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headings list	keywords list	title stringlengths 20 281	id stringlengths 20 20	toc stringlengths 57 522 ⌀	sections list	abstract list	summary list	year stringclasses 13 values
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "fungal genetics", "statistics", "light microscopy", "fungal structure", "fungi", "statistical data", "confocal laser microscopy", "mathematics", "dna replication", "microscopy", "genome analysis", "confocal microscopy", "dna", "research and analysis methods", "mycology", "gene express...	Danger signals activate a putative innate immune system during regeneration in a filamentous fungus	journal.pgen.1007390	null	[ [ "The idea of regenerating lost body parts has fascinated humans since the beginning of history [1] .", "Human imagination was further captured upon witnessing the extraordinary capacity of species from almost all Phyla to , upon damage , regenerate a lost part or structure [1] .", "Nevertheless , our ...	[ "The ability to respond to injury is a biological process shared by organisms of different kingdoms that can even result in complete regeneration of a part or structure that was lost .", "Due to their immobility , multicellular fungi are prey to various predators and are therefore constantly exposed to mechanical...	[ "The idea of regenerating lost body parts has always fascinated humans due to its impact on human health .", "Recently , the study of the response to damage has gained importance not only in regenerative medicine , but also in organ transplantation .", "We have established a microbial model that given its relat...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Dominant Mutations in S. cerevisiae PMS1 Identify the Mlh1-Pms1 Endonuclease Active Site and an Exonuclease 1-Independent Mismatch Repair Pathway	journal.pgen.1003869	null	[ [ "DNA mismatch repair ( MMR ) acts to repair the potentially mutagenic misincorporation errors that occur during normal DNA replication and the absence of MMR results in increased rates of accumulating mutations .", "Consequently , defects in human MMR genes cause the hereditary cancer susceptibility syndr...	[ "Lynch syndrome ( hereditary nonpolypsis colorectal cancer or HNPCC ) is a common cancer predisposition syndrome .", "Predisposition to cancer in this syndrome results from increased accumulation of mutations due to defective mismatch repair ( MMR ) caused by a mutation in one of the mismatch repair genes MLH1 , ...	[ "Lynch syndrome ( hereditary nonpolypsis colorectal cancer or HNPCC ) is a common cancer predisposition syndrome .", "Predisposition to cancer in this syndrome results from increased accumulation of mutations due to defective mismatch repair ( MMR ) caused by a mutation in one of the mismatch repair genes MLH1 , ...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "immune physiology", "spleen", "ears", "immunology", "microbiology", "parasitic diseases", "parasitic protozoans", "protozoan life cycles", "animal models", "preventive medicine", "developmental biology", "model organisms", "protozoans", "leishmania", "e...	Vaccination with a Leishmania infantum HSP70-II null mutant confers long-term protective immunity against Leishmania major infection in two mice models	journal.pntd.0005644	null	[ [ "Leishmaniases are a group of vector-borne diseases caused by the transmission of the protozoan parasite Leishmania in different mammalian hosts , during the blood meal of the invertebrate vectors ( phlebotomine sandflies ) .", "Depending on the species of the parasite and the immune response of the host ...	[ "The immunization with genetically attenuated Leishmania cell lines has been associated to the induction of memory and effector T cell responses against Leishmania able to control subsequent challenges .", "A Leishmania infantum null mutant for the HSP70-II genes has been described , possessing a non-virulent phe...	[ "Despite numerous efforts made , a vaccine against leishmaniasis for humans is not available .", "Attempts based on parasite fractions or selected antigens failed to confer long lasting protection .", "On the other side , leishmanization , which consists in the inoculation of live virulent parasites in hidden p...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "microbiology/microbial physiology and metabolism", "cell biology/chemical biology of the cell", "computational biology/metabolic networks", "computational biology/systems biology" ]	A Minimal Model of Metabolism-Based Chemotaxis	journal.pcbi.1001004	null	[ [ "Behavioral analysis of chemotaxis in E . coli has shown that up-gradient or down-gradient directional movement is achieved through the combination of two basic types of movements , tumbling and running ( see Figure 1 ) .", "These two behaviors are both achieved through the rotation of flagella .", "R...	[ "Since the pioneering work by Julius Adler in the 1960's , bacterial chemotaxis has been predominantly studied as metabolism-independent .", "All available simulation models of bacterial chemotaxis endorse this assumption .", "Recent studies have shown , however , that many metabolism-dependent chemotactic patt...	[ "Traditionally , bacterial chemotaxis has been treated as metabolism-independent .", "Under this assumption , dedicated chemotaxis signalling pathways operate independently of metabolic processes .", "There is however , in various strains of bacteria , growing evidence of metabolism-dependent chemotaxis where m...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "acoustics", "vocalization", "medicine and health sciences", "engineering and technology", "ears", "vertebrates", "animals", "mammals", "animal signaling and communication", "echoes", "animal behavior", "computer vision", "remote sensing", "zoology", "computer and information sciences", ...	Action Enhances Acoustic Cues for 3-D Target Localization by Echolocating Bats	journal.pbio.1002544	As an echolocating bat tracks a moving target, it produces head waggles and adjusts the separation of the tips of its ears to enhance cues for target detection and localization. These findings suggest parallels in active sensing between echolocation and vision.	[ [ "Animals experience complex and noisy sensory information when navigating in the natural environment , and they must employ strategies to selectively sample and process biologically relevant signals in dynamic contexts [1 , 2] .", "One strategy for parsing complex sensory information is “active sensing , ...	[ "Under natural conditions , animals encounter a barrage of sensory information from which they must select and interpret biologically relevant signals .", "Active sensing can facilitate this process by engaging motor systems in the sampling of sensory information .", "The echolocating bat serves as an excellent...	[ "As animals operate in the natural environment , they must detect and process relevant sensory information embedded in complex and noisy signals .", "One strategy to overcome this challenge is to use active sensing or behavioral adjustments to extract sensory information from a selected region of the environment ...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Selectivity by Small-Molecule Inhibitors of Protein Interactions Can Be Driven by Protein Surface Fluctuations	journal.pcbi.1004081	null	[ [ "Selectivity of a compound for its desired protein target—or targets—is an important property optimized in the course of small-molecule drug discovery [1] .", "Some diseases , such as chronic myeloid leukemia , can be traced to dysfunction of a single protein target ( BCR-ABL ) ; in such cases , drugs suc...	[ "Small-molecules that inhibit interactions between specific pairs of proteins have long represented a promising avenue for therapeutic intervention in a variety of settings .", "Structural studies have shown that in many cases , the inhibitor-bound protein adopts a conformation that is distinct from its unbound a...	[ "Despite intense interest and considerable effort , there are few examples of small molecules that directly inhibit protein-protein interactions .", "Crystal structures of early successes have highlighted the plasticity of the protein surface , as some inhibitor-bound proteins are captured in conformations that a...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "immune physiology", "ears", "immunology", "cytomegalovirus infection", "neuroscience", "animal models", "outer hair cells", "otology", "inner ear", "model organisms", "microscopy", "experimental organism systems", "hearing...	Natural killer cells attenuate cytomegalovirus-induced hearing loss in mice	journal.ppat.1006599	null	[ [ "Cytomegalovirus ( CMV ) is the most common infectious cause of congenital sensorineural hearing loss ( SNHL ) in humans [1] with between 15–30% of pediatric hearing loss attributable to this infection [2–4] .", "The consequences of hearing loss for affected children include speech and language delay , po...	[ "Congenital cytomegalovirus ( CMV ) infection is the most common non-hereditary cause of sensorineural hearing loss ( SNHL ) yet the mechanisms of hearing loss remain obscure .", "Natural Killer ( NK ) cells play a critical role in regulating murine CMV infection via NK cell recognition of the Ly49H cell surface ...	[ "Cytomegalovirus ( CMV ) transmission from an infected mother to her fetus is a leading cause of permanent hearing loss in children , but the contributing processes are not clear .", "In this report , we utilized a mouse model , which recapitulates many features of congenital CMV mediated childhood hearing loss ,...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "gene networks", "animal genetics", "gene regulation", "microbiology", "parasitology", "dna transcription", "gene function", "parasite physiology", "genome analysis tools", "genome databases", "molecular genetics", "microbial growth and development", "quantitative parasitology", "gene expr...	Transcriptome Analyses of Inhibitor-treated Schistosome Females Provide Evidence for Cooperating Src-kinase and TGFβ Receptor Pathways Controlling Mitosis and Eggshell Formation	journal.ppat.1003448	null	[ [ "Blood-dwelling endoparasites of the genus Schistosoma are the only trematodes that have evolved a gender dimorphism [1] , [2] .", "These parasites cause schistosomiasis , which is of worldwide significance for humans and animals in tropical and sub-tropical areas [3] .", "About 780 million people liv...	[ "Schistosome parasites cause schistosomiasis , one of the most prevalent parasitemias worldwide affecting humans and animals .", "Constant pairing of schistosomes is essential for female sexual maturation and egg production , which causes pathogenesis .", "Female maturation involves signaling pathways controlli...	[ "As one of the most prevalent parasitic infections worldwide , schistosomiasis is caused by blood-flukes of the genus Schistosoma .", "Pathology coincides with egg production , which is started upon pairing of the dioeciously living adults .", "A constant pairing contact is required to induce mitoses and differ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics of disease", "insulin-dependent signal transduction", "signal transduction", "developmental biology", "cell biology", "molecular development", "genetics", "tor signaling", "biology and life sciences", "molecular cell biology", "cell signaling", "gene function" ]	Ribosomal Protein Mutations Induce Autophagy through S6 Kinase Inhibition of the Insulin Pathway	journal.pgen.1004371	null	[ [ "Diseases linked to mutations affecting the ribosome include inherited disorders such as Diamond-Blackfan anemia ( DBA ) , Shwachman-Diamond syndrome ( SDS ) , and dyskeratosis congenita ( DC ) [1] .", "They may also be acquired as with 5q-myelodysplastic syndrome ( 5q-MDS ) [2] .", "While the phenoty...	[ "Mutations affecting the ribosome lead to several diseases known as ribosomopathies , with phenotypes that include growth defects , cytopenia , and bone marrow failure .", "Diamond-Blackfan anemia ( DBA ) , for example , is a pure red cell aplasia linked to the mutation of ribosomal protein ( RP ) genes .", "He...	[ "Diseases linked to mutations affecting the ribosome , ribosomopathies , have an exceptionally wide range of phenotypes .", "However , many ribosomopathies have some features in common including cytopenia and growth defects .", "Our study aims to clarify the mechanisms behind these common phenotypes .", "We f...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "reproductive system", "spermatocytes", "rna interference", "cloning", "cell differentiation", "germ cells", "developmental biology", "stem cells", "molecular biology techniques", "epigenetics", "sperm", "research and analysis methods", "adult stem cells", ...	DREF Genetically Counteracts Mi-2 and Caf1 to Regulate Adult Stem Cell Maintenance	journal.pgen.1008187	null	[ [ "Adult stem cells maintain tissues during the lifetime of an organism by replenishing short-lived differentiated cells such as in the skin , intestinal epithelium and blood .", "Adult stem cells also give rise to differentiated cells upon injury in tissues such as skeletal muscle and lung .", "To main...	[ "Active adult stem cells maintain a bipotential state with progeny able to either self-renew or initiate differentiation depending on extrinsic signals from the surrounding microenvironment .", "However , the intrinsic gene regulatory networks and chromatin states that allow adult stem cells to make these cell fa...	[ "Many adult tissues are maintained throughout life by the dual ability of adult stem cells to produce progeny that either self-renew or differentiate to replace specialized cells lost to turnover or damage .", "Although signals from the surrounding microenvironment have been shown to regulate the choice between s...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "learning and memory", "developmental neuroscience", "cellular neuroscience", "ion channels", "synaptic plasticity", "synapses", "computational neuroscience", "single neuron function", "biology", "neuroscience", "neurophysiology" ]	The Effects of NMDA Subunit Composition on Calcium Influx and Spike Timing-Dependent Plasticity in Striatal Medium Spiny Neurons	journal.pcbi.1002493	null	[ [ "The striatum is the main input structure of the basal ganglia , which is necessary for proper motor function and habit formation .", "The medium spiny projection neurons ( MSPNs ) , which comprise ∼95% of striatal neurons , undergo changes in synaptic strength during the learning of a motor task [1] .", ...	[ "Calcium through NMDA receptors ( NMDARs ) is necessary for the long-term potentiation ( LTP ) of synaptic strength; however , NMDARs differ in several properties that can influence the amount of calcium influx into the spine .", "These properties , such as sensitivity to magnesium block and conductance decay kin...	[ "The striatum of the basal ganglia plays a key role in fluent motor control; pathology in this structure causes the motor symptoms of Parkinson's Disease and Huntington's Chorea .", "A putative cellular mechanism underlying learning of motor control is synaptic plasticity , which is an activity dependent change i...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "neuroscience/behavioral neuroscience", "genetics and genomics/gene function" ]	A Constant Light-Genetic Screen Identifies KISMET as a Regulator of Circadian Photoresponses	journal.pgen.1000787	null	[ [ "The rotation of the Earth on its axis is responsible for the mild temperatures found in most regions of the globe , which allow for a complex biosphere to thrive .", "However , this rotation is accompanied by important variations in light intensity and temperature , which are challenges for most organism...	[ "Circadian pacemakers are essential to synchronize animal physiology and behavior with the day∶night cycle .", "They are self-sustained , but the phase of their oscillations is determined by environmental cues , particularly light intensity and temperature cycles .", "In Drosophila , light is primarily detected...	[ "In most organisms , intracellular molecular pacemakers called circadian clocks coordinate metabolic , physiological , and behavioral processes during the course of the day .", "For example , they determine when animals are active or resting .", "Circadian clocks are self-sustained oscillators , but their free-...	2009
