Split (3)

train · 24.8k rows

headings list	keywords list	title stringlengths 20 281	id stringlengths 20 20	toc stringlengths 57 522 ⌀	sections list	abstract list	summary list	year stringclasses 13 values
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "genome-wide association studies", "medicine and health sciences", "variant genotypes", "population genetics", "genetic mapping", "regression analysis", "linkage disequilibrium", "mathematics", "statistics (mathematics)", "genome analysis", "population biology", "research and analysis methods"...	Structured mating: Patterns and implications	journal.pgen.1006655	null	[ [ "The mating pattern determines the genetic structure of a population [1 , 2 , 3] .", "The genetic structure of a population refers to the distribution of alleles and genotypes in the population .", "Characterizing the genetic structure of a study population is important because ignoring it can lead to...	[ "Genetic similarity of spouses can reflect factors influencing mate choice , such as physical/behavioral characteristics , and patterns of social endogamy .", "Spouse correlations for both genetic ancestry and measured traits may impact genotype distributions ( Hardy Weinberg and linkage equilibrium ) , and there...	[ "We analyzed three generations of whites from the Framingham Heart Study ( FHS ) using genome-wide genotype data to characterize their genetic ancestry .", "By examination of spouse-pairs , we observed that individuals of Northern/Western European , Southern European and Ashkenazi ancestry preferentially chose sp...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "evolutionary biology/microbial evolution and genomics", "genetics and genomics/functional genomics", "microbiology/microbial evolution and genomics", "computational biology/genomics", "infectious diseases/bacterial infections", "computational biology/systems biology" ]	Identifying Cognate Binding Pairs among a Large Set of Paralogs: The Case of PE/PPE Proteins of Mycobacterium tuberculosis	journal.pcbi.1000174	null	[ [ "The PE and PPE gene families in Mtb make up nearly 10% of the bacterium's coding DNA [2] .", "The two families combined have about 150 members , amounting to 4% of the open reading frames ( ORFs ) in Mtb .", "The PE and PPE gene families account for much of the genomic difference between Mtb and othe...	[ "We consider the problem of how to detect cognate pairs of proteins that bind when each belongs to a large family of paralogs .", "To illustrate the problem , we have undertaken a genomewide analysis of interactions of members of the PE and PPE protein families of Mycobacterium tuberculosis .", "Our computation...	[ "We consider the problem of detecting protein interactions from genome sequences when the potential interacting partners belong to large families of similar ( homologous ) proteins .", "Many computational methods for predicting protein interactions rely on similarity to a pair of known interacting proteins .", ...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Inter-kingdom Signaling by the Legionella Quorum Sensing Molecule LAI-1 Modulates Cell Migration through an IQGAP1-Cdc42-ARHGEF9-Dependent Pathway	journal.ppat.1005307	null	[ [ "Bacteria accomplish intra-species and inter-species communication through the production , secretion and detection of low molecular weight compounds [1 , 2] .", "Many of these compounds , termed “autoinducers” , trigger above a certain concentration threshold transmembrane phosphorylation signaling and u...	[ "Small molecule signaling promotes the communication between bacteria as well as between bacteria and eukaryotes .", "The opportunistic pathogenic bacterium Legionella pneumophila employs LAI-1 ( 3-hydroxypentadecane-4-one ) for bacterial cell-cell communication .", "LAI-1 is produced and detected by the Lqs ( ...	[ "Legionella pneumophila is a ubiquitous environmental bacterium , which upon inhalation causes a severe pneumonia termed Legionnaires’ disease .", "The opportunistic pathogen employs the small molecule LAI-1 ( Legionella autoinducer-1 ) for bacterial cell-cell communication .", "LAI-1 is produced and detected b...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "physiology", "in vitro", "diabetes and endocrinology", "homo (human)", "rattus (rat)" ]	A KATP Channel-Dependent Pathway within α Cells Regulates Glucagon Release from Both Rodent and Human Islets of Langerhans	journal.pbio.0050143	Elevated glucose levels reduce electrical activity and the release of glucagon via inactivation of ion channels in pancreatic islet cells.	[ [ "Blood glucose levels are under the control of two hormones released from the pancreatic islets of Langerhans .", "Islet β cells secrete insulin when glucose is high , decreasing glucose production by the liver and increasing glucose storage in multiple tissues .", "Regulated insulin secretion is rela...	[ "Glucagon , secreted from pancreatic islet α cells , stimulates gluconeogenesis and liver glycogen breakdown .", "The mechanism regulating glucagon release is debated , and variously attributed to neuronal control , paracrine control by neighbouring β cells , or to an intrinsic glucose sensing by the α cells them...	[ "Glucagon is a critical regulator of glucose homeostasis .", "Its major action is to mobilize glucose from the liver .", "Glucagon secretion from α cells of the pancreatic islets of Langerhans is suppressed by elevated blood sugar , a response that is often perturbed in diabetes .", "Much work has focused on ...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular neuroscience", "cellular neuroscience", "neuronal morphology", "signaling pathways", "biology", "neuroscience" ]	An Autism-Associated Variant of Epac2 Reveals a Role for Ras/Epac2 Signaling in Controlling Basal Dendrite Maintenance in Mice	journal.pbio.1001350	Epac2 disruption impairs basal (but not apical) dendrite complexity in cortical neurons, and an autism-associated mutation in Epac2 implicates a Ras/Epac2 signaling pathway in the active maintenance of basal dendritic arbors.	[ [ "Dendritic structure is critical for neuronal function , as the size and shape of the dendritic arbor defines the neuron's receptive field [1] .", "Generating and maintaining proper arborization is therefore crucial for neural circuit function [2] .", "The importance of maintaining dendritic arborizat...	[ "The architecture of dendritic arbors determines circuit connectivity , receptive fields , and computational properties of neurons , and dendritic structure is impaired in several psychiatric disorders .", "While apical and basal dendritic compartments of pyramidal neurons are functionally specialized and differe...	[ "A fundamental feature of a neuron is the morphology of its dendrites , which are the processes that receive and integrate synaptic signals from other neurons .", "Neurons in the mammalian cortex exhibit two distinct dendritic arbors: apical dendrites , which extend far from the cell body , and basal dendrites , ...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "evolutionary biology", "molecular biology", "genetics and genomics" ]	Trans-Regulation of Mouse Meiotic Recombination Hotspots by Rcr1	journal.pbio.1000036	Rcr1 is identified as atrans-regulator of meiotic recombination hotspots that appears to act at the initiation of recombination and that maps to a 5.3-megabase region on mouse Chromosome 17.	[ [ "Meiotic homologous recombination is responsible for generating genetic variety among offspring as well as ensuring accurate chromosome segregation during meiotic cell divisions .", "The process of recombination is initiated by the formation of DNA double-strand breaks ( DSBs ) created by the highly conse...	[ "Meiotic recombination is required for the orderly segregation of chromosomes during meiosis and for providing genetic diversity among offspring .", "Among mammals , as well as yeast and higher plants , recombination preferentially occurs at highly delimited chromosomal sites 1–2 kb long known as hotspots .", "...	[ "Recombination is an essential aspect of meiosis , ensuring proper contact and exchange of genetic material between homologous parental chromosomes , as well as their subsequent segregation to produce haploid gametes .", "In humans and mice , recombination events are located at preferential sites termed hotspots ...	2009
[ "Introduction", "Results and discussion", "Materials and methods" ]	[ "biotechnology", "invertebrates", "medicine and health sciences", "caenorhabditis", "neuroscience", "animals", "animal models", "caenorhabditis elegans", "model organisms", "oils", "experimental organism systems", "genetic engineering", "digestive system", "research and analysis methods", ...	Pheromone-sensing neurons regulate peripheral lipid metabolism in Caenorhabditis elegans	journal.pgen.1006806	null	[ [ "In relation to fat metabolism and energy balance , the central nervous system plays a more intricate role than historically thought .", "Initially believed to exert its effects on adiposity predominantly through promoting food intake , several studies have now demonstrated that the underlying neuronal ci...	[ "It is now established that the central nervous system plays an important role in regulating whole body metabolism and energy balance .", "However , the extent to which sensory systems relay environmental information to modulate metabolic events in peripheral tissues has remained poorly understood .", "In addit...	[ "The central nervous system plays a vital role in regulating whole body metabolism and energy balance .", "However , the precise cellular , genetic and molecular mechanisms underlying these effects remain a major unsolved mystery .", "C . elegans has emerged as a tractable and highly informative model to study ...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "legs", "pathology and laboratory medicine", "chemical compounds", "sports and exercise medicine", "salts", "limbs (anatomy)", "database searching", "physical activity", "health care", "signs and symptoms", "edema", "research and analysis methods", "public a...	Self-Care for Management of Secondary Lymphedema: A Systematic Review	journal.pntd.0004740	null	[ [ "Lymphedema is a high protein edema which forms when the lymphatic system is chronically overwhelmed .", "Earlier fluid rich stages progress gradually toward enlargement and fibrosis of the subcutaneous compartment and hyperkeratosis of the skin ( elephantiasis ) [1] .", "This can occur as a result of...	[ "Lymphedema is a debilitating and disfiguring sequela of an overwhelmed lymphatic system .", "The most common causes of secondary lymphedema are lymphatic filariasis ( LF ) , a vector-borne , parasitic disease endemic in 73 tropical countries , and treatment for cancer in developed countries .", "Lymphedema is ...	[ "Secondary lymphedema is a major cause of disability worldwide .", "The most common causes are treatment for cancer or infection with lymphatic filariasis .", "In both cases , the lymphatic system is damaged and unable to perform its normal function of removing extracellular fluid and wastes .", "Protein rich...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Accuracy of Individual Rapid Tests for Serodiagnosis of Gambiense Sleeping Sickness in West Africa	journal.pntd.0003480	null	[ [ "Human African trypanosomiasis ( HAT ) or sleeping sickness is a fatal parasitic infection affecting rural populations in sub-Saharan Africa .", "During the last decade , active case finding by specialized mobile teams has considerably contributed to the reduction of the prevalence of HAT caused by Trypan...	[ "Individual rapid tests for serodiagnosis ( RDT ) of human African trypanosomiasis ( HAT ) are particularly suited for passive screening and surveillance .", "However , so far , no large scale evaluation of RDTs has been performed for diagnosis of Trypanosoma brucei gambiense HAT in West Africa .", "The objecti...	[ "Screening for gambiense human African trypanosomiasis ( HAT ) or sleeping sickness is traditionally based on detection of trypanosome specific antibodies in blood .", "Whereas the card agglutination test is particularly suited for mass screening , individual rapid serodiagnostic tests ( RDTs ) are rather adapted...	2015
[ "Introduction", "Results", "Network Co-activation Differences among Emotion Categories", "Discussion", "Methods" ]	[]	A Bayesian Model of Category-Specific Emotional Brain Responses	journal.pcbi.1004066	null	[ [ "To develop a model for emotion categories and test its accuracy in diagnosing the emotions being cultivated in specific studies , we constructed a generative , Bayesian Spatial Point Process ( BSPP ) model of the joint posterior distribution of peak activation locations over the brain for each emotion catego...	[ "Understanding emotion is critical for a science of healthy and disordered brain function , but the neurophysiological basis of emotional experience is still poorly understood .", "We analyzed human brain activity patterns from 148 studies of emotion categories ( 2159 total participants ) using a novel hierarchic...	[ "Neuroimaging provides a unique way of understanding the ‘emotional brain’ by identifying patterns across multiple systems that imbue each instance of emotion with its particular qualities .", "In this meta-analysis across 148 studies , we ask whether it is possible to identify patterns that differentiate five em...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "cell biology", "genetics and genomics", "cardiovascular disorders" ]	Genetic and Physiologic Dissection of the Vertebrate Cardiac Conduction System	journal.pbio.0060109	By characterizing the genetic underpinnings of the vertebrate cardiac conduction system, a new study sheds light on the mechanisms underlying cardiac arrhythmias, which cause the sudden death of hundreds of thousands of people each year.	[ [ "Vertebrate hearts have evolved into multichambered structures requiring coordinated beating of their chambers to achieve antegrade blood flow throughout the organism .", "Unidirectional blood flow is achieved through two specialized structures that are unique to vertebrates: cardiac valves and the specia...	[ "Vertebrate hearts depend on highly specialized cardiomyocytes that form the cardiac conduction system ( CCS ) to coordinate chamber contraction and drive blood efficiently and unidirectionally throughout the organism .", "Defects in this specialized wiring system can lead to syncope and sudden cardiac death .", ...	[ "Aberrant electrical activity of the heart , otherwise known as cardiac arrhythmia , may disrupt heart contractions , leading to loss of consciousness and sudden death .", "Every year , approximately 450 , 000 individuals in the United States die suddenly from this event .", "Currently , the only proven prevent...	2008
