphatic filariasis ( elephantiasis ) and onchocerciasis ( river blindness ) .", "Other filarial species are important veterinary pathogens ( e . g . D...	[ "Most filarial parasite species contain Wolbachia , obligatory bacterial endosymbionts that are crucial for filarial development and reproduction .", "They are targets for alternative chemotherapy , but their role in the biology of filarial nematodes is not well understood .", "Light microscopy provides importa...	[ "Most filarial nematodes contain Wolbachia endobacteria that are essential for development and reproduction .", "An antibody against a Wolbachia surface protein was used to monitor the distribution of endobacteria during the B . malayi life cycle .", "In situ hybridization with probes binding to Wolbachia 16S r...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "biochemistry", "biochemical simulations", "computer and information sciences", "computational chemistry", "computer modeling", "molecular dynamics", "dna replication", "biology and life sciences", "dna", "physical sciences", "computational biology", "chemical biology", "chemistry" ]	Molecular Dynamics Study of the Opening Mechanism for DNA Polymerase I	journal.pcbi.1003961	null	[ [ "DNA polymerase , which is responsible for copying DNA , is a vital enzyme involved in the transfer of genetic information for living organisms .", "It is also utilized by scientists to replicate DNA sequences during polymerase chain reactions ( PCR ) .", "DNA polymerase has the ability to quickly and...	[ "During DNA replication , DNA polymerases follow an induced fit mechanism in order to rapidly distinguish between correct and incorrect dNTP substrates .", "The dynamics of this process are crucial to the overall effectiveness of catalysis .", "Although X-ray crystal structures of DNA polymerase I with substrat...	[ "All organisms are dependent on the proper replication of their DNA for survival .", "DNA polymerase is the enzyme responsible for copying our DNA during cell division .", "We have performed computational simulations on DNA polymerase to understand the fundamental dynamics of the enzyme .", "Our simulations p...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "organismal evolution", "protein interactions", "signaling networks", "protein abundance", "molecular cell biology", "network analysis", "eukaryotic evolution", "computer and information sciences", "proteins", "proteomics", "systems biology", "biochemistry", "signal transduction", "cell bi...	Protein Conservation and Variation Suggest Mechanisms of Cell Type-Specific Modulation of Signaling Pathways	journal.pcbi.1003659	null	[ [ "Proteins do not act in isolation but interact with other proteins to fulfill important cellular functions .", "Often proteins are organized into pathways , which are tightly controlled cascades of protein binding events ( and those of other biomolecules ) .", "One important cellular function controll...	[ "Many proteins and signaling pathways are present in most cell types and tissues and yet perform specialized functions .", "To elucidate mechanisms by which these ubiquitous pathways are modulated , we overlaid information about cross-cell line protein abundance and variability , and evolutionary conservation ont...	[ "Cell function is determined by highly organized networks of biological molecules .", "An important class of protein pathways maintains the transmission of signals from the cell membrane to the nucleus .", "These signaling pathways are reused for different purposes at an evolutionary scale and in different cell...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "mathematics", "genome evolution", "statistics (mathematics)", "epidemiology", "biology and life sciences", "population biology", "physical sciences", "computational biology", "evolutionary biology", "evolutionary genetics" ]	Heterogeneity in the Frequency and Characteristics of Homologous Recombination in Pneumococcal Evolution	journal.pgen.1004300	null	[ [ "The evolution of many bacterial species is largely driven by horizontal exchange of sequence .", "Often , this can be attributed to the movement of autonomously mobile genetic elements ( MGEs ) .", "Many of those are able to insert into the host chromosome through site-specific recombination mediated...	[ "The bacterium Streptococcus pneumoniae ( pneumococcus ) is one of the most important human bacterial pathogens , and a leading cause of morbidity and mortality worldwide .", "The pneumococcus is also known for undergoing extensive homologous recombination via transformation with exogenous DNA .", "It has been ...	[ "Streptococcus pneumoniae , a bacterium commonly carried asymptomatically by children , is a major cause of diseases such as pneumonia and meningitis .", "The species is genetically diverse and is known to frequently undergo the remarkable process of transformation via homologous recombination .", "In this proc...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "computational biology/molecular dynamics", "computational biology" ]	Multiscale Coarse-Graining of the Protein Energy Landscape	journal.pcbi.1000827	null	[ [ "Despite continuing advances in computing power , atomistic simulation remains a considerable challenge at increasingly large time and length scales for processes of biological importance such as protein folding , conformational change and assembly .", "Coarse-grained ( CG ) approaches have therefore enjo...	[ "A variety of coarse-grained ( CG ) models exists for simulation of proteins .", "An outstanding problem is the construction of a CG model with physically accurate conformational energetics rivaling all-atom force fields .", "In the present work , atomistic simulations of peptide folding and aggregation equilib...	[ "Biological function originates from the dynamical motions of proteins in response to cellular stimuli .", "Protein dynamics arise from physical interactions that are well-predicted by detailed atomistic simulations .", "In order to examine large protein complexes on long timescales of biological importance , h...	2010
[ "Introduction", "Results", "Discussion", "Material and Methods" ]	[ "bacteriology", "plant microbiology", "gene expression", "genetics", "molecular genetics", "biology", "microbiology", "host-pathogen interaction", "genetics and genomics", "bacterial pathogens" ]	Acid-Induced Type VI Secretion System Is Regulated by ExoR-ChvG/ChvI Signaling Cascade in Agrobacterium tumefaciens	journal.ppat.1002938	null	[ [ "Pathogenic bacteria have evolved several specialized secretion systems to transport protein or DNA across membranes to extracellular milieu or even to the host cells in response to specific environmental cues .", "Among the 6 types of secretion systems , named type I to VI ( T1SS to T6SS ) identified in ...	[ "The type VI secretion system ( T6SS ) is a widespread , versatile protein secretion system in pathogenic Proteobacteria .", "Several T6SSs are tightly regulated by various regulatory systems at multiple levels .", "However , the signals and/or regulatory mechanisms of many T6SSs remain unexplored .", "Here ,...	[ "The bacterial type VI secretion system ( T6SS ) has diverse functions that contribute to the survival or fitness of many pathogenic bacteria in response to environmental cues .", "Numerous studies have shown that T6SS is highly regulated via multiple mechanisms , but the regulatory mechanisms of most T6SSs remai...