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "body fluids", "pathology and laboratory medicine", "ears", "parasitic diseases", "animals", "glossina", "otology", "ear infections", "tsetse fly", "insect vectors", "digestive system", "epidemiology", "exocrine glands", "head", "otorh...	The Dermis as a Delivery Site of Trypanosoma brucei for Tsetse Flies	journal.ppat.1005744	null	[ [ "Human African trypanosomiasis , also known as sleeping sickness , is indigenous for the African continent and is caused by two subspecies of Trypanosoma brucei , namely T . brucei rhodesiense and T . brucei gambiense .", "A range of other trypanosome species including T . congolense , T . vivax and T . b...	[ "Tsetse flies are the sole vectors of Trypanosoma brucei parasites that cause sleeping sickness .", "Our knowledge on the early interface between the infective metacyclic forms and the mammalian host skin is currently highly limited .", "Glossina morsitans flies infected with fluorescently tagged T . brucei par...	[ "Sleeping sickness is caused by trypanosomes that are transmitted by the blood feeding tsetse flies .", "The present study has established an experimental transmission model with fluorescently labeled parasites in mice that allows us to study their fate following natural transmission by a tsetse fly bite .", "P...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Predictive Coding of Dynamical Variables in Balanced Spiking Networks	journal.pcbi.1003258	null	[ [ "Neural systems need to integrate , store , and manipulate sensory information before acting upon it .", "Various neurophysiological and psychophysical experiments have provided examples of how these feats are accomplished in the brain , from the integration of sensory stimuli to decision-making [1] , fro...	[ "Two observations about the cortex have puzzled neuroscientists for a long time .", "First , neural responses are highly variable .", "Second , the level of excitation and inhibition received by each neuron is tightly balanced at all times .", "Here , we demonstrate that both properties are necessary conseque...	[ "Two observations about the cortex have puzzled and fascinated neuroscientists for a long time .", "First , neural responses are highly variable .", "Second , the level of excitation and inhibition received by each neuron is tightly balanced at all times .", "Here , we demonstrate that both properties are nec...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular biology" ]	Activator Control of Nucleosome Occupancy in Activation and Repression of Transcription	journal.pbio.0060317	A new nucleosome-occupancy technique reveals how the transcriptional activator Gal4 determines chromatin structure as genes are activated and repressed.	[ [ "Gal4 is an intensively studied transcriptional activator found in the yeast Saccharomyces cerevisiae .", "Galactose , added to the growth medium , frees Gal4 of its inhibitor Gal80 , and the DNA-bound activator quickly and strongly induces genes required to metabolize the sugar .", "Two such genes ar...	[ "The relationship between chromatin structure and gene expression is a subject of intense study .", "The universal transcriptional activator Gal4 removes promoter nucleosomes as it triggers transcription , but how it does so has remained obscure .", "The reverse process , repression of transcription , has often...	[ "In this paper , we examine activation and repression of transcription of a gene in yeast .", "This gene , like the typical human gene , is wrapped in DNA-protein packets called nucleosomes .", "It is widely believed that these condensed packets are unwrapped , in a process called nucleosome removal , as transc...	2008
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "atmospheric science", "geographical locations", "mathematical models", "electromagnetic radiation", "mathematics", "forecasting", "statistics (mathematics)", "atmospheric dynamics", "humidity", "research and analysis methods", "random walk", "south america", ...	Bayesian dynamic modeling of time series of dengue disease case counts	journal.pntd.0005696	null	[ [ "Dengue is an arboviral disease caused by a Flavivirus , leading to high morbidity in children and adults in tropical countries of Asia and Latin America [1] .", "There are four genetically distinct but antigenically related ( different serotypes ) dengue viruses named DEN-1 , DEN-2 , DEN-3 , and DEN-4 ."...	[ "The aim of this study is to model the association between weekly time series of dengue case counts and meteorological variables , in a high-incidence city of Colombia , applying Bayesian hierarchical dynamic generalized linear models over the period January 2008 to August 2015 .", "Additionally , we evaluate the...	[ "Time series analysis of dengue disease case counts are currently employed to establish associations between dengue disease and environmental , socioeconomic and climatic variables and to predict the evolution of dengue epidemics .", "Nowadays there is acceptance that climatic factors like environmental temperatu...	2017
[ "Introduction", "Method", "Results", "Discussion", "Discussion" ]	[ "haplotypes", "biology and life sciences", "population genetics", "computational biology", "evolutionary biology" ]	HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data	journal.pcbi.1003502	null	[ [ "While human and other eukaryotic genomes typically contain two copies of every chromosome , plants , yeast and fish such as salmon can have strictly more than two copies of each chromosome .", "By running standard genotype calling tools , it is possible to accurately identify the number of “wild type” an...	[ "As the more recent next-generation sequencing ( NGS ) technologies provide longer read sequences , the use of sequencing datasets for complete haplotype phasing is fast becoming a reality , allowing haplotype reconstruction of a single sequenced genome .", "Nearly all previous haplotype reconstruction studies ha...	[ "While human and other eukaryotic genomes typically contain two copies of every chromosome , plants , yeast and fish such as salmon can have strictly more than two copies of each chromosome .", "By running standard genotype calling tools , it is possible to accurately identify the number of “wild type” and “mutan...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunocytochemistry", "animal genetics", "genetic mutation", "protein interactions", "gene function", "developmental biology", "organism development", "molecular development", "molecular genetics", "morphogenesis", "sequence analysis", "cytochemistry", "proteins", "adhesion molecules", ...	Alp/Enigma Family Proteins Cooperate in Z-Disc Formation and Myofibril Assembly	journal.pgen.1003342	null	[ [ "Vertebrate muscles consist of three major types , skeletal , cardiac , and smooth muscles , which correspond in Drosophila to body wall , heart , and visceral muscle .", "Common to all is an actomyosin contractile system with thin filaments anchored at Z-discs .", "A crucial component of Z-discs is α...	[ "The Drosophila Alp/Enigma family protein Zasp52 localizes to myotendinous junctions and Z-discs .", "It is required for terminal muscle differentiation and muscle attachment .", "Its vertebrate ortholog ZASP/Cypher also localizes to Z-discs , interacts with α-actinin through its PDZ domain , and is involved in...	[ "Muscles are comprised of huge , multinucleated cells that feature a highly organized cytoskeletal architecture consisting of variable numbers of myofibrils , whose formation is not well understood .", "Each myofibril is an array of sarcomeres , the smallest contractile unit of muscles .", "The contractile syst...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "innate immune system", "medicine and health sciences", "sleep deprivation", "immune physiology", "cytokines", "rna interference", "sleep", "astrocytes", "immunology", "vertebrates", "neuroscience", "macroglial cells", "animals", "mammals", "animal models", "physiolo...	Astrocyte expression of the Drosophila TNF-alpha homologue, Eiger, regulates sleep in flies	journal.pgen.1007724	null	[ [ "The function of sleep and the neurobiology underlying the detrimental effects of sleep deprivation on physiological function are poorly understood .", "Understanding phylogenetic conservation of mechanisms that regulate sleep and the neurobiological consequences associated with sleep loss may provide imp...	[ "Sleep contributes to cognitive functioning and is sufficient to alter brain morphology and function .", "However , mechanisms underlying sleep regulation remain poorly understood .", "In mammals , tumor necrosis factor-alpha ( TNFα ) is known to regulate sleep , and cytokine expression may represent an evoluti...	[ "Every animal sleeps , from fruit flies to humans .", "However , the function of sleep is still currently unknown .", "Identifying conserved mechanisms of sleep regulation in evolutionarily ancient organisms may help us to understand the function of sleep .", "Therefore , we have examined whether Eiger , the ...	2018
[ "Introduction", "Results/Discussion", "Methods" ]	[ "biotechnology", "biochemistry", "secondary metabolism", "genomics", "genome evolution", "genetics", "synthetic biology", "biosynthesis", "biology and life sciences", "comparative genomics", "computational biology", "evolutionary biology", "microbiology", "metabolism", "microbial genomic...	A Systematic Computational Analysis of Biosynthetic Gene Cluster Evolution: Lessons for Engineering Biosynthesis	journal.pcbi.1004016	null	[ [ "Bacterial secondary metabolites are widely used as pharmaceutical , agricultural , and dietary agents .", "They consist of many classes of compounds including polyketides ( PKs ) , nonribosomal peptides ( NRPs ) , ribosomally synthesized and post-translationally modified peptides ( RiPPs ) , terpenoids ,...	[ "Bacterial secondary metabolites are widely used as antibiotics , anticancer drugs , insecticides and food additives .", "Attempts to engineer their biosynthetic gene clusters ( BGCs ) to produce unnatural metabolites with improved properties are often frustrated by the unpredictability and complexity of the enzy...	[ "Bacterial secondary metabolites mediate a broad range of microbe-microbe and microbe-host interactions , and are widely used in human medicine , agriculture and manufacturing .", "Despite recent advances in synthetic biology , efforts to engineer their biosynthetic genes for the production of unnatural variants ...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular biology/recombination", "genetics and genomics/gene discovery", "molecular biology/dna repair" ]	The Caenorhabditis elegans Homolog of Gen1/Yen1 Resolvases Links DNA Damage Signaling to DNA Double-Strand Break Repair	journal.pgen.1001025	null	[ [ "The correct maintenance and duplication of genetic information is constantly challenged by genotoxic stress .", "DNA double-strand breaks ( DSBs ) are amongst the most deleterious lesions .", "DSBs can be induced by ionizing irradiation ( IR ) or caused by the stalling of DNA replication forks .", ...	[ "DNA double-strand breaks ( DSBs ) can be repaired by homologous recombination ( HR ) , which can involve Holliday junction ( HJ ) intermediates that are ultimately resolved by nucleolytic enzymes .", "An N-terminal fragment of human GEN1 has recently been shown to act as a Holliday junction resolvase , but littl...	[ "Coordination of DNA repair with cell cycle progression and apoptosis is a central task of the DNA damage response machinery .", "A key intermediate of recombinational repair and meiotic recombination , first proposed in 1964 , involves four-stranded DNA structures .", "These intermediates have to be resolved u...	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "immune physiology", "nuclear staining", "pathology and laboratory medicine", "pathogens", "immunology", "tropical diseases", "microbiology", "light microscopy", "green fluorescent protein", "viruses", "rabies", "luminescent proteins", "rna viruses", "micr...	A high throughput neutralization test based on GFP expression by recombinant rabies virus	journal.pntd.0007011	null	[ [ "Human rabies is a zoonotic disease transmitted predominantly through bites from infected animals [1] .", "Although , rabies is nearly 100% fatal after onset of symptoms , it is preventable by post exposure prophylaxis ( PEP ) when administered immediately and appropriately after a suspect exposure .", ...	[ "The effectiveness of rabies vaccination in both humans and animals is determined by the presence of virus neutralizing antibodies ( VNAs ) .", "The Rapid Fluorescent Focus Inhibition Test ( RFFIT ) is the method traditionally used for detection and quantification of VNAs .", "It is a functional in vitro test f...	[ "The potency of rabies vaccine is demonstrated by the presence of virus neutralizing antibodies ( VNAs ) in serum .", "It is critical to evaluate immunologic status of individuals who work directly with rabies virus ( RABV ) ( laboratorians ) or at high risk of infection due to interaction with animals ( veterina...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cadherins", "mitosis", "developmental biology", "cell division", "cell adhesion", "adhesion molecules", "molecular development", "cell migration", "biology", "molecular cell biology", "morphogenesis", "cell differentiation", "cyclins" ]	Mitogen-Activated Protein Kinase (MAPK) Pathway Regulates Branching by Remodeling Epithelial Cell Adhesion	journal.pgen.1004193	null	[ [ "Receptor tyrosine kinase ( RTK ) signaling is a key mechanism through which extracellular stimuli guide development of the kidney and many other organs , but the specific in vivo functions of intracellular cascades activated downstream of RTKs remain poorly characterized .", "The kidney develops as a res...	[ "Although the growth factor ( GF ) signaling guiding renal branching is well characterized , the intracellular cascades mediating GF functions are poorly understood .", "We studied mitogen-activated protein kinase ( MAPK ) pathway specifically in the branching epithelia of developing kidney by genetically abrogat...	[ "Development of the ureter and collecting ducts of the kidney requires extensive growth and branching of an epithelial tube , the ureteric bud .", "While many genes that control this process are known , the intracellular signaling pathways that underlie renal morphogenesis remain poorly understood .", "The cell...	2014
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "toxins", "enzyme-linked immunoassays", "pathology and laboratory medicine", "tropical diseases", "geographical locations", "vertebrates", "animals", "toxicology", "toxic agents", "vaccines", "cobras", "reptiles", "neglected tropical diseases", "infectious...	Preclinical antivenom-efficacy testing reveals potentially disturbing deficiencies of snakebite treatment capability in East Africa	journal.pntd.0005969	null	[ [ "Snakebite annually kills over 95 , 000 people [1] residing in some of the most disadvantaged rural communities [2] , and leaves about 300 , 000 surviving victims with permanent physical disabilities and stigmatising disfigurements .", "Since it is the most economically-productive and educationally-vulner...	[ "Antivenom is the treatment of choice for snakebite , which annually kills an estimated 32 , 000 people in sub-Saharan Africa and leaves approximately 100 , 000 survivors with permanent physical disabilities that exert a considerable socioeconomic burden .", "Over the past two decades , the high costs of the most...	[ "Snakebite is one of the most under-researched , under-resourced high morbidty/high mortality NTDs , as reflected by the fact that many of the antivenoms used to treat snakebite victims in sub-Saharan Africa are of uncertain and untested efficacy .", "This Kenya case study is the first examination of the preclini...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "pathology and laboratory medicine", "helminths", "gene regulation", "immunology", "parasitic diseases", "animals", "mathematics", "statistics (mathematics)", "research and analysis methods", "mathematical and statistical techniques", "gene ex...	Comprehensive Transcriptome Meta-analysis to Characterize Host Immune Responses in Helminth Infections	journal.pntd.0004624	null	[ [ "Helminth infections , also known as helminthiases , are estimated to affect > 2 billion people and especially prevalent in developing countries .", "Despite recent progress in helminth control programs , much work remains to be done to achieve eradication [1] .", "To develop effective intervention st...	[ "Helminth infections affect more than a third of the world’s population .", "Despite very broad phylogenetic differences among helminth parasite species , a systemic Th2 host immune response is typically associated with long-term helminth infections , also known as the “helminth effect” .", "Many investigations...	[ "Many studies have been conducted to understand the immune modulatory effects in helminth infections .", "To determine whether there is a common transcriptomic signature characteristic of the helminth effect , we performed a comprehensive meta-analysis of publicly available gene expression datasets .", "The res...	2016