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "liver", "immune physiology", "diagnostic radiology", "body fluids", "biopsy", "spleen", "fibrosis", "liver diseases", "surgical and invasive medical procedures", "magnetic resonance imaging", "physiological processes", "developmental biology", "gastroentero...	Model-inferred mechanisms of liver function from magnetic resonance imaging data: Validation and variation across a clinically relevant cohort	journal.pcbi.1007157	null	[ [ "Measurements of liver function are important to determine the optimal therapeutic strategy in cases of severe chronic liver disease ( CLD ) , and for prevention of post-treatment hepatic failure [1] .", "Estimating liver function is also important when planning surgical treatment , because postoperative ...	[ "Estimation of liver function is important to monitor progression of chronic liver disease ( CLD ) .", "A promising method is magnetic resonance imaging ( MRI ) combined with gadoxetate , a liver-specific contrast agent .", "For this method , we have previously developed a model for an average healthy human .",...	[ "Being able to accurately and reliably estimate liver function is important when monitoring the progression of patients with liver disease , as well as when identifying drug-induced liver injury during drug development .", "A promising method for quantifying liver function is to use magnetic resonance imaging com...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "interaction networks", "protein interactions", "protein interaction networks", "mutation", "network analysis", "nonsense mutation", "protein structure", "mutation databases", "frameshift mutation", "research and analysis methods", "computer and information sciences", "proteins", "biological...	3D spatial organization and network-guided comparison of mutation profiles in Glioblastoma reveals similarities across patients	journal.pcbi.1006789	null	[ [ "Cancer mostly occurs when somatic mutations accumulate and eventually change the behavior , structure and properties of the cell .", "Understanding which mutations cause cancer is of crucial importance .", "The large-scale cancer genome sequencing projects including The Cancer Genome Atlas ( TCGA ) [...	[ "Glioblastoma multiforme ( GBM ) is the most aggressive type of brain tumor .", "Molecular heterogeneity is a hallmark of GBM tumors that is a barrier in developing treatment strategies .", "In this study , we used the nonsynonymous mutations of GBM tumors deposited in The Cancer Genome Atlas ( TCGA ) and appli...	[ "Precision medicine aims to find the best treatment strategy based on the information about the patient’s tumor .", "Molecular heterogeneity is the main obstacle in developing treatment strategies .", "Therefore , transforming patient specific molecular data into clinically interpretable knowledge is fundamenta...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Modeling the Effects of Vorinostat In Vivo Reveals both Transient and Delayed HIV Transcriptional Activation and Minimal Killing of Latently Infected Cells	journal.ppat.1005237	null	[ [ "Treatment of HIV-infected individuals with combination antiretroviral therapy ( cART ) effectively suppresses HIV to levels below the limit of detection of conventional assays and substantially reduces morbidity and mortality of HIV infected patients [1] .", "However , it does not eradicate the virus and...	[ "Recent efforts to cure human immunodeficiency virus type-1 ( HIV-1 ) infection have focused on developing latency reversing agents as a first step to eradicate the latent reservoir .", "The histone deacetylase inhibitor , vorinostat , has been shown to activate HIV RNA transcription in CD4+ T-cells and alter hos...	[ "Combination antiretroviral therapy ( cART ) for HIV infection must be taken for life due to the existence of long lived latently infected cells .", "Recent efforts have focused on developing latency reversing agents to eliminate latently infected cells by activating HIV production .", "In this work , we assess...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "taxonomy", "organismal evolution", "medicine and health sciences", "pathology and laboratory medicine", "evolutionary biology", "hepacivirus", "pathogens", "population genetics", "microbiology", "retroviruses", "viruses", "immunodeficiency viruses", "phylogenetics", "data management", "...	Exceptional Heterogeneity in Viral Evolutionary Dynamics Characterises Chronic Hepatitis C Virus Infection	journal.ppat.1005894	null	[ [ "An estimated 3% of the global human population has been infected with the hepatitis C virus ( HCV ) , many of whom are unaware of their infection status .", "Unlike other members of the virus family Flaviviridae , HCV causes acute and chronic infection in humans .", "Symptoms of acute infection are t...	[ "The treatment of HCV infection has seen significant progress , particularly since the approval of new direct-acting antiviral drugs .", "However these clinical achievements have been made despite an incomplete understanding of HCV replication and within-host evolution , especially compared with HIV-1 .", "Here...	[ "Our knowledge of HCV within-host evolution is substantially limited , which is surprising given that highly successful therapies against the virus have been developed .", "Key aspects of HCV infection , such as rapid fluctuations in viral diversity and the reappearance of viral strains years after their initial ...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "mycobacterium ulcerans", "bacterial diseases", "infectious diseases", "buruli ulcer", "medicine and health sciences", "anatomical pathology", "histopathology", "animal models of infection", "pathology and laboratory medicine", "animal studies", "animal models of disease", "neglected tropical ...	Experimental Infection of the Pig with Mycobacterium ulcerans: A Novel Model for Studying the Pathogenesis of Buruli Ulcer Disease	journal.pntd.0002968	null	[ [ "Buruli ulcer ( BU ) , caused by infection with Mycobacterium ulcerans , is a human disease of the skin primarily affecting subcutaneous fat tissue and leading to ulceration of the overlying dermal and epidermal layers [1] , [2] .", "The disease is reported from countries worldwide but has its highest pre...	[ "Buruli ulcer ( BU ) is a slowly progressing , necrotising disease of the skin caused by infection with Mycobacterium ulcerans .", "Non-ulcerative manifestations are nodules , plaques and oedema , which may progress to ulceration of large parts of the skin .", "Histopathologically , BU is characterized by coagu...	[ "Buruli ulcer caused by Mycobacterium ulcerans infection is a necrotizing disease of the skin and the underlying subcutaneous tissue .", "Since the skin of pigs ( Sus scrofa ) has striking structural and physiological similarities with human skin , we investigated whether it is possible to develop an experimental...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology/virion structure, assembly, and egress", "virology/host invasion and cell entry" ]	A Capsid-Encoded PPxY-Motif Facilitates Adenovirus Entry	journal.ppat.1000808	null	[ [ "Many viruses use the microtubule network of the host cell for transport to their site of replication ( i . e . the nucleus ) [1] .", "Access to the microtubule network is achieved through recruitment of cytoplasmic dynein motor proteins followed by efficient retrograde transport towards the nucleus [2] ,...	[ "Viruses use cellular machinery to enter and infect cells .", "In this study we address the cell entry mechanisms of nonenveloped adenoviruses ( Ads ) .", "We show that protein VI , an internal capsid protein , is rapidly exposed after cell surface attachment and internalization and remains partially associated...	[ "Viruses exploit cellular functions during entry and exit of cells .", "To redirect cellular functions for their own purpose , viruses encode high-affinity binding sites for key-cellular factors .", "One such domain is the PPxY motif , which is present in structural proteins of several , mainly enveloped viruse...	2010
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "phosphorylation", "transfection", "medicine and health sciences", "gene regulation", "293t cells", "regulatory proteins", "biological cultures", "rna extraction", "dna-binding proteins", "oncology", "transcription factors", "bioassays and physiological analysis", "molecular biology techniqu...	A human endogenous retrovirus-derived gene that can contribute to oncogenesis by activating the ERK pathway and inducing migration and invasion	journal.ppat.1006451	null	[ [ "Retroviruses are responsible for a broad range of diseases in animals and humans , the most common of which is the development of cancers .", "The mechanisms by which they contribute to oncogenesis are diverse and include:", "( i ) insertional mutagenesis , due to activation of cellular proto-oncogen...	[ "Endogenous retroviruses are cellular genes of retroviral origin captured by their host during the course of evolution and represent around 8% of the human genome .", "Although most are defective and transcriptionally silenced , some are still able to generate retroviral-like particles and proteins .", "Among t...	[ "Nearly half the DNA of mammals consists of reitarated , selfish elements that can move and amplify within the genome .", "With time , some of these elements are recruited by the host and the proteins they encode are used to fulfill physiological functions , whereas other elements have conserved some of their pat...	2017
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "comparative sequence analysis", "chemical characterization", "statistics", "vertebrates", "animals", "mammals", "mathematics", "forecasting", "sequence motif analysis", "epigenomics", "research and analysis methods", "sequence analysis", "genomics", "bioinformatics", "mathematical and s...	Functional conservation of sequence determinants at rapidly evolving regulatory regions across mammals	journal.pcbi.1006451	null	[ [ "Epigenomic modifications such as histone modifications and DNA methylation play critical roles in development , regulation , and diseases .", "The study of epigenetic modifications has made great strides in recent decades , and the specific combinations of different epigenome components in distinct biolo...	[ "Recent advances in epigenomics have made it possible to map genome-wide regulatory regions using empirical methods .", "Subsequent comparative epigenomic studies have revealed that regulatory regions diverge rapidly between genome of different species , and that the divergence is more pronounced in enhancers tha...	[ "Regions of the genome that do not encode genes but affect expression of other genes , such as enhancers and promoters , are referred to as regulatory regions .", "Because of their regulatory functions , it was thought that enhancers and promoters should be evolutionarily conserved .", "Regulatory regions can b...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "antimicrobials", "medicine and health sciences", "drugs", "population genetics", "microbiology", "antifungals", "epistasis", "mutation", "sign epistasis", "pharmacology", "population biology", "mycology", "lipids", "fitness epistasis", "mutant strains", "sterols", "reciprocal sign e...	Widespread Genetic Incompatibilities between First-Step Mutations during Parallel Adaptation of Saccharomyces cerevisiae to a Common Environment	journal.pbio.1002591	A study of yeast adapted to the fungicide nystatin finds that the first step toward speciation (partial postzygotic reproductive isolation) can evolve rapidly in populations under similar selective pressures.	[ [ "The nature of epistasis is critical to broad-scale evolutionary phenomena .", "If all possible alleles have the same effect in all genetic backgrounds , we might expect populations that diverge initially to converge to a similar genotype and/or phenotype over time at the fitness optimum .", "In contr...	[ "Independently evolving populations may adapt to similar selection pressures via different genetic changes .", "The interactions between such changes , such as in a hybrid individual , can inform us about what course adaptation may follow and allow us to determine whether gene flow would be facilitated or hampere...	[ "We crossed yeast bearing different genetic mutations to determine the fitness of their hybrid offspring .", "These strains had previously evolved in the presence of the fungicide nystatin .", "Even though the initial strains had nearly identical genomes , differing only in the mutation they carried within the ...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "white light", "medicine and health sciences", "sleep", "vertebrates", "light", "mice", "animals", "mammals", "electromagnetic radiation", "physiological processes", "animal behavior", "adrenal glands", "visible light", "zoology", "behavior", "gene expression", "light pulses", "phy...	Melanopsin Regulates Both Sleep-Promoting and Arousal-Promoting Responses to Light	journal.pbio.1002482	Light can produce either sleep or arousal in mice. This study reveals that these opposing effects depend upon the wavelength of light and appear to involve separate pathways, both modulated by the photopigment melanopsin.	[ [ "In addition to its familiar visual function the mammalian retina mediates a broad range of non-image forming responses to light , including the entrainment of circadian rhythms [1] , regulation of pineal melatonin synthesis [2] , pupillary light constriction [3] and the regulation of sleep [4–6] .", "Res...	[ "Light plays a critical role in the regulation of numerous aspects of physiology and behaviour , including the entrainment of circadian rhythms and the regulation of sleep .", "These responses involve melanopsin ( OPN4 ) -expressing photosensitive retinal ganglion cells ( pRGCs ) in addition to rods and cones .",...	[ "Light exerts profound effects on our physiology and behaviour , setting our biological clocks to the correct time and regulating when we are asleep and we are awake .", "The photoreceptors mediating these responses include the rods and cones involved in vision , as well as a subset of photosensitive retinal gang...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunopathology", "immune cells", "cell biology", "animal cells", "clinical immunology", "biology and life sciences", "cellular types", "immunology" ]	Alveolar Macrophages Are Essential for Protection from Respiratory Failure and Associated Morbidity following Influenza Virus Infection	journal.ppat.1004053	null	[ [ "Alveolar macrophages ( AM ) are lung-resident macrophages important for the maintenance of surfactant homeostasis in the alveolar space [1] .", "Their importance for lung physiology becomes evident in a rare human syndrome termed “pulmonary alveolar proteinosis” ( PAP ) , which is characterized by the ac...	[ "Alveolar macrophages ( AM ) are critical for defense against bacterial and fungal infections .", "However , a definitive role of AM in viral infections remains unclear .", "We here report that AM play a key role in survival to influenza and vaccinia virus infection by maintaining lung function and thereby prot...	[ "Acute respiratory viral infections can cause severe morbidity and pneumonia in infected individuals .", "Alveolar macrophages and various subsets of dendritic cells have been implicated in innate immunity and induction of anti-viral T cell responses that contribute to host defense against influenza virus infecti...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	The Rise and Fall of an Evolutionary Innovation: Contrasting Strategies of Venom Evolution in Ancient and Young Animals	journal.pgen.1005596	null	[ [ "Venom is an intriguing evolutionary innovation that is utilized by various animals for predation and/or defense .", "This complex biochemical cocktail is characterized by a myriad of organic and inorganic molecules , such as proteins , peptides , polyamines and salts that disrupt the normal physiology of...	[ "Animal venoms are theorized to evolve under the significant influence of positive Darwinian selection in a chemical arms race scenario , where the evolution of venom resistance in prey and the invention of potent venom in the secreting animal exert reciprocal selection pressures .", "Venom research to date has m...	[ "While the influence of positive selection in diversifying animal venoms is widely recognized , the role of purifying selection that conserves the amino acid sequence of venom components such as peptide toxins has never been considered .", "In addition to unraveling the unique strategies of evolution of toxin gen...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "computational neuroscience", "biology", "neuroscience" ]	Spectral Analysis of Input Spike Trains by Spike-Timing-Dependent Plasticity	journal.pcbi.1002584	null	[ [ "Organization in neuronal networks is hypothesized to rely to a large extent on synaptic plasticity based on their spiking activity .", "The importance of spike timing for synaptic plasticity has been observed in many brain areas for many types of neurons [1] , [2] , which was termed spike-timing-dependen...	[ "Spike-timing-dependent plasticity ( STDP ) has been observed in many brain areas such as sensory cortices , where it is hypothesized to structure synaptic connections between neurons .", "Previous studies have demonstrated how STDP can capture spiking information at short timescales using specific input configur...	[ "Tuning feature extraction of sensory stimuli is an important function for synaptic plasticity models .", "A widely studied example is the development of orientation preference in the primary visual cortex , which can emerge using moving bars in the visual field .", "A crucial point is the decomposition of stim...	2012