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "viral entry", "viral transmission and infection", "virology", "biology", "microbiology" ]	The Membrane Fusion Step of Vaccinia Virus Entry Is Cooperatively Mediated by Multiple Viral Proteins and Host Cell Components	journal.ppat.1002446	null	[ [ "Entry of enveloped viruses into cells can be divided into three steps:", "( i ) close apposition of viral and cellular membranes ,", "( ii ) lipid mixing of the outer membrane leaflets leading to formation of a hemifusion intermediate , and", "( iii ) formation and expansion of a fusion pore allo...	[ "For many viruses , one or two proteins allow cell attachment and entry , which occurs through the plasma membrane or following endocytosis at low pH . In contrast , vaccinia virus ( VACV ) enters cells by both neutral and low pH routes; four proteins mediate cell attachment and twelve that are associated in a memb...	[ "Poxviruses are large DNA viruses that cause diseases in humans and other animals .", "To initiate infection , the core of the large , membrane-enveloped particle must penetrate into the cytoplasm where replication occurs .", "For most enveloped viruses only one or two proteins are needed for attachment and pen...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "b vitamins", "invertebrates", "vitamin b12 deficiency", "medicine and health sciences", "megaloblastic anemia", "rna interference", "chemical compounds", "pathology and laboratory medicine", "caenorhabditis", "pathogens", "microbiology", "diet", "animals", "organic compounds", "anemia",...	Interplay between mitochondria and diet mediates pathogen and stress resistance in Caenorhabditis elegans	journal.pgen.1008011	null	[ [ "Like it's genome , an organism's diet and microbiota tremendously influence its life history .", "Attempts to understand this have led to the development of the host-microbiota-nutrition axis model [1] .", "Although an avalanche of literature has reported on variations in the microbiota , diet , and ...	[ "Diet is a crucial determinant of organismal biology; interactions between the host , its diet , and its microbiota are critical to determining the health of an organism .", "A variety of genetic and biochemical means were used to assay stress sensitivity in C . elegans reared on two standard laboratory diets: E ...	[ "Vitamin B12 deficiency affects ~10–40% of US adults , causing a range of health issues ranging from anemia to neurological defects .", "Here we provide a mechanistic link between dietary B12 deficiency and mitochondrial dysfunction .", "Our data indicate that B12 supports clearance of propionate , an intermedi...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "reverse transcriptase-polymerase chain reaction", "medicine and health sciences", "pathology and laboratory medicine", "togaviruses", "chikungunya infection", "respiratory infections", "pathogens", "tropical diseases", "microbiology", "geographical locations", "alphaviruses", "pulmonology", ...	Chikungunya Fever Cases Identified in the Veterans Health Administration System, 2014	journal.pntd.0004630	null	[ [ "Chikungunya virus ( CHIKV ) , an alphavirus most commonly transmitted by Aedes species mosquitoes , causes chikungunya fever ( CHIK ) , characterized by acute-onset of fever and what is frequently described as incapacitating polyarthralgia [1 , 2] .", "Since CHIKV was first identified in Tanzania in 1953...	[ "During December 2013 , the first locally transmitted chikungunya virus ( CHIKV ) infections in the Americas were reported in the Caribbean .", "Although CHIKV infection is rarely fatal , risk for severe disease increases with age and medical comorbidities .", "Herein we describe characteristics of Veterans Hea...	[ "Infection with mosquito-borne chikungunya virus causes fever and severe diffuse joint pain—an illness known as chikungunya fever , or \"that which bends up . \"", "Epidemics of chikungunya fever have occurred in Asia , Africa , and Europe .", "Not until December 2013 were there reports of chikungunya virus inf...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "antimicrobials", "medicine and health sciences", "pathology and laboratory medicine", "pneumococcus", "pathogens", "drugs", "microbiology", "epistasis", "antibiotic resistance", "linkage disequilibrium", "antibiotics", "pharmacology", "bacteria", "bacterial pathogens", "antimicrobial re...	On the evolutionary ecology of multidrug resistance in bacteria	journal.ppat.1007763	null	[ [ "Antibiotic resistance and , in particular , multidrug resistance ( MDR ) are public health threats .", "Multidrug resistant infections are associated with poorer clinical outcomes and higher cost of treatment than other infections [1 , 2] and there is concern that the emergence of pan-resistant strains (...	[ "Resistance against different antibiotics appears on the same bacterial strains more often than expected by chance , leading to high frequencies of multidrug resistance .", "There are multiple explanations for this observation , but these tend to be specific to subsets of antibiotics and/or bacterial species , wh...	[ "Antibiotic resistance is a serious public health concern , yet the ecology and evolution of drug resistance are not fully understood .", "This impacts our ability to design effective interventions to combat resistance .", "From a public health point of view , multidrug resistance is particularly problematic be...	2019
[ "Introduction", "Results", "Discussion", "Material and methods" ]	[ "blood cells", "cell death", "medicine and health sciences", "autophagic cell death", "immune cells", "pathology and laboratory medicine", "intracellular pathogens", "molecular probe techniques", "pathogens", "immunology", "cell processes", "microbiology", "immunoblotting", "inflammasomes"...	MyD88-dependent inflammasome activation and autophagy inhibition contributes to Ehrlichia-induced liver injury and toxic shock	journal.ppat.1006644	null	[ [ "Human monocytic ehrlichiosis ( HME ) is the most prevalent emerging tick-borne , life threatening rickettsial disease and is caused by the obligate intracellular bacterium E . chaffeensis .", "Patients with HME develop severe liver inflammation and dysfunction followed by multi-organ failure and toxic sh...	[ "Severe hepatic inflammation is a common cause of acute liver injury following systemic infection with Ehrlichia , obligate Gram-negative intracellular bacteria that lack lipopolysaccharide ( LPS ) .", "We have previously shown that type I IFN ( IFN-I ) and inflammasome activation are key host-pathogenic mediator...	[ "Human monocytic ehrlichiosis ( HME ) is the most prevalent emerging infectious disease in the United States .", "Ehrlichia chaffeensis , etiologic agent of HME , is a Gram negative obligate intracellular bacterium transmitted by infected tick bites and can infect different cell type .", "Although Ehrlichia lac...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "physiology", "signal processing", "biology", "anatomy and physiology", "cardiovascular system", "biophysics", "computational biology", "engineering" ]	Uncovering the Dynamics of Cardiac Systems Using Stochastic Pacing and Frequency Domain Analyses	journal.pcbi.1002399	null	[ [ "In cardiac physiology , alternans designates the alternation of action potential ( AP ) parameters ( e . g . , AP duration ( APD ) , calcium transient ) from beat to beat [1] , [2] .", "It leads to dispersion of refractoriness and represents a well established mechanism of conduction block and thus of se...	[ "Alternans of cardiac action potential duration ( APD ) is a well-known arrhythmogenic mechanism which results from dynamical instabilities .", "The propensity to alternans is classically investigated by examining APD restitution and by deriving APD restitution slopes as predictive markers .", "However , experi...	