[ "Introduction", "Materials and methods", "Results and discussion" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "microbiology", "viruses", "genomic databases", "filoviruses", "rna viruses", "genome analysis", "microbial genomics", "research and analysis methods", "sequence analysis", "viral genomics", "sequence alignme...	Flavivirus and Filovirus EvoPrinters: New alignment tools for the comparative analysis of viral evolution	journal.pntd.0005673	null	[ [ "Flaviruses , including Dengue , Yellow Fever , Japanese Encephalitis and West Nile viruses , are significant public-health pathogens responsible for wide-spread epidemics .", "Recently , another member of this genus , Zika virus ( ZIKV ) , has emerged as a global public health threat ( reviewed in [1] ."...	[ "Flavivirus and Filovirus infections are serious epidemic threats to human populations .", "Multi-genome comparative analysis of these evolving pathogens affords a view of their essential , conserved sequence elements as well as progressive evolutionary changes .", "While phylogenetic analysis has yielded impor...	[ "Flaviviruses , including Zika and Dengue viruses , and Filoviruses , including Ebola and Marburg viruses , are significant global public health threats .", "Genetic surveillance of viral isolates provides important insights into the origin of outbreaks , reveals lineage heterogeneity and diversification , and fa...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "clinical research design", "clinical immunology", "clinical trials", "meta-analyses", "immune response" ]	HIV-1 Vaccine-Induced T-Cell Reponses Cluster in Epitope Hotspots that Differ from Those Induced in Natural Infection with HIV-1	journal.ppat.1003404	null	[ [ "The HIV epidemic is a major global health challenge leading to more than 1 . 8 million deaths annually , and despite significant efforts the search for an efficacious and safe vaccine continues .", "Many different formulations of candidate HIV vaccines have been proposed and tested in recent years [1] ."...	[ "Several recent large clinical trials evaluated HIV vaccine candidates that were based on recombinant adenovirus serotype 5 ( rAd-5 ) vectors expressing HIV-derived antigens .", "These vaccines primarily elicited T-cell responses , which are known to be critical for controlling HIV infection .", "In the current...	[ "The HIV epidemic is a major global health challenge leading to more than 1 . 8 million deaths annually , and despite significant efforts , the search for an efficacious and safe vaccine continues .", "Several candidate vaccines were designed to elicit CD8+ T-cell responses and were based on using recombinant Ade...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Tissue Expression Pattern of PMK-2 p38 MAPK Is Established by the miR-58 Family in C. elegans	journal.pgen.1004997	null	[ [ "Since the initial genetic identification of microRNAs in Caenorhabditis elegans [1 , 2] , biochemical cloning methods and computational approaches have identified hundreds of microRNAs [3 , 4] , though genetic analysis has defined functional roles for relatively few of these [5 , 6] .", "A single microRN...	[ "Analyses of gene expression profiles in evolutionarily diverse organisms have revealed a role for microRNAs in tuning tissue-specific gene expression .", "Here , we show that the relatively abundant and constitutively expressed miR-58 family of microRNAs sharply defines the tissue-specific expression of the broa...	[ "MicroRNAs are small , noncoding RNAs that act post-transcriptionally to inhibit expression of their target mRNAs .", "Gene expression studies of microRNAs and their target transcripts in diverse organisms have suggested that microRNAs may function to shape patterns of tissue expression .", "In this paper , we ...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "classical mechanics", "chemical compounds", "fluid mechanics", "quantum tunneling", "neuroscience", "organic compounds", "turbulence", "probability distribution", "animal behavior", "mathematics", "odorants", "materials science", "zoology", "quantum mechanics", "thermodynamics", "entr...	Information-theoretic analysis of realistic odor plumes: What cues are useful for determining location?	journal.pcbi.1006275	null	[ [ "Diverse species throughout the animal kingdom use olfactory cues for navigation tasks critical to survival , including locating food sources and mating partners .", "However , olfactory navigation is not simple: odorants are often volatile and carried on rapidly changing currents , resulting in spatiotem...	[ "Many species rely on olfaction to navigate towards food sources or mates .", "Olfactory navigation is a challenging task since odor environments are typically turbulent .", "While time-averaged odor concentration varies smoothly with the distance to the source , instaneous concentrations are intermittent and o...	[ "Navigating towards a food source or mating partner based on an animals’ sense of smell is a difficult task due to the complex spatiotemporal distribution of odor molecules .", "The most basic aspect of this task is the acquisition of samples from the environment .", "It is clear that odor concentration does no...	2018
[ "Introduction", "Results", "Discussion", "Methods and Materials" ]	[ "signal transduction", "fungi", "feedback regulation", "cell biology", "mechanisms of signal transduction", "cell cycle and cell division", "biology and life sciences", "cell processes", "saccharomyces cerevisiae", "saccharomyces", "organisms", "yeast" ]	Nur1 Dephosphorylation Confers Positive Feedback to Mitotic Exit Phosphatase Activation in Budding Yeast	journal.pgen.1004907	null	[ [ "Cellular reproduction is a highly regulated process that is controlled on a multiplicity of levels , ensuring orderly progression through the different phases of the cell cycle and accurate partitioning of the genome .", "At the heart of eukaryotic cell cycle control lie cyclin-dependent kinases ( Cdks )...	[ "Substrate dephosphorylation by the cyclin-dependent kinase ( Cdk ) -opposing phosphatase , Cdc14 , is vital for many events during budding yeast mitotic exit .", "Cdc14 is sequestered in the nucleolus through inhibitory binding to Net1 , from which it is released in anaphase following Net1 phosphorylation .", ...	[ "During the cell cycle , a specific sequence of events leads to the formation of two daughter cells from one mother cell .", "Progression through the cell cycle is tightly controlled , with events occurring in the right place at the right time .", "Exactly how this is achieved is still being elucidated .", "I...	2015
[ "Introduction", "Results", "Discussion", "Availability of data and materials" ]	[ "transfer rna", "small nucleolar rnas", "chemical bonding", "chemical characterization", "vesicles", "gene regulation", "messenger rna", "cellular structures and organelles", "physical chemistry", "research and analysis methods", "rna structure", "gene expression", "chemistry", "cross-link...	Transcriptome-wide analysis of alternative routes for RNA substrates into the exosome complex	journal.pgen.1006699	null	[ [ "In Eukaryotes , the exosome is the major RNA degradation complex responsible for quality control of most transcripts in both the nucleus and cytoplasm , processing of stable RNA precursors and turnover of pre-mRNAs , mRNAs and large numbers of non-coding RNAs ( ncRNAs ) .", "A puzzling aspect of exosome ...	[ "The RNA exosome complex functions in both the accurate processing and rapid degradation of many classes of RNA .", "Functional and structural analyses indicate that RNA can either be threaded through the central channel of the exosome or more directly access the active sites of the ribonucleases Rrp44 and Rrp6 ,...	[ "In all organisms , diverse classes of RNA perform a wide range of functions , including programing of protein synthesis , transcriptional and post-transcriptional regulation of gene expression and forming key structural and functional components for pre-mRNA splicing , ribosome synthesis and translation .", "In ...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "physiology/cardiovascular physiology and circulation", "neurological disorders/cerebrovascular disease", "non-clinical medicine/research methods", "pharmacology/drug development", "cardiovascular disorders/cardiovascular pharmacology", "genetics and genomics/gene function", "neurological disorders/neur...	Post-Stroke Inhibition of Induced NADPH Oxidase Type 4 Prevents Oxidative Stress and Neurodegeneration	journal.pbio.1000479	The identification of NOX4 as a major source of oxidative stress in stroke and demonstration of dramatic protection after stroke in mice by NOX4 deletion or NOX inhibition, opens up new avenues for treatment.	[ [ "Ischemic stroke has outstanding medical relevance as it is the second leading cause of death in industrialized countries [1] .", "Due to the aging of the population , the incidence of stroke is projected to rise even further in the future [2] .", "Despite tremendous research activity , with more than...	[ "Ischemic stroke is the second leading cause of death worldwide .", "Only one moderately effective therapy exists , albeit with contraindications that exclude 90% of the patients .", "This medical need contrasts with a high failure rate of more than 1 , 000 pre-clinical drug candidates for stroke therapies .", ...	[ "Stroke is the second leading cause of death worldwide .", "Today , only one approved therapy exists—a drug that breaks down blood clots—the effectiveness of which is moderate , and it can only be used in about 10% of patients because of contraindications .", "New therapeutic strategies that are translatable to...	2010
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "japanese encephalitis virus", "invertebrates", "medicine and health sciences", "body fluids", "pathology and laboratory medicine", "pathogens", "geographical locations", "microbiology", "vector-borne diseases", "vertebrates", "saliva", "animals", "viruses", "rna viruses", "insect vector...	Differential Infectivities among Different Japanese Encephalitis Virus Genotypes in Culex quinquefasciatus Mosquitoes	journal.pntd.0005038	null	[ [ "Japanese encephalitis virus ( JEV ) is a zoonotic flavivirus endemic in the Asian Pacific region .", "Transmission of JEV in endemic regions predominantly alternates between amplification hosts and Culex tritaeniorhynchus mosquitoes .", "Infected ardeid birds and pigs often develop high-titer viremia...	[ "During the last 20 years , the epidemiology of Japanese encephalitis virus ( JEV ) has changed significantly in its endemic regions due to the gradual displacement of the previously dominant genotype III ( GIII ) with clade b of GI ( GI-b ) .", "Whilst there is only limited genetic difference distinguishing the ...	[ "Japanese encephalitis virus ( JEV ) is a zoonotic flavivirus , which is primarily transmitted by Culex species mosquitoes and a leading cause of pediatric encephalitis in Asia .", "JEV is also an important public health threat to countries outside the endemic region because collections of Cx .", "quinquefascia...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Prevalence of Neurocysticercosis in People with Epilepsy in the Eastern Province of Zambia	journal.pntd.0003972	null	[ [ "Neurocysticercosis ( NCC ) is a parasitic infection of the brain caused by the metacestode larval stage of the pork tapeworm Taenia solium and occurs primarily in low-income countries .", "Pigs are the natural intermediate host for the tapeworm , while humans are the only definitive host but may accident...	[ "Zambia is endemic for Taenia solium taeniosis and cysticercosis .", "In this single-centered , cross-sectional , community-based study , the role of neurocysticercosis ( NCC ) as a cause of epilepsy was examined .", "People with epilepsy ( PWE , n = 56 ) were identified in an endemic area using a screening que...	[ "Neurocysticercosis , an infection caused by the larval stage of Taenia solium ( the pork tapeworm ) , is a preventable and treatable disease and one of the main causes of epilepsy in low-income countries .", "Studies in Zambia have indicated high endemicity of T . solium in rural communities where a high prevale...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Flexibility of Oral Cholera Vaccine Dosing—A Randomized Controlled Trial Measuring Immune Responses Following Alternative Vaccination Schedules in a Cholera Hyper-Endemic Zone	journal.pntd.0003574	null	[ [ "As a disease of poverty and inequity , cholera is often prevalent in areas of compromised sanitation , overcrowded conditions , and poor quality of water supply .", "An increasing number of longer lasting outbreaks have dramatically impacted the least developed countries ( LDCs ) , including those in Afr...	[ "A bivalent killed whole cell oral cholera vaccine has been found to be safe and efficacious for five years in the cholera endemic setting of Kolkata , India , when given in a two dose schedule , two weeks apart .", "A randomized controlled trial revealed that the immune response was not significantly increased f...	[ "The five year efficacy results of the bivalent , killed whole cell oral cholera vaccine was shown to offer 65% protection in cholera endemic Kolkata .", "Currently , two oral cholera vaccines ( OCV ) are prequalified by the World Health Organization: the whole cell recombinant cholera toxin B subunit vaccine ( D...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "physiology/cardiovascular physiology and circulation", "non-clinical medicine", "pharmacology/drug resistance", "physiology/muscle and connective tissue", "physiology/neuronal signaling mechanisms", "chemical biology" ]	A Genetic Screen for Dihydropyridine (DHP)-Resistant Worms Reveals New Residues Required for DHP-Blockage of Mammalian Calcium Channels	journal.pgen.1000067	null	[ [ "Calcium influx into the cell can make both an immediate and a long-term impact on many cellular processes , including membrane excitability , neurotransmitter release , muscle contraction , transcription , and proliferation [1] .", "It is therefore not surprising that calcium current through calcium-perm...	[ "Dihydropyridines ( DHPs ) are L-type calcium channel ( Cav1 ) blockers prescribed to treat several diseases including hypertension .", "Cav1 channels normally exist in three states: a resting closed state , an open state that is triggered by membrane depolarization , followed by a non-conducting inactivated stat...	[ "L-type calcium channels are important drug targets because they regulate many physiological processes throughout the body .", "For example , L-type calcium channels regulate cardiac myocytes and vascular smooth muscle contraction .", "Antagonists are therefore commonly used to lower blood pressure and treat ot...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "genetics and genomics/genomics", "genetics and genomics/comparative genomics", "genetics and genomics/functional genomics", "genetics and genomics/gene expression", "genetics and genomics/nuclear structure and function", "molecular biology/chromosome structure", "genetics and genomics/chromosome biolog...	The Role of Nucleosome Positioning in the Evolution of Gene Regulation	journal.pbio.1000414	A comparative genomics study maps nucleosomes across the entire genomes of 12 fungal species, identifying multiple distinct mechanisms linking changes in chromatin architecture to evolution of gene regulation.	[ [ "Regulatory differences affecting gene expression can play a major role in species evolution [1] and can help elucidate the functional mechanisms that control gene regulation [2] , [3] .", "Although specific examples of regulatory divergence are known in bacteria [4] , fungi [5] , , flies [9] , and mammal...	[ "Chromatin organization plays a major role in gene regulation and can affect the function and evolution of new transcriptional programs .", "However , it can be difficult to decipher the basis of changes in chromatin organization and their functional effect on gene expression .", "Here , we present a large-scal...	