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "respiratory infections", "ears", "immunology", "parasitic diseases", "parasitic protozoans", "pulmonology", "otology", "ear infections", "protozoans", "signs and symptoms", "leishmania", ...	Divergent roles for Ly6C+CCR2+CX3CR1+ inflammatory monocytes during primary or secondary infection of the skin with the intra-phagosomal pathogen Leishmania major	journal.ppat.1006479	null	[ [ "Immature bone marrow-derived monocytes are cells of the innate immune system that undergo maturation to populate numerous peripheral cell subsets [1–4] .", "Under different inflammatory and steady state conditions monocytes have been shown to acquire effector [5] , regulatory [6] , suppressor [7] , homeo...	[ "Inflammatory monocytes can be manipulated by environmental cues to perform multiple functions .", "To define the role of monocytes during primary or secondary infection with an intra-phagosomal pathogen we employed Leishmania major-red fluorescent protein ( RFP ) parasites and multi-color flow cytometry to defin...	[ "Many infectious diseases are initiated in the context of inflammation .", "This inflammatory response may be initiated by the pathogen itself or by damage to barrier sites associated with the infectious process .", "In the case of the vector-transmitted intra-phagosomal pathogen Leishmania , the parasite must ...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biophysics", "cell biology", "biology and life sciences", "ion transport" ]	Electrochemical Regulation of Budding Yeast Polarity	journal.pbio.1002029	Manipulation of yeast cell polarity by external electric fields reveals electrochemical pathways that influence the distribution of membrane lipids and the polarity regulator Cdc4p.	[ [ "Cell polarization arises from the asymmetric accumulation of cellular components near a region of the plasma membrane .", "Although the roles of polarity proteins such as small GTPases and cytoskeletal elements have been studied extensively [1] , much less is known about the possible contribution of elec...	[ "Cells are naturally surrounded by organized electrical signals in the form of local ion fluxes , membrane potential , and electric fields ( EFs ) at their surface .", "Although the contribution of electrochemical elements to cell polarity and migration is beginning to be appreciated , underlying mechanisms are n...	[ "The ability of cells to orient towards spatial cues is critical for processes such as migration , wound healing , and development .", "Although the role of electrochemical signals is well characterized in processes such as neuronal signaling , their function in cell polarity is much less understood or appreciate...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "mosquitoes", "rna interference", "emerging infectious diseases", "viral transmission and infection", "vector biology", "virology", "gene expression", "genetics", "gene regulation", "molecular genetics", "emerging viral diseases", "biology", "microbiology", "viral vectors" ]	Cooler Temperatures Destabilize RNA Interference and Increase Susceptibility of Disease Vector Mosquitoes to Viral Infection	journal.pntd.0002239	null	[ [ "There is a great deal of uncertainty concerning how climate change will affect the distribution and incidence of infectious diseases , particularly vector-borne diseases .", "Although there have been predictions of increased vector-borne disease with increasing global temperatures [1] , modeling such cha...	[ "The impact of global climate change on the transmission dynamics of infectious diseases is the subject of extensive debate .", "The transmission of mosquito-borne viral diseases is particularly complex , with climatic variables directly affecting many parameters associated with the prevalence of disease vectors ...	[ "Although a link between the increased susceptibility of mosquitoes for arthropod-borne viruses and exposure to lower rearing temperatures has been known for many years , the molecular basis of this has remained unknown .", "We investigated this phenomenon using an engineered strain of mosquito where the expressi...	2013
[ "Introduction", "Results", "Discussion", "Material and methods" ]	[ "genome-wide association studies", "plant anatomy", "quantitative trait loci", "plant products", "genetic mapping", "plant science", "oils", "genome analysis", "crops", "lipids", "genomics", "crop science", "gene expression", "seeds", "genetic loci", "agriculture", "vegetable oils", ...	Artificial selection on GmOLEO1 contributes to the increase in seed oil during soybean domestication	journal.pgen.1008267	null	[ [ "Soybean ( Glycine max ( L . ) Merr .", ") is an important food and oil crop .", "Soybean seeds accumulate large amounts of oil and protein and have been intensively targeted for human consumption during long-term domestication and cultivation .", "Given the high percentage of oil in soybean seeds...	[ "Increasing seed oil content is one of the most important breeding goals for soybean due to a high global demand for edible vegetable oil .", "However , genetic improvement of seed oil content has been difficult in soybean because of the complexity of oil metabolism .", "Determining the major variants and molec...	[ "Soybean seed oil is an important quality trait targeted during domestication and breeding .", "However , the molecular mechanism of soybean oil regulation is largely unknown due to its complex genetic architecture and environmental sensitivity .", "In this paper , we integrated GWAS across multiple environment...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "clinical laboratory sciences", "body fluids", "enzyme-linked immunoassays", "cost-effectiveness analysis", "economic analysis", "geographical locations", "social sciences", "parasitic protozoans", "health care", "north america", "organisms", "protozoans", "...	Cost-Effectiveness of Blood Donation Screening for Trypanosoma cruzi in Mexico	journal.pntd.0004528	null	[ [ "Chagas disease is caused by the unicellular parasite Trypanosoma cruzi , capable of movement directly from one person to another via blood transfusion , organ transplant , or maternal-fetal transfer [1 , 2] .", "Although the most prevalent mode of transmission is via the excreta of infected reduviid bugs...	[ "An estimated 2 million inhabitants are infected with Chagas disease in Mexico , with highest prevalence coinciding with highest demographic density in the southern half of the country .", "After vector-borne transmission , Trypanosoma cruzi is principally transmitted to humans via blood transfusion .", "Despit...	[ "Chagas disease continues to be a neglected disease in Mexico and Latin-American .", "Although an estimated 96% of Trypanosoma cruzi transmission to humans occurs via 32 triatomine vector species , the only transmission prevention in Mexico has been sparse and based on heterogeneous blood donation screening .", ...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "immunology/immune response", "infectious diseases/epidemiology and control of infectious diseases", "biotechnology/protein chemistry and proteomics" ]	Immunogenic Salivary Proteins of Triatoma infestans: Development of a Recombinant Antigen for the Detection of Low-Level Infestation of Triatomines	journal.pntd.0000532	null	[ [ "Control programs for Chagas disease in South America , such as the ‘Southern Cone Initiative’ have relied mainly upon vector control using insecticide spraying [1] .", "These campaigns have reduced the distribution of T . infestans to an area of 14 . 6% of the initial endemic area .", "However , espe...	[ "Triatomines are vectors of Trypanosoma cruzi , the etiological agent of Chagas disease in Latin America .", "The most effective vector , Triatoma infestans , has been controlled successfully in much of Latin America using insecticide spraying .", "Though rarely undertaken , surveillance programs are necessary ...	[ "Chagas disease , caused by Trypanosoma cruzi , is a neglected disease with 20 million people at risk in Latin America .", "The main control strategies are based on insecticide spraying to eliminate the domestic vectors , the most effective of which is Triatoma infestans .", "This approach has been very success...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/disease models", "genetics and genomics/genetics of disease", "biochemistry/protein folding" ]	Activation of Mutant Enzyme Function In Vivo by Proteasome Inhibitors and Treatments that Induce Hsp70	journal.pgen.1000807	null	[ [ "Missense mutations are genetic alterations that result in the production of proteins with single amino acid changes and are an especially common cause of a variety of diseases [1] .", "Most disease causing missense mutations do not target key catalytic residues , but rather cause problems in protein fold...	[ "Missense mutant proteins , such as those produced in individuals with genetic diseases , are often misfolded and subject to processing by intracellular quality control systems .", "Previously , we have shown using a yeast system that enzymatic function could be restored to I278T cystathionine β-synthase ( CBS ) ...	[ "Genetic diseases are often caused by missense mutations: single nucleotide changes that cause a single incorrect amino acid to be substituted into the underlying protein .", "Most missense mutations cause the encoded protein to fold incorrectly and therefore not function properly .", "Examples of missense muta...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "signal transduction", "medicine and health sciences", "cancer genetics", "cell biology", "chromosome biology", "gastroenterology and hepatology", "gene expression", "genetics", "biology and life sciences", "gastrointestinal cancers", "molecular cell biology", "cell signaling", "chromatin" ]	Brg1 Loss Attenuates Aberrant Wnt-Signalling and Prevents Wnt-Dependent Tumourigenesis in the Murine Small Intestine	journal.pgen.1004453	null	[ [ "More than 90% of colorectal cancers ( CRC ) are characterised by aberrant activation of the canonical Wnt/β-catenin pathway , which is proposed to play a major role in the initiation and progression of CRC [1] .", "Despite this clear link between deregulated Wnt signalling and disease , therapies which t...	[ "Tumourigenesis within the intestine is potently driven by deregulation of the Wnt pathway , a process epigenetically regulated by the chromatin remodelling factor Brg1 .", "We aimed to investigate this interdependency in an in vivo setting and assess the viability of Brg1 as a potential therapeutic target .", ...	[ "Aberrant Wnt signalling is responsible for the majority of colorectal cancers , the third leading cause of cancer-related mortality in the UK .", "However , no therapies directly targeting Wnt signalling are currently available .", "Using mouse models of intestinal cancer , we demonstrate that deleting chromat...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "elderly", "tropical diseases", "geographical locations", "health care", "age groups", "chi square tests", "adults", "mathematics", "statistics (mathematics)", "neglected tropical diseases", "research and analysis methods", "infectious diseases", "dengue fev...	Factors Associated with the Time of Admission among Notified Dengue Fever Cases in Region VIII Philippines from 2008 to 2014	journal.pntd.0005050	null	[ [ "Dengue fever is endemic in the Philippines .", "The Department of Health ( DOH ) reported 59 , 943 cases between January and September 2014 , with an incidence of 60 cases per 100 , 000 [1] .", "Sixty five percent of the cases in the country were admitted , while 35% were treated as outpatient [2] ."...	[ "In cases of Dengue fever , late hospital admission can lead to treatment delay and even death .", "In order to improve early disease notification and management , it is essential to investigate the factors affecting the time of admission of Dengue cases .", "This study determined the factors associated with th...	[ "A variety of factors affect the time of admission of Dengue fever cases .", "These must be investigated , as delayed treatment of this disease can result in death .", "The authors of this study determined the factors associated with the time of admission among notified Dengue cases of Region VIII , Philippines...	2016
[ "Introduction", "Results", "Discussion", "Model" ]	[ "acidosis", "medicine and health sciences", "action potentials", "pathology and laboratory medicine", "membrane potential", "brain", "electrophysiology", "neuroscience", "surgical and invasive medical procedures", "signs and symptoms", "functional electrical stimulation", "cellular structures ...	Theoretical perspectives on central chemosensitivity: CO2/H+-sensitive neurons in the locus coeruleus	journal.pcbi.1005853	null	[ [ "Central chemoreception is a neuronal sensory mechanism by which changes in CO2 and H+ levels in the brain are detected [1–3] .", "It occurs in specialized CO2/H+-sensitive centers in the brainstem that are involved in the neuronal network that regulates autonomic ventilation [4–10] .", "Regular venti...	[ "Central chemoreceptors are highly sensitive neurons that respond to changes in pH and CO2 levels .", "An increase in CO2/H+ typically reflects a rise in the firing rate of these neurons , which stimulates an increase in ventilation .", "Here , we present an ionic current model that reproduces the basic electro...	[ "The sensory mechanism by which changes in CO2 and H+ levels are detected in the brain is known as central chemoreception .", "Altered chemoreception is common to a wide variety of clinical conditions , including sleep apnea , sudden infant death syndrome , hyperventilation , depression , anxiety and asthma .", ...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/gene expression", "genetics and genomics/functional genomics", "virology/immunodeficiency viruses", "virology/animal models of infection", "immunology/innate immunity", "virology/mechanisms of resistance and susceptibility, including host genetics", "infectious diseases/hiv infect...	Transcriptional Profiling in Pathogenic and Non-Pathogenic SIV Infections Reveals Significant Distinctions in Kinetics and Tissue Compartmentalization	journal.ppat.1000296	null	[ [ "Natural reservoir hosts of simian immunodeficiency virus ( SIV ) do not develop AIDS in response to infection and live a normal lifespan .", "This is in contrast to non-natural hosts , such as Asian pig-tailed macaques ( PTs ) , which , when experimentally infected with SIV , develop AIDS in a similar ma...	[ "Simian immunodeficiency virus ( SIV ) infection leads to AIDS in experimentally infected macaques , whereas natural reservoir hosts exhibit limited disease and pathology .", "It is , however , unclear how natural hosts can sustain high viral loads , comparable to those observed in the pathogenic model , without ...	[ "Simian immunodeficiency virus ( SIV ) does not cause disease in African green monkeys ( a natural host for the virus ) , whereas experimentally infected Asian macaques ( a non-natural host ) develop a progressive disease that is similar to that which occurs in HIV-infected humans .", "Insight into how HIV causes...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	The Pattern of Adipose Tissue Accumulation during Early Infancy Provides an Environment for the Development of Dengue Hemorrhagic Fever	journal.pntd.0004267	null	[ [ "Dengue is the most prevalent arthropod-borne viral illness in humans with half of the world’s population at risk .", "The global burden of symptomatic dengue is on the order of 100 million cases/year [1] .", "The dengue viruses ( DENVs ) are single-stranded , positive-sense , RNA-containing enveloped...	[ "Dengue is the most prevalent arthropod-borne viral illness in humans with half of the world’s population at risk .", "During early infancy , severe dengue can develop after a primary dengue virus infection .", "There has been a clinical observation that severe dengue during the first year of life is seen only ...	[ "Dengue is the most prevalent arthropod-borne viral illness in humans with half of the world’s population at risk .", "During early infancy , severe dengue can develop after a primary dengue virus infection .", "There has been a clinical observation that severe dengue during the first year of life is seen only ...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "phosphorylation", "medicine and health sciences", "nucleic acid synthesis", "nuclear staining", "hela cells", "biological cultures", "messenger rna", "brain", "microbiology", "red nucleus", "cell cultures", "rna synthesis", "chemical synthesis", "research and analysis methods", "specime...	Inclusion bodies of human parainfluenza virus type 3 inhibit antiviral stress granule formation by shielding viral RNAs	journal.ppat.1006948	null	[ [ "Human parainfluenza virus type 3 ( HPIV3 ) , a member of the Paramyxoviridae family , can cause acute respiratory tract diseases such as pneumonia and bronchitis in infants and children [1] .", "The genome of HPIV3 contains a non-segmented negative-strand RNA , which encodes 6 proteins: the nucleoprotein...	