Split (3)

train · 24.8k rows

Search is not available for this dataset

article stringlengths 4.36k 149k	summary stringlengths 32 3.35k	section_headings listlengths 1 91	keywords listlengths 0 141	year stringclasses 13 values	title stringlengths 20 281
Ligand binding to death receptors activates apoptosis in cancer cells . Stimulation of death receptors results in the formation of intracellular multiprotein platforms that either activate the apoptotic initiator Caspase-8 to trigger cell death , or signal through kinases to initiate inflammatory and cell survival sign...	Death receptors are targets of novel cancer therapeutics . Most of them signal through flexible multiprotein platforms to either activate apoptotic or necroptotic cell death , or propagate cell survival and pro-inflammatory signals . We focused our study on the role of dynamic assembly and composition of these platform...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "death", "hela", "cells", "cell", "processes", "biological", "cultures", "simulation", "and", "modeling", "fluorophotometry", "cell", "cultures", "research", "and", "analysis", "methods", "chemical", "properties", "physical", "chemistry", "fluorescence", "resona...	2019	Heterogeneous responses to low level death receptor activation are explained by random molecular assembly of the Caspase-8 activation platform
The NF-κB signaling pathway is central to the innate and adaptive immune responses . Upon their detection of pathogen-associated molecular patterns , Toll-like receptors on the cell surface initiate signal transduction and activate the NF-κB pathway , leading to the production of a wide array of inflammatory cytokines ...	Enteropathogenic Escherichia coli ( EPEC ) and enterohemorrhagic E . coli ( EHEC ) cause food-borne diseases , including watery diarrhea or severe bloody diarrhea and life-threatening kidney disease ( hemolytic uremic syndrome ) . Upon ingestion , EPEC/EHEC colonize the cells of the epithelial lining in the intestinal ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/cellular", "microbiology", "and", "pathogenesis" ]	2010	NleC, a Type III Secretion Protease, Compromises NF-κB Activation by Targeting p65/RelA
Mammarenaviruses are associated with human hemorrhagic fever diseases in Africa and America . Recently , a rodent mammarenavirus , Wēnzhōu virus ( WENV ) and related viruses , have been reported in China , Cambodia , and Thailand . Moreover , in Cambodia , these viruses were suspected to be associated with human diseas...	Rodents are natural reservoirs of mammarenavirus . Lymphocytic choriomeningitis virus ( LCMV ) , isolated in Asian countries during the 1990s , has a worldwide distribution and was the first mammarenavirus isolated . In 2014 , a second mammarenavirus , Wēnzhōu virus ( WENV ) , was identified in rodents in Zhejiang Prov...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "taxonomy", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "vertebrates", "animals", "mammals", "viruses", "phylogenetics", "data", ...	2019	Prevalence of Wēnzhōu virus in small mammals in Yunnan Province, China
Dietary fatty acids can be incorporated directly into phospholipids . This poses a specific challenge to cellular membranes since their composition , hence properties , could greatly vary with different diets . That vast variations in diets are tolerated therefore implies the existence of regulatory mechanisms that mon...	Our cells and their internal organelles are bound by membranes composed primarily of phospholipids , i . e . polar molecules containing two fatty acids attached to a hydrophilic head group . The types of fatty acids in phospholipids greatly influence membrane properties: saturated fatty acids make the membranes rigid w...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "carbohydrate", "metabolism", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "caenorhabditis", "gene", "regulation", "light", "microscopy", "glucose", "metabolism", "animals", "toxicology", "animal", "models", "toxi...	2017	The adiponectin receptor AdipoR2 and its Caenorhabditis elegans homolog PAQR-2 prevent membrane rigidification by exogenous saturated fatty acids
There are no effective therapeutics that antagonize or reverse the protein-misfolding events underpinning polyglutamine ( PolyQ ) disorders , including Spinocerebellar Ataxia Type-3 ( SCA3 ) . Here , we augment the proteostasis network of Drosophila SCA3 models with Hsp104 , a powerful protein disaggregase from yeast ,...	There are no effective therapeutics for any of the neurodegenerative disorders caused by expanded polyglutamine ( PolyQ ) tracts including Spinocerebellar Ataxia Type-3 ( SCA3 ) . These disorders are connected with the misfolding and aggregation of proteins bearing expanded PolyQ tracts in the neurons of affected indiv...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Hsp104 Suppresses Polyglutamine-Induced Degeneration Post Onset in a Drosophila MJD/SCA3 Model
The category B agent of bioterrorism , Entamoeba histolytica has a two-stage life cycle: an infective cyst stage , and an invasive trophozoite stage . Due to our inability to effectively induce encystation in vitro , our knowledge about the cyst form remains limited . This also hampers our ability to develop cyst-speci...	We used tandem mass spectrometry to identify E . histolytica cyst proteins in 5 cyst positive stool samples . We report the identification of 417 non-redundant E . histolytica proteins including 195 proteins that were not identified in existing trophozoite derived proteome or EST datasets , consistent with cyst specifi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "biochemistry", "infectious", "diseases", "diagnostic", "medicine", "global", "health", "biology", "microbiology", "proteomics" ]	2012	Proteomic Analysis of the Cyst Stage of Entamoeba histolytica
Interactions between genes and proteins are crucial for efficient processing of internal or external signals , but this connectivity also amplifies stochastic fluctuations by propagating noise between components . Linear ( unbranched ) cascades were shown to exhibit an interplay between the sensitivity to changes in in...	Biological circuits need to be sensitive to changes in environmental signals but at the same time buffer rapid fluctuations ( noise ) that might be imposed on this input . In this paper , we analyze the interplay between sensitivity to signals and the ability to buffer noise . Previous studies reported that negative fe...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "saccharomyces", "biophysics", "none", "computational", "biology" ]	2008	Noise Propagation and Signaling Sensitivity in Biological Networks: A Role for Positive Feedback