[ "Divergence in gene regulation plays a major role in organismal evolution .", "Evidence suggests that changes in the packaging of eukaryotic genomes into chromatin can underlie the evolution of divergent gene expression patterns .", "Here , we explore the role of chromatin structure in regulatory evolution by w...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "skin", "merkel cells", "medicine and health sciences", "integumentary system", "epithelial cells", "developmental signaling", "epidermis", "research and analysis methods", "specimen preparation and treatment", "staining", "hair", "animal cells", "biological tissue", "hair follicles", "h...	A Cascade of Wnt, Eda, and Shh Signaling Is Essential for Touch Dome Merkel Cell Development	journal.pgen.1006150	null	[ [ "The Hedgehog ( Hh ) pathway is conserved across the Metazoa subkingdom , and is one of a small number of intercellular signaling pathways that regulate the differentiation and pattering of morphologically diverse structures during development [1 , 2] .", "Postnatally , Hh ligands regulate tissue specific...	[ "The Sonic hedgehog ( Shh ) signaling pathway regulates developmental , homeostatic , and repair processes throughout the body .", "In the skin , touch domes develop in tandem with primary hair follicles and contain sensory Merkel cells .", "The developmental signaling requirements for touch dome specification ...	[ "Sonic hedgehog ( Shh ) is one of a limited set of signaling molecules that cells use to drive organ formation during development and tissue regeneration after birth .", "How Shh signaling achieves different biological effects in the same tissue is incompletely understood .", "Touch domes are unique sensory str...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "immune physiology", "pathology and laboratory medicine", "microbial cultures", "pathogens", "vibrio", "biological cultures", "tropical diseases", "microbiology", "geographical locations", "immunology", "diarrhea", "bacterial diseases", "crystals", "vibrio...	Field evaluation of a locally produced rapid diagnostic test for early detection of cholera in Bangladesh	journal.pntd.0007124	null	[ [ "Even with the development of modern established treatments and preventative measures , cholera still remains a major health burden in low-income countries with limited resources , particularly in the developing world .", "Cholera is a water-borne infectious disease which can be characterized by life-thre...	[ "Cholera remains a substantial health burden in Asia and Africa particularly in resource poor settings .", "The standard procedures to identify the etiological organism V . cholerae are isolation from microbiological culture from stool as well as Polymerase Chain Reaction ( PCR ) .", "Both the processes are hig...	[ "Cholera still remains a burning public health issue in the developing world .", "Microbiological culture is the gold standard method for cholera diagnosis .", "However , it requires well equipped laboratories and 24–72 hours’ time for the isolation of pathogens , which may not be feasible for hard to reach are...	2019
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "carbachol", "action potentials", "medicine and health sciences", "engineering and technology", "paracrine signaling", "drugs", "membrane potential", "electrophysiology", "neuroscience", "endocrine physiology", "probability distribution", "mathematics", "pharmacology", "statistical distrib...	A Bayesian approach to modelling heterogeneous calcium responses in cell populations	journal.pcbi.1005794	null	[ [ "Transient changes in the intracellular calcium ( Ca2+ ) concentration have long been associated with the activation of plasma membrane receptors [1] .", "Since the seminal work by Woods et al . [2] linking the frequency of cytosolic Ca2+ oscillations in hepatocytes to the concentration of various hormone...	[ "Calcium responses have been observed as spikes of the whole-cell calcium concentration in numerous cell types and are essential for translating extracellular stimuli into cellular responses .", "While there are several suggestions for how this encoding is achieved , we still lack a comprehensive theory .", "To...	[ "Upon stimulation a large number of cell types respond with transient increases of the intracellular calcium concentration , which often take the form of repetitive spikes .", "It is therefore believed that calcium spikes play a central role in cellular signal transduction .", "A critical feature of these calci...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "public health and epidemiology/epidemiology", "infectious diseases/viral infections", "public health and epidemiology/global health", "public health and epidemiology/infectious diseases" ]	High Dengue Case Capture Rate in Four Years of a Cohort Study in Nicaragua Compared to National Surveillance Data	journal.pntd.0000633	null	[ [ "Dengue is a mosquito-borne illness that is a major public health problem in tropical and subtropical regions , causing millions of cases annually [1] .", "However , under-reporting of dengue cases to national surveillance systems hinders accurate local , regional and global calculations of disease burden...	[ "Dengue is a major public health problem in tropical and subtropical regions; however , under-reporting of cases to national surveillance systems hinders accurate knowledge of disease burden and costs .", "Laboratory-confirmed dengue cases identified through the Nicaraguan Pediatric Dengue Cohort Study ( PDCS ) w...	[ "National public health and epidemiology programs are often tasked with tracking certain infectious diseases , but many barriers lead to under-reporting .", "In tropical and subtropical countries where dengue fever is endemic , under-reporting may be due to misdiagnosis , limitations of the WHO case classificatio...	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "biotechnology", "medicine", "public health and epidemiology", "small molecules", "microbiology", "host-pathogen interaction", "developmental biology", "emerging infectious diseases", "microbial growth and development", "applied microbiology", "infectious diseases", "medical microbiology", "...	Inhibition of Dengue Virus Entry and Multiplication into Monocytes Using RNA Interference	journal.pntd.0001410	null	[ [ "Dengue infection ranks as one of the most clinically significant and prevalent mosquito-borne viral diseases of the globe .", "It is an expanding public health problem particularly in the tropical and subtropical areas [1] .", "Following an incubation period of 3 to 14 days , fever and a variety of s...	[ "Dengue infection ranks as one of the most significant viral diseases of the globe .", "Currently , there is no specific vaccine or antiviral therapy for prevention or treatment .", "Monocytes/macrophages are the principal target cells for dengue virus and are responsible for disseminating the virus after its t...	[ "Prevention and treatment of dengue infection remain a serious global public health priority .", "Extensive efforts are required toward the development of vaccines and discovery of potential therapeutic compounds against the dengue viruses .", "Dengue virus entry is a critical step for virus reproduction and es...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "phosphorylation", "gene regulation", "regulatory proteins", "messenger rna", "dna-binding proteins", "circadian oscillators", "transcription factors", "chronobiology", "molecular biology techniques", "research and analysis methods", "transcriptional control", "proteins", "hyperexpression te...	Transcription factor CBF-1 is critical for circadian gene expression by modulating WHITE COLLAR complex recruitment to the frq locus	journal.pgen.1007570	null	[ [ "Circadian rhythms exist in almost all kingdoms of life [1–3] .", "The circadian clock is a highly conserved timekeeping system that allows organisms to anticipate and adjust to daily environmental changes [4] .", "These rhythms are generated by self-sustained molecular oscillators , based on transcri...	[ "Transcription of the Neurospora crassa circadian clock gene frequency ( frq ) is an essential process in the negative feedback loop that controls circadian rhythms .", "WHITE COLLAR 1 ( WC-1 ) and WHITE COLLAR 2 ( WC-2 ) forms the WC complex ( WCC ) that is the main activator of frq transcription by binding to i...	[ "Circadian clocks , which measure time on a scale of approximately 24 hours , are generated by a cell-autonomous circadian oscillator comprised of autoregulatory feedback loops .", "In the Neurospora crassa circadian oscillator , WHITE COLLAR complex ( WCC ) actives transcription of the frequency ( frq ) gene .",...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "death rates", "livestock", "medicine and health sciences", "body fluids", "insect metamorphosis", "ruminants", "demography", "vertebrates", "sand flies", "animals", "mammals", "developmental biology", "pupae", "population biology", "infectious disease control", "insect vectors", "zo...	Visceral Leishmaniasis on the Indian Subcontinent: Modelling the Dynamic Relationship between Vector Control Schemes and Vector Life Cycles	journal.pntd.0004868	null	[ [ "The known VL vector on the Indian subcontinent is the sand fly species Phlebotomus argentipes [6] .", "Phlebotomine sand flies are small Diptera , rarely exceeding a length of 3 mm , in the family Psychodidae and subfamily Phlebotominae [7] and are holometabolous consisting of four life stages: eggs , la...	[ "Visceral leishmaniasis ( VL ) is a disease caused by two known vector-borne parasite species ( Leishmania donovani , L . infantum ) , transmitted to man by phlebotomine sand flies ( species: Phlebotomus and Lutzomyia ) , resulting in ≈50 , 000 human fatalities annually , ≈67% occurring on the Indian subcontinent ....	[ "Visceral leishmaniasis is a disease caused by a virulent vector-borne parasite transmitted to man by phlebotomine sand flies .", "Fipronil-based drugs , administered to cattle orally , provide a potential means of sand fly control by permeating in cattle blood and being excreted in cattle feces , targeting adult...	2016
[ "Introduction", "Results/Discussion", "Methods" ]	[ "systems biology", "model organisms", "plant and algal models", "mathematics", "theoretical biology", "plant biology", "regulatory networks", "biology", "computational biology", "signaling networks", "nonlinear dynamics", "genetics and genomics", "arabidopsis thaliana" ]	A Circadian Clock-Regulated Toggle Switch Explains AtGRP7 and AtGRP8 Oscillations in Arabidopsis thaliana	journal.pcbi.1002986	null	[ [ "Circadian clocks are endogenous timekeepers that can be found among all taxa of life [1]–[3] .", "They are able to generate stable oscillations with a period of approximately 24h that persist even under constant ( free-running ) conditions , i . e . in the absence of any rhythmic environmental influences...	[ "The circadian clock controls many physiological processes in higher plants and causes a large fraction of the genome to be expressed with a 24h rhythm .", "The transcripts encoding the RNA-binding proteins AtGRP7 ( Arabidopsis thaliana Glycine Rich Protein 7 ) and AtGRP8 oscillate with evening peaks .", "The c...	[ "The circadian clock organizes the day in the life of a plant by causing 24h rhythms in gene expression .", "For example , the core clockwork of the model plant Arabidopsis thaliana causes the transcripts encoding the RNA-binding proteins AtGRP7 and AtGRP8 to undergo high amplitude oscillations with a peak at the...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "plant anatomy", "chemical compounds", "ethylene signaling cascade", "ethylene", "gene regulation", "regulatory proteins", "brassica", "dna-binding proteins", "organic compounds", "hormones", "root hairs", "mutation", "plant science", "model organisms", "plant hormones", "transcription...	The Molecular Mechanism of Ethylene-Mediated Root Hair Development Induced by Phosphate Starvation	journal.pgen.1006194	null	[ [ "As an essential macronutrient , phosphorus ( P ) plays vital roles in plant growth , development , and metabolism .", "P not only serves as structural elements of nucleic acids and phospholipids , but is also involved in many important biological processes , including photosynthesis , oxidative phosphory...	[ "Enhanced root hair production , which increases the root surface area for nutrient uptake , is a typical adaptive response of plants to phosphate ( Pi ) starvation .", "Although previous studies have shown that ethylene plays an important role in root hair development induced by Pi starvation , the underlying mo...	[ "Phytohormone ethylene has previously been known to play an important role in mediating root hair development induced by phosphate starvation; however , the underlying molecular mechanism is not understood .", "Using combined molecular , genetic , and genomic approaches , we identify a group of genes that affect ...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases" ]	Cis and Trans Acting Factors Involved in Human Cytomegalovirus Experimental and Natural Latent Infection of CD14 (+) Monocytes and CD34 (+) Cells	journal.ppat.1003366	null	[ [ "Human cytomegalovirus ( HCMV ) is a ubiquitous herpesvirus that infects 60–90% of the population and is usually subclinical , however virus infection can cause severe disease and mortality in immune compromised patients [1] .", "Disease manifestations include retinitis , pneumonia and hepatitis [2] .", ...	[ "The parameters involved in human cytomegalovirus ( HCMV ) latent infection in CD14 ( + ) and CD34 ( + ) cells remain poorly identified .", "Using next generation sequencing we deduced the transcriptome of HCMV latently infected CD14 ( + ) and CD34 ( + ) cells in experimental as well as natural latency settings ....	[ "Human cytomegalovirus ( HCMV ) is a ubiquitous herpesvirus where infection is usually subclinical .", "HCMV initial infection is followed by the establishment of latency in CD34 ( + ) myeloid cells and CD14 ( + ) monocytes .", "Primary infection or reactivation from latency can be associated with significant m...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "phosphorylation", "gene regulation", "fungal structure", "fungi", "plant science", "model organisms", "experimental organism systems", "gene types", "appressoria", "plant pathology", "molecular biology techniques", "mutagenesis and gene deletion techniques", "research and analysis methods",...	PKA activity is essential for relieving the suppression of hyphal growth and appressorium formation by MoSfl1 in Magnaporthe oryzae	journal.pgen.1006954	null	[ [ "Magnaporthe oryzae is the causal agent of rice blast , which is one of the most important rice diseases worldwide .", "In the past two decades , M . oryzae has been developed as a model organism to study fungal-plant interactions because of its economic importance and the experimental tractability [1–3] ...	[ "In the rice blast fungus Magnaporthe oryzae , the cAMP-PKA pathway regulates surface recognition , appressorium turgor generation , and invasive growth .", "However , deletion of CPKA failed to block appressorium formation and responses to exogenous cAMP .", "In this study , we generated and characterized the ...	[ "The cAMP-PKA signaling pathway plays a critical role in regulating various cellular processes in eukaryotic cells in response to extracellular cues .", "In the rice blast fungus , this important pathway is involved in surface recognition , appressorium morphogenesis , and infection .", "However , the exact rol...	2017