[ "Viral invasion triggers the activation of the host antiviral response .", "Besides the innate immune response , stress granules ( SGs ) also act as an additional defense response to combat viral replication .", "However , many viruses have evolved various strategies to suppress SG formation to facilitate their...	[ "Human parainfluenza virus type 3 ( HPIV3 ) is one of the major causes of acute respiratory tract diseases such as pneumonia and bronchitis in infants and children .", "Virus invasion activates cellular stress responses .", "One of these responses is the formation of SGs which counteract viral replication .", ...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	The Rapid-Heat LAMPellet Method: A Potential Diagnostic Method for Human Urogenital Schistosomiasis	journal.pntd.0003963	null	[ [ "Human schistosomiasis , a parasitic freshwater snail transmitted disease caused by several species of genus Schistosoma trematode worms , is one of the 17 neglected tropical diseases ( NTDs ) considered by World Health Organization ( WHO ) [1] .", "It is estimated that 732 million persons are at risk of ...	[ "Urogenital schistosomiasis due to Schistosoma haematobium is a serious underestimated public health problem affecting 112 million people - particularly in sub-Saharan Africa .", "Microscopic examination of urine samples to detect parasite eggs still remains as definitive diagnosis .", "This work was focussed o...	[ "Human schistosomiasis is a disease caused by several species of parasitic worms of the genus Schistosoma that is affecting 200 million people , especially in sub-Saharan Africa .", "Most people are infected with Schistosoma haematobium , the species that causes urogenital schistosomiasis and also bladder cancer ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "cell biology", "genetics", "biology and life sciences", "neuroscience" ]	Genetic Analysis of a Novel Tubulin Mutation That Redirects Synaptic Vesicle Targeting and Causes Neurite Degeneration in C. elegans	journal.pgen.1004715	null	[ [ "Microtubule and molecular motors mediate polarized transport of neuronal proteins to either axons or dendrites [1] .", "Microtubules are oriented uniformly with their plus ends towards the distal end of the axon , which facilitates kinesin-dependent targeting of presynaptic proteins [2] .", "By contr...	[ "Neuronal cargos are differentially targeted to either axons or dendrites , and this polarized cargo targeting critically depends on the interaction between microtubules and molecular motors .", "From a forward mutagenesis screen , we identified a gain-of-function mutation in the C . elegans α-tubulin gene mec-12...	[ "Axons and dendrites are two classes of neuronal process that differ in their functions and molecular compositions .", "Proteins important for synaptic functions are mostly synthesized in the cell body and sorted differentially into the axon or dendrites .", "Microtubules in the axon and dendrite maintain their...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immune cells", "immune activation", "antigen-presenting cells", "immunity to infections", "immunology", "microbiology", "emerging viral diseases", "host-pathogen interaction", "mechanisms of resistance and susceptibility", "emerging infectious diseases", "immune defense", "animal models of in...	A Systems Biology Approach Reveals that Tissue Tropism to West Nile Virus Is Regulated by Antiviral Genes and Innate Immune Cellular Processes	journal.ppat.1003168	null	[ [ "Acute virus infection induces host innate immune defense programs that serve to control virus replication , prevent virus-mediated pathology , and aid in developing sterilizing immunity ( i . e . humoral and cell-mediated immunity ) .", "During RNA virus infection , intracellular viral RNA is recognized ...	[ "The actions of the RIG-I like receptor ( RLR ) and type I interferon ( IFN ) signaling pathways are essential for a protective innate immune response against the emerging flavivirus West Nile virus ( WNV ) .", "In mice lacking RLR or IFN signaling pathways , WNV exhibits enhanced tissue tropism , indicating that...	[ "West Nile virus ( WNV ) , a mosquito-transmitted RNA flavivirus , is an NIAID Category B infectious agent that has emerged in the Western hemisphere as a serious public health threat .", "The innate immune effectors that impart restriction of WNV infection are not well defined .", "WNV infection is sensed by t...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology", "biology", "microbiology" ]	Influenza Virus Respiratory Infection and Transmission Following Ocular Inoculation in Ferrets	journal.ppat.1002569	null	[ [ "Despite reports of conjunctivitis following infection with numerous respiratory pathogens ( including influenza , adenovirus , respiratory syncytial virus , and others ) , research investigating the role of ocular infection in virus pathogenicity and transmissibility has been underrepresented [1]–[4] .", ...	[ "While influenza viruses are a common respiratory pathogen , sporadic reports of conjunctivitis following human infection demonstrates the ability of this virus to cause disease outside of the respiratory tract .", "The ocular surface represents both a potential site of virus replication and a portal of entry for...	[ "Most infections with influenza virus result in respiratory disease .", "However , influenza viruses of the H7 subtype frequently cause ocular and not respiratory symptoms during human infection , demonstrating that the eye represents an alternate location for influenza viruses to infect humans .", "Using a fer...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology/viral replication and gene regulation", "virology/immune evasion" ]	Hepatitis B Virus Polymerase Blocks Pattern Recognition Receptor Signaling via Interaction with DDX3: Implications for Immune Evasion	journal.ppat.1000986	null	[ [ "Hepatitis B virus ( HBV ) is the prototypic member of the hepadnavirus family and a major cause of liver diseases .", "An estimated 400 million people are persistently infected with HBV worldwide .", "A significant subset of these HBV carriers progresses to severe liver disease , such as hepatocellul...	[ "Viral infection leads to induction of pattern-recognition receptor signaling , which leads to interferon regulatory factor ( IRF ) activation and ultimately interferon ( IFN ) production .", "To establish infection , many viruses have strategies to evade the innate immunity .", "For the hepatitis B virus ( HBV...	[ "Viral infection is sensed by the host innate immune system , which acts to limit viral infection by inducing antiviral cytokines such as the interferons .", "To establish infection , many viruses have strategies to evade the innate immunity .", "For the hepatitis B virus ( HBV ) , which causes chronic infectio...	2010
[ "Introduction", "Model", "Results", "Discussion" ]	[ "mathematics", "computational biology/systems biology", "cell biology/gene expression" ]	Model-Based Deconvolution of Cell Cycle Time-Series Data Reveals Gene Expression Details at High Resolution	journal.pcbi.1000460	null	[ [ "Recent technological advances have made feasible studies of biological systems at the single-cell level [1]–[4] .", "However , our current understanding of single-cell biochemistry and physiology has been largely inferred from averaged population measurements that often mask individual cell dynamics and ...	[ "In both prokaryotic and eukaryotic cells , gene expression is regulated across the cell cycle to ensure “just-in-time” assembly of select cellular structures and molecular machines .", "However , present in all time-series gene expression measurements is variability that arises from both systematic error in the ...	[ "Time-series analyses of cellular regulatory processes have successfully drawn attention to the importance of temporal regulation in biological systems .", "A number of model systems can be synchronized such that data collected on cell populations better reflect the dynamic properties of the individual cell .", ...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "action potentials", "medicine and health sciences", "membrane potential", "electrophysiology", "neuroscience", "systems science", "mathematics", "forecasting", "statistics (mathematics)", "computational neuroscience", "cellular structures and organelles", "research and analysis methods", "c...	Enhanced Sensitivity to Rapid Input Fluctuations by Nonlinear Threshold Dynamics in Neocortical Pyramidal Neurons	journal.pcbi.1004761	null	[ [ "How do pyramidal neurons transform their input into output spike trains ?", "The answer to this question is of fundamental importance because it determines potential coding strategies of the brain [1–5] .", "Theoretical studies of the Integrate-and-Fire model responding to in vivo-like fluctuating cu...	[ "The way in which single neurons transform input into output spike trains has fundamental consequences for network coding .", "Theories and modeling studies based on standard Integrate-and-Fire models implicitly assume that , in response to increasingly strong inputs , neurons modify their coding strategy by prog...	[ "Over the last decades , a variety of simplified spiking models have been shown to achieve a surprisingly high performance in predicting the neuronal responses to in vitro somatic current injections .", "Because of the complex adaptive behavior featured by cortical neurons , this success is however restricted to ...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Existing Infection Facilitates Establishment and Density of Malaria Parasites in Their Mosquito Vector	journal.ppat.1005003	null	[ [ "Interactions between pathogen strains within hosts can be profound and affect many aspects of infectious disease biology , including disease severity and infectiousness , as well as the evolution of virulence and the spread of drug resistance [1–7] .", "Yet for medically important vector-borne diseases ,...	[ "Very little is known about how vector-borne pathogens interact within their vector and how this impacts transmission .", "Here we show that mosquitoes can accumulate mixed strain malaria infections after feeding on multiple hosts .", "We found that parasites have a greater chance of establishing and reach high...	[ "Very little is known about how malaria parasite strains interact with each other inside mosquitoes .", "In this study we show that mosquitoes that have already been infected with one strain of malaria parasites are more likely to become infected with a new strain .", "Moreover , the presence of an existing inf...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/bacterial infections", "immunology/genetics of the immune system", "immunology/immunity to infections", "immunology/innate immunity" ]	Rudra Interrupts Receptor Signaling Complexes to Negatively Regulate the IMD Pathway	journal.ppat.1000120	null	[ [ "Insects rely primarily on innate immune responses to fight pathogens .", "The Drosophila immune response has proven to be an experimentally powerful and conserved model system for the study of innate immunity [1] , [2] , [3] , [4] .", "In particular , the insect immune response relies on evolutionary...	[ "Insects rely primarily on innate immune responses to fight pathogens .", "In Drosophila , antimicrobial peptides are key contributors to host defense .", "Antimicrobial peptide gene expression is regulated by the IMD and Toll pathways .", "Bacterial peptidoglycans trigger these pathways , through recognition...	[ "The innate immune system controls the immediate response to infection .", "Innate immunity relies on germline encoded receptors , receptors that are present at birth , to recognize germs and trigger a protective response .", "Invertebrates ( i . e . , insects ) rely on innate immunity to survive in microbial-r...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "evolutionary ecology", "plant biology", "population genetics", "quantitative traits", "plant science", "linkage (genetics)", "plant genetics", "biology", "evolutionary genetics", "genotypes", "trait locus", "plant evolution", "phenotypes", "heredity", "genetics", "gene flow", "evolu...	Indirect Evolution of Hybrid Lethality Due to Linkage with Selected Locus in Mimulus guttatus	journal.pbio.1001497	Ecological selection on an adaptive allele causes a tightly linked hybrid incompatibility factor to rapidly hitchhike to high frequency in a population of the wildflower Mimulus guttatus.	[ [ "Adaptation to local environmental conditions by natural selection is the primary cause of evolutionary change in natural populations .", "Ecological adaptation can cause reproductive isolation when selection acts on traits that influence the likelihood of intermating in nature , such as habitat preferenc...	[ "Most species are superbly and intricately adapted to the environments in which they live .", "Adaptive evolution by natural selection is the primary force shaping biological diversity .", "Differences between closely related species in ecologically selected characters such as habitat preference , reproductive ...	[ "Adaptive evolution by natural selection is the primary force generating biological diversity .", "A critical question is whether the evolution of hybrid incompatibility , which is essential for the maintenance of species diversity , is caused by adaptive evolution .", "In this article , we investigate one of t...	2013
[ "Introduction", "Discussion" ]	[ "physics/condensed matter", "biophysics/theory and simulation", "biophysics/biomacromolecule-ligand interactions", "mathematics/statistics", "computational biology/molecular dynamics", "physics/interdisciplinary physics" ]	Perturbation-Response Scanning Reveals Ligand Entry-Exit Mechanisms of Ferric Binding Protein	journal.pcbi.1000544	null	[ [ "Functional proteins are complex structures , which may remain mainly unmodified as a result of a multitude of mutations [1] , yet may have their energy surface go through significant changes upon perturbing highly specific regions [2]–[4] .", "The various accessible states populated may be manipulated by...	[ "We study apo and holo forms of the bacterial ferric binding protein ( FBP ) which exhibits the so-called ferric transport dilemma: it uptakes iron from the host with remarkable affinity , yet releases it with ease in the cytoplasm for subsequent use .", "The observations fit the “conformational selection” model ...	[ "Upon binding ligands , many proteins undergo structural changes compared to the unbound form .", "We introduce a methodology to monitor these changes and to study which mechanisms arrange conformational shifts between the liganded and free forms .", "Our method is simple , yet it efficiently characterizes the ...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cellular stress responses", "molecular cell biology", "cell biology", "gene regulation", "genetics", "molecular genetics", "biology", "genetics and genomics" ]	Iron-Responsive miR-485-3p Regulates Cellular Iron Homeostasis by Targeting Ferroportin	journal.pgen.1003408	null	[ [ "While iron is an essential nutrient for all cells , high levels of iron can lead to toxicity .", "Therefore , cellular iron homeostasis is carefully maintained by an exquisite system of iron regulatory proteins ( IRPs ) that respond to iron levels and coordinate the expression of targets important for ba...	[ "Ferroportin ( FPN ) is the only known cellular iron exporter in mammalian cells and plays a critical role in the maintenance of both cellular and systemic iron balance .", "During iron deprivation , the translation of FPN is repressed by iron regulatory proteins ( IRPs ) , which bind to the 5′ untranslated regio...	[ "Cellular iron homeostasis is maintained by a sophisticated system that responds to iron levels and coordinates the expression of targets important for balancing iron export and uptake with intracellular storage and utilization .", "Ferroportin is the only known cellular iron exporter in mammalian cells and plays...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "model organisms", "genetics", "biology", "molecular cell biology", "genetics and genomics" ]	Duox, Flotillin-2, and Src42A Are Required to Activate or Delimit the Spread of the Transcriptional Response to Epidermal Wounds in Drosophila	journal.pgen.1002424	null	[ [ "The development of a specialized epidermal barrier layer represents a key step during the evolution of multi-cellular organisms .", "This outer integument provides protection from the environment and helps maintain cellular homeostasis .", "Epidermal barriers consist of epithelial cells that are tigh...	[ "The epidermis is the largest organ of the body for most animals , and the first line of defense against invading pathogens .", "A breach in the epidermal cell layer triggers a variety of localized responses that in favorable circumstances result in the repair of the wound .", "Many cellular and genetic respons...	[ "An epidermal wound provides signals that initiate a variety of localized responses , some of which act to regenerate and repair the breach in the epidermal barrier .", "The Drosophila melanogaster embryonic epidermis provides an excellent system to discover new genes that regulate wound-healing processes .", "...	2011