[ "Cardiac arrhythmias are frequent complications of heart disease and an important cause of morbidity and mortality .", "The rhythmic activity of the heart relies on the action potential , a bioelectrical signal characterized by complex dynamics involving ion currents and intracellular calcium cycling .", "When ...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "medicinal chemistry", "virology", "chemistry", "biology", "microbiology", "viral structure" ]	Small-Molecule Inhibitors of Dengue-Virus Entry	journal.ppat.1002627	null	[ [ "Enveloped viruses penetrate into the cytosol of their target cell by fusion of viral and cellular membranes [1] , [2] .", "Flaviviruses , such as dengue , penetrate from endosomes , following uptake by clathrin-mediated endocytosis [3] , [4] .", "At endosomal pH , proton binding by their envelope pro...	[ "Flavivirus envelope protein ( E ) mediates membrane fusion and viral entry from endosomes .", "A low-pH induced , dimer-to-trimer rearrangement and reconfiguration of the membrane-proximal “stem\" of the E ectodomain draw together the viral and cellular membranes . We found stem-derived peptides from dengue viru...	[ "Fusion of viral and cellular membranes is necessary to establish infection by an enveloped virus .", "This process is facilitated by rearrangement of protein ( s ) present on the virion surface in response to molecular cues from the compartment from which fusion occurs , such as low pH of an endosome .", "Deng...	2012
[ "Introduction", "Results/Discussion", "Supporting Information" ]	[ "homo (human)", "computational biology", "evolutionary biology", "molecular biology", "mus (mouse)" ]	The (In)dependence of Alternative Splicing and Gene Duplication	journal.pcbi.0030033	null	[ [ "Alternative splicing ( AS ) and gene duplication ( GD ) are two main contributors to the diversity of the protein repertoire with enormous impact on protein sequence , structure , and function [1–5] .", "Interestingly , several recent studies point to a direct equivalence between AS and GD .", "There...	[ "Alternative splicing ( AS ) and gene duplication ( GD ) both are processes that diversify the protein repertoire .", "Recent examples have shown that sequence changes introduced by AS may be comparable to those introduced by GD .", "In addition , the two processes are inversely correlated at the genomic scale:...	[ "Alternative splicing ( AS ) and gene duplication ( GD ) followed by sequence divergence constitute two fundamental biological processes contributing to proteome variability .", "The former reflects the ability of many genes to express different products , while the latter results in several copies of the same ge...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "learning", "medicine and health sciences", "engineering and technology", "neurodegenerative diseases", "amyotrophic lateral sclerosis", "brain electrophysiology", "social sciences", "electrophysiology", "contingency tables", "neuroscience", "learning and memory", "human factors engineering", ...	Brain–Computer Interface–Based Communication in the Completely Locked-In State	journal.pbio.1002593	"Locked in" patients suffering from advanced amyotrophic lateral sclerosis, with no reliable means of communication, can learn to answer questions requiring a “yes” or “no” thought using frontocentral oxygenation changes measurable by functional near-infrared spectroscopy.	[ [ "Communication is the process of expressing and sharing feelings , thoughts , and intentions with one another by verbal and various nonverbal means .", "Communication skills appear automatic but can pose severe challenges to individuals suffering from motor neuron disorders .", "The most devastating o...	[ "Despite partial success , communication has remained impossible for persons suffering from complete motor paralysis but intact cognitive and emotional processing , a state called complete locked-in state ( CLIS ) .", "Based on a motor learning theoretical context and on the failure of neuroelectric brain–compute...	[ "Despite scientific and technological advances , communication has remained impossible for persons suffering from complete motor paralysis but intact cognitive and emotional processing , a condition that is called completely locked-in state .", "Brain–computer interfaces based on neuroelectrical technology ( like...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "antimicrobials", "taxonomy", "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "drugs", "microbiology", "vertebrates", "staphylococcus aureus", "animals", "mammals", "methicillin-resistant staphylococcus aureus", "antibiotic resistance", "phylogenetics", ...	Evidence for the evolutionary steps leading to mecA-mediated β-lactam resistance in staphylococci	journal.pgen.1006674	null	[ [ "The most important antibiotic resistance mechanism in staphylococci is associated with the mecA gene , which confers resistance to the large class of β-lactam antibiotics .", "mecA is carried on a mobile genetic element called staphylococcal cassette chromosome mec ( SCCmec ) [1] , which always inserts a...	[ "The epidemiologically most important mechanism of antibiotic resistance in Staphylococcus aureus is associated with mecA–an acquired gene encoding an extra penicillin-binding protein ( PBP2a ) with low affinity to virtually all β-lactams .", "The introduction of mecA into the S . aureus chromosome has led to the...	[ "The emergence and rise of mecA-mediated β-lactam resistance in staphylococci has been one of the greatest concerns of the scientific and medical communities worldwide .", "However , little is known regarding the origin of the mecA gene determinant .", "In this study we demonstrate that antibiotic pressure in t...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology/membranes and sorting", "genetics and genomics/disease models" ]	The C. elegans Opa1 Homologue EAT-3 Is Essential for Resistance to Free Radicals	journal.pgen.1000022	null	[ [ "Dominant optic atrophy ( DOA ) is one of the leading causes of inherited blindness .", "DOA is a progressive eye disease caused by degeneration of the retinal ganglion cell layer with ascending atrophy of the optic nerve [1] .", "The most prevalent form of DOA is caused by heterozygous mutations in t...	[ "The C . elegans eat-3 gene encodes a mitochondrial dynamin family member homologous to Opa1 in humans and Mgm1 in yeast .", "We find that mutations in the C . elegans eat-3 locus cause mitochondria to fragment in agreement with the mutant phenotypes observed in yeast and mammalian cells .", "Electron microscop...	[ "Dominant Optic Atrophy is a progressive eye disease caused by degeneration of retinal ganglion cells .", "The most prevalent form of DOA is caused by mutations in the Opa1 protein .", "This protein is required for fusion between mitochondria , it has an anti-apoptotic function , and it is required for mitochon...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "mus (mouse)", "in vitro", "genetics and genomics" ]	An Unmethylated 3′ Promoter-Proximal Region Is Required for Efficient Transcription Initiation	journal.pgen.0030027	null	[ [ "DNA methylation is essential for mammalian development [1 , 2] , playing an important role in maintaining transcriptional silencing of genes on the inactive X chromosome , imprinted genes , and parasitic elements [3 , 4] .", "In mammals , DNA methylation occurs predominantly on cytosines in the context o...	[ "The promoter regions of approximately 40% of genes in the human genome are embedded in CpG islands , CpG-rich regions that frequently extend on the order of one kb 3′ of the transcription start site ( TSS ) region .", "CpGs 3′ of the TSS of actively transcribed CpG island promoters typically remain methylation-f...	