[ "Introduction" ]	[ "biophysics/theory and simulation", "biophysics/biomacromolecule-ligand interactions", "computational biology/protein structure prediction", "computational biology/molecular dynamics", "biochemistry/drug discovery" ]	Conformational Transitions upon Ligand Binding: Holo-Structure Prediction from Apo Conformations	journal.pcbi.1000634	null	[ [ "Interactions between proteins and small molecules are involved in many biochemical phenomena .", "Insight into these processes relies on detailed knowledge about the structure of protein/ligand complexes , e . g . how enzymes stabilize substrates and cofactors in close proximity .", "Moreover , almos...	[ "Biological function of proteins is frequently associated with the formation of complexes with small-molecule ligands .", "Experimental structure determination of such complexes at atomic resolution , however , can be time-consuming and costly .", "Computational methods for structure prediction of protein/ligan...	[ "Structure-based drug design has become a powerful tool in modern drug discovery pipelines .", "A critical prerequisite is a structure of the target protein close to its ligand bound conformation which is often difficult to determine experimentally .", "In many cases , a structure of the unbound receptor is ava...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology" ]	An Initial Step of GAS-Containing Autophagosome-Like Vacuoles Formation Requires Rab7	journal.ppat.1000670	null	[ [ "Streptococcus pyogenes , also known as Group A Streptococcus ( GAS ) is a common pathogen that causes a variety of acute infections including pharyngitis , skin infections , acute rheumatic fever and life-threatening necrotizing fasciitis [1] .", "The bacterium enters non-phagocytic human cells via endoc...	[ "Group A streptococcus ( GAS; Streptococcus pyogenes ) is a common pathogen that invades non-phagocytic human cells via endocytosis .", "Once taken up by cells , it escapes from the endocytic pathway to the cytoplasm , but here it is contained within a membrane-bound structure termed GAS-containing autophagosome-...	[ "Autophagy has become one of the leading edge subjects in science .", "Autophagy occurs when a cell eats some of its cellular components and digests them .", "These cellular components may include cytosol and organelles as well as bacteria that has invaded the cell .", "Thus , autophagy plays an important rol...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "antigen processing and recognition", "epstein-barr virus infectious mononucleosis", "immunology", "biology", "viral diseases", "immune response" ]	Messenger RNA Sequence Rather than Protein Sequence Determines the Level of Self-synthesis and Antigen Presentation of the EBV-encoded Antigen, EBNA1	journal.ppat.1003112	null	[ [ "Members of the viral family Herpesviridae , which are widely distributed throughout the animal kingdom , are characterized by their large double-stranded , linear DNA genomes .", "The gammaherpesviruses , one of three sub-families of Herpesviridae , predominantly replicate and persist in lymphoid cells w...	[ "Unique purine-rich mRNA sequences embedded in the coding sequences of a distinct group of gammaherpesvirus maintenance proteins underlie the ability of the latently infected cell to minimize immune recognition .", "The Epstein-Barr virus nuclear antigen , EBNA1 , a well characterized lymphocryptovirus maintenanc...	[ "Viruses establishing persistent latent infections have evolved various mechanisms to avoid immune surveillance .", "The Epstein-Barr virus-encoded nuclear antigen , EBNA1 , expressed in all EBV-associated malignancies , modulates its own protein levels at quantities sufficient to maintain viral infection but low...	2012
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "rheumatology", "knee joints", "medicine and health sciences", "immune cells", "diagnostic radiology", "pathology and laboratory medicine", "pathogens", "immunology", "microbiology", "staphylococcus aureus", "magnetic resonance imaging", "bacteria", "neutrophils", "bacteri...	The YIN and YANG of lipoproteins in developing and preventing infectious arthritis by Staphylococcus aureus	journal.ppat.1007877	null	[ [ "Despite colonizing more than half of the human population at some stage during their life [1] , Staphylococcus aureus ( S . aureus ) is a highly pathogenic microorganism responsible for a broad range of infections in humans [2] .", "Septic arthritis , considered to be one of the most aggressive joint dis...	[ "Rapid bone destruction often leads to permanent joint dysfunction in patients with septic arthritis , which is mainly caused by Staphylococcus aureus ( S . aureus ) .", "Staphylococcal cell wall components are known to induce joint inflammation and bone destruction .", "Here , we show that a single intra-artic...	[ "Rapid bone destruction often leads to permanent joint dysfunction in septic arthritis , which is mainly caused by S . aureus .", "Despite advances in the use of antibiotics , permanent reductions in joint function occur in up to 50% of patients , who may also need joint replacement surgery .", "Additional chal...	2019
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "public health and epidemiology", "biomarker epidemiology", "clinical laboratory sciences", "diagnostic medicine", "chagas disease", "epidemiology", "neglected tropical diseases", "epidemiological methods" ]	Antigenicity and Diagnostic Potential of Vaccine Candidates in Human Chagas Disease	journal.pntd.0002018	null	[ [ "The protozoan parasite Trypanosoma cruzi , transmitted by blood-sucking triatomines , causes Chagas disease , which is a health threat for an estimated 10 million people , living mostly in Latin America .", "More than 25 million people are at risk of the disease [1] .", "Increasing travel and immigra...	[ "Chagas disease , caused by Trypanosoma cruzi , is endemic in Latin America and an emerging infectious disease in the US and Europe .", "We have shown TcG1 , TcG2 , and TcG4 antigens elicit protective immunity to T . cruzi in mice and dogs .", "Herein , we investigated antigenicity of the recombinant proteins i...	[ "Chagas disease is the most common cause of congestive heart failure related deaths among young adults in the endemic areas of South and Central America and Mexico .", "Diagnosis and treatment of T . cruzi infection has remained difficult and challenging after 100 years of its identification .", "In >95% of hum...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "mathematics", "computer science" ]	A Flexible Bayesian Model for Studying Gene–Environment Interaction	journal.pgen.1002482	null	[ [ "Genome-wide association studies that focus on detecting the main effect from individual single nucleotide polymorphisms ( SNPs ) have successfully identified more than 4 , 000 SNPs associated with different diseases [1] .", "To achieve a better understanding of the mechanisms underlying disease developme...	[ "An important follow-up step after genetic markers are found to be associated with a disease outcome is a more detailed analysis investigating how the implicated gene or chromosomal region and an established environment risk factor interact to influence the disease risk .", "The standard approach to this study of...	[ "Many common diseases result from a complex interplay of genetic and environmental risk factors .", "It is important to study the potential genetic and environmental risk factors jointly in order to achieve a better understanding of the mechanisms underlying disease development .", "The standard single-marker a...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "bacterial diseases", "infectious diseases", "geography", "public health and epidemiology", "computer science", "epidemiology", "earth sciences", "public health", "geoinformatics", "human geography" ]	Analysing Spatio-Temporal Clustering of Meningococcal Meningitis Outbreaks in Niger Reveals Opportunities for Improved Disease Control	journal.pntd.0001577	null	[ [ "Meningococcal meningitis ( MM ) , caused by the bacterium Neisseria meningitidis ( Nm ) , is a major health problem in sub-Saharan Africa .", "The highest incidences of the disease are observed in the so-called “African Meningitis Belt” where annual recurrent epidemics occur during the very hot , dry sea...	[ "Meningococcal meningitis is a major health problem in the “African Meningitis Belt” where recurrent epidemics occur during the hot , dry season .", "In Niger , a central country belonging to the Meningitis Belt , reported meningitis cases varied between 1 , 000 and 13 , 000 from 2003 to 2009 , with a case-fatali...	[ "Meningococcal meningitis ( MM ) is an infection of the meninges caused by a bacterium , Neisseria meningitidis , transmitted through respiratory and throat secretions .", "It can cause brain damage and results in death in 5–15% of cases .", "Large epidemics of MM occur almost every year in sub-Saharan Africa d...	2012
[ "Introduction", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "population genetics", "genomic library construction", "animals", "invertebrate genomics", "genome analysis", "dna construction", "molecular biology techniques", "population biology", "insect vectors", "research and analysis methods", "infecti...	Population genomics of Culiseta melanura, the principal vector of Eastern equine encephalitis virus in the United States	journal.pntd.0006698	null	[ [ "Eastern equine encephalitis ( EEE ) virus ( Alphavirus , Togaviridae ) causes severe disease in humans and equines with high case mortality and persistent neurologic impairment in survivors [1] .", "Historically , outbreaks of this relatively rare but highly pathogenic arthropod-borne virus occurred inte...	[ "Eastern Equine Encephalitis ( EEE ) ( Togaviridae , Alphavirus ) is a highly pathogenic mosquito-borne arbovirus that circulates in an enzootic cycle involving Culiseta melanura mosquitoes and wild Passeriformes birds in freshwater swamp habitats .", "Recently , the northeastern United States has experienced an ...	[ "Eastern equine encephalitis ( EEE ) is a highly pathogenic mosquito-borne virus responsible for outbreaks of severe disease in humans and equines , causing high mortality and neurological impairment in most survivors .", "In the past , human disease outbreaks in the northeastern United States occurred intermitte...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "schistosoma", "invertebrates", "medicine and health sciences", "helminths", "gene regulation", "tropical diseases", "fibrosis", "parasitic diseases", "animals", "liver diseases", "collagens", "animal models", "developmental biology", "micrornas", "model organisms", "gastroenterology a...	Down-regulation of microRNA-203-3p initiates type 2 pathology during schistosome infection via elevation of interleukin-33	journal.ppat.1006957	null	[ [ "Schistosomiasis is a serious but neglected tropical infectious disease , affecting more than 230 million people worldwide [1] .", "Hepatic granuloma and secondary fibrosis caused by lodged eggs from the parasite are the primary cause of morbidity and mortality from this chronic and debilitating disease ....	[ "The type 2 immune response is the central mechanism of disease progression in schistosomiasis , but the signals that induce it after infection remain elusive .", "Aberrant microRNA ( miRNA ) expression is a hallmark of human diseases including schistosomiasis , and targeting the deregulated miRNA can mitigate di...	[ "Schistosomiasis is a serious but neglected tropical infectious disease .", "Hepatic fibrosis caused by lodged eggs from the parasite is the primary cause of morbidity and mortality from this disease .", "Type 2 immune response , featured by the T helper 2 cell associated cytokines such as IL-4 and IL-13 , is t...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The Arabidopsis IDD14, IDD15, and IDD16 Cooperatively Regulate Lateral Organ Morphogenesis and Gravitropism by Promoting Auxin Biosynthesis and Transport	journal.pgen.1003759	null	[ [ "Auxin is a key plant hormone that plays critical roles in the regulation of plant growth and development .", "A combination of physiological , genetic , biochemical , and molecular studies has greatly enriched our understanding of auxin biosynthesis , transport , and signal transduction [1]–[3] .", "...	[ "The plant hormone auxin plays a critical role in regulating various aspects of plant growth and development , and the spatial accumulation of auxin within organs , which is primarily attributable to local auxin biosynthesis and polar transport , is largely responsible for lateral organ morphogenesis and the establ...	[ "Auxin is a key plant hormone and the spatial accumulation of auxin is essential for lateral organ morphogenesis and gravitropic responses in higher plants .", "However , the various mechanisms through which spatial auxin accumulation is regulated remain to be fully elucidated .", "Here , we identify a gain-of-...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "genetics and genomics/microbial evolution and genomics", "ophthalmology/eye infections", "public health and epidemiology/infectious diseases", "infectious diseases/bacterial infections", "genetics and genomics/population genetics" ]	Chlamydia trachomatis ompA Variants in Trachoma: What Do They Tell Us?	journal.pntd.0000306	null	[ [ "Trachoma is the leading infectious cause of blindness worldwide [1] .", "Repeated infection by Chlamydia trachomatis provokes chronic follicular conjunctivitis ( clinically active trachoma ) , which leads to conjunctival scarring , entropion , trichiasis and ultimately blinding corneal opacification .", ...	[ "Trachoma , caused by Chlamydia trachomatis ( Ct ) , is the leading infectious cause of blindness .", "Sequence-based analysis of the multiple strains typically present in endemic communities may be informative for epidemiology , transmission , response to treatment , and understanding the host response .", "Co...	[ "Trachoma is an important cause of blindness resulting from transmission of the bacterium Chlamydia trachomatis .", "One way to understand better how this infection is transmitted and how the human immune system controls it is to study the strains of bacteria associated with infection .", "Comparing strains bef...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Incorporating Motif Analysis into Gene Co-expression Networks Reveals Novel Modular Expression Pattern and New Signaling Pathways	journal.pgen.1003840	null	[ [ "The advancement in technologies in recent years has resulted in many large data sets cataloging the biological systems at various levels .", "Biological networks inferred from these data have become an important tool to describe and analyze biological signaling systems [1]–[3] .", "Depending on the s...	[ "Understanding of gene regulatory networks requires discovery of expression modules within gene co-expression networks and identification of promoter motifs and corresponding transcription factors that regulate their expression .", "A commonly used method for this purpose is a top-down approach based on clusterin...	[ "Gene co-expression networks unite genes with similar expression patterns .", "From these networks , gene co-expression modules can be identified .", "A specific family of transcription factor ( s ) may regulate the genes within a co-expression module .", "Thus , module identification is important to decipher...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular biology/histone modification", "genetics and genomics/gene expression", "genetics and genomics/chromosome biology", "genetics and genomics/genome projects", "molecular biology/dna methylation", "genetics and genomics/epigenetics" ]	DNA Methylation Analysis of Chromosome 21 Gene Promoters at Single Base Pair and Single Allele Resolution	journal.pgen.1000438	null	[ [ "After deciphering the sequence of the human genome , the study of epigenetic processes which initiate and maintain heritable patterns of gene expression and gene function without changing the DNA sequence , has moved into the center of research [1] .", "The epigenome comprises different modifications of ...	[ "Differential DNA methylation is an essential epigenetic signal for gene regulation , development , and disease processes .", "We mapped DNA methylation patterns of 190 gene promoter regions on chromosome 21 using bisulfite conversion and subclone sequencing in five human cell types .", "A total of 28 , 626 sub...	[ "Epigenetics is defined as the inheritance of changes in gene function without changing the DNA sequence .", "Epigenetic signals comprise methylation of cytosine bases of the DNA and chemical modifications of the histone proteins .", "DNA methylation plays important roles in development and disease processes ."...	2009