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Malaria in Pregnancy Interacts with and Alters the Angiogenic Profiles of the Placenta	journal.pntd.0003824	null	[ [ "In countries endemic for Plasmodium spp .", ", malaria in pregnancy ( MiP ) remains an important health burden that can result in maternal anaemia , small-for-gestational-age babies , low birth weight , and even miscarriages and stillbirths [1–3] .", "Most of the studies looking at possible mechanism...	[ "Malaria in pregnancy remains a substantial public health problem in malaria-endemic areas with detrimental outcomes for both the mother and the foetus .", "The placental changes that lead to some of these detrimental outcomes have been studied , but the mechanisms that lead to these changes are still not fully e...	[ "Plasmodium infections during pregnancy represent a substantial health burden for mothers and their neonates leading to underweight babies , preterm deliveries , abortions , stillbirths , and even maternal mortality .", "The placenta , in its role as a bridge between mother and foetus , will either suffer or medi...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "death rates", "invertebrates", "parasite groups", "medicine and health sciences", "body fluids", "oocysts", "plasmodium", "tropical diseases", "parasitic diseases", "animals", "parasitology", "apicomplexa", "pharmacology", "population biology", "insect vectors", "drug metabolism", "...	Promising approach to reducing Malaria transmission by ivermectin: Sporontocidal effect against Plasmodium vivax in the South American vectors Anopheles aquasalis and Anopheles darlingi	journal.pntd.0006221	null	[ [ "The 2016 World Malaria Report ( WHO ) estimated 212 million cases of malaria worldwide , leading to 429 , 000 deaths , which illustrates that malaria remains an important public health problem .", "In the Americas , 389 , 390 cases and 87 deaths were reported in 2016 with Brazil reporting 24% and Peru 19...	[ "The mosquito resistance to the insecticides threatens malaria control efforts , potentially becoming a major public health issue .", "Alternative methods like ivermectin ( IVM ) administration to humans has been suggested as a possible vector control to reduce Plasmodium transmission .", "Anopheles aquasalis a...	[ "Malaria is one of the most important infectious diseases in the world with hundreds of millions of new cases every year .", "The disease is caused by parasites of the genus Plasmodium where Plasmodium vivax represent most of the cases in the Americas .", "Current strategies to combat malaria transmission are b...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology" ]	Survival Response to Increased Ceramide Involves Metabolic Adaptation through Novel Regulators of Glycolysis and Lipolysis	journal.pgen.1003556	null	[ [ "Energy balance is regulated by complex homeostatic control of lipid and glucose metabolism involving signaling pathways in multiple tissues and organs .", "Aberrant glucose and lipid metabolism arising from defects in these pathways accompanies a number of diseases including cardiovascular disorders , ty...	[ "The sphingolipid ceramide elicits several stress responses , however , organisms survive despite increased ceramide but how they do so is poorly understood .", "We demonstrate here that the AKT/FOXO pathway regulates survival in increased ceramide environment by metabolic adaptation involving changes in glycolys...	[ "Ceramide belongs to an important class of lipids called sphingolipids .", "An increase in ceramide levels elicits several stress responses .", "We have used Drosophila mutated in ceramide kinase , an enzyme involved in metabolizing ceramide to understand how an organism adapts to stress imposed by ceramide .",...	2013
[ "Introduction", "Histones are found in some newly discovered Archaea", "Conclusion", "Methods" ]	[ "chemical compounds", "dna-binding proteins", "microbiology", "organic compounds", "review", "archaea", "basic amino acids", "amino acids", "epigenetics", "chromatin", "chromosome biology", "proteins", "gene expression", "chemistry", "histones", "nucleosomes", "archaean biology", "...	Structure and function of archaeal histones	journal.pgen.1007582	null	[ [ "In eukaryotes , octameric histone cores compact DNA by wrapping an approximately 150-bp unit twice around its surface , forming a nucleosome [12 , 13] .", "Nucleosomes interact with each other , yielding an additional level of DNA organization in the form of a fibre .", "Besides a role in compaction ...	[ "The genomes of all organisms throughout the tree of life are compacted and organized in chromatin by association of chromatin proteins .", "Eukaryotic genomes encode histones , which are assembled on the genome into octamers , yielding nucleosomes .", "Post-translational modifications of the histones , which o...	[ "Both Archaea and eukaryotes express histones , but whereas the tertiary structure of histones is conserved , the quaternary structure of histone–DNA complexes is very different .", "In a recent study , the crystal structure of the archaeal hypernucleosome was revealed to be an “endless” core of interacting histo...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "blood cells", "flow cytometry", "innate immune system", "medicine and health sciences", "immune cells", "immune physiology", "cytokines", "spleen", "immunology", "developmental biology", "molecular development", "cytotoxic t cells", "research and analysis methods", "specimen preparation a...	IL-12p40/IL-10 Producing preCD8α/Clec9A+ Dendritic Cells Are Induced in Neonates upon Listeria monocytogenes Infection	journal.ppat.1005561	null	[ [ "Early life is a period of immune maturation characterized by a high susceptibility to infectious diseases .", "The underdeveloped immune system gives a Th2-biased response and has an impaired ability to develop long-lasting protective CD8+ T cell immunity [1 , 2] .", "We are particularly interested i...	[ "Infection by Listeria monocytogenes ( Lm ) causes serious sepsis and meningitis leading to mortality in neonates .", "This work explored the ability of CD11chigh lineage DCs to induce CD8+ T-cell immune protection against Lm in mice before 7 days of life , a period symbolized by the absence of murine IL-12p70-pr...	[ "Lm is a gram-positive food-borne pathogen that is the ethiological agent of listeriosis , a worldwide disease reported most frequently in developed countries .", "It can cause spontaneous septic abortions , fatal meningitis or encephalitis in immunocompromised and pregnant individuals .", "The murine model of ...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "rna", "micrornas", "plant science", "plant disease resistance", "gene expression", "genetics", "gene regulation", "biology and life sciences", "plant pathology", "plant pathogens" ]	MicroRNAs Suppress NB Domain Genes in Tomato That Confer Resistance to Fusarium oxysporum	journal.ppat.1004464	null	[ [ "MicroRNAs ( miRNAs ) are single-stranded RNA molecules of approximately 20–24 nucleotides in length that are endogenously transcribed from single-stranded non-coding RNA species [1] , [2] .", "Plant miRNAs were first identified in 2002 [1] , [3] and have been shown to play vital roles in multiple biologi...	[ "MicroRNAs ( miRNAs ) suppress the transcriptional and post-transcriptional expression of genes in plants .", "Several miRNA families target genes encoding nucleotide-binding site–leucine-rich repeat ( NB-LRR ) plant innate immune receptors .", "The fungus Fusarium oxysporum f .", "sp .", "lycopersici cause...	[ "Fusarium oxysporum is a fungal pathogen that represents a species complex , with members that infect numerous crops .", "In spite of its importance to agriculture , very little is known about roles of small RNAs in plant immunity against F . oxysporum .", "In this study , we set up a screen for tomato microRNA...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "genetics and genomics/gene expression", "genetics and genomics/complex traits", "genetics and genomics/genetics of disease", "genetics and genomics/epigenetics", "genetics and genomics", "genetics and genomics/population genetics" ]	Single-Tissue and Cross-Tissue Heritability of Gene Expression Via Identity-by-Descent in Related or Unrelated Individuals	journal.pgen.1001317	null	[ [ "The genome contains a complex set of instructions for the assembly and maintenance of an organism .", "A fundamental goal in biology is to understand the relationship between genotype and phenotype .", "This goal can be achieved in part by studying the genetic basis of gene expression , as many genot...	[ "Family studies of individual tissues have shown that gene expression traits are genetically heritable .", "Here , we investigate cis and trans components of heritability both within and across tissues by applying variance-components methods to 722 Icelanders from family cohorts , using identity-by-descent ( IBD ...	[ "An important goal in biology is to understand how genotype affects gene expression .", "Because gene expression varies across tissues , the relationship between genotype and gene expression may be tissue-specific .", "In this study , we used heritability approaches to study the regulation of gene expression in...	2011
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "evolutionary biology", "evolutionary biology/human evolution", "genetics and genomics/population genetics" ]	Ancient DNA from European Early Neolithic Farmers Reveals Their Near Eastern Affinities	journal.pbio.1000536	The first farmers from Central Europe reveal a genetic affinity to modern-day populations from the Near East and Anatolia, which suggests a significant demographic input from this area during the early Neolithic.	[ [ "The transition from a hunter–gatherer existence to a “Neolithic lifestyle , ” which was characterized by increasing sedentarism and the domestication of animals and plants , has profoundly altered human societies around the world [1] , [2] .", "In Europe , archaeological and population genetic views of t...	[ "In Europe , the Neolithic transition ( 8 , 000–4 , 000 b . c . ) from hunting and gathering to agricultural communities was one of the most important demographic events since the initial peopling of Europe by anatomically modern humans in the Upper Paleolithic ( 40 , 000 b . c . ) .", "However , the nature and s...	[ "The transition from a hunter–gatherer existence to a sedentary farming-based lifestyle has had key consequences for human groups around the world and has profoundly shaped human societies .", "Originating in the Near East around 11 , 000 y ago , an agricultural lifestyle subsequently spread across Europe during ...	2010
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Crystal Structures of a Piscine Betanodavirus: Mechanisms of Capsid Assembly and Viral Infection	journal.ppat.1005203	null	[ [ "Nodaviridae is a family of positive-sense single-stranded RNA viruses with a non-enveloped T = 3 capsid .", "These viruses are characterized by a viral genome comprising two RNA molecules–RNA1 and RNA2 .", "RNA1 ( 3 . 1 kb ) encodes protein A , which is a RNA-dependent RNA polymerase ( RdRp ) respons...	[ "Betanodaviruses cause massive mortality in marine fish species with viral nervous necrosis .", "The structure of a T = 3 Grouper nervous necrosis virus-like particle ( GNNV-LP ) is determined by the ab initio method with non-crystallographic symmetry averaging at 3 . 6 Å resolution .", "Each capsid protein ( C...	[ "Betanodaviruses belong to the family Nodaviridae and cause the mortality of numerous larval-stage fish species .", "Here we report protein crystal structures of a piscine betanodavirus , the Grouper nervous necrosis virus ( GNNV ) , in four different forms .", "Highlights are two structural features that contr...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "neuromuscular junctions", "nervous system", "cell processes", "electrophysiology", "pigments", "neuroscience", "surgical and invasive medical procedures", "developmental biology", "functional electrical stimulation", "materials science", "nerve fibers", "dyes...	A Ca2+ channel differentially regulates Clathrin-mediated and activity-dependent bulk endocytosis	journal.pbio.2000931	null	[ [ "In the presynaptic terminal , continuous release of synaptic vesicles ( SVs ) results in vesicle pool depletion , plasma membrane expansion , and SV protein overloading at the release site [1] .", "Endocytosis is therefore tightly coupled to exocytosis [2] .", "Among the different modes of SV endocyt...	[ "Clathrin-mediated endocytosis ( CME ) and activity-dependent bulk endocytosis ( ADBE ) are two predominant forms of synaptic vesicle ( SV ) endocytosis , elicited by moderate and strong stimuli , respectively .", "They are tightly coupled with exocytosis for sustained neurotransmission .", "However , the under...	[ "The arrival of an action potential at the nerve end induces synaptic vesicle ( SV ) exocytosis to allow the release of chemical neurotransmitters and the rapid transmission of signals .", "SV endocytosis is in turn elicited in order to rapidly replenish the vesicle pool in neurons .", "Therefore , tight coupli...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "fish", "medicine and health sciences", "morpholino", "rna interference", "skeletal muscles", "messenger rna", "vertebrates", "nucleotides", "animals", "animal models", "osteichthyes", "developmental biology", "model organisms", "untranslated regions", "experimental organism systems", ...	Genetic compensation triggered by actin mutation prevents the muscle damage caused by loss of actin protein	journal.pgen.1007212	null	[ [ "Genetic compensation exists as a mechanism to buffer the organism against gene loss that would otherwise be deleterious to survival .", "Whilst this term has been used to describe dosage compensation , evolution resulting in reversion to ancestral phenotypes , and gene duplication compensating for mutati...	[ "The lack of a mutant phenotype in homozygous mutant individuals’ due to compensatory gene expression triggered upstream of protein function has been identified as genetic compensation .", "Whilst this intriguing process has been recognized in zebrafish , the presence of homozygous loss of function mutations in h...	[ "Many healthy individuals carry loss of function mutations in essential genes that would normally be deleterious for survival .", "Intriguingly , it may be the presence of the genomic lesion itself in these individuals that triggers the compensatory pathways .", "It is not known how widespread this phenomenon i...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "mycology", "biology", "microbiology", "host-pathogen interaction", "pathogenesis" ]	In vivo Hypoxia and a Fungal Alcohol Dehydrogenase Influence the Pathogenesis of Invasive Pulmonary Aspergillosis	journal.ppat.1002145	null	[ [ "The incidence of life-threatening human fungal infections has increased during the last three decades as medical therapies , organ transplantations , an increasing geriatric population , and HIV infections have generated a significant rise in the number of susceptible patients [1] , [2] , [3] .", "Asperg...	[ "Currently , our knowledge of how pathogenic fungi grow in mammalian host environments is limited .", "Using a chemotherapeutic murine model of invasive pulmonary aspergillosis ( IPA ) and 1H-NMR metabolomics , we detected ethanol in the lungs of mice infected with Aspergillus fumigatus .", "This result suggest...	[ "Metabolic flexibility is important for human pathogens like Aspergillus fumigatus as it allows adaptation to dynamic infection induced microenvironments .", "Consequently , identification of fungal metabolic pathways critical for in vivo growth may uncover novel virulence mechanisms and new therapeutic opportuni...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics", "developmental biology", "diabetes and endocrinology", "cell biology/neuronal signaling mechanisms" ]	Loss of the Transcriptional Repressor PAG-3/Gfi-1 Results in Enhanced Neurosecretion that is Dependent on the Dense-Core Vesicle Membrane Protein IDA-1/IA-2	journal.pgen.1000447	null	[ [ "Dense core vesicles ( DCVs ) mediate the storage and secretion of hormones ( e . g . insulin ) and neuropeptides ( e . g . vasoactive intestinal peptide , VIP ) from a variety of neuroendocrine cells ( e . g . pancreatic β-cells ) .", "The biogenesis of DCVs and cargo is coordinately regulated , allowing...	[ "It is generally accepted that neuroendocrine cells regulate dense core vesicle ( DCV ) biogenesis and cargo packaging in response to secretory demands , although the molecular mechanisms of this process are poorly understood .", "One factor that has previously been implicated in DCV regulation is IA-2 , a cataly...	[ "Within secretory cells , hormones are packaged into vesicles ( called DCVs ) that are released upon stimulation .", "The number of DCVs is regulated to meet the secretory demands of the cell by a mechanism that is poorly understood , although a protein in the membrane of DCVs , called IA-2 , is thought to play a...	2009