Comparative analyses of pathogen genomes provide new insights into how pathogens have evolved common and divergent virulence strategies to invade related plant species . Fusarium crown and root rots are important diseases of wheat and barley world-wide . In Australia , these diseases are primarily caused by the fungal ...	Cereals are our most important staple crops and are subject to attack from a diverse range of fungal pathogens . A major goal of molecular plant pathology research is to understand how pathogens infect plants to allow the development of durable plant protection measures . Comparing the genomes of different pathogens of...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "functional", "genomics", "plant", "biology", "genome", "sequencing", "plant", "science", "cereals", "crops", "plant", "pathology", "comparative", "genomics", "crop", "diseases", "biology", "agriculture", "plant", "pathogens", "genomics", "genetics", "and", "genomics" ]	2012	Comparative Pathogenomics Reveals Horizontally Acquired Novel Virulence Genes in Fungi Infecting Cereal Hosts
Parasitic helminths establish chronic infections in mammalian hosts . Helminth/Plasmodium co-infections occur frequently in endemic areas . However , it is unclear whether Plasmodium infections compromise anti-helminth immunity , contributing to the chronicity of infection . Immunity to Plasmodium or helminths requires...	Approximately a third of the world’s population is burdened with chronic intestinal parasitic helminth infections , causing significant morbidities . Identifying the factors that contribute to the chronicity of infection is therefore essential . Co-infection with other pathogens , which is extremely common in helminth ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	IFNγ and IL-12 Restrict Th2 Responses during Helminth/Plasmodium Co-Infection and Promote IFNγ from Th2 Cells
The nematode C . elegans is an important model for the study of social behaviors . Recent investigations have shown that a family of small molecule signals , the ascarosides , controls population density sensing and mating behavior . However , despite extensive studies of C . elegans aggregation behaviors , no intraspe...	Chemical signaling is an ancient form of inter-organismal communication . The nematode Caenorhabditis elegans exhibits a wide range of social behaviors , including mutual attraction and aggregation , and has served as a useful model towards investigating the signaling pathways that regulate these behaviors . Recent inv...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "behavioral", "neuroscience", "model", "organisms", "ecology", "chemical", "biology", "chemistry", "biology", "neuroscience", "behavioral", "ecology" ]	2012	A Modular Library of Small Molecule Signals Regulates Social Behaviors in Caenorhabditis elegans
Cryptococcus neoformans is an encapsulated pathogenic yeast that can change the size of the cells during infection . In particular , this process can occur by enlarging the size of the capsule without modifying the size of the cell body , or by increasing the diameter of the cell body , which is normally accompanied by...	Cryptococcus neoformans is a fungal pathogen that has a significant incidence in HIV+ patients in particular , in Sub-saharan Africa , Asia and South America . This yeast poses an excellent model to investigate fungal virulence because it develops many strategies to adapt to the host and evade the immune response . One...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "blood", "cells", "cell", "physiology", "cryptococcus", "neoformans", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "cryptococcus", "immune", "cells", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "atmos...	2018	Cryptococcus neoformans can form titan-like cells in vitro in response to multiple signals
Genome-wide association studies ( GWAS ) are now used routinely to identify SNPs associated with complex human phenotypes . In several cases , multiple variants within a gene contribute independently to disease risk . Here we introduce a novel Gene-Wide Significance ( GWiS ) test that uses greedy Bayesian model selecti...	Genome-wide association studies ( GWAS ) have successfully identified genetic variants associated with complex human phenotypes . Despite a proliferation of analysis methods , most studies rely on simple , robust SNP–by–SNP univariate tests with ever-larger population sizes . Here we introduce a new test motivated by t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "statistics", "bayes", "theorem", "algorithms", "genome", "analysis", "tools", "mathematics", "biostatistics", "statistical", "methods", "biology", "probability", "theory", "computer", "science", "genetics", "genomics", "genetics", ...	2011	Gene-Based Tests of Association
Heritability of bone mineral density ( BMD ) varies across skeletal sites , reflecting different relative contributions of genetic and environmental influences . To quantify the degree to which common genetic variants tag and environmental factors influence BMD , at different sites , we estimated the genetic ( rg ) and...	The heritability of bone mineral density ( BMD ) varies across skeletal sites , reflecting different relative contributions of genetic and environmental influences . To investigate whether the genes underlying bone acquisition act in a site-specific manner , we quantified the shared genetic influences across axial and ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "biochemistry", "rheumatology", "medicine", "and", "health", "sciences", "genome", "analysis", "genetics", "biology", "and", "life", "sciences", "computational", "biology", "metabolism", "bone", "and", "mineral", "metabolism", "h...	2014	Phenotypic Dissection of Bone Mineral Density Reveals Skeletal Site Specificity and Facilitates the Identification of Novel Loci in the Genetic Regulation of Bone Mass Attainment
Stable rhythmic neural activity depends on the well-coordinated interplay of synaptic and cell-intrinsic conductances . Since all biophysical processes are temperature dependent , this interplay is challenged during temperature fluctuations . How the nervous system remains functional during temperature perturbations re...	All physiological processes are influenced by temperature . This is a particular problem for the nervous system , as temperature changes can disrupt the well-balanced flow of ions across the cell membrane necessary for maintaining nerve cell function . Possessing compensatory mechanisms that counterbalance detrimental ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Neuromodulation to the Rescue: Compensation of Temperature-Induced Breakdown of Rhythmic Motor Patterns via Extrinsic Neuromodulatory Input