[ "Genes , the functional units of heredity , are made up of DNA , which is packaged inside the nuclei of eukaryotic cells in association with a number of proteins in a structure called chromatin .", "In order for transcription , the process of transferring genetic information from DNA to RNA , to take place , chro...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "eye infections", "dermatology", "otology", "medicine and health sciences", "genetic dominance", "autosomal dominant traits", "epidemiology", "ophthalmology", "genetics", "keratitis", "biology and life sciences", "hearing disorders", "dermatologic pathology", "otorhinolaryngology", "pedi...	Revertant Mutation Releases Confined Lethal Mutation, Opening Pandora's Box: A Novel Genetic Pathogenesis	journal.pgen.1004276	null	[ [ "A nonsense mutation may , in theory , disrupt and thus “confine” the effects of another dominant pathogenic mutation when the two mutations coexist in the same allele of a single gene .", "Furthermore , in such cases , reversion of the confining nonsense mutation may paradoxically elicit a congenital dis...	[ "When two mutations , one dominant pathogenic and the other “confining” nonsense , coexist in the same allele , theoretically , reversion of the latter may elicit a disease , like the opening of Pandora's box .", "However , cases of this hypothetical pathogenic mechanism have never been reported .", "We describ...	[ "Loss of gene functions due to nonsense mutations is a typical pathogenic mechanism of hereditary diseases .", "They may , however , in certain genetic contexts , confine the effects of other dominant pathogenic mutations and suppress disease manifestations .", "We report the first instance in the literature wh...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Emergence of Slow-Switching Assemblies in Structured Neuronal Networks	journal.pcbi.1004196	null	[ [ "Neuronal ensembles exhibit a broad repertoire of activity patterns .", "Such dynamics are governed by a time-evolving network of synaptic connections with an intricate , yet structured , organization .", "Due to the advancement of connectomics , our knowledge about such networks is rapidly growing , ...	[ "Unraveling the interplay between connectivity and spatio-temporal dynamics in neuronal networks is a key step to advance our understanding of neuronal information processing .", "Here we investigate how particular features of network connectivity underpin the propensity of neural networks to generate slow-switch...	[ "Neural networks display a wide range of spatio-temporal behaviors .", "Understanding how this complex orchestration of neuronal firing activity is determined by the structure of the network ( i . e . , its wiring ) is an important step towards comprehending how neural computation is manifested , especially given...	2015
[ "Introduction", "Methods", "Results", "Discussion", "Conclusion" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "ruminants", "immunology", "tropical diseases", "geographical locations", "vertebrates", "south sudan", "animals", "mammals", "surgical and invasive medical procedures", "health care", "bacterial diseases", "signs and sym...	Burden of trachoma in five counties of Eastern Equatoria state, South Sudan: Results from population-based surveys	journal.pntd.0005658	null	[ [ "Trachoma , the leading cause of preventable blindness , is a disease caused by ocular infection with the bacterium Chlamydia trachomatis [1] .", "Over time , repeated infections can lead to conjunctival scarring of the upper eyelid , which may result in the eyelid turning inwards against the globe and co...	[ "In order to decrease the prevalence of trachoma within the country , the Republic of South Sudan has implemented components of the SAFE strategy in various counties since 2001 .", "Five counties in Eastern Equatoria state were surveyed in order to monitor progress of programmatic interventions and determine if a...	[ "Trachoma is the leading cause of preventable blindness in the world; however , with proper interventions the disease can be controlled .", "Despite a paucity of experienced trachoma graders , insecurity , and difficulty accessing some villages , population-based impact surveys were conducted in five counties of ...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "sequencing techniques", "genome sequencing", "genetics", "biology and life sciences", "molecular biology techniques", "microbiology", "genomics", "molecular biology", "parasitology" ]	A High Resolution Case Study of a Patient with Recurrent Plasmodium vivax Infections Shows That Relapses Were Caused by Meiotic Siblings	journal.pntd.0002882	null	[ [ "Plasmodium vivax is the most widespread of the human malaria parasite species with 2 . 85 billion people living in areas at risk for P . vivax infection [1] .", "Worldwide there are approximately 100 million cases of P . vivax annually , and the severity of P . vivax infection is increasingly recognized ...	[ "Plasmodium vivax infects a hundred million people annually and endangers 40% of the world's population .", "Unlike Plasmodium falciparum , P . vivax parasites can persist as a dormant stage in the liver , known as the hypnozoite , and these dormant forms can cause malaria relapses months or years after the initi...	[ "Plasmodium vivax is capable of remaining dormant in the human liver for months to years after an initial infection , creating an asymptomatic human reservoir .", "This unique aspect of parasite biology makes eliminating P . vivax distinctly different from P . falciparum elimination , and yet very little is known...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "systems biology", "biochemical simulations", "immunodeficiency viruses", "virology", "microbiology", "biology", "computational biology" ]	Gag-Pol Processing during HIV-1 Virion Maturation: A Systems Biology Approach	journal.pcbi.1003103	null	[ [ "The morphological maturation of human immunodeficiency virus type 1 ( HIV-1 ) depends on the proteolytic processing of the Gag and Gag-Pol polyproteins by the virus encoded PR that occurs concomitant with or shortly after virus release [1] .", "PR inhibitors ( PIs ) that interfere with this process resul...	[ "Proteolytic processing of Gag and Gag-Pol polyproteins by the viral protease ( PR ) is crucial for the production of infectious HIV-1 , and inhibitors of the viral PR are an integral part of current antiretroviral therapy .", "The process has several layers of complexity ( multiple cleavage sites and substrates;...	[ "Human Immunodeficiency Virus ( HIV ) produces its structural proteins and key enzymes in the form of polyproteins , from which the individual proteins need to be released in a complex and tightly regulated series of cleavage reactions to give rise to a morphologically mature , infectious virus particle .", "This...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biofilms", "bacteriology", "bacterial physiology", "bacterial biofilms", "ecology", "biology and life sciences", "microbiology", "microbial ecology" ]	A Central Role for Carbon-Overflow Pathways in the Modulation of Bacterial Cell Death	journal.ppat.1004205	null	[ [ "The balanced progression of cell division and apoptotic events is a classic hallmark of eukaryotic development [1] .", "Intriguingly , a similar homeostatic control of cell death , lysis and proliferation is predicted to benefit the development of adherent multicellular bacterial assemblages ( called bio...	[ "Similar to developmental programs in eukaryotes , the death of a subpopulation of cells is thought to benefit bacterial biofilm development .", "However mechanisms that mediate a tight control over cell death are not clearly understood at the population level .", "Here we reveal that CidR dependent pyruvate ox...	