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "virology", "emerging viral diseases", "biology", "microbiology" ]	Genotype V Japanese Encephalitis Virus Is Emerging	journal.pntd.0001231	null	[ [ "Japanese encephalitis ( JE ) , which is caused by JE virus ( JEV ) , is one of the most important viral encephalitis in the world [1]–[4] .", "It is prevalent mostly in Asia including eastern Asia [5]–[7] , southern Asia [8] and southeast Asia [9] , [10] .", "JE has extended its geographic range to t...	[ "Japanese encephalitis ( JE ) is a global public health issue that has spread widely to more than 20 countries in Asia and has extended its geographic range to the south Pacific region including Australia .", "JE has become the most important cause of viral encephalitis in the world .", "Japanese encephalitis v...	[ "Japanese encephalitis virus ( JEV ) is a mosquito-borne virus that causes Japanese encephalitis ( JE ) with significant morbidity and mortality .", "Five genotypes ( genotype I–V ) have been identified based on the nucleotide sequence of viral envelope ( E ) gene of JEV .", "To date , the only known strain of ...	2011
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "nervous system", "membrane potential", "electrophysiology", "neuroscience", "simulation and modeling", "bioassays and physiological analysis", "neuronal dendrites", "research and analysis methods", "excitatory postsynaptic potentials", "animal cells", "electrop...	Determination of effective synaptic conductances using somatic voltage clamp	journal.pcbi.1006871	null	[ [ "Neurons receive myriad excitatory ( E ) and inhibitory ( I ) synaptic inputs at dendrites .", "The spatiotemporal interaction between these E and I inputs are crucial for neuronal computation [1–3] , for instance , to shape neural activity [4 , 5] , to enhance feature selectivity [6 , 7] , to modulate ne...	[ "The interplay between excitatory and inhibitory neurons imparts rich functions of the brain .", "To understand the synaptic mechanisms underlying neuronal computations , a fundamental approach is to study the dynamics of excitatory and inhibitory synaptic inputs of each neuron .", "The traditional method of de...	[ "To understand synaptic mechanisms underlying neuronal computations , a fundamental approach is to use voltage clamp to measure the dynamics of excitatory and inhibitory input conductances .", "Due to the space clamp effect , the measured conductance in general deviates from the local input conductance on the den...	2019
[ "Introduction", "Methods", "Results", "Discussion", "Conclusions" ]	[ "sequencing techniques", "schistosoma", "invertebrates", "schistosoma mansoni", "helminths", "gene regulation", "animals", "invertebrate genomics", "micrornas", "genome analysis", "molecular biology techniques", "rna sequencing", "research and analysis methods", "schistosoma japonicum", ...	The small RNA complement of adult Schistosoma haematobium	journal.pntd.0006535	null	[ [ "Human schistosomiasis is a chronic , snail-borne , neglected tropical disease ( NTD ) caused predominantly by infections with the blood flukes Schistosoma haematobium , S . mansoni and S . japonicum [1] .", "This disease is highly prevalent in sub-Saharan Africa , where infections with S . haematobium an...	[ "Blood flukes of the genus Schistosoma cause schistosomiasis—a neglected tropical disease ( NTD ) that affects more than 200 million people worldwide .", "Studies of schistosome genomes have improved our understanding of the molecular biology of flatworms , but most of them have focused largely on protein-coding ...	[ "Human schistosomiasis is a chronic , neglected tropical disease ( NTD ) that is predominantly caused by the blood flukes Schistosoma haematobium , S . mansoni and S . japonicum .", "Infections by S . haematobium and/or S . mansoni are highly prevalent in Africa , affecting ~ 200 million people .", "The decodin...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology", "chromosome biology", "centromeres", "biology", "molecular cell biology" ]	Histone H3 Localizes to the Centromeric DNA in Budding Yeast	journal.pgen.1002739	null	[ [ "During eukaryotic cell division sister chromatids , containing identical copies of genetic information , are pulled apart and driven towards opposite spindle poles by the microtubules of the mitotic spindle , which attach to the centromeric DNA sequences of the sisters via kinetochore protein complexes .", ...	[ "During cell division , segregation of sister chromatids to daughter cells is achieved by the poleward pulling force of microtubules , which attach to the chromatids by means of a multiprotein complex , the kinetochore .", "Kinetochores assemble at the centromeric DNA organized by specialized centromeric nucleoso...	[ "During cell division , replicated DNA molecules are pulled to daughter cells by microtubules , which originate at the spindle poles and attach to a multiprotein complex , the kinetochore .", "The kinetochore assembles at a special region of the chromosome , termed the centromere .", "The kinetochore is compris...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry", "developmental biology", "model organisms", "cell biology", "genetics", "biology and life sciences", "proteomics", "molecular cell biology", "research and analysis methods" ]	The Specification and Global Reprogramming of Histone Epigenetic Marks during Gamete Formation and Early Embryo Development in C. elegans	journal.pgen.1004588	null	[ [ "The totipotency of a new embryo depends upon the reprogramming of epigenetic information carried over from the sperm and oocyte , each of which distinctly packages its DNA .", "For example , canonical histones H2A , H2B , H3 , H4 and the linker histone H1 within mammalian sperm are replaced by sperm nucl...	[ "In addition to the DNA contributed by sperm and oocytes , embryos receive parent-specific epigenetic information that can include histone variants , histone post-translational modifications ( PTMs ) , and DNA methylation .", "However , a global view of how such marks are erased or retained during gamete formatio...	[ "Successful reproduction depends upon the receipt and processing of distinct chromatin packages from sperm and oocytes .", "This includes not only a unique complement of DNA , but information in the form of proteins , such as histones , that differentially package the DNA in each cell type .", "For example , hi...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "evolutionary biology/animal behavior" ]	Environmental Change Enhances Cognitive Abilities in Fish	journal.pbio.1000351	Cichlid fish subjected to a single change in food ration early in life show enhanced learning abilities during juvenile and adult stages.	[ [ "The ability of adapting to changes in the environment is an important driving force of evolution , as recognized already by Darwin in his famous quote: “It is not the strongest of the species that survives…it is the one that is the most adaptable to change” [1] .", "Animals may adapt by altering their be...	[ "Flexible or innovative behavior is advantageous , especially when animals are exposed to frequent and unpredictable environmental perturbations .", "Improved cognitive abilities can help animals to respond quickly and adequately to environmental dynamics , and therefore changing environments may select for highe...	[ "Animals with higher cognitive abilities should be better capable of producing new , modified , or innovative behaviors as this ability could allow them to cope better with unpredictable environmental changes .", "Changing environments may hence select for higher cognitive abilities .", "Similarly , changing co...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Elucidation of Ligand-Dependent Modulation of Disorder-Order Transitions in the Oncoprotein MDM2	journal.pcbi.1004282	null	[ [ "A large fraction of proteins contain substantial regions that are unstructured in native conditions [1 , 2] .", "Protein disorder plays a key role in biomolecular function , enabling proteins to tune binding affinity and specificity to diverse partners [3] .", "In particular protein-complexes that in...	[ "Numerous biomolecular interactions involve unstructured protein regions , but how to exploit such interactions to enhance the affinity of a lead molecule in the context of rational drug design remains uncertain .", "Here clarification was sought for cases where interactions of different ligands with the same dis...	[ "Life as we know it depends on interactions between proteins .", "There is substantial evidence that many interactions between proteins involve very flexible protein regions .", "These disordered regions may undergo disorder/order transitions upon forming an interaction with another protein .", "Many successf...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics", "epigenetics", "biology", "chromatin", "genetics and genomics" ]	DNA Topoisomerase III Localizes to Centromeres and Affects Centromeric CENP-A Levels in Fission Yeast	journal.pgen.1003371	null	[ [ "Centromeres are unique regions of eukaryotic chromosomes that are essential for chromosome segregation at mitosis and meiosis .", "The specialized centromeric chromatin directs assembly of kinetochores , which serve as points of attachment for the spindle apparatus .", "In all eukaryotes , centromeri...	[ "Centromeres are specialized chromatin regions marked by the presence of nucleosomes containing the centromere-specific histone H3 variant CENP-A , which is essential for chromosome segregation .", "Assembly and disassembly of nucleosomes is intimately linked to DNA topology , and DNA topoisomerases have previous...	[ "Centromeres are unique regions on eukaryotic chromosomes that are essential for chromosome segregation at mitosis and meiosis .", "Centromere identity and function depends on the presence of specialized chromatin with nucleosomes containing the centromere-specific histone H3 variant CENP-A .", "Assembly and di...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "dermatology", "medicine and health sciences", "immune cells", "herpes simplex", "immune activation", "antigen-presenting cells", "immunology", "microbiology", "infectious disease immunology", "skin infections", "sexually transmitted diseases", "animal models of infection", ...	Distinct APC Subtypes Drive Spatially Segregated CD4+ and CD8+ T-Cell Effector Activity during Skin Infection with HSV-1	journal.ppat.1004303	null	[ [ "Infection results in the priming of pathogen-specific T-cell responses in LNs draining the site of infection .", "Depending on the nature of the pathogen , this critical step in generating adaptive immunity involves the interaction of naive T cells with various types of migrating and LN-resident DCs [1] ...	[ "Efficient infection control requires potent T-cell responses at sites of pathogen replication .", "However , the regulation of T-cell effector function in situ remains poorly understood .", "Here , we show key differences in the regulation of effector activity between CD4+ and CD8+ T-cells during skin infectio...	[ "HSV-1 is a widely distributed pathogen causing a life-long latent infection associated with periodic bouts of reactivation and severe clinical complications .", "Adaptive immune responses encompassing CD4+ and CD8+ T-cell activities are key to both the clearance of infectious virus and the control of latent infe...	2014
[ "Introduction", "Results and Discussion", "Materials and Methods" ]	[]	Identification of Astrotactin2 as a Genetic Modifier That Regulates the Global Orientation of Mammalian Hair Follicles	journal.pgen.1005532	null	[ [ "In complex multi-cellular organisms , individual surface structures such as hairs , feathers , scales , and bristles typically exhibit a high degree of spatial order .", "In birds and mammals , the stereotyped orientations of feathers and hairs reflect the underlying orientations of follicles within the ...	[ "Planar cell polarity ( PCP ) signaling controls the global orientation of surface structures , such as hairs and bristles , in both vertebrates and invertebrates .", "In Frizzled6-/- ( Fz6-/- ) mice , hair follicle orientations on the head and back are nearly random at birth , but reorient during early postnatal...	[ "Hair , feather , and scale patterns are a universal feature of vertebrate surface morphology .", "These patterns are under precise genetic control as seen by their species-specificity and by their alterations in different breeds of domesticated animals .", "The first clues to the mechanism of hair patterning i...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "functional genomics", "cell biology", "chromosome biology", "genomic imprinting", "gene expression", "genetics", "gene regulation", "biology and life sciences", "epigenetics", "molecular genetics", "genomics", "chromatin" ]	Allele-Specific Genome-wide Profiling in Human Primary Erythroblasts Reveal Replication Program Organization	journal.pgen.1004319	null	[ [ "DNA replication in eukaryotes starts at DNA sequences termed origins of replication .", "The timing of DNA replication within the S-phase of the cell cycle depends on the distribution and the relative order of activation of those origins .", "Eukaryotic DNA replication is mediated by the sequential f...	[ "We have developed a new approach to characterize allele-specific timing of DNA replication genome-wide in human primary basophilic erythroblasts .", "We show that the two chromosome homologs replicate at the same time in about 88% of the genome and that large structural variants are preferentially associated wit...	[ "DNA replication in mammalian cells proceeds according to a distinct order .", "Genes that are expressed tend to replicate before genes that are not expressed .", "We report here that we have developed a method to measure the timing of replication of the maternal and paternal chromosomes separately .", "We fo...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "parasite groups", "medicine and health sciences", "body fluids", "respiratory infections", "plasmodium", "tropical diseases", "parasitic diseases", "parasitic protozoans", "pulmonology", "parasitology", "parasitemia", "apicomplexa", "protozoans", "molecular biology techniques", "quantit...	Assessment of false negative rates of lactate dehydrogenase-based malaria rapid diagnostic tests for Plasmodium ovale detection	journal.pntd.0007254	null	[ [ "Plasmodium ovale has a wide geographic distribution across tropical countries , especially in Africa , Asia and some Western Pacific islands [1] .", "P . ovale has been overshadowed by other human malaria parasites in the field of medicine and medical research because of the relatively low morbidity and ...	[ "Currently , malaria rapid diagnostic tests ( RDTs ) are widely used for malaria diagnosis , but test performance and the factors that lead to failure of Plasmodium ovale detection are not well understood .", "In this study , three pLDH-based RDTs were evaluated using cases in China that originated in Africa .", ...	[ "Plasmodium ovale ( P . ovale ) are under-estimated and overshadowed by other malaria parasites in tropical countries , which can cause chronic infections that last from months to years .", "The chronic infection caused by P . ovale should be of concern in the context of the long-term goal of eliminating malaria ...	2019