Epidemic dengue fever ( DF ) and dengue hemorrhagic fever/dengue shock syndrome ( DHF/DSS ) are overwhelming public health capacity for diagnosis and clinical care of dengue patients throughout the tropical and subtropical world . The ability to predict severe dengue disease outcomes ( DHF/DSS ) using acute phase clini...	Epidemics of dengue fever ( DF ) and dengue hemorrhagic fever/dengue shock syndrome ( DHF/DSS ) are overwhelming public health capacity for diagnosis and patient care . Developing a panel of biomarkers in acute-phase serum specimens for prognosis of severe dengue disease would be of enormous value for appropriate triag...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "chemical", "compounds", "liquid", "chromatography", "tropical", "diseases", "organic", "compounds", "pediatrics", "metabolomics", "metabolites", "neglected", "tropical", "diseases", "pediatric", "infections", "research", "and", "a...	2016	Metabolomics-Based Discovery of Small Molecule Biomarkers in Serum Associated with Dengue Virus Infections and Disease Outcomes
Spike timing dependent plasticity ( STDP ) is a learning rule that modifies synaptic strength as a function of the relative timing of pre- and postsynaptic spikes . When a neuron is repeatedly presented with similar inputs , STDP is known to have the effect of concentrating high synaptic weights on afferents that syste...	The paper describes a new biologically plausible mechanism for generating intermediate-level visual representations using an unsupervised learning scheme . These representations can then be used very effectively to perform categorization tasks using natural images . While the basic hierarchical architecture of the syst...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "primates", "neuroscience", "computational", "biology" ]	2007	Unsupervised Learning of Visual Features through Spike Timing Dependent Plasticity
Osteoporosis is a common polygenic disease and global healthcare priority but its genetic basis remains largely unknown . We report a high-throughput multi-parameter phenotype screen to identify functionally significant skeletal phenotypes in mice generated by the Wellcome Trust Sanger Institute Mouse Genetics Project ...	Chronic disease represents a global healthcare burden but its genetic basis is largely unknown . To address this , a massive international investment is generating a resource of mutant mice to investigate the function of every gene . Although current characterization of mutants is broadbased , it lacks specificity . He...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "rheumatology", "animal", "genetics", "integrative", "physiology", "anatomy", "and", "physiology", "biomechanics", "gene", "function", "animal", "models", "genetics", "of", "disease", "physiological", "processes", "model", "organisms", "bone", "homeostasis", ...	2012	Rapid-Throughput Skeletal Phenotyping of 100 Knockout Mice Identifies 9 New Genes That Determine Bone Strength
Emerging evidence implies that STAT6 plays an important role in both the adaptive and innate immune responses to virus infection . Kaposi’s sarcoma-associated herpesvirus ( KSHV ) is an oncogenic γ-herpesvirus agent associated with several human malignancies , including Kaposi’s sarcoma ( KS ) and primary effusion lymp...	STAT6 , a member of the signal transducer and activator of transcription ( STAT ) family , has been shown to play an important role in viral infection . STAT6 activation is linked to reactivation of oncogenic herpesvirus and their associated cancers . However , the precise mechanism by which KSHV modulates STAT6 regula...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "phosphorylation", "medicine", "and", "health", "sciences", "luciferase", "pathology", "and", "laboratory", "medicine", "molecular", "probe", "techniques", "enzymes", "pathogens", "immunoblotting", "microbiology", "enzymology", "viruses", "immunoprecipitation", "dna", "viru...	2017	Nuclear Localization and Cleavage of STAT6 Is Induced by Kaposi’s Sarcoma-Associated Herpesvirus for Viral Latency
DNA sequence and local chromatin landscape act jointly to determine transcription factor ( TF ) binding intensity profiles . To disentangle these influences , we developed an experimental approach , called protein/DNA binding followed by high-throughput sequencing ( PB–seq ) , that allows the binding energy landscape t...	Transcription factors ( TFs ) bind DNA to modulate levels of gene expression . TF binding sites change throughout development , in response to environmental stimuli , and different tissues have distinct TF binding profiles . The mechanism by which TFs discriminate between binding sites in a context dependent manner is ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computer", "science", "biology" ]	2012	Accurate Prediction of Inducible Transcription Factor Binding Intensities In Vivo
The Mediator is a highly conserved , large multiprotein complex that is involved essentially in the regulation of eukaryotic mRNA transcription . It acts as a general transcription factor by integrating regulatory signals from gene-specific activators or repressors to the RNA Polymerase II . The internal network of int...	Phenotypic diversity and environmental adaptation in genetically identical cells is achieved by an exact tuning of their transcriptional program . It is a challenging task to unravel parts of the complex network of involved gene regulatory components and their interactions . Here , we shed light on the role of the Medi...	[ "Abstract", "Introduction", "Methods", "Results/Discussion" ]	[ "statistics", "microbiology", "dna", "transcription", "mathematical", "computing", "model", "organisms", "mathematics", "signaling", "in", "cellular", "processes", "transcriptional", "signaling", "gene", "expression", "computing", "methods", "biology", "molecular", "biology...	2012	MC EMiNEM Maps the Interaction Landscape of the Mediator