[ "Many bacterial species including the pathogen Staphylococcus aureus are capable of adhering to surfaces and forming complex communities called biofilms .", "This mode of growth can be particularly challenging from an infection control standpoint , as they are often refractory to antibiotics and host immune syste...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "disease mapping", "infectious diseases", "public health and epidemiology", "epidemiology", "infectious disease epidemiology", "african trypanosomiasis", "neglected tropical diseases", "parasitic diseases" ]	Estimating and Mapping the Population at Risk of Sleeping Sickness	journal.pntd.0001859	null	[ [ "Human African trypanosomiasis ( HAT ) , or sleeping sickness , is a vector-borne disease caused by two sub-species of the parasitic protozoa Trypanosoma brucei ( i . e . T . b . gambiense and T . b . rhodesiense ) .", "Trypanosomes are transmitted to humans by the infected bite of various species of tset...	[ "Human African trypanosomiasis ( HAT ) , also known as sleeping sickness , persists as a public health problem in several sub-Saharan countries .", "Evidence-based , spatially explicit estimates of population at risk are needed to inform planning and implementation of field interventions , monitor disease trends ...	[ "The present thrust towards the elimination of human African trypanosomiasis ( HAT , or sleeping sickness ) requires accurate information on how many people are at risk of contracting the disease , and where they live .", "This information is crucial to target field interventions effectively and efficiently , as ...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "ecology and environmental sciences", "medicine and health sciences", "surface water", "limnology", "malacology", "tropical diseases", "parasitic diseases", "animals", "gastropods", "aquatic environments", "geology", "bodies of water", "neglected tropical diseases", "sna...	Impact of the Three Gorges project on ecological environment changes and snail distribution in Dongting Lake area	journal.pntd.0005661	null	[ [ "The Three Gorges Dam ( TGD ) is located at the upper reaches of the Yangtze River , and it is a remarkable , comprehensive hydropower project [1] .", "Sediment discharge and water impoundment at the dam started in 2003 .", "Following the cofferdam power generation period ( 2003–2005 , water level 135...	[ "The Three Gorges Dam ( TGD ) is a remarkable , far-reaching project in China .", "This study was conducted to assess the impact of TGD on changes in the ecological environment , snail distribution and schistosomiasis transmission in Dongting Lake area .", "Hydrological data were collected from 12 monitoring si...	[ "Three Gorges Dam ( TGD ) is a tremendous hydrological project in China , it affects the ecological environment and influences the survival of animals downstream .", "The Dongting Lake is the first large lake that connects Yangtze River after it flows out of TGD , meanwhile , it accounts for 48% of the total snai...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "evolutionary biology", "gene function", "germ cells", "animal models", "developmental biology", "model organisms", "cell division", "organism development", "dna", "biology", "mouse", "somatic cells", "biochemistry", "nucleic acids", "genetic screens", "genetics", "cellular types", ...	Acute Versus Chronic Loss of Mammalian Azi1/Cep131 Results in Distinct Ciliary Phenotypes	journal.pgen.1003928	null	[ [ "Centrosomes are conserved animal organelles which function as the major microtubule organising centre ( MTOC ) , and are required for diverse processes including formation of cilia and flagella , intracellular trafficking events , cell polarity and division .", "Structurally , the centrosome consists of ...	[ "Defects in cilium and centrosome function result in a spectrum of clinically-related disorders , known as ciliopathies .", "However , the complex molecular composition of these structures confounds functional dissection of what any individual gene product is doing under normal and disease conditions .", "As pa...	[ "Cilia are slender projections from the surface of most mammalian cells and have sensory and sometimes motile functions .", "They are essential for mammalian development and defects in cilia lead to a group of human diseases , termed ciliopathies , with variable symptoms including embryonic lethality , lung and k...	2013
[ "Introduction", "Material and methods", "Results", "Discussion" ]	[ "blood cells", "innate immune system", "medicine and health sciences", "immune physiology", "cytokines", "pathology and laboratory medicine", "immune cells", "body fluids", "pathogens", "immunology", "microbiology", "opportunistic infections", "cloning", "retroviruses", "viruses", "dev...	Switching and loss of cellular cytokine producing capacity characterize in vivo viral infection and malignant transformation in human T- lymphotropic virus type 1 infection	journal.ppat.1006861	null	[ [ "Human T- lymphotropic virus type-1 ( HTLV-1 ) is a complex delta retrovirus infecting an estimated 10 million individuals worldwide [1] .", "In the majority , infection leads to a chronic asymptomatic carrier state ( AC ) but 2% to 6% develop adult T-cell leukaemia/lymphoma ( ATL ) and another 3% inflamm...	[ "Adult T-cell leukaemia/lymphoma ( ATL ) arises from chronic non-malignant human T lymphotropic virus type-1 ( HTLV-1 ) infection which is characterized by high plasma pro-inflammatory cytokines whereas ATL is characterized by high plasma anti-inflammatory ( IL-10 ) concentrations .", "The poor prognosis of ATL i...	[ "Human T-cell lymphotropic virus type-1 ( HTLV-1 ) infection of CD4+ T cells is associated with a change in their cytokine producing capacity and is responsible for the different plasma cytokine profiles in patients with adult T-cell leukaemia/Lymphoma ( ATL ) and non-malignant HTLV-1 infection .", "Dominant mali...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Two Portable Recombination Enhancers Direct Donor Choice in Fission Yeast Heterochromatin	journal.pgen.1003762	null	[ [ "Fission yeast cells switch mating type by directed recombination events where the information in the expressed mat1 locus is replaced with information copied from one of two silent loci , mat2 or mat3 ( reviewed in [1] ) .", "The system allows investigating multiple facets of recombination , including ef...	[ "Mating-type switching in fission yeast results from gene conversions of the active mat1 locus by heterochromatic donors .", "mat1 is preferentially converted by mat2-P in M cells and by mat3-M in P cells .", "Here , we report that donor choice is governed by two portable recombination enhancers capable of prom...	[ "The state of chromatin , heterochromatin or euchromatin , affects homologous recombination in eukaryotes .", "We study mating-type switching in fission yeast to learn how recombination is regulated in heterochromatin .", "Fission yeast exists as two mating-types , P or M , determined by the allele present at t...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases/neglected tropical diseases", "public health and epidemiology/epidemiology", "infectious diseases/helminth infections", "public health and epidemiology/screening", "infectious diseases/epidemiology and control of infectious diseases" ]	Occurrence of Strongyloides stercoralis in Yunnan Province, China, and Comparison of Diagnostic Methods	journal.pntd.0000075	null	[ [ "Soil-transmitted helminthiases are caused by infections with intestinal nematodes , of which Ascaris lumbricoides , Trichuris trichiura and the hookworms ( Ancylostoma duodenale and Necator americanus ) are the most widespread species [1–3] .", "Collectively , these soil-transmitted helminths affect over...	