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "arthropoda", "public and occupational health", "invertebrates", "disease vectors", "mosquitoes", "medicine and health sciences", "infectious diseases", "helminth infections", "filariasis", "epidemiology", "global health", "biology and life sciences", "lymphatic filariasis", "malaria", "...	Multiple Resistances and Complex Mechanisms of Anopheles sinensis Mosquito: A Major Obstacle to Mosquito-Borne Diseases Control and Elimination in China	journal.pntd.0002889	null	[ [ "Malaria and filariasis are two of the most important vector-borne parasitic diseases in Southeast Asia .", "Although China and several other countries in the region have reported a marked downward trend in malaria cases , high malaria incidence has been observed in the major neighboring endemic countries...	[ "Malaria , dengue fever , and filariasis are three of the most common mosquito-borne diseases worldwide .", "Malaria and lymphatic filariasis can occur as concomitant human infections while also sharing common mosquito vectors .", "The overall prevalence and health significance of malaria and filariasis have ma...	[ "Malaria and lymphatic filariasis are two of the most important mosquito-borne parasitic diseases worldwide , which can occur as concomitant human infections .", "The Anopheles sinensis mosquito is the most common malaria and lymphatic filariasis vector in Southeast Asia .", "Disease-vector control is an import...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "genetics", "biology", "morphogenesis", "gene networks", "genetics and genomics" ]	A Bow-Tie Genetic Architecture for Morphogenesis Suggested by a Genome-Wide RNAi Screen in Caenorhabditis elegans	journal.pgen.1002010	null	[ [ "Morphogenesis involves the coordinated change in the shape of cells and tissues during development , eventually giving rise to functional structures in the adult animal .", "Such coordinated change must occur at the correct time and in the proper position .", "In the case of structures that differ be...	[ "During animal development , cellular morphogenesis plays a fundamental role in determining the shape and function of tissues and organs .", "Identifying the components that regulate and drive morphogenesis is thus a major goal of developmental biology .", "The four-celled tip of the Caenorhabditis elegans male...	[ "Morphogenesis is a process in which cells change their shape and position to give rise to mature structures .", "Elucidation of the molecular basis of morphogenesis and its regulation would be a major step towards understanding organ formation and functionality .", "We focus on a powerful model for morphogenes...	2011
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "global health" ]	Early Diagnosis, Treatment and Follow-Up of Cystic Echinococcosis in Remote Rural Areas in Patagonia: Impact of Ultrasound Training of Non-Specialists	journal.pntd.0001444	null	[ [ "Hydatidosis or cystic echinococcosis ( CE ) is a disease caused by the larval stage of the cestode Echinococcus granulosus .", "It is endemic in sheep raising areas and is among the most neglected diseases in the world today [1] , [2] .", "Despite a global burden calculated at 1 009 662 disability ad...	[ "Cystic echinococcosis ( CE ) is a chronic , complex and neglected disease caused by the larval stage of Echinococcus granulosus .", "The effects of this neglect have a stronger impact in remote rural areas whose inhabitants have no chances of being diagnosed and treated properly without leaving their jobs and tr...	[ "Cystic echinococcosis ( CE ) is an important and widespread disease that affects sheep , cattle , and humans living in areas where sheep and cattle are raised .", "CE is highly endemic in rural sections of Rio Negro , Argentina , where our group is based .", "However , it requires continuous monitoring of both...	2012
[ "Introduction", "Materials and methods", "Results and discussion", "Conclusion" ]	[ "medicine and health sciences", "linguistics", "statistics", "natural antisense transcripts", "gene regulation", "cancers and neoplasms", "social sciences", "oncology", "hematologic cancers and related disorders", "micrornas", "mathematics", "forecasting", "lymphomas", "information technol...	LMTRDA: Using logistic model tree to predict MiRNA-disease associations by fusing multi-source information of sequences and similarities	journal.pcbi.1006865	null	[ [ "MicroRNAs ( miRNAs ) are a small class of endogenous non-coding RNAs with a length of about 20–24 nucleotides [1] .", "They bind to the 3'-untranslated region of target miRNA through sequence-specific base pairing , resulting in cleavage or translation inhibition of target miRNA , and thereby regulating ...	[ "Emerging evidence has shown microRNAs ( miRNAs ) play an important role in human disease research .", "Identifying potential association among them is significant for the development of pathology , diagnose and therapy .", "However , only a tiny portion of all miRNA-disease pairs in the current datasets are ex...	[ "Identification of miRNA-disease associations is considered as an important step for the development of diagnose and therapy .", "Computational methods contribute to discovering the potential disease-related miRNAs .", "Based on the assumption that functionally related miRNAs tend to be involved disease , the m...	2019
[ "Introduction", "Materials and Methods", "Results/Discussion" ]	[ "physics", "biochemistry", "biochemistry simulations", "proteins", "biophysics simulations", "chemistry", "biology", "computational chemistry", "biophysics", "thermodynamics", "physical chemistry" ]	Kinetics of Amyloid Aggregation: A Study of the GNNQQNY Prion Sequence	journal.pcbi.1002782	null	[ [ "The aggregation of misfolded amyloid proteins into fibrils is a hallmark of many neurodegenerative diseases such as Alzheimer's , Parkinson's , and Huntington's diseases [1]–[5] and understanding amyloid aggregation mechanisms is crucial for controlling their destructive consequences .", "Fibrils are kno...	[ "The small amyloid-forming GNNQQNY fragment of the prion sequence has been the subject of extensive experimental and numerical studies over the last few years .", "Using unbiased molecular dynamics with the OPEP coarse-grained potential , we focus here on the onset of aggregation in a 20-mer system .", "With a ...	[ "Protein aggregation plays an important pathological role in numerous neurodegenerative diseases such as Alzheimer's , Parkinson's , Creutzfeldt-Jakob , the Prion disease and diabetes mellitus .", "In most cases , misfolded proteins are involved and aggregate irreversibly to form highly ordered insoluble macrostr...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Prevalence and Transmission of Trypanosoma cruzi in People of Rural Communities of the High Jungle of Northern Peru	journal.pntd.0003779	null	[ [ "Chagas disease is caused by the protozoan parasite Trypanosoma cruzi , and is primarily transmitted by triatomine vectors .", "Chagas disease is endemic to poor rural regions of Central and South America and is responsible for the largest public health burden of any parasitic infection in the Western Hem...	[ "Vector-borne transmission of Trypanosoma cruzi is seen exclusively in the Americas where an estimated 8 million people are infected with the parasite .", "Significant research in southern Peru has been conducted to understand T . cruzi infection and vector control , however , much less is known about the burden ...	[ "Chagas disease causes significant morbidity and mortality throughout Central and South America .", "The epidemiology and control of this disease is subject to unique regional particularities , including the behavior and ecology of the local insect vector species .", "Significant resources have been allocated t...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Exome and Transcriptome Sequencing of Aedes aegypti Identifies a Locus That Confers Resistance to Brugia malayi and Alters the Immune Response	journal.ppat.1004765	null	[ [ "The rate at which parasites are transmitted by mosquitoes is an important determinant of the prevalence of vector-borne diseases in human populations .", "Alongside factors like the number of mosquitoes and their biting preferences , the rate of transmission depends on the ability of mosquitoes to acquir...	[ "Many mosquito species are naturally polymorphic for their abilities to transmit parasites , a feature which is of great interest for controlling vector-borne disease .", "Aedes aegypti , the primary vector of dengue and yellow fever and a laboratory model for studying lymphatic filariasis , is genetically variab...	[ "Within mosquito populations , genetic differences between individuals affect their ability to transmit human diseases such as malaria , dengue fever , and lymphatic filariasis .", "In the mosquito Aedes aegypti , some individuals are genetically resistant to Brugia malayi , a mosquito-vectored parasite that caus...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Maintenance of Glia in the Optic Lamina Is Mediated by EGFR Signaling by Photoreceptors in Adult Drosophila	journal.pgen.1005187	null	[ [ "The degeneration of the nervous system can be viewed as a failure to maintain cell survival and function within the nervous system .", "In mammals , the survival of neurons during development and adulthood is actively maintained by the neurotrophic factors produced by other neurons or glias [1 , 2] .", ...	[ "The late onset of neurodegeneration in humans indicates that the survival and function of cells in the nervous system must be maintained throughout adulthood .", "In the optic lamina of the adult Drosophila , the photoreceptor axons are surrounded by multiple types of glia .", "We demonstrated that the adult p...	[ "Degeneration of the nervous system can be viewed as a failure to maintain cell survival or function in the nervous system .", "The late onset of neurodegeneration in humans indicates that the cell survival in the nervous system must be maintained throughout our lives .", "Neuronal survival is maintained by neu...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "immune cells", "immunity to infections", "immunology", "immune suppression", "microbiology", "animal models", "histology", "adaptive immunity", "model organisms", "immune defense", "animal models of infection", "infectious diseases", "biology", "infectious disease modeling",...	Measles Immune Suppression: Lessons from the Macaque Model	journal.ppat.1002885	null	[ [ "Measles is associated with a transient but profound immune suppression , which may last for several weeks to months after the acute stage of the disease .", "The clinical importance of this immune suppression is illustrated by the observation that measles mortality is typically caused by secondary infect...	[ "Measles remains a significant childhood disease , and is associated with a transient immune suppression .", "Paradoxically , measles virus ( MV ) infection also induces robust MV-specific immune responses .", "Current hypotheses for the mechanism underlying measles immune suppression focus on functional impair...	[ "Measles is associated with a transient immune suppression , resulting in increased susceptibility to opportunistic infections .", "Indeed , the main causes of measles mortality are secondary infections in the respiratory and digestive tract .", "Although measles is associated with lymphopenia , depletion of ly...	2012
[ "Introduction", "Results/Discussion", "Methods" ]	[ "sequence analysis", "systems biology", "biochemistry", "genomics", "biology", "computational biology", "comparative genomics", "proteomics", "pharmacogenomics" ]	Proteins with Complex Architecture as Potential Targets for Drug Design: A Case Study of Mycobacterium tuberculosis	journal.pcbi.1002118	null	[ [ "Tuberculosis ( TB ) remains a major world-wide health hazard , causing to roughly 2 million deaths per year .", "Approximately , one third of the world's population is currently infected with Mycobacterium tuberculosis ( MTB ) , the causative agent of TB [1] , [2] .", "MTB is an intracellular parasit...	[ "Lengthy co-evolution of Homo sapiens and Mycobacterium tuberculosis , the main causative agent of tuberculosis , resulted in a dramatically successful pathogen species that presents considerable challenge for modern medicine .", "The continuous and ever increasing appearance of multi-drug resistant mycobacteria ...	[ "Mycobacterium tuberculosis ( MTB ) , the causative agent of TB , is a dramatically successful pathogen that poses a considerable challenge for modern medicine .", "The increase in multi-drug resistant TB necessitates the identification of novel drug targets and drugs with new mechanisms of action .", "In this ...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "mycology", "immune cells", "immunology", "biology", "microbiology" ]	Stage Specific Assessment of Candida albicans Phagocytosis by Macrophages Identifies Cell Wall Composition and Morphogenesis as Key Determinants	journal.ppat.1002578	null	[ [ "Invasive C . albicans infection can present a serious clinical complication , especially in patients with an impaired immune system .", "Host defence against systemic candidiasis relies mainly on the ingestion and elimination of fungal cells by cells of the innate immune system , especially neutrophils a...	[ "Candida albicans is a major life-threatening human fungal pathogen .", "Host defence against systemic Candida infection relies mainly on phagocytosis of fungal cells by cells of the innate immune system .", "In this study , we have employed video microscopy , coupled with sophisticated image analysis tools , t...	[ "Host defence against systemic candidiasis relies mainly on the ingestion and elimination of fungal cells by cells of the innate immune system , especially neutrophils and macrophages .", "Here we have used live cell video microscopy coupled with sophisticated image analysis to generate a temporal and spatial ana...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	From Cellular Characteristics to Disease Diagnosis: Uncovering Phenotypes with Supercells	journal.pcbi.1003215	null	[ [ "In the life sciences , there is now a wealth of quantitative information from simultaneous measurements on many proteins and genes , from small tissue samples down to a single cell at a time [1]–[6] .", "Likewise , bioimaging is following a similar trend through multicolor fluorescent imaging and the eme...	[ "Cell heterogeneity and the inherent complexity due to the interplay of multiple molecular processes within the cell pose difficult challenges for current single-cell biology .", "We introduce an approach that identifies a disease phenotype from multiparameter single-cell measurements , which is based on the conc...	[ "The behavior of organisms is based on the concerted action occurring on an astonishing range of scales from the molecular to the organismal level .", "Molecular properties control the function of a cell , while cell ensembles form tissues and organs , which work together as an organism .", "In order to underst...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	DUX4 Binding to Retroelements Creates Promoters That Are Active in FSHD Muscle and Testis	journal.pgen.1003947	null	[ [ "The transcription factor DUX4 is a member of a small family of double-homeodomain genes that also includes paralogs DUXA , DUXB , DUXBL , DUXC and murine Dux [1]–[3] .", "The primate-specific DUX4 gene likely arose from retrotransposition of the DUXC mRNA , with subsequent deletion of the DUXC gene from ...	[ "The human double-homeodomain retrogene DUX4 is expressed in the testis and epigenetically repressed in somatic tissues .", "Facioscapulohumeral muscular dystrophy ( FSHD ) is caused by mutations that decrease the epigenetic repression of DUX4 in somatic tissues and result in mis-expression of this transcription ...	[ "Transposable elements ( TEs ) are found in most genomes , and many TEs create extra copies of themselves in new genomic locations by a process called retrotransposition .", "TEs are often thought of as genomic parasites that must be suppressed , because retrotransposition can cause great harm to their host organ...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "auditory cortex", "medicine and health sciences", "action potentials", "neural networks", "nervous system", "membrane potential", "brain", "electrophysiology", "neuroscience", "computational neuroscience", "mood disorders", "neuronal tuning", "sensory physiology", "computer and informatio...	Stimulus-specific adaptation in a recurrent network model of primary auditory cortex	journal.pcbi.1005437	null	[ [ "Stimulus-specific adaptation ( SSA ) is the decrease in responses to a repeating stimulus ( standard ) that does not generalize to another , rarely-occurring stimulus ( deviant ) .", "SSA is a robust and widespread finding in the auditory system .", "It has been demonstrated in single neurons in prim...	[ "Stimulus-specific adaptation ( SSA ) occurs when neurons decrease their responses to frequently-presented ( standard ) stimuli but not , or not as much , to other , rare ( deviant ) stimuli .", "SSA is present in all mammalian species in which it has been tested as well as in birds .", "SSA confers short-term ...	