In the last two decades , mitochondrial DNA ( mtDNA ) and the non-recombining portion of the Y chromosome ( NRY ) have been extensively used in order to measure the maternally and paternally inherited genetic structure of human populations , and to infer sex-specific demography and history . Most studies converge towar...	Human evolutionary history has been investigated mainly through the prism of genetic variation of the Y chromosome and mitochondrial DNA . These two uniparentally inherited markers reflect the demographic history of males and females , respectively . Their contrasting patterns of genetic differentiation reveal that wom...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "genetics", "and", "genomics/population", "genetics", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics" ]	2008	Sex-Specific Genetic Structure and Social Organization in Central Asia: Insights from a Multi-Locus Study
Fungal pathogens have evolved diverse strategies to sense host-relevant cues and coordinate cellular responses , which enable virulence and drug resistance . Defining circuitry controlling these traits opens new opportunities for chemical diversity in therapeutics , as the cognate inhibitors are rarely explored by conv...	Invasive fungal infections pose a serious threat to human health worldwide , with Candida albicans being a leading fungal pathogen . Mortality is in part due to the limited arsenal of effective antifungals , with drug resistance on the rise . The echinocandins , which target the fungal cell wall , are the newest class ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "antimicrobials", "cell", "walls", "medicine", "and", "health", "sciences", "cellular", "stress", "responses", "pathology", "and", "laboratory", "medicine", "pathogens", "drugs", "cell", "processes", "microbiology", "antifungals", "fungi", "model", "organisms", "pharmac...	2016	Metal Chelation as a Powerful Strategy to Probe Cellular Circuitry Governing Fungal Drug Resistance and Morphogenesis
Streptococcus pneumoniae isolates typically express one of over 90 immunologically distinguishable polysaccharide capsules ( serotypes ) , which can be classified into “serogroups” based on cross-reactivity with certain antibodies . Pneumococci can alter their serotype through recombinations affecting the capsule polys...	Streptococcus pneumoniae is a major respiratory pathogen responsible for a high burden of morbidity and mortality worldwide . Current anti-pneumococcal vaccines target the bacterium’s polysaccharide capsule , of which at least 95 different variants ( ‘serotypes’ ) are known , which are classified into ‘serogroups’ . Ba...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Selective and Genetic Constraints on Pneumococcal Serotype Switching
Incidence of Leishmania donovani infection and Visceral Leishmaniasis ( VL ) was assessed in a prospective study in Indian and Nepalese high-endemic villages . DAT-seroconversion was used as marker of incident infection in 3 yearly surveys . The study population was followed up to month 30 to identify incident clinical...	Visceral Leishmaniasis is well known as a public health problem in North-Indian Bihar state and adjacent districts in Nepal , with about 300 . 000 new cases per year . As not all infections with L . donovani lead to disease , the impact of control programs should not only be measured in numbers of VL cases , but also i...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "leishmaniasis", "neglected", "tropical", "diseases" ]	2011	Incidence of Symptomatic and Asymptomatic Leishmania donovani Infections in High-Endemic Foci in India and Nepal: A Prospective Study
Pluripotent embryonic stem cells are of paramount importance for biomedical sciences because of their innate ability for self-renewal and differentiation into all major cell lines . The fateful decision to exit or remain in the pluripotent state is regulated by complex genetic regulatory networks . The rapid growth of ...	In the embryonic stage mammalian cells are pluripotent: they have not yet committed to any specific cell type . The commitment to a cell type is controlled by pluripotency networks , the bio-molecular inventory which is unsurprisingly complex , spanning a myriad of transcription factors , genes and epigenetic factors ....	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetic", "networks", "gene", "regulation", "regulatory", "proteins", "dna-binding", "proteins", "signaling", "networks", "dna", "transcription", "stem", "cells", "network", "analysis", "transcription", "factors", "computer", "and", "information", "sciences", "cell", "...	2018	A stochastic and dynamical view of pluripotency in mouse embryonic stem cells
Eukaryotic cells extend a variety of surface protrusions to direct cell motility . Formation of protrusions is mediated by coordinated actions between the plasma membrane and the underlying actin cytoskeleton . Here , we found that the single calponin homology ( CH ) domain-containing protein CHDP-1 induces the formati...	In response to intra- and extracellular cues , remodeling of the sub-membranous cortical actin cytoskeleton constantly reorganizes the plasma membrane . Thus , distinct types of actin-rich invaginations or protrusions , such as filopodia and lamellipodia , enable cells to explore territory and pull themselves around . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "caenorhabditis", "neurites", "neuroscience", "animals", "membrane", "proteins", "animal", "models", "caenorhabditis", "elegans", "model", "organisms", "cellular", "structures", "and", "organelles", "neuronal", "dendrites", "cytoskeleton", "research", "and"...	2016	The Calponin Family Member CHDP-1 Interacts with Rac/CED-10 to Promote Cell Protrusions
Collective behaviour is a widespread phenomenon in biology , cutting through a huge span of scales , from cell colonies up to bird flocks and fish schools . The most prominent trait of collective behaviour is the emergence of global order: individuals synchronize their states , giving the stunning impression that the g...	Our perception of collective behaviour in biological systems is closely associated to the emergence of order on a group scale . For example , birds within a flock align their directions of motion , giving the stunning impression that the group is just one organism . Large swarms of midges , mosquitoes and flies , howev...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "behavioral", "ecology", "ecology", "and", "environmental", "sciences", "ecology", "biology", "and", "life", "sciences", "computational", "biology", "biophysics", "biophysical", "simulations" ]	2014	Collective Behaviour without Collective Order in Wild Swarms of Midges