[ "Strongyloides stercoralis is a neglected soil-transmitted helminth species , and there is a lack of parasitologic and epidemiologic data pertaining to this parasite in China and elsewhere .", "We studied the local occurrence of S . stercoralis in a village in Yunnan province , China , and comparatively assessed ...	[ "An estimated 30 million to 100 million people are infected with the parasitic worm Strongyloides stercoralis , the causative agent of strongyloidiasis , and yet this is a neglected tropical disease .", "The diagnosis of this parasite requires specialized techniques ( e . g . Baermann and Koga agar plate method )...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology" ]	Variants in SUP45 and TRM10 Underlie Natural Variation in Translation Termination Efficiency in Saccharomyces cerevisiae	journal.pgen.1002211	null	[ [ "Translational fidelity is essential for functional integrity of the cell .", "Efficient termination is an important aspect of translational fidelity , and a multitude of mechanisms participate in this highly regulated process .", "Translation termination in eukaryotes is mediated by two termination f...	[ "Translation termination is a highly controlled process in the cell .", "In Saccharomyces cerevisiae , various regulatory factors employ genetic and epigenetic mechanisms to control this process .", "We used a quantitative dual luciferase reporter assay to demonstrate a difference in translation termination eff...	[ "Translation , the process of protein synthesis from messenger RNA ( mRNA ) , cannot be successfully completed without proper termination .", "The ends of the mRNA coding regions are marked by one of the three stop codons , which are recognized by termination factors rather than by the transfer RNAs ( tRNAs ) tha...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "neurochemistry", "action potentials", "engineering and technology", "signal processing", "depolarization", "membrane potential", "electrophysiology", "neuroscience", "signal filtering", "synaptic plasticity", "neuronal dendrites", "excitatory postsynaptic pot...	Control of Ca2+ Influx and Calmodulin Activation by SK-Channels in Dendritic Spines	journal.pcbi.1004949	null	[ [ "Associative learning is underpinned by Hebbian synaptic plasticity at glutamatergic synapses .", "Spike timing-dependent plasticity ( STDP ) is the classical manifestation of Hebbian plasticity where temporally correlated pre- and post-synaptic activity induces NMDA receptor ( NMDAR ) - and Ca2+ -depende...	[ "The key trigger for Hebbian synaptic plasticity is influx of Ca2+ into postsynaptic dendritic spines .", "The magnitude of [Ca2+] increase caused by NMDA-receptor ( NMDAR ) and voltage-gated Ca2+ -channel ( VGCC ) activation is thought to determine both the amplitude and direction of synaptic plasticity by diffe...	[ "Hebbian or associative plasticity is triggered by postsynaptic Ca2+ influx which activates calmodulin and CaMKII .", "The influx of Ca2+ through voltage-dependent NMDA receptors and Ca2+ channels is regulated by Ca2+ -activated K+ channels ( SK-channels ) providing negative feedback regulation of postsynaptic [C...	2016
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "antimicrobials", "medicine and health sciences", "pathology and laboratory medicine", "drugs", "tropical diseases", "microbiology", "rna extraction", "physiological processes", "bacterial diseases", "signs and symptoms", "antibiotics", "neglected tropical diseases", "pharmacology", "cellu...	Clearance of viable Mycobacterium ulcerans from Buruli ulcer lesions during antibiotic treatment as determined by combined 16S rRNA reverse transcriptase /IS 2404 qPCR assay	journal.pntd.0005695	null	[ [ "Buruli ulcer is a neglected tropical disease caused by infection with Mycobacterium ulcerans ( Mu ) which is common in rural parts of West African countries including Ghana [1] .", "It causes large , disfiguring skin ulcers mainly in children aged 5 to 15 years although any age can be affected [2] .", ...	[ "Buruli ulcer ( BU ) caused by Mycobacterium ulcerans is effectively treated with rifampicin and streptomycin for 8 weeks but some lesions take several months to heal .", "We have shown previously that some slowly healing lesions contain mycolactone suggesting continuing infection after antibiotic therapy .", "...	[ "Buruli ulcer ( BU ) caused by Mycobacterium ulcerans is effectively treated with rifampicin and streptomycin for 8 weeks but some lesions take several months to heal .", "We have shown previously that some slowly healing lesions contain the M . ulcerans toxin , mycolactone , suggesting continuing infection after...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "learning", "cognitive neuroscience", "psychology", "social and behavioral sciences", "cognitive psychology", "decision making", "biology", "neuroscience", "learning and memory" ]	A Mixture of Delta-Rules Approximation to Bayesian Inference in Change-Point Problems	journal.pcbi.1003150	null	[ [ "Decisions are often guided by beliefs about the probability and utility of potential outcomes .", "These beliefs are learned through past experiences that , in stable environments , can be used to generate accurate predictions .", "However , in dynamic environments , changes can occur that render pas...	[ "Error-driven learning rules have received considerable attention because of their close relationships to both optimal theory and neurobiological mechanisms .", "However , basic forms of these rules are effective under only a restricted set of conditions in which the environment is stable .", "Recent studies ha...	[ "The ability to make accurate predictions is important to thrive in a dynamic world .", "Many predictions , like those made by a stock picker , are based , at least in part , on historical data thought also to reflect future trends .", "However , when unexpected changes occur , like an abrupt change in the valu...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "evolutionary biology/animal genetics", "geriatrics/geriatric ophthalmology", "ophthalmology/retinal disorders", "developmental biology/aging", "genetics and genomics/disease models" ]	The Identification of Zebrafish Mutants Showing Alterations in Senescence-Associated Biomarkers	journal.pgen.1000152	null	[ [ "Chronic oxidative stress has been shown to reduce lifespan in many species and lead to accelerated aging [1]–[3] .", "It has also been reported that oxidative stress is involved in neurodegeneration , sarcopenia and other muscle wasting conditions , which are accompanied by multiple aging symptoms [4]–[6...	[ "There is an interesting overlap of function in a wide range of organisms between genes that modulate the stress responses and those that regulate aging phenotypes and , in some cases , lifespan .", "We have therefore screened mutagenized zebrafish embryos for the altered expression of a stress biomarker , senesc...	[ "By performing genetic mutant screens using senescence-associated biomarkers , we show that the zebrafish is a tractable model system for the study of aging .", "In vertebrate organisms , it has not previously been possible to carry out systematic screens for genes that are important for stress responses and agin...	2008