[ "We present a possible mechanism for the way auditory cortex emphasizes stimuli that are deviant within a regular , repetitive sequence .", "This enhancement is strong and widespread in auditory cortex , but not in its major thalamic input , the ventral division of the medial geniculate body .", "In contrast wi...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cancer genetics", "signaling in selected disciplines", "neuroscience", "model organisms", "oncogenic signaling", "biology", "phospholipid signaling cascade", "signal transduction", "genetic screens", "genetics", "molecular cell biology", "genetics of disease", "genetics and genomics", "si...	A Kinome-Wide RNAi Screen in Drosophila Glia Reveals That the RIO Kinases Mediate Cell Proliferation and Survival through TORC2-Akt Signaling in Glioblastoma	journal.pgen.1003253	null	[ [ "Glioblastoma ( GBM ) , the most common primary malignant brain tumor , infiltrates the brain , grows rapidly , and is refractory to current therapies .", "Signature genetic lesions in GBM include amplification , mutation , and/or overexpression of receptor tyrosine kinases ( RTKs ) , such as EGFR and PDG...	[ "Glioblastoma , the most common primary malignant brain tumor , is incurable with current therapies .", "Genetic and molecular analyses demonstrate that glioblastomas frequently display mutations that activate receptor tyrosine kinase ( RTK ) and Pi-3 kinase ( PI3K ) signaling pathways .", "In Drosophila melano...	[ "Glioblastomas , the most common primary brain tumor , harbor mutations in receptor tyrosine kinases ( RTKs ) , such as EGFR , and components of the Pi-3 kinase ( PI3K ) signaling pathway .", "However , the genes that act downstream of RTK and PI3K signaling to drive glioblastoma remain unclear .", "To investig...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "biophysics", "molecular biology" ]	Human and Drosophila Cryptochromes Are Light Activated by Flavin Photoreduction in Living Cells	journal.pbio.0060160	Cryptochromes are blue-light-absorbing receptors found in plants, animals, and humans. In mammals, they are not thought to respond to light, but this study demonstrates contrary evidence that indeed, human cryptochromes undergo a photochemical transformation in response to light.	[ [ "Cryptochromes are blue-light–absorbing photoreceptors found throughout the biological kingdom , involved in diverse and important signaling roles [1–3] .", "Cryptochromes were first identified in plants from a mutant of Arabidopsis thaliana ( A . thaliana ) , hy4 , which failed to show normal plant growt...	[ "Cryptochromes are a class of flavoprotein blue-light signaling receptors found in plants , animals , and humans that control plant development and the entrainment of circadian rhythms .", "In plant cryptochromes , light activation is proposed to result from photoreduction of a protein-bound flavin chromophore th...	[ "Vision in animals is generally associated with light-sensitive rhodopsin pigments located in the eyes .", "However , animals ranging from flies to humans also possess ancient visual receptors known as cryptochromes in multiple cell types .", "In this work , we study the mechanism of light sensing in two repres...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/epigenetics", "developmental biology/developmental molecular mechanisms", "molecular biology/transcription initiation and activation", "genetics and genomics/gene expression" ]	A Single cis Element Maintains Repression of the Key Developmental Regulator Gata2	journal.pgen.1001103	null	[ [ "Metazoan development is characterized by complex transcriptional programs specified by gene regulatory networks [1] , [2] .", "Transcription factors in these networks occupy specific cis elements at target gene loci where they modulate chromatin remodeling and modification , and thereby transcription .",...	[ "In development , lineage-restricted transcription factors simultaneously promote differentiation while repressing alternative fates .", "Molecular dissection of this process has been challenging as transcription factor loci are regulated by many trans-acting factors functioning through dispersed cis elements .",...	[ "Different cell types are formed and maintained by proteins called transcription factors that directly bind to specific DNA sequences to activate or repress gene expression .", "While numerous DNA sequences bound by transcription factors are established , many questions remain unanswered regarding how they functi...	2010
[ "Introduction", "Methods", "Results and Discussion" ]	[ "emerging infectious diseases", "virology", "emerging viral diseases", "biology", "microbiology", "viral evolution" ]	Re-Emergence of Crimean-Congo Hemorrhagic Fever Virus in Central Africa	journal.pntd.0001350	null	[ [ "Crimean-Congo hemorrhagic fever virus ( CCHFV , family Bunyaviridae , genus Nairovirus ) is a tick-borne virus .", "It causes severe illness throughout Africa , Asia , Southeast Europe and the Middle East , with case fatality rates ranging from 3% to 30% .", "Its worldwide distribution closely matche...	[ "Crimean-Congo hemorrhagic fever ( CCHF ) is a severe tick-borne disease well recognized through Europe and Asia where diagnostic tests and medical surveillance are available .", "However , it is largely neglected in Africa , especially in the tropical rainforest of Central Africa where only sporadic human cases ...	[ "Crimean-Congo hemorrhagic fever virus ( CCHFV ) is transmitted to humans through tick-bite or contact with infected blood or tissues from livestock , the main vertebrate hosts in a peri-domestic natural cycle .", "With numerous outbreaks , a high case fatality rate ( 3%–30% ) and a high risk for nosocomial trans...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "plant science", "plant biology", "genetics", "biology", "molecular cell biology", "genetics and genomics" ]	OSD1 Promotes Meiotic Progression via APC/C Inhibition and Forms a Regulatory Network with TDM and CYCA1;2/TAM	journal.pgen.1002865	null	[ [ "Meiosis is a key step in the life cycle of sexually reproducing eukaryotes , such as the majority of flowering plants .", "At meiosis ploidy is reduced by two , leading to the production of typically haploid gametes whose fusion during fertilization restores diploidy of the next generation .", "This ...	[ "Cell cycle control is modified at meiosis compared to mitosis , because two divisions follow a single DNA replication event .", "Cyclin-dependent kinases ( CDKs ) promote progression through both meiosis and mitosis , and a central regulator of their activity is the APC/C ( Anaphase Promoting Complex/Cyclosome )...	[ "In the life cycle of sexual organisms , a specialized cell division—meiosis—reduces the number of chromosomes from two sets ( 2n , diploid ) to one set ( n , haploid ) , while fertilization restores the original chromosome number .", "Meiosis reduces ploidy because it consists of two cellular divisions following...	2012
[ "Introduction", "Methods", "Results and Discussion" ]	[ "sequencing techniques", "protein interactions", "protein structure prediction", "protein structure", "molecular biology techniques", "rna alignment", "research and analysis methods", "sequence analysis", "rna structure", "protein structure determination", "sequence alignment", "proteins", "...	Template-Based Modeling of Protein-RNA Interactions	journal.pcbi.1005120	null	[ [ "About three quarters of the human genome could be transcribed into RNA , including 4 , 693 miRNAs [1] and 105 , 255 long noncoding RNAs [2] .", "The function of most of these RNAs is unknown .", "RNAs never act alone .", "One hypothesis is that the long noncoding RNA are molecular scaffolds for p...	[ "Protein-RNA complexes formed by specific recognition between RNA and RNA-binding proteins play an important role in biological processes .", "More than a thousand of such proteins in human are curated and many novel RNA-binding proteins are to be discovered .", "Due to limitations of experimental approaches , ...	[ "Structures of protein-RNA complexes are important for characterization of biological processes .", "The number of experimentally determined protein-RNA complexes is limited .", "Thus modeling of these complexes is important .", "Reliable structural predictions of proteins and their complexes are provided by ...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Multi-locus Analysis of Genomic Time Series Data from Experimental Evolution	journal.pgen.1005069	null	[ [ "There is a small but growing literature on the analysis of evolve-and-resequence data .", "Feder et al . [30] present a statistical test for detecting selection at a single biallelic locus in time series data .", "( Although it is not a major focus , their method can also be used to estimate the sele...	[ "Genomic time series data generated by evolve-and-resequence ( E&R ) experiments offer a powerful window into the mechanisms that drive evolution .", "However , standard population genetic inference procedures do not account for sampling serially over time , and new methods are needed to make full use of modern e...	[ "A growing number of experimental biologists are generating “evolve-and-resequence” ( E&R ) data in which the genomes of an experimental population are repeatedly sequenced over time .", "The resulting time series data provide important new insights into the dynamics of evolution .", "This type of analysis has ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/gene discovery", "genetics and genomics/genetics of the immune system" ]	Genome-Wide Association Study Identifies Two Novel Regions at 11p15.5-p13 and 1p31 with Major Impact on Acute-Phase Serum Amyloid A	journal.pgen.1001213	null	[ [ "Serum amyloid A ( SAA ) is a sensitive marker of the acute inflammatory state .", "Its isoforms are expressed constitutively ( C-SAA ) and show a rapid ( up to 1000-fold ) increased expression in response to inflammatory stimuli such as trauma , infection , injury , and stress during the acute phase ( A-...	[ "Elevated levels of acute-phase serum amyloid A ( A-SAA ) cause amyloidosis and are a risk factor for atherosclerosis and its clinical complications , type 2 diabetes , as well as various malignancies .", "To investigate the genetic basis of A-SAA levels , we conducted the first genome-wide association study on b...	[ "An elevated level of acute-phase serum amyloid A ( A-SAA ) , a sensitive marker of the acute inflammatory state with high heritability estimates , causes amyloidosis and is a risk factor for atherosclerosis and its clinical complications , type 2 diabetes , as well as various malignancies .", "This study describ...	2010
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Non-Invasive Sampling of Schistosomes from Humans Requires Correcting for Family Structure	journal.pntd.0002456	null	[ [ "Infectious disease research is rapidly adopting the tools of evolutionary biology and molecular ecology [1]–[5] .", "Molecular genetic data , evolutionary theory , and population genetic tools can provide methodology to uncover epidemiological processes that cannot be easily determined otherwise .", ...	[ "For ethical and logistical reasons , population-genetic studies of parasites often rely on the non-invasive sampling of offspring shed from their definitive hosts .", "However , if the sampled offspring are naturally derived from a small number of parents , then the strong family structure can result in biased p...	[ "Genetic epidemiology uses genetic data to uncover patterns of disease processes .", "To acquire data for these analyses , individual pathogens are collected and scored at genetic markers , and the resultant data are analyzed to infer biological patterns about the pathogen populations .", "In lieu of invasive s...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "action potentials", "neural networks", "decision making", "nervous system", "membrane potential", "social sciences", "electrophysiology", "neuroscience", "cognitive psychology", "cognition", "network analysis", "computer and information sciences", "animal c...	Predicting how and when hidden neurons skew measured synaptic interactions	journal.pcbi.1006490	null	[ [ "Establishing relationships between a network’s architecture and its function is a fundamental problem in neuroscience and network science in general .", "Not only is the architecture of a neural circuit intimately related to its function , but pathologies in wiring between neurons are believed to contrib...	[ "A major obstacle to understanding neural coding and computation is the fact that experimental recordings typically sample only a small fraction of the neurons in a circuit .", "Measured neural properties are skewed by interactions between recorded neurons and the “hidden” portion of the network .", "To properl...	[ "No experiment in neuroscience can record from more than a tiny fraction of the total number of neurons present in a circuit .", "This severely complicates measurement of a network’s true properties , as unobserved neurons skew measurements away from what would be measured if all neurons were observed .", "For ...	2018
[ "Introduction", "Methods", "Results", "Discussion", "Conclusion" ]	[ "guinea", "medicine and health sciences", "clinical laboratory sciences", "body fluids", "pathology and laboratory medicine", "education", "pathogens", "sociology", "geographical locations", "tropical diseases", "social sciences", "ebola hemorrhagic fever", "microbiology", "viruses", "re...	What motivates Ebola survivors to donate plasma during an emergency clinical trial? The case of Ebola-Tx in Guinea	journal.pntd.0006885	null	[ [ "The urgency to contain the 2013–2016 West-African Ebola virus disease ( EVD ) epidemic led to the World Health Organization’s prioritization of the clinical evaluation of convalescent plasma ( CP ) or whole blood in September 2014 [1–4] as a potential cure , resulting in fast-tracked non-randomized clinical ...	[ "During the 2014 Ebola Virus Disease ( EVD ) epidemic , the Ebola-Tx trial evaluated the use of convalescent plasma ( CP ) in Guinea .", "The effectiveness of plasmapheresis trials depends on the recruitment of plasma donors .", "This paper describes what motivated or deterred EVD survivors to donate CP , provi...	[ "During the 2014 West-African Ebola Virus Disease epidemic , the Ebola-Tx clinical trial in Guinea aimed to determine whether the administration of Ebola antibodies from the blood plasma of Ebola survivors could increase Ebola patients’ survival rate .", "Ebola-Tx was the first trial to solicit and evaluate blood...	2018
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "blood cells", "schistosoma", "invertebrates", "schistosoma mansoni", "medicine and health sciences", "reactive oxygen species", "immune cells", "pathology and laboratory medicine", "helminths", "immunology", "membrane potential", "electrophysiology", "animals", "molecular biology techniqu...	H+ channels in embryonic Biomphalaria glabrata cell membranes: Putative roles in snail host-schistosome interactions	journal.pntd.0005467	null	[ [ "Schistosomiasis , a neglected tropical disease afflicting over 250 million people worldwide [1] , is caused by parasitic flatworms of the genus Schistosoma .", "Schistosoma spp .", "have a two-host life cycle involving sexual reproduction within a mammalian host and asexual reproduction within a snai...	[ "The human blood fluke Schistosoma mansoni causes intestinal schistosomiasis , a widespread neglected tropical disease .", "Infection of freshwater snails Biomphalaria spp .", "is an essential step in the transmission of S . mansoni to humans , although the physiological interactions between the parasite and it...	[ "Schistosoma mansoni is one of four major species of human blood flukes that , together , infect over 250 million people worldwide .", "Transmission of S . mansoni to humans requires infection of freshwater intermediate host snails , Biomphalaria spp .", ", in order to complete its life cycle .", "The B . gla...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "rna interference", "caenorhabditis", "gene regulation", "animals", "invertebrate genomics", "animal models", "age groups", "developmental biology", "caenorhabditis elegans", "model organisms", "genome analysis", "experimental organism systems", "epigenetics", "embryos",...	Maternal and zygotic gene regulatory effects of endogenous RNAi pathways	journal.pgen.1007784	null	[ [ "A plethora of pathways based on non-coding small RNAs ( sRNAs ) regulates gene expression in every domain of life .", "These are collectively known as RNA interference ( RNAi ) or RNAi-like pathways .", "In invertebrates , which lack adaptive immune systems and interferon response , RNAi-like pathway...	[ "Endogenous small RNAs ( sRNAs ) and Argonaute proteins are ubiquitous regulators of gene expression in germline and somatic tissues .", "sRNA-Argonaute complexes are often expressed in gametes and are consequently inherited by the next generation upon fertilization .", "In Caenorhabditis elegans , 26G-RNAs are...	[ "Small RNAs ( sRNAs ) and their partner Argonaute proteins regulate the expression of target RNAs .", "When sperm and egg meet upon fertilization , a diverse set of proteins and RNA , including sRNA-Argonaute complexes , is passed on to the developing progeny .", "Thus , these two players are important to initi...	2019