There is great interindividual variability in HIV-1 viral setpoint after seroconversion , some of which is known to be due to genetic differences among infected individuals . Here , our focus is on determining , genome-wide , the contribution of variable gene expression to viral control , and to relate it to genomic DN...	There has been recent progress in understanding the genetic factors that modulate susceptibility to HIV-1 infection . Genetic variation explains to a certain extent differences in disease progression among individuals . Less is known regarding the contribution of differences in gene expression to viral control . The pr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genetics", "of", "disease", "genetics", "and", "genomics/population", "genetics", "infectious", "diseases/hiv", "infection", "and", "aids", "genetics", "and", "genomics/gene", "expression" ]	2010	Genome-Wide mRNA Expression Correlates of Viral Control in CD4+ T-Cells from HIV-1-Infected Individuals
Numerous plant viruses that cause significant agricultural problems are persistently transmitted by insect vectors . We wanted to see if apoptosis was involved in viral infection process in the vector . We found that a plant reovirus ( rice gall dwarf virus , RGDV ) induced typical apoptotic response during viral repli...	Of the approximately 700 known plant viruses , more than 75% are transmitted by insects . Numerous plant viruses can replicate inside the cells of the insects . Unlike in the plant hosts , the viruses do not seem to cause disease in the insect vectors that carry them . Here , we report that the replication of a plant r...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "death", "medicine", "and", "health", "sciences", "viral", "transmission", "and", "infection", "cell", "processes", "biological", "cultures", "microbiology", "vector-borne", "diseases", "viral", "structure", "cell", "cultures", "mitochondria", "bioenergetics", "...	2019	Fibrillar structures induced by a plant reovirus target mitochondria to activate typical apoptotic response and promote viral infection in insect vectors
CD8 T cell responses have three phases: expansion , contraction , and memory . Dynamic alterations in proliferation and apoptotic rates control CD8 T cell numbers at each phase , which in turn dictate the magnitude of CD8 T cell memory . Identification of signaling pathways that control CD8 T cell memory is incomplete ...	CD8 T cells are vital for controlling infections with viruses , intracellular bacteria and protozoa . Induction of T and B cell memory is the basis of vaccinations and cellular immunity to intracellular pathogens depends upon the number and quality of memory CD8 T cells . Understanding the mechanisms that control vario...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "immunology", "biology" ]	2012	FOXO3 Regulates CD8 T Cell Memory by T Cell-Intrinsic Mechanisms
Soil-transmitted helminths , such as Trichuris trichiura , are of major concern in public health . Current efforts to control these helminth infections involve periodic mass treatment in endemic areas . Since these large-scale interventions are likely to intensify , monitoring the drug efficacy will become indispensibl...	Worldwide , millions of people are infected with soil-transmitted helminths , particularly in developing countries . Efforts to control these infections involve periodic mass drug treatment in endemic areas . Since these large-scale interventions are likely to intensify , monitoring of drug efficacy has become a key is...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/antimicrobials", "and", "drug", "resistance", "infectious", "diseases/neglected", "tropical", "diseases", "public", "health", "and", "epidemiology/preventive", "medicine", "public", "health", "and", "epidemiology/infectious", "diseases", "public", "hea...	2009	Field Validity and Feasibility of Four Techniques for the Detection of Trichuris in Simians: A Model for Monitoring Drug Efficacy in Public Health?
Haiti's cholera epidemic has been devastating partly due to underlying weak infrastructure and limited clean water and sanitation . A comprehensive approach to cholera control is crucial , yet some have argued that oral cholera vaccination ( OCV ) might result in reduced hygiene practice among recipients . We evaluated...	In October 2010 , Haiti experienced a cholera outbreak that is now considered one of the largest cholera epidemics in recent history . A comprehensive approach is necessary to successfully fight the epidemic and proven methods for controlling cholera include improving access to clean water and sanitation as well as wid...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2013	Cholera Vaccination Campaign Contributes to Improved Knowledge Regarding Cholera and Improved Practice Relevant to Waterborne Disease in Rural Haiti
Rhodopsin mistrafficking can cause photoreceptor ( PR ) degeneration . Upon light exposure , activated rhodopsin 1 ( Rh1 ) in Drosophila PRs is internalized via endocytosis and degraded in lysosomes . Whether internalized Rh1 can be recycled is unknown . Here , we show that the retromer complex is expressed in PRs wher...	Upon light exposure , rhodopsins—light-sensing proteins in the eye—trigger visual transduction signaling to activate fly photoreceptor cells . After activation , rhodopsins can be internalized from the cell surface into endosomes and then degraded in lysosomes . This mechanism prevents constant activation of the visual...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience", "visual", "system", "biology", "and", "life", "sciences", "sensory", "systems" ]	2014	The Retromer Complex Is Required for Rhodopsin Recycling and Its Loss Leads to Photoreceptor Degeneration
Alternative 3′ and 5′ splice site ( ss ) events constitute a significant part of all alternative splicing events . These events were also found to be related to several aberrant splicing diseases . However , only few of the characteristics that distinguish these events from alternative cassette exons are known currentl...	Alternative splicing is the mechanism that is responsible for the creation of multiple mRNA products from a single gene . It is considered a key player in genomic complexity achievement . Alternative 3′ and 5′ splicing events in which part of the exon is alternatively included or excluded in the mRNA constitute a signi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "evolutionary", "biology", "molecular", "biology", "vertebrates" ]	2007	The Emergence of Alternative 3′ and 5′ Splice Site Exons from Constitutive Exons