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "heme", "medicine and health sciences", "gut bacteria", "pathology and laboratory medicine", "animal models of disease", "microbiology", "operons", "toxicology", "animal models", "toxicity", "model organisms", "gastroenterology and hepatology", "experimental organism systems", "dna", "ba...	Heme sensing and detoxification by HatRT contributes to pathogenesis during Clostridium difficile infection	journal.ppat.1007486	null	[ [ "Clostridium difficile is a spore-forming , Gram-positive obligate anaerobe that is the most common cause of nosocomial infections in the United States [1] .", "C . difficile infects the colon , causing a wide range of diseases that vary from infectious diarrhea to pseudomembranous colitis .", "During...	[ "Clostridium difficile is a Gram-positive , spore-forming anaerobic bacterium that infects the colon , causing symptoms ranging from infectious diarrhea to fulminant colitis .", "In the last decade , the number of C . difficile infections has dramatically risen , making it the leading cause of reported hospital a...	[ "Clostridium difficile is a pathogenic bacterium that infects the colon and is the leading cause of infectious diarrhea in the United States .", "C . difficile mediated disease is driven by the production of two toxins , TcdA and TcdB .", "The toxins cause severe damage to the intestinal epithelial layer of the...	2018
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "neural networks", "nervous system", "social sciences", "electrophysiology", "neuroscience", "synaptic plasticity", "vision", "eyes", "neuronal plasticity", "mood disorders", "developmental neuroscience", "computer and information sciences", "animal cells", ...	Synaptic plasticity onto inhibitory neurons as a mechanism for ocular dominance plasticity	journal.pcbi.1006834	null	[ [ "Throughout development , sensory cortex can experience periods of heightened sensitivity to sensory inputs .", "The rewiring of neuronal networks is very flexible during these periods , but there is less such plasticity otherwise .", "Having normal sensory experiences during these periods is crucial ...	[ "Ocular dominance plasticity is a well-documented phenomenon allowing us to study properties of cortical maturation .", "Understanding this maturation might be an important step towards unravelling how cortical circuits function .", "However , it is still not fully understood which mechanisms are responsible fo...	[ "During the development of the brain , visual cortex has a period of increased plasticity .", "Closing one eye for multiple days during this period can have a profound and life-long impact on neuronal responses .", "A well-established hypothesis is that the absolute level of inhibition regulates this period .",...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "mosquitoes", "zoonoses", "disease ecology", "infectious disease epidemiology", "epidemiology", "neglected tropical diseases", "arboviral infections", "vectors and hosts", "public health" ]	The Changing Epidemiology of Murray Valley Encephalitis in Australia: The 2011 Outbreak and a Review of the Literature	journal.pntd.0002656	null	[ [ "Murray Valley encephalitis virus ( MVEV ) causes the most serious of the mosquito-borne virus diseases endemic to Australia .", "It also occurs on the island of New Guinea , and little is known about its epidemiology there [1] .", "It is a member of the Japanese encephalitis serogroup of flaviviruses...	[ "Murray Valley encephalitis virus ( MVEV ) is the most serious of the endemic arboviruses in Australia .", "It was responsible for six known large outbreaks of encephalitis in south-eastern Australia in the 1900s , with the last comprising 58 cases in 1974 .", "Since then MVEV clinical cases have been largely c...	[ "An outbreak of Murray Valley encephalitis with 17 confirmed cases occurred across Australia in 2011 .", "This outbreak involved parts of Australia where cases had not occurred for many decades .", "The epidemiology in this outbreak reflects a change that has occurred over the past 15 years , with more non-Abor...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "computational biology/macromolecular structure analysis", "biophysics/theory and simulation", "computational biology" ]	Using Entropy Maximization to Understand the Determinants of Structural Dynamics beyond Native Contact Topology	journal.pcbi.1000816	null	[ [ "Associated with each protein fold is a set of intrinsically accessible global motions that arise solely from the 3-dimensional geometry of the fold and involve the entire architecture .", "For a number of systems it has been shown that these intrinsic motions play an important role in protein function [1...	[ "Comparison of elastic network model predictions with experimental data has provided important insights on the dominant role of the network of inter-residue contacts in defining the global dynamics of proteins .", "Most of these studies have focused on interpreting the mean-square fluctuations of residues , or de...	[ "As more protein structures are solved , we are able to perform a more critical assessment of the relationship between protein structure and dynamics , and to gain a deeper understanding of the major determinants of structural dynamics .", "Here we perform a systematic study on a set of proteins structurally dete...	2010
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "neurochemistry", "engineering and technology", "signal processing", "membrane potential", "social sciences", "light", "electrophysiology", "neuroscience", "animals", "electromagnetic radiation", "animal models", "serotonin", "drosophila m...	Modulation of voltage-dependent K+ conductances in photoreceptors trades off investment in contrast gain for bandwidth	journal.pcbi.1006566	null	[ [ "The activity of neurons and neural circuits is modulated to adjust their properties to changes in state , affecting behaviour .", "Modulation can occur at large spatial scales , encompassing large numbers of neurons , or may be more localised , being restricted to small circuits or single neurons [1–5] ....	[ "Modulation is essential for adjusting neurons to prevailing conditions and differing demands .", "Yet understanding how modulators adjust neuronal properties to alter information processing remains unclear , as is the impact of neuromodulation on energy consumption .", "Here we combine two computational models...	[ "The properties of neurons and neural circuits can be adjusted by neuromodulators , molecules that alter their ability to respond to future activity .", "Many neuromodulators target voltage-dependent ion channels , molecular components of cell membranes that influence the electrical activity of neurons .", "Bec...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "computational biology/metagenomics" ]	Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples	journal.pcbi.1000352	null	[ [ "The increasing availability of high-throughput , inexpensive sequencing technologies has led to the birth of a new scientific field , metagenomics , encompassing large-scale analyses of microbial communities .", "Broad sequencing of bacterial populations allows us a first glimpse at the many microbes tha...	[ "Numerous studies are currently underway to characterize the microbial communities inhabiting our world .", "These studies aim to dramatically expand our understanding of the microbial biosphere and , more importantly , hope to reveal the secrets of the complex symbiotic relationship between us and our commensal ...	[ "The emerging field of metagenomics aims to understand the structure and function of microbial communities solely through DNA analysis .", "Current metagenomics studies comparing communities resemble large-scale clinical trials with multiple subjects from two general populations ( e . g . sick and healthy ) .", ...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "cell biology/cell signaling", "cell biology", "neurological disorders/movement disorders", "neuroscience/neurobiology of disease and regeneration" ]	PINK1 Is Selectively Stabilized on Impaired Mitochondria to Activate Parkin	journal.pbio.1000298	Mutations in PINK1 or Parkin lead to familial parkinsonism. The authors suggest that PINK1 and Parkin form a pathway that senses damaged mitochondria and selectively targets them for degradation.	[ [ "Parkinson disease is a common neurodegenerative disorder with no disease-modifying therapy presently available for its treatment [1] .", "Study of recessive forms of familial Parkinson disease , such as those resulting from mutations in the E3 ubiquitin ligase Parkin ( GeneID: 5071 ) or the mitochondrial...	[ "Loss-of-function mutations in PINK1 and Parkin cause parkinsonism in humans and mitochondrial dysfunction in model organisms .", "Parkin is selectively recruited from the cytosol to damaged mitochondria to trigger their autophagy .", "How Parkin recognizes damaged mitochondria , however , is unknown .", "Her...	[ "Mutations in the PINK1 or Parkin genes lead to an inherited form of Parkinson disease .", "Understanding how the products of these genes work may give us insights into what goes wrong in these patients and in Parkinson disease more generally .", "Previous studies in flies and mice , and in human cells suggest ...	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases/neglected tropical diseases", "infectious diseases/tropical and travel-associated diseases" ]	A Randomized Controlled Trial of Local Heat Therapy Versus Intravenous Sodium Stibogluconate for the Treatment of Cutaneous Leishmania major Infection	journal.pntd.0000628	null	[ [ "Cutaneous leishmaniasis is a parasitic infection transmitted by the bite of an infected sand fly , with an estimated worldwide incidence of 1 . 5 million cases [1] .", "Generally self resolving within months , infection with Leishmania major can leave disfiguring scars or chronic ulcers , usually in area...	[ "Cutaneous Leishmania major has affected many travelers including military personnel in Iraq and Afghanistan .", "Optimal treatment for this localized infection has not been defined , but interestingly the parasite is thermosensitive .", "Participants with parasitologically confirmed L . major infection were ra...	[ "Cutaneous leishmaniasis , a parasitic skin infection transmitted by the bite of a sand fly , can result in chronic skin sores and is estimated to affect more than 1 . 5 million persons worldwide .", "While the infection generally heals on its own in months to years , treatment can be expensive and difficult .", ...	2010
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "body fluids", "rna interference", "pathology and laboratory medicine", "enzymes", "pathogens", "enzymology", "microbiology", "animals", "viruses", "rna viruses", "epigenetics", "insect vectors", "infectious diseases", "aedes aegypti", ...	Catalase protects Aedes aegypti from oxidative stress and increases midgut infection prevalence of Dengue but not Zika	journal.pntd.0005525	null	[ [ "Arthropod-borne viral ( arboviral ) diseases , such as Dengue , Chikungunya , and especially Zika , have recently occupied a central spot in the global discussions concerning infectious diseases due to the rapid spread of cases worldwide and the associated increase in syndromes such as microcephaly and Guill...	[ "Digestion of blood in the midgut of Aedes aegypti results in the release of pro-oxidant molecules that can be toxic to the mosquito .", "We hypothesized that after a blood meal , the antioxidant capacity of the midgut is increased to protect cells against oxidative stress .", "Concomitantly , pathogens present...	[ "Mosquitoes ingest large amounts of blood , a rich and abundant source of energy to sustain egg production .", "Blood digestion offers challenges to the insect , like managing high concentrations of heme and iron , pro-oxidant and potentially toxic molecules derived from hemoglobin .", "Mosquitoes and other blo...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "humoral immunity", "medicine and health sciences", "immune cells", "immunology", "vaccines", "infectious disease immunology", "sexually transmitted diseases", "class switching", "vaccination and immunization", "antibody response", "infectious diseases", "white blood cells", ...	Characteristics of Memory B Cells Elicited by a Highly Efficacious HPV Vaccine in Subjects with No Pre-existing Immunity	journal.ppat.1004461	null	[ [ "The quadrivalent HPV ( qHPV ) vaccine provides near-complete protection against sexually transmitted HPV infections that most commonly cause anogenital and oropharyngeal cancers ( HPV types 16 and 18 ) and genital warts ( HPV 6 and 11 ) when administered to individuals naive to these types [1]–[6] .", "I...	[ "Licensed human papillomavirus ( HPV ) vaccines provide near complete protection against the types of HPV that most commonly cause anogenital and oropharyngeal cancers ( HPV 16 and 18 ) when administered to individuals naive to these types .", "These vaccines , like most other prophylactic vaccines , appear to pr...	[ "There is an urgent need to better understand how to reliably generate effective vaccines , particularly subunit vaccines , as certain pathogens are considered to pose too great of a safety risk to be developed as live , attenuated or killed vaccines ( e . g . , HIV-1 ) .", "The human papillomavirus ( HPV ) vacci...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "humoral immunity", "biochemistry", "immunochemistry", "clinical immunology", "immunity", "biology and life sciences", "immunology", "vaccination and immunization", "immunotherapy" ]	Use of a Synthetic Biosensor for Neutralizing Activity-Biased Selection of Monoclonal Antibodies against Atroxlysin-I, an Hemorrhagic Metalloproteinase from Bothrops atrox Snake Venom	journal.pntd.0002826	null	[ [ "Snakebites cause up to 1 , 800 000 envenomations per year , mainly in tropical areas [1]–[4] .", "Snakebites might be considered as a daily occupational hazard since rural subsistent farming communities are the main population suffering from this condition [3] , [4] , considered as a Neglected Tropical C...	[ "The snake Bothrops atrox is responsible for the majority of envenomings in the northern region of South America .", "Severe local effects , including hemorrhage , which are mainly caused by snake venom metalloproteinases ( SVMPs ) , are not fully neutralized by conventional serum therapy .", "Little is known a...	[ "In this work , we propose a new screening strategy to produce monoclonal antibodies against Atr-I , a P-I class SVMP from Bothrops atrox , which is the snake responsible for the majority of the accidents in South America .", "SVMPs are the main toxic factors in Bothrops venom causing systemic and local hemorrhag...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The Highly Prolific Phenotype of Lacaune Sheep Is Associated with an Ectopic Expression of the B4GALNT2 Gene within the Ovary	journal.pgen.1003809	null	[ [ "Women , cattle , goats and ewes have generally one or two offspring , whereas other mammals , such as sows , rodents and dogs are prolific and produce more than three offspring .", "It relies on the number of ovulations at each estrus cycle i . e . the ovulation rate ( OR ) , for which the underlying gen...	[ "Prolific sheep have proven to be a valuable model to identify genes and mutations implicated in female fertility .", "In the Lacaune sheep breed , large variation in litter size is genetically determined by the segregation of a fecundity major gene influencing ovulation rate , named FecL and its prolific allele ...	[ "Prolific sheep have proven to be a valuable model to identify genes and mutations implicated in ovarian function and female fertility .", "Indeed , fecundity genes of the Bone Morphogenetic Protein ( BMP ) family discovered in sheep was evidenced as genetic candidates to explain female infertility pathologies ."...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "infectious disease epidemiology", "immunology", "geographical locations", "animals", "vaccines", "preventive medicine", "north america", "infectious disease control", "vaccination and immunization", "insect vectors", "public and occupational ...	Projected Impact of Dengue Vaccination in Yucatán, Mexico	journal.pntd.0004661	null	[ [ "Dengue is currently the most important arboviral disease of humans and has an increasing global public health burden [1] .", "Worldwide , the combined annual number of infections by the four dengue serotypes has been estimated to be close to 400 million , of which 96 million develop symptomatic disease [...	