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "antimicrobials", "medicine and health sciences", "pathology and laboratory medicine", "chikungunya infection", "drugs", "immunology", "tropical diseases", "microbiology", "parasitic diseases", "salmonellosis", "bacterial diseases", "signs and symptoms", "antibiotics", "neglected tropical ...	A novel diagnostic algorithm equipped on an automated hematology analyzer to differentiate between common causes of febrile illness in Southeast Asia	journal.pntd.0007183	null	[ [ "Arboviruses and bacterial infections such as salmonellosis , leptospirosis , and rickettsiosis are common causes of acute febrile illness in tropical and subtropical countries [1–3] .", "Discriminating between these infections is of great importance to triage patients in need of antibiotics or monitoring...	[ "Distinguishing arboviral infections from bacterial causes of febrile illness is of great importance for clinical management .", "The Infection Manager System ( IMS ) is a novel diagnostic algorithm equipped on a Sysmex hematology analyzer that evaluates the host response using novel techniques that quantify cell...	[ "Distinguishing arboviral infections , such as dengue , from bacterial causes of febrile illness is of great importance for clinical management and antimicrobial stewardship .", "In resource-limited countries , costly and expertise-reliant diagnostic assays cannot be performed routinely .", "The Infection Manag...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "neuroscience/behavioral neuroscience", "mathematics", "neuroscience/cognitive neuroscience", "neuroscience/theoretical neuroscience" ]	Can Monkeys Choose Optimally When Faced with Noisy Stimuli and Unequal Rewards?	journal.pcbi.1000284	null	[ [ "There is increasing evidence from in vivo recordings in monkeys that oculomotor decision making in the brain mimics a drift-diffusion ( DD ) process , with neural activity rising to a threshold before movement initiation [1]–[4] .", "In one well-studied task , monkeys are trained to decide the direction ...	[ "We review the leaky competing accumulator model for two-alternative forced-choice decisions with cued responses , and propose extensions to account for the influence of unequal rewards .", "Assuming that stimulus information is integrated until the cue to respond arrives and that firing rates of stimulus-selecti...	[ "Decisions are commonly based on multiple sources of information .", "In a forced choice task , for example , sensory information about the identity of a stimulus may be combined with prior information about the amount of reward associated with each choice .", "We employed a well-characterized motion discrimina...	2009
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Histamine 1 Receptor Blockade Enhances Eosinophil-Mediated Clearance of Adult Filarial Worms	journal.pntd.0003932	null	[ [ "Filariae are vector-borne tissue-invasive nematodes that infect over 100 million people worldwide and cause the debilitating conditions of river blindness and elephantiasis [1] .", "A major obstacle to ongoing efforts to control and potentially eradicate these diseases is the limited ability of anti-fila...	[ "Filariae are tissue-invasive nematodes that cause diseases such as elephantiasis and river blindness .", "The goal of this study was to characterize the role of histamine during Litomosoides sigmodontis infection of BALB/c mice , a murine model of filariasis .", "Time course studies demonstrated that while exp...	[ "Filariae are tissue-invasive parasitic roundworms that infect over 100 million people worldwide and cause debilitating conditions such as river blindness and elephantiasis .", "One of the major factors limiting our ability to eliminate these infections is the lack of drugs that kill adult worms when given as a s...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Effectiveness Study of Paromomycin IM Injection (PMIM) for the Treatment of Visceral Leishmaniasis (VL) in Bangladesh	journal.pntd.0004118	null	[ [ "Visceral leishmaniasis ( VL ) , also known as kala-azar , remains one of the most neglected diseases in Bangladesh with an estimated 65 million people at risk of the disease [1] .", "Widely available , safe , and affordable therapies for visceral leishmaniasis are needed .", "Although VL was nearly e...	[ "This study was conducted in Bangladeshi patients in an outpatient setting to support registration of Paromomycin Intramuscular Injection ( PMIM ) as a low-cost treatment option in Bangladesh .", "This Phase IIIb , open-label , multi-center , single-arm trial assessed the efficacy and safety of PMIM administered ...	[ "Effective and safe therapies for visceral leishmaniasis ( VL ) , also known as kala-azar , at an affordable cost are urgently needed in Bangladesh .", "Although sodium stibogluconate , miltefosine , and paromomycin are included in the National Essential Drug List for VL , only miltefosine is currently registered...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Auditory Frequency and Intensity Discrimination Explained Using a Cortical Population Rate Code	journal.pcbi.1003336	null	[ [ "The nature of the neural code for perception is a fundamental question in neuroscience 1–5 .", "In auditory neuroscience , the search for the neural code for pitch—an essential perceptual attribute of sound classes such as music and speech—has attracted considerable interest [6]–[9] .", "Two main typ...	[ "The nature of the neural codes for pitch and loudness , two basic auditory attributes , has been a key question in neuroscience for over century .", "A currently widespread view is that sound intensity ( subjectively , loudness ) is encoded in spike rates , whereas sound frequency ( subjectively , pitch ) is enc...	[ "A widely held view among auditory scientists is that the neural code for sound intensity ( or loudness ) involves temporally coarse spike-rate information , whereas the code for sound frequency ( or pitch ) requires more fine-grained and precise spike timing information .", "One problem with this view is that ne...	2013
[ "Introduction", "Results", "Discussion", "Conclusion", "Methods" ]	[ "medicine and health sciences", "tissue proteins", "phase iii clinical investigation", "protein expression", "clinical medicine", "mathematics", "artificial intelligence", "pharmacology", "molecular biology techniques", "discrete mathematics", "combinatorics", "research and analysis methods", ...	Systematic interrogation of diverse Omic data reveals interpretable, robust, and generalizable transcriptomic features of clinically successful therapeutic targets	journal.pcbi.1006142	null	[ [ "More than half of drug candidates that advance beyond phase I clinical trials fail due to lack of efficacy [1 , 2] .", "One possible explanation for these failures is sub-optimal target selection [3] .", "Many factors must be considered when selecting a target for drug discovery [4 , 5] .", "Intr...	[ "Target selection is the first and pivotal step in drug discovery .", "An incorrect choice may not manifest itself for many years after hundreds of millions of research dollars have been spent .", "We collected a set of 332 targets that succeeded or failed in phase III clinical trials , and explored whether Omi...	[ "Drug discovery often begins with a hypothesis that changing the abundance or activity of a target—a biological molecule , usually a protein—will cure a disease or ameliorate its symptoms .", "Whether a target hypothesis translates into a successful therapy depends in part on the characteristics of the target , b...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "mitogenic signaling", "host-pathogen interaction", "microbiology", "g-protein signaling", "pasteurellosis", "bacterial diseases", "gtpase signaling", "mapk signaling cascades", "bacterial pathogens", "erk signaling cascade", "infectious diseases", "signaling in cellular processe...	