The posttranslational modifiers SUMO and ubiquitin critically regulate the DNA damage response ( DDR ) . Important crosstalk between these modifiers at DNA lesions is mediated by the SUMO-targeted ubiquitin ligase ( STUbL ) , which ubiquitinates SUMO chains to generate SUMO-ubiquitin hybrids . These SUMO-ubiquitin hybr...	Since its discovery in 2007 , SUMO-targeted ubiquitin ligase ( STUbL ) activity has been identified as a key regulator of diverse cellular processes such as DNA repair , mitosis and DNA replication . In each of these processes , STUbL has been shown to promote the chromatin extraction and/or degradation of SUMO chain m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "chemical", "compounds", "chromosome", "structure", "and", "function", "organic", "compounds", "telomeres", "fungi", "model", "organisms", "sumoylation", "experimental", "organism", "systems", "basic", "amino", "acids", "amino", "acids", "protein", "structure", "dna", ...	2017	SUMO-targeted ubiquitin ligase activity can either suppress or promote genome instability, depending on the nature of the DNA lesion
Monocyte dysfunction by filarial antigens has been a major mechanism underlying immune evasion following hyporesponsiveness during patent lymphatic filariasis . Recent studies have initiated a paradigm shift to comprehend the immunological interactions of Wolbachia and its antigens in inflammation , apoptosis , lymphoc...	Despite knowing the significance of Wolbachia in helminth infections , our understanding of immunity and pathogenesis remains incomplete . Therefore , considering the gravity of the problem , the present study provides evidence that Wolbachia heat shock protein 60 induces apoptosis and senescence through TLR-4 . Also ,...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Autophagy Protects Monocytes from Wolbachia Heat Shock Protein 60–Induced Apoptosis and Senescence
Leprosy reactions , reversal reactions/RR and erythema nodosum leprosum/ENL , can cause irreversible nerve damage , handicaps and deformities . The study of Mycobacterium leprae-specific serologic responses at diagnosis in the cohort of patients enrolled at the Clinical Trial for Uniform Multidrug Therapy Regimen for L...	Leprosy is a debilitating dermato-neurologic disease caused by Mycobacterium leprae . One of the main difficulties in the clinical management of leprosy patients is the development of leprosy reactions which are immune inflammatory episodes that can cause irreversible handicaps , incapacities and deformities . There ar...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "mycobacterium", "leprae", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "immunology", "tropical", "diseases", "bacterial", "diseases", "neglected", "tropical", "diseases", "...	2017	Leprosy reactions: The predictive value of Mycobacterium leprae-specific serology evaluated in a Brazilian cohort of leprosy patients (U-MDT/CT-BR)
Cells of the innate immune system act in synergy to provide a first line of defense against pathogens . Here we describe that dendritic cells ( DCs ) , matured with viral products or mimics thereof , including Epstein-Barr virus ( EBV ) , activated natural killer ( NK ) cells more efficiently than other mature DC prepa...	Epstein-Barr virus ( EBV ) establishes a persistent infection in nearly all human adults . Due to its tumor causing potential EBV infection has to be continuously controlled by the immune system in virus carriers . We demonstrate here that in the first week after infection , when other EBV-specific immune responses are...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "viruses", "none", "virology", "in", "vitro", "immunology", "homo", "(human)" ]	2008	Tonsilar NK Cells Restrict B Cell Transformation by the Epstein-Barr Virus via IFN-γ
While we have good understanding of bacterial metabolism at the population level , we know little about the metabolic behavior of individual cells: do single cells in clonal populations sometimes specialize on different metabolic pathways ? Such metabolic specialization could be driven by stochastic gene expression and...	This study addresses a fundamental question in bacterial metabolism: do all individuals in a clonal population express the same metabolic functions , or do individuals specialize on different metabolic functions and assimilate different substrates ? Reports about stochastic gene expression in bacterial populations rais...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "physiology", "carbohydrate", "metabolism", "chemical", "compounds", "particle", "physics", "biological", "cultures", "carbohydrates", "cell", "metabolism", "organic", "compounds", "glucose", "glucose", "metabolism", "dna", "transcription", "atoms", "composite", "...	2017	Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations
Auditory neurons encode stimulus history , which is often modelled using a span of time-delays in a spectro-temporal receptive field ( STRF ) . We propose an alternative model for the encoding of stimulus history , which we apply to extracellular recordings of neurons in the primary auditory cortex of anaesthetized fer...	The responses of neurons in the primary auditory cortex depend on the recent history of sounds over seconds or less . Typically , this dependence on the past has been modelled by applying a wide span of time delays to the input , although this is likely to be biologically unrealistic . Real neurons integrate the histor...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "auditory", "cortex", "medicine", "and", "health", "sciences", "neural", "networks", "brain", "vertebrates", "neuroscience", "learning", "and", "memory", "animals", "mammals", "bacterial", "diseases", "cognition", "network", "analysis", "memory", "cellular", "structures...	2019	A dynamic network model of temporal receptive fields in primary auditory cortex
The dynamics of tumor progression is driven by multiple factors , which can be exogenous to the tumor ( microenvironment ) or intrinsic ( genetic , epigenetic or due to intercellular interactions ) . While tumor heterogeneity has been extensively studied on the level of cell genetic profiles or cellular composition , t...	Primary tumors and tumor metastases grow as three-dimensional ( 3D ) masses of cells . Depending on the surrounding stroma , they may acquire various shapes , more or less irregular . Tumor organoids are the 3D experimental cultures that mimic growth of in vivo tumors , as well as their response to treatments . However...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "organoids", "medicine", "and", "health", "sciences", "cell", "cycle", "inhibitors", "cell", "cycle", "and", "cell", "division", "cancer", "treatment", "biological", "cultures", "cell", "processes", "radii", "geometry", "simulation", "and", "modeling", "oncology", "...	2019	Morphophenotypic classification of tumor organoids as an indicator of drug exposure and penetration potential