[ "Dengue vaccines will soon provide a new tool for reducing dengue disease , but the effectiveness of widespread vaccination campaigns has not yet been determined .", "We developed an agent-based dengue model representing movement of and transmission dynamics among people and mosquitoes in Yucatán , Mexico , and s...	[ "Dengue is a mosquito-transmitted viral disease that is common throughout the tropics .", "Despite a long history in humans and extensive efforts to control dengue transmission in many countries , the number , severity , and geographic range of reported cases is increasing .", "Most control efforts have focused...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "energy flow", "ecology and environmental sciences", "marine ecosystems", "marine biology", "biomass (ecology)", "plant science", "herbivory", "plant ecology", "research facilities", "research and analysis methods", "ecological metrics", "mesocosms", "ecosystems", "food web structure", "...	Climate change could drive marine food web collapse through altered trophic flows and cyanobacterial proliferation	journal.pbio.2003446	null	[ [ "Forecasting the effect of global change on ecosystem functioning is a major challenge in ecology [1] , partly because future climate shifts are likely to reorganize complex food webs , generating novel communities composed of new combinations of species [2] .", "In marine ecosystems , multiple anthropoge...	[ "Global warming and ocean acidification are forecast to exert significant impacts on marine ecosystems worldwide .", "However , most of these projections are based on ecological proxies or experiments on single species or simplified food webs .", "How energy fluxes are likely to change in marine food webs in re...	[ "Healthy marine ecosystems are crucial for people’s livelihoods and food production .", "Global climate stressors , such as warming and ocean acidification , can drastically impact the structure and function of marine food webs , diminishing the production of goods and services .", "Our ability to predict how f...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "bacterial diseases", "infectious diseases", "mycobacterium", "immunity", "innate immunity", "microbial pathogens", "biology", "microbiology" ]	Targeting of Mycobacterium tuberculosis Heparin-Binding Hemagglutinin to Mitochondria in Macrophages	journal.ppat.1002435	null	[ [ "Tuberculosis remains a serious global problem , although many researchers have made a persistent effort for several decades .", "Mycobacterium tuberculosis , a major causative agent of pulmonary tuberculosis , is responsible for 1 . 8 million deaths per year worldwide [1] .", "Innate immune system pl...	[ "Mycobacterium tuberculosis heparin-binding hemagglutinin ( HBHA ) , a virulence factor involved in extrapulmonary dissemination and a strong diagnostic antigen against tuberculosis , is both surface-associated and secreted .", "The role of HBHA in macrophages during M . tuberculosis infection , however , is less...	[ "Cell death is a common outcome during infection with a number of pathogenic microorganisms .", "Therefore , defining the factors responsible for killing of host cells is important to uncovering mechanisms of pathogenesis .", "World-wide , two billon people are latently infected with Mycobacterium tuberculosis ...	2011
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "turkey (country)", "sequencing techniques", "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "population genetics", "geographical locations", "microbiology", "sand flies", "gene pool", "viruses", "signs and symptoms", "phylogenetic analysis", "genome analy...	Sandfly-Borne Phlebovirus Isolations from Turkey: New Insight into the Sandfly fever Sicilian and Sandfly fever Naples Species	journal.pntd.0004519	null	[ [ "The genus Phlebovirus ( family Bunyaviridae ) currently contains 9 viral species Sandfly fever Naples ( SFNV ) , Salehabad ( SALV ) , Rift Valley fever ( RVFV ) , Uukuniemi ( UUKV ) , Bujaru ( BUJV ) , Candiru ( CRUV ) , Chilibre ( CHIV ) , Frijoles ( FRIV ) and Punta Toro ( PTV ) including 33 distinct serot...	[ "Many studies have presented virus sequences which suggest the existence of a variety of putative new phleboviruses transmitted by sandflies in the Old World .", "However , in most of these studies , only partial sequences in the polymerase or the nucleoprotein genes were characterised .", "Therefore to further...	[ "We provide evidence that sandfly-borne phleboviruses belonging to 3 distinct genetic and phylogenetic groups ( Sandfly fever Naples virus [SFNV] , Sandfly fever Sicilian virus [SFSV] , and Salehabad virus [SALV] ) co-circulate in Adana city , in Mediterranean Turkey .", "While Adana virus was recently described ...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Learning and forgetting using reinforced Bayesian change detection	journal.pcbi.1006713	null	[ [ "The adaptation of learning to contingency changes and noise has numerous connections to various scientific fields from cognitive psychology to machine learning .", "A classical finding in behavioural neuroscience is that instrumental behaviours tend to be less and less flexible as subjects repeatedly rec...	[ "Agents living in volatile environments must be able to detect changes in contingencies while refraining to adapt to unexpected events that are caused by noise .", "In Reinforcement Learning ( RL ) frameworks , this requires learning rates that adapt to past reliability of the model .", "The observation that be...	[ "In stable contexts , animals and humans exhibit automatic behaviour that allows them to make fast decisions .", "However , these automatic processes exhibit a lack of flexibility when environmental contingencies change .", "In the present paper , we propose a model of behavioural automatization that is based o...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "death rates", "invertebrates", "medicine and health sciences", "ruminants", "african trypanosomiasis", "tropical diseases", "vertebrates", "parasitic diseases", "animals", "mammals", "parasitic protozoans", "glossina", "simulation and modeling", "seasons", "developmental biology", "pr...	An agent-based model of tsetse fly response to seasonal climatic drivers: Assessing the impact on sleeping sickness transmission rates	journal.pntd.0006188	null	[ [ "The tsetse fly ( genus: Glossina ) is the vector for human African trypanosomiasis ( HAT ) or sleeping sickness , a neglected tropical disease caused by two sub-species of the protozoan parasite Trypanosoma brucei s . l . : T . b .", "rhodesiense , in eastern and southern Africa and T . b .", "gambie...	[ "This paper presents the development of an agent-based model ( ABM ) to incorporate climatic drivers which affect tsetse fly ( G . m . morsitans ) population dynamics , and ultimately disease transmission .", "The model was used to gain a greater understanding of how tsetse populations fluctuate seasonally , and ...	[ "African trypanosomiasis is a parasitic disease which affects humans and other animals in 36 sub-Saharan African countries .", "The disease is transmitted by the tsetse fly , and the human form of the diseases is known as sleeping sickness .", "In an attempt to improve our understanding of the mechanisms which ...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology" ]	The Role of Response Elements Organization in Transcription Factor Selectivity: The IFN-β Enhanceosome Example	journal.pcbi.1002077	null	[ [ "Cellular response to environmental signals relies on tight gene regulation .", "Specific recognition of response elements ( REs ) by transcription factors ( TFs ) [1]–[4] and their combinatorial assembly [1] , [5] , [6] on promoters and enhancers is crucial for functional , gene-specific transcription in...	[ "What is the mechanism through which transcription factors ( TFs ) assemble specifically along the enhancer DNA ?", "The IFN-β enhanceosome provides a good model system: it is small; its components' crystal structures are available; and there are biochemical and cellular data .", "In the IFN-β enhanceosome , th...	[ "An enhanceosome is a functional unit that consists of DNA segment called enhancer; its transcription factors ( TFs ) ; and their interacting cofactors .", "To function , the TFs must assemble on their corresponding response elements ( REs ) cooperatively .", "Understanding how TFs assemble is important because...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "musculoskeletal system", "bone", "physiology", "genetics", "biology", "anatomy and physiology", "genetics and genomics" ]	Inactivation of a Novel FGF23 Regulator, FAM20C, Leads to Hypophosphatemic Rickets in Mice	journal.pgen.1002708	null	[ [ "FAM20C is a member of the “family with sequence similarity 20” .", "In mammals , this evolutionarily conserved protein family consists of three members: FAM20A , FAM20B and FAM20C .", "FAM20A was originally observed in the lung and liver and displays obvious differential expression in hematopoietic c...	[ "Family with sequence similarity 20 , -member C ( FAM20C ) is highly expressed in the mineralized tissues of mammals .", "Genetic studies showed that the loss-of-function mutations in FAM20C were associated with human lethal osteosclerotic bone dysplasia ( Raine Syndrome ) , implying an inhibitory role of this mo...	[ "A recent study demonstrated that the inactivating mutations in the FAM20C gene were associated with lethal osteosclerotic bone dysplasia characterized by a generalized hardening of all bones; this observation implied an inhibitory role of FAM20C during bone formation .", "However , in vitro studies revealed a co...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "public and occupational health", "infectious diseases", "computer and information sciences", "data management", "ecology and environmental sciences", "computer modeling", "nature-society interactions", "medicine and health sciences", "disease ecology", "data acquisition", "behavioral and social...	Global Disease Monitoring and Forecasting with Wikipedia	journal.pcbi.1003892	null	[ [ "Infectious disease remains extremely costly in both human and economic terms .", "For example , the majority of global child mortality is due to conditions such as acute respiratory infection , measles , diarrhea , malaria , and HIV/AIDS [1] .", "Even in developed countries , infectious disease has g...	[ "Infectious disease is a leading threat to public health , economic stability , and other key social structures .", "Efforts to mitigate these impacts depend on accurate and timely monitoring to measure the risk and progress of disease .", "Traditional , biologically-focused monitoring techniques are accurate b...	[ "Even in developed countries , infectious disease has significant impact; for example , flu seasons in the United States take between 3 , 000 and 49 , 000 lives .", "Disease surveillance , traditionally based on patient visits to health providers and laboratory tests , can reduce these impacts .", "Motivated by...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "face", "chemical compounds", "engineering and technology", "tropical diseases", "salts", "geographical locations", "cell phones", "bacterial diseases", "eye diseases", "neglected tropical diseases", "ethiopia", "eyes", "africa", "public and occupational h...	‘If an Eye Is Washed Properly, It Means It Would See Clearly’: A Mixed Methods Study of Face Washing Knowledge, Attitudes, and Behaviors in Rural Ethiopia	journal.pntd.0005099	null	[ [ "Trachoma is the leading cause of infectious blindness globally .", "[1–3] Caused by the bacterium Chlamydia trachomatis , trachoma is thought to be transmitted by direct contact from infected persons and clothing , as well as the moisture-seeking fly Musca sorbens . [4 , 5]", "Currently endemic in 53...	[ "Face cleanliness is a core component of the SAFE ( Surgery , Antibiotics , Facial cleanliness , and Environmental improvements ) strategy for trachoma control .", "Understanding knowledge , attitudes , and behaviors related to face washing may be helpful for designing effective interventions for improving facial...	[ "Facial cleanliness is a core component of the SAFE ( Surgery , Antibiotics , Facial cleanliness , and Environmental improvements ) strategy for trachoma control .", "We conducted a mixed methods study in a trachoma hyperendemic region of rural Ethiopia to better understand knowledge , attitudes , and behaviors r...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "sequencing techniques", "alleles", "genetic mapping", "genome analysis", "copy number variation", "molecular genetics", "molecular biology techniques", "research and analysis methods", "sequence analysis", "genome complexity", "sequence alignment", "bioinformatics", "molecular biology", "...	Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets	journal.pcbi.1006080	null	[ [ "The emergence and maturation of next-generation sequencing technologies , including whole genome sequencing , whole exome sequencing , and targeted sequencing approaches , has enabled researchers to perform increasingly more complex analysis of copy number variants ( CNVs ) [1] .", "While genome sequenci...	[ "Somatic copy number variations ( CNVs ) play a crucial role in development of many human cancers .", "The broad availability of next-generation sequencing data has enabled the development of algorithms to computationally infer CNV profiles from a variety of data types including exome and targeted sequence data; ...	[ "We present Bamgineer , a software program to introduce user-defined , haplotype-specific copy number variants ( CNVs ) at any frequency into standard Binary Alignment Mapping ( BAM ) files .", "Copy number gains are simulated by introducing new DNA sequencing read pairs sampled from existing reads and modified t...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "crystal structure", "pathology and laboratory medicine", "manganese", "pathogens", "condensed matter physics", "microbiology", "enzymology", "orthomyxoviruses", "viruses", "organisms", "hantavirus", "monomers (chemistry)", "rna viruses", "andes virus", ...	Atomic Structure and Biochemical Characterization of an RNA Endonuclease in the N Terminus of Andes Virus L Protein	journal.ppat.1005635	null	[ [ "Andes virus ( ANDV ) belongs to the genus Hantavirus within the family Bunyaviridae .", "Hantaviruses can be pathogenic to humans and are distributed worldwide [1–3] .", "Their natural hosts are various rodent species [4] .", "ANDV is endemic in Argentina and Chile and its main reservoir host is ...	[ "Andes virus ( ANDV ) is a human-pathogenic hantavirus .", "Hantaviruses presumably initiate their mRNA synthesis by using cap structures derived from host cell mRNAs , a mechanism called cap-snatching .", "A signature for a cap-snatching endonuclease is present in the N terminus of hantavirus L proteins .", ...	[ "Hantaviruses may cause severe disease in humans , either hemorrhagic fever or cardiopulmonary syndrome .", "Both conditions are associated with high lethality .", "Vaccines and effective treatments approved for application in humans are not available .", "The L protein plays a central role in hantavirus repl...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology/virus evolution and symbiosis", "virology/vaccines", "virology/immunodeficiency viruses", "virology/animal models of infection", "virology", "infectious diseases/hiv infection and aids", "virology/immune evasion", "infectious diseases/sexually transmitted diseases", "virology/host invasion...	High Multiplicity Infection by HIV-1 in Men Who Have Sex with Men	journal.ppat.1000890	null	[ [ "An effective sterilizing HIV-1 vaccine ideally should target virus in the earliest stages of transmission , prior to dissemination and establishment of persistent infection [1] , [2] , [3] , [4] .", "To be broadly protective , such a vaccine must defend against a genetically diverse set of viruses transm...	[ "Elucidating virus-host interactions responsible for HIV-1 transmission is important for advancing HIV-1 prevention strategies .", "To this end , single genome amplification ( SGA ) and sequencing of HIV-1 within the context of a model of random virus evolution has made possible for the first time an unambiguous ...	[ "Understanding the biology of sexual transmission of HIV-1 could contribute importantly to the development of effective prevention measures .", "However , different routes of virus transmission ( vaginal , rectal , penile or oral ) and inaccessibility of tissues at or near the time of virus transmission make this...	2010

Subsets and Splits

No community queries yet

The top public SQL queries from the community will appear here once available.