Pasteurella Multocida Toxin Prevents Osteoblast Differentiation by Transactivation of the MAP-Kinase Cascade via the Gαq/11 - p63RhoGEF - RhoA Axis	journal.ppat.1003385	null	[ [ "Bone tissue is a common target for bacterial infections .", "Diseases like caries , periodontitis or osteomyelitis are due to infections by Streptococcus mutans , Actinobacillus actinomycetemcomitans or Staphylococcus aureus inter alia .", "The mechanism of bacterial-induced bone damage may be caused...	[ "The 146-kDa Pasteurella multocida toxin ( PMT ) is the main virulence factor to induce P . multocida-associated progressive atrophic rhinitis in various animals .", "PMT leads to a destruction of nasal turbinate bones implicating an effect of the toxin on osteoblasts and/or osteoclasts .", "The toxin induces c...	[ "Pasteurella multocida causes as a facultative pathogen various diseases in men and animals .", "One induced syndrome is atrophic rhinitis , which is a form of osteopenia , mainly characterized by facial distortion due to degradation of nasal turbinate bones .", "Strains , which especially affect bone tissue , ...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "antimicrobials", "cell death", "invertebrates", "medicine and health sciences", "rna interference", "drugs", "cell processes", "permeability", "microbiology", "diet", "animals", "animal models", "drosophila melanogaster", "model organisms", "nutrition", "antibiotics", "materials sci...	Dietary restriction improves intestinal cellular fitness to enhance gut barrier function and lifespan in D. melanogaster	journal.pgen.1007777	null	[ [ "The intestinal epithelium forms a permeable barrier that segregates the internal and external environments , allowing for the absorption of nutrients , but at the same time keeping toxic substances and pathogens from entering the body .", "The intestine also manages the interaction between the host and t...	[ "Loss of gut integrity is linked to various human diseases including inflammatory bowel disease .", "However , the mechanisms that lead to loss of barrier function remain poorly understood .", "Using D . melanogaster , we demonstrate that dietary restriction ( DR ) slows the age-related decline in intestinal in...	[ "Dietary restriction ( DR ) is a robust environmental method to slow aging and age-related diseases in diverse organisms .", "Age-related disruption of gut integrity has been observed in both mammals and fruit flies and is a determinant of lifespan .", "In Drosophila , DR is able to slow the age-related decline...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Optimising and Communicating Options for the Control of Invasive Plant Disease When There Is Epidemiological Uncertainty	journal.pcbi.1004211	null	[ [ "Impacts of invading pathogens can be extremely severe , and so understanding how controls can be optimised is imperative [1] .", "We focus here on plant disease , motivated by the serious and potentially irreparable ecological damage that can follow introductions of plant pathogens into natural host popu...	[ "Although local eradication is routinely attempted following introduction of disease into a new region , failure is commonplace .", "Epidemiological principles governing the design of successful control are not well-understood .", "We analyse factors underlying the effectiveness of reactive eradication of local...	[ "Increases in global trade and travel suggest outbreaks of plant disease caused by invasive pathogens will increase in frequency .", "We use mathematical modelling to show how control of such disease outbreaks can be optimised .", "Although our methods and analyses are generic , we use the attempted eradication...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "nucleic acid synthesis", "pathology and laboratory medicine", "togaviruses", "chikungunya infection", "pathogens", "biological cultures", "tropical diseases", "microbiology", "alphaviruses", "viruses", "chikungunya virus", "rna viruses", "neglected tropical...	New World and Old World Alphaviruses Have Evolved to Exploit Different Components of Stress Granules, FXR and G3BP Proteins, for Assembly of Viral Replication Complexes	journal.ppat.1005810	null	[ [ "The Alphavirus genus of the Togaviridae family contains a wide variety of human and animal pathogens .", "Alphaviruses are broadly distributed on all continents , where they are transmitted between vertebrate hosts by mosquito vectors .", "The alphavirus genome is a single-stranded RNA of positive po...	[ "The positive-strand RNA viruses initiate their amplification in the cell from a single genome delivered by virion .", "This single RNA molecule needs to become involved in replication process before it is recognized and degraded by cellular machinery .", "In this study , we show that distantly related New Worl...	[ "Many viruses encode proteins containing intrinsically disordered domains , whose functions are as yet unknown .", "Here we show that such a domain ( HVD ) in the alphavirus nsP3 protein orchestrates assembly of viral replication complexes through interaction with RNA-binding cellular factors .", "Surprisingly ...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "learning", "medicine and health sciences", "social sciences", "neuroscience", "learning and memory", "perceptual learning", "perception", "cognitive psychology", "computer vision", "vision", "neuronal tuning", "research and analysis methods", "sensory physiology", "computer and informatio...	Feature reliability determines specificity and transfer of perceptual learning in orientation search	journal.pcbi.1005882	null	[ [ "Training in fundamental visual perceptual tasks can lead to substantial improvement , a phenomenon known as Visual Perceptual Learning ( VPL ) , which is associated with adult brain plasticity .", "VPL has powerful real-word applications [1–3] including improving the vision of adults with cortical blindn...	[ "Training can modify the visual system to produce a substantial improvement on perceptual tasks and therefore has applications for treating visual deficits .", "Visual perceptual learning ( VPL ) is often specific to the trained feature , which gives insight into processes underlying brain plasticity , but limits...	[ "Training can modify the visual system to produce improvements on perceptual tasks ( visual perceptual learning ) , which is associated with adult brain plasticity .", "Visual perceptual learning has important clinical applications: it improves the vision of adults with visual deficits , e . g . amblyopia and cor...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "homo (human)", "genetics and genomics" ]	Combined Genome Scans for Body Stature in 6,602 European Twins: Evidence for Common Caucasian Loci	journal.pgen.0030097	null	[ [ "Human adult stature ( body height ) has been the target of numerous genetic quantitative trait linkage studies in the past few years [1–17] .", "Despite high heritability estimates for all populations , based on either twin comparison [18–21] or on actual genetic resemblance in siblings [22] , the result...	[ "Twin cohorts provide a unique advantage for investigations of the role of genetics and environment in the etiology of variation in common complex traits by reducing the variance due to environment , age , and cohort differences .", "The GenomEUtwin ( http://www . genomeutwin . org ) consortium consists of eight ...	[ "Twin cohorts provide a unique advantage for research of the role of genetics and environment behind common complex traits by reducing the variance due to environment , age , and cohort differences .", "The GenomEUtwin consortium consists of eight twin cohorts with the total resource of hundreds of thousands of t...	2007

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