To date , studies on papillary renal-cell carcinoma ( pRCC ) have largely focused on coding alterations in traditional drivers , particularly the tyrosine-kinase , Met . However , for a significant fraction of tumors , researchers have been unable to determine a clear molecular etiology . To address this , we perform t...	Renal cell carcinoma accounts for more than 90% of kidney cancers . Papillary renal cell carcinoma ( pRCC ) is the second most common subtype of renal cell carcinoma . Previous studies , focusing mostly on the protein-coding regions , have identified several key genomic alterations that are critical to cancer initiatio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cancer", "genomics", "renal", "cell", "carcinoma", "medicine", "and", "health", "sciences", "carcinomas", "cancers", "and", "neoplasms", "basic", "cancer", "research", "genitourinary", "tract", "tumors", "oncology", "mutation", "dna", "replication", "epigenetics", "d...	2017	Whole-genome analysis of papillary kidney cancer finds significant noncoding alterations
Infectious diseases pose a severe worldwide threat to human and livestock health . While early diagnosis could enable prompt preventive interventions , the majority of diseases are found in rural settings where basic laboratory facilities are scarce . Under such field conditions , point-of-care immunoassays provide an ...	The lack of diagnostic tests that are sensitive , affordable and user-friendly is the impediment to early detection and containment of infectious diseases . For these reasons , African trypanosomosis continues to pose serious threat to the communities that are unable to access laboratory services . Assays that are able...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "livestock", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "ruminants", "immunology", "vertebrates", "parasitic", "diseases", "animals", "mammals", "molecular", "biology", "t...	2016	An Anti-proteome Nanobody Library Approach Yields a Specific Immunoassay for Trypanosoma congolense Diagnosis Targeting Glycosomal Aldolase
Bacterial pathogens of plant and animals share a homologous group of virulence factors , referred to as the YopJ effector family , which are translocated by the type III secretion ( T3S ) system into host cells during infection . Recent work indicates that some of these effectors encode acetyltransferases that suppress...	How host disease resistance pathways are activated in response to pathogens remains a fundamental question in host-pathogen interactions . In this work , we used the Pseudomonas-Arabidopsis pathosystem to study how the AvrBsT effector activates plant immune signaling . AvrBsT belongs to the YopJ effector family , a gro...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "cell", "biology", "plant", "pathology", "plant", "science", "biology" ]	2014	AvrBsT Acetylates Arabidopsis ACIP1, a Protein that Associates with Microtubules and Is Required for Immunity
Influenza vaccination is the primary approach to prevent influenza annually . WHO/CDC recommendations prioritize vaccinations mainly on the basis of age and co-morbidities , but have never considered influenza infection history of individuals for vaccination targeting . We evaluated such influenza vaccination policies ...	WHO/CDC recommendations prioritize influenza vaccinations primarily on the basis of age co-morbidities , but have never considered targeting vaccination for individuals previously infected with influenza . An individual's infection risk is governed by his or her contacts as manifested by his or her social interactions ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biology", "and", "life", "sciences", "population", "biology", "medicine", "and", "health", "sciences", "epidemiology" ]	2014	An Innovative Influenza Vaccination Policy: Targeting Last Season's Patients
Thousands of long intergenic non-coding RNAs ( lincRNAs ) are encoded by the mammalian genome . However , the function of most of these lincRNAs has not been identified in vivo . Here , we demonstrate a role for a novel lincRNA , linc-MYH , in adult fast-type myofiber specialization . Fast myosin heavy chain ( MYH ) ge...	Adult skeletal muscles are classified into fast-type and slow-type , which display different resistance to muscle atrophy and metabolic protection against obesity . We identify in this manuscript a new mechanism controlling in vivo adult muscle fiber-type specification implicating a long intergenic non-coding RNA , lin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "gene", "expression", "genetics", "biology", "and", "life", "sciences", "cell", "differentiation", "dna", "transcription", "gene", "function" ]	2014	Six Homeoproteins and a linc-RNA at the Fast MYH Locus Lock Fast Myofiber Terminal Phenotype
Mathematical models of mitochondrial bioenergetics provide powerful analytical tools to help interpret experimental data and facilitate experimental design for elucidating the supporting biochemical and physical processes . As a next step towards constructing a complete physiologically faithful mitochondrial bioenerget...	Mathematically modeling biological systems challenges our current understanding of the physical and biochemical events contributing to the observed dynamics . It requires careful consideration of hypothesized mechanisms , model development assumptions and details regarding the experimental conditions . We have adopted ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/systems", "biology", "biophysics/theory", "and", "simulation", "biochemistry/theory", "and", "simulation" ]	2010	Modeling Mitochondrial Bioenergetics with Integrated Volume Dynamics
Many eukaryotic cell-surface proteins are anchored to the membrane via glycosylphosphatidylinositol ( GPI ) . There are at least 26 genes involved in biosynthesis and remodeling of GPI anchors . Hypomorphic coding mutations in seven of these genes have been reported to cause decreased expression of GPI anchored protein...	Glycosylphosphatidylinositols ( GPI ) are glycolipid anchors that anchor various proteins to the cell surface . At least 26 genes are involved in biosynthesis and modification of the GPI anchors . Recently , mutations in eight of those genes have been described . Although those mutations do not fully abolish the functi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "epilepsy", "medicine", "and", "health", "sciences", "child", "growth", "genetic", "dominance", "growth", "restriction", "child", "development", "autosomal", "recessive", "traits", "neurology", "neurodegenerative", "diseases", "genetics", "biology", "and", "life", "scie...	2014	Null Mutation in PGAP1 Impairing Gpi-Anchor Maturation in Patients with Intellectual Disability and Encephalopathy