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "mathematics", "applied mathematics", "biology", "computational biology", "nonlinear dynamics", "biophysics", "neuroscience" ]	Bayesian Comparison of Neurovascular Coupling Models Using EEG-fMRI	journal.pcbi.1002070	null	[ [ "Functional magnetic resonance imaging ( fMRI ) is an extensively employed neuroimaging technique that allows the non-invasive recordings from human brain of neuronal activity with relatively high spatial resolution .", "However , the blood oxygenation level-dependent ( BOLD ) contrast on which fMRI is ba...	[ "Functional magnetic resonance imaging ( fMRI ) , with blood oxygenation level-dependent ( BOLD ) contrast , is a widely used technique for studying the human brain .", "However , it is an indirect measure of underlying neuronal activity and the processes that link this activity to BOLD signals are still a topic ...	[ "Functional magnetic resonance imaging ( fMRI ) , with blood oxygenation level-dependent ( BOLD ) contrast , is a widely used technique for studying the human brain .", "However , the relationship between neuronal activity and blood flow , the basis of fMRI , is still under much debate .", "A growing body of ev...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "population modeling", "influenza", "infectious disease modeling", "biology", "viral diseases", "computational biology" ]	Multiple Estimates of Transmissibility for the 2009 Influenza Pandemic Based on Influenza-like-Illness Data from Small US Military Populations	journal.pcbi.1003064	null	[ [ "Novel strains of influenza emerge as pandemics either from animal reservoirs [1] or from reassortment in humans [2] .", "Pandemic strains are characterized by low levels of population immunity that permit higher levels of incidence .", "However , pandemic strains are not necessarily intrinsically mor...	[ "Rapidly characterizing the amplitude and variability in transmissibility of novel human influenza strains as they emerge is a key public health priority .", "However , comparison of early estimates of the basic reproduction number during the 2009 pandemic were challenging because of inconsistent data sources and...	[ "The ability to rapidly and reliably characterize novel strains of influenza in terms of their transmissibility is crucial for health planners: without good estimates for key parameters it is not possible to identify the appropriate strength of interventions or the spatial optimization of interventions based on var...	2013
[ "Introduction", "Methods", "Discussion" ]	[ "infectious diseases/viral infections", "ecology/population ecology" ]	The Extinction of Dengue through Natural Vulnerability of Its Vectors	journal.pntd.0000922	null	[ [ "Dengue fever is a public health problem of global importance , producing a spectrum of disease spanning febrile arthralgia to hemorrhagic death .", "Dengue viruses are transmitted between human hosts almost exclusively by Aedes ( Stegomyia ) aegypti and Aedes ( Stg . ) albopictus mosquitoes , both of whi...	[ "Dengue is the world's most important mosquito-borne viral illness .", "Successful future management of this disease requires an understanding of the population dynamics of the vector , especially in the context of changing climates .", "Our capacity to predict future dynamics is reflected in our ability to exp...	[ "Dengue transmission has not always been confined to tropical areas .", "In some cases , this has been due to a reduced geographic range of the mosquitoes that are able to carry dengue viruses .", "In Australia , Aedes aegypti mosquitoes once occurred throughout temperate , drier parts of the country but are no...	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "action potentials", "medicine and health sciences", "neural networks", "applied mathematics", "membrane potential", "electrophysiology", "neuroscience", "simulation and modeling", "algorithms", "probability distribution", "mathematics", "convolution", "research and analysis methods", "com...	ASSET: Analysis of Sequences of Synchronous Events in Massively Parallel Spike Trains	journal.pcbi.1004939	null	[ [ "Synchronous input spikes to a receiving neuron are considered most effective in generating an output spike , as predicted by theoretical studies coining the term coincidence detector [1] .", "The argument rests on the premise that excitatory post-synaptic potentials ( EPSPs ) in the cortex are typically ...	[ "With the ability to observe the activity from large numbers of neurons simultaneously using modern recording technologies , the chance to identify sub-networks involved in coordinated processing increases .", "Sequences of synchronous spike events ( SSEs ) constitute one type of such coordinated spiking that pro...	[ "Neurons in the cerebral cortex are highly interconnected .", "However , the mechanisms of coordinated processing in the neuronal network are not yet understood .", "Theoretical studies have proposed synchronized electrical impulses ( spikes ) propagating between groups of nerve cells as a basis of cortical pro...	2016
[ "Introduction", "Methods", "Results and discussion" ]	[ "schistosoma", "invertebrates", "schistosoma mansoni", "medicine and health sciences", "ultraviolet radiation", "helminths", "tropical diseases", "database searching", "light", "parasitic diseases", "animals", "electromagnetic radiation", "neglected tropical diseases", "research and analys...	The effectiveness of water treatment processes against schistosome cercariae: A systematic review	journal.pntd.0006364	null	[ [ "Schistosomiasis is a water-borne helminthic disease caused by schistosomes , which are parasitic worms .", "Infection occurs through dermal-contact with cercaria-infested freshwater .", "Cercariae are released by snails infected with miracidia which hatch from the eggs in human urine and feces .", ...	[ "Schistosomiasis is one of the most disabling neglected tropical diseases , ranking second in terms of years lived with disability .", "While treatment with the drug praziquantel can have immediate beneficial effects , reinfection can occur rapidly if people are in contact with cercaria-infested water .", "Wate...	[ "Schistosomiasis control currently focuses on preventive chemotherapy ( PC ) with praziquantel , which is effective , safe , and inexpensive .", "However , this treatment does not prevent subsequent reinfection .", "As schistosomiasis control targets become more ambitious and move towards elimination , interest...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "blood cells", "medicine and health sciences", "clinical laboratory sciences", "body fluids", "pathology and laboratory medicine", "blood counts", "immunology", "tropical diseases", "preventive medicine", "signs and symptoms", "platelets", "neglected tropical diseases", "transfusion medicine...	Potential Harm of Prophylactic Platelet Transfusion in Adult Dengue Patients	journal.pntd.0004576	null	[ [ "Dengue is estimated to cause 390 million infections annually of which a quarter are symptomatic [1] .", "In the last 5 decades , the incidence of dengue cases has increased 30 -fold with expanding geographical distribution , leading to major international public health concern[2] .", "Dengue infectio...	[ "Thrombocytopenia is a hallmark of dengue infection , and bleeding is a dreaded complication of dengue fever .", "Prophylactic platelet transfusion has been used to prevent bleeding in the management of dengue fever , although the evidence for its benefit is lacking .", "In adult dengue patients with platelet c...	[ "Thrombocytopenia is one of the most prominent clinical features in dengue infection .", "This may manifest clinically as bleeding , which carries significant morbidity and mortality .", "For many years , clinicians have given dengue patients platelet transfusion in a bid to increase their platelet counts to pr...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "machine learning algorithms", "action potentials", "medicine and health sciences", "neural networks", "applied mathematics", "membrane potential", "social sciences", "electrophysiology", "neuroscience", "learning and memory", "simulation and modeling", "algorithms", "recurrent neural networ...	Efficient neural decoding of self-location with a deep recurrent network	journal.pcbi.1006822	null	[ [ "Place cells , pyramidal neurons found in CA1 and CA3 of the mammalian hippocampus [1–4] , exhibit spatially constrained receptive fields , referred to as place fields .", "In general , the activity of place cells is considered to be stable [5 , 6]; place fields are typically robust to the removal of spec...	[ "Place cells in the mammalian hippocampus signal self-location with sparse spatially stable firing fields .", "Based on observation of place cell activity it is possible to accurately decode an animal’s location .", "The precision of this decoding sets a lower bound for the amount of information that the hippoc...	[ "Being able to accurately self-localize is critical for most motile organisms .", "In mammals , place cells in the hippocampus appear to be a central component of the brain network responsible for this ability .", "In this work we recorded the activity of a population of hippocampal neurons from freely moving r...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Practices of Dengue Fever Prevention and the Associated Factors among the Orang Asli in Peninsular Malaysia	journal.pntd.0003954	null	[ [ "Dengue fever is a serious problem overwhelming the world: annually , there are about 50–100 million dengue infections [1] which include 500 , 000 dengue hemorrhagic fever DHF cases with 22 , 000 deaths , mostly among children [2] .", "In the year 2085 , is it estimated at least 50–60% of the world popula...	[ "Dengue is prevalent among Malaysia's indigenous peoples , known as the Orang Asli , and it poses a serious health threat to them .", "The study aims to look at the socio-demographic factors , health beliefs , and knowledge about dengue and its association to dengue prevention practices among Orang Asli communiti...	[ "Dengue poses a threat to everyone worldwide , including the Orang Asli community in Peninsular Malaysia .", "Social demographic , knowledge and behavioral factors are essential aspects to control and prevent dengue .", "This study is aimed to examine these factors and their association with dengue prevention p...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology/membranes and sorting", "infectious diseases/hiv infection and aids", "virology/virulence factors and mechanisms" ]	Multilayered Mechanism of CD4 Downregulation by HIV-1 Vpu Involving Distinct ER Retention and ERAD Targeting Steps	journal.ppat.1000869	null	[ [ "Human Immunodeficiency Virus-1 and -2 ( HIV-1 and -2 ) , as well as Simian Immunodeficiency Virus ( SIV ) , selectively target helper T-lymphocytes and macrophages/monocytes by binding of their viral envelope protein , Env , to a combination of two cell-type-specific surface receptors: a type 1 transmembrane...	[ "A key function of the Vpu protein of HIV-1 is the targeting of newly-synthesized CD4 for proteasomal degradation .", "This function has been proposed to occur by a mechanism that is fundamentally distinct from the cellular ER-associated degradation ( ERAD ) pathway .", "However , using a combination of genetic...	[ "HIV-1 devotes two accessory proteins , Nef and Vpu , to the task of removing the viral receptor , CD4 , from the cell surface .", "Whereas Nef delivers surface CD4 for degradation in lysosomes , Vpu targets newly-made CD4 in the endoplasmic reticulum for degradation by cytosolic proteasomes .", "This latter pr...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "embryology", "developmental neuroscience", "neural circuit formation", "axon guidance", "molecular development", "biology", "neuroscience", "pattern formation", "cell fate determination" ]	A Novel Approach to Selectively Target Neuronal Subpopulations Reveals Genetic Pathways That Regulate Tangential Migration in the Vertebrate Hindbrain	journal.pgen.1002099	null	[ [ "Understanding cell-specific regulatory mechanisms is a major challenge in the post-genome era .", "Particularly in mammals , the reiterated usage of the same transcription factor in distinct subsets of cells or during distinct developmental time points provides the basis to generate thousands of individu...	[ "Vertebrate genes often play functionally distinct roles in different subsets of cells; however , tools to study the cell-specific function of gene products are poorly developed .", "Therefore , we have established a novel mouse model that enables the visualization and manipulation of defined subpopulations of ne...	[ "In mammals , many genes execute a unique set of distinctive and common functions in different cell types .", "Strategies to address these individual roles often involve the generation of series of transgenic animals .", "Here , we present a novel approach that combines a single transgenic mouse line with tissu...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "sequencing techniques", "cell physiology", "carbohydrate metabolism", "medicine and health sciences", "pathology and laboratory medicine", "oxygen", "pathogens", "microbiology", "cell metabolism", "glucose metabolism", "viruses", "dna viruses", "hypoxia", "molecular biology techniques", ...	Metabolic reprogramming of Kaposi’s sarcoma associated herpes virus infected B-cells in hypoxia	journal.ppat.1007062	null	[ [ "Kaposi’s sarcoma associated herpesvirus ( KSHV ) is the etiological agent of Kaposi sarcoma , primary effusion lymphoma and multicentric Castleman disease [1–3] .", "By altering the expression of core metabolic enzymes , KSHV infected cells acquire a metabolic strategy of aerobic glycolysis generally ref...	[ "Kaposi’s sarcoma associated herpesvirus ( KSHV ) infection stabilizes hypoxia inducible factors ( HIFs ) .", "The interaction between KSHV encoded factors and HIFs plays a critical role in KSHV latency , reactivation and associated disease phenotypes .", "Besides modulation of large-scale signaling , KSHV infe...	[ "Hypoxia inducible factors ( HIFs ) play a critical role in survival and growth of cancerous cells , in addition to modulating cellular metabolism .", "Kaposi’s sarcoma associated herpesvirus ( KSHV ) infection stabilizes HIFs .", "Several factors encoded by KSHV are known to interact with up or downstream targ...	2018
[ "Introduction", "Model", "Results", "Discussion" ]	[ "control engineering", "computer science", "behavioral neuroscience", "control systems", "computational neuroscience", "biology", "neuroscience" ]	Speed/Accuracy Trade-Off between the Habitual and the Goal-Directed Processes	journal.pcbi.1002055	null	[ [ "A very basic assumption in theories of animal decision making is that animals possess a complicated learning machinery that aims for maximizing rewards and minimizing threats to homeostasis [1] .", "The primary question within this framework is then how the brain , constrained by computational limitation...	[ "Instrumental responses are hypothesized to be of two kinds: habitual and goal-directed , mediated by the sensorimotor and the associative cortico-basal ganglia circuits , respectively .", "The existence of the two heterogeneous associative learning mechanisms can be hypothesized to arise from the comparative adv...	[ "When confronted with different alternatives , animals can respond either based on their pre-established habits , or by considering the short- and long-term consequences of each option .", "Whereas habitual decision making is fast , goal-directed thinking is a time-consuming task .", "Instead , habits are infle...	2011

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