Parkinson's disease ( PD ) , the second most prevalent neurodegenerative disease after Alzheimer's disease , is linked to the gradual loss of dopaminergic neurons in the substantia nigra . Disease loci causing hereditary forms of PD are known , but most cases are attributable to a combination of genetic and environment...	Parkinson's disease ( PD ) is characterized by the progressive loss of dopaminergic neurons . While hereditary forms are known , most cases are attributable to a combination of genetic and environmental risk factors . In PD models , dopaminergic neurodegeneration can be triggered by neurotoxins such as 6-hydroxydopamin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "model", "organisms", "genetics", "biology", "and", "life", "sciences", "neuroscience", "research", "and", "analysis", "methods" ]	2014	Tetraspanin (TSP-17) Protects Dopaminergic Neurons against 6-OHDA-Induced Neurodegeneration in C. elegans
Natural variation separates Epstein-Barr virus ( EBV ) into type 1 and type 2 strains . Type 2 EBV is less transforming in vitro due to sequence differences in the EBV transcription factor EBNA2 . This correlates with reduced activation of the EBV oncogene LMP1 and some cell genes . Transcriptional activation by type 1...	Epstein-Barr virus ( EBV ) drives the development of many human cancers worldwide including specific types of lymphoma and carcinoma . EBV infects B lymphocytes and immortalises them , thus contributing to lymphoma development . The virus promotes B lymphocyte growth and survival by altering the level at which hundreds...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "chemical", "characterization", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "organisms", "viruses", "materials", "science", "dna", "viruses", "sequ...	2019	Increased association between Epstein-Barr virus EBNA2 from type 2 strains and the transcriptional repressor BS69 restricts EBNA2 activity
Selective pressures between hosts and their parasites can result in reciprocal evolution or adaptation of specific life history traits . Local adaptation of resident hosts and parasites should lead to increase parasite infectivity/virulence ( higher compatibility ) when infecting hosts from the same location ( in sympa...	Schistosomiasis , the second most widespread human parasitic disease after malaria , is caused by helminth parasites of the genus Schistosoma . More than 200 million people in 74 countries suffer from the pathological , and societal consequences of this disease . To complete its life cycle , the parasite requires an in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "schistosoma", "invertebrates", "schistosoma", "mansoni", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "biomphalaria", "helminths", "natural", "antisense", "transcripts", "gene", "regulation", ...	2019	Sympatric versus allopatric evolutionary contexts shape differential immune response in Biomphalaria / Schistosoma interaction
Metabolic rate , heart rate , lifespan , and many other physiological properties vary with body mass in systematic and interrelated ways . Present empirical data suggest that these scaling relationships take the form of power laws with exponents that are simple multiples of one quarter . A compelling explanation of thi...	The rate at which an organism produces energy to live increases with body mass to the 3/4 power . Ten years ago West , Brown , and Enquist posited that this empirical relationship arises from the structure and dynamics of resource distribution networks such as the cardiovascular system . Using assumptions that capture ...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "physiology/cardiovascular", "physiology", "and", "circulation", "biophysics/theory", "and", "simulation", "physics/general", "physics", "mathematics/statistics", "computational", "biology/systems", "biology" ]	2008	Sizing Up Allometric Scaling Theory
Tropical diseases caused by parasites continue to cause socioeconomic devastation that reverberates worldwide . There is a growing need for new control measures for many of these diseases due to increasing drug resistance exhibited by the parasites and problems with drug toxicity . One new approach is to apply host def...	Protozoan parasites cause serious diseases in large areas of the tropics . Control of these diseases depends to a great extent on the use of therapeutic drugs , many of which are highly toxic . In addition , parasite resistance to several of the front-line drugs is increasing . Host defense peptides ( HDP; formerly cal...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/antimicrobials", "and", "drug", "resistance", "cell", "biology/cell", "growth", "and", "division", "biochemistry/protein", "chemistry", "immunology/immunity", "to", "infections" ]	2009	Killing of Trypanosomatid Parasites by a Modified Bovine Host Defense Peptide, BMAP-18
An important problem in neuronal computation is to discern how features of stimuli control the timing of action potentials . One aspect of this problem is to determine how an action potential , or spike , can be elicited with the least energy cost , e . g . , a minimal amount of applied current . Here we show in the Ho...	Computational neuroscience seeks to understand the mechanisms by which signals excite a neuron or a neuronal network . An important consideration in these studies is optimality , i . e . , what signal most effectively causes excitation . Optimization of neuronal signaling is important for networks that need to minimize...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "mathematics", "biology" ]	2011	Optimal Stimulus Shapes for Neuronal Excitation
The Josephin Domain ( JD ) , i . e . the N-terminal domain of Ataxin 3 ( At3 ) protein , is an interesting example of competition between physiological function and aggregation risk . In fact , the fibrillogenesis of Ataxin 3 , responsible for the spinocerebbellar ataxia 3 , is strictly related to the JD thermodynamic ...	Proteins are fascinating molecular machines capable of organizing themselves into well-defined hierarchical structures through a huge number of conformational changes to accomplish a wide range of cellular functions . Protein conformational changes may be characterized by transitions from a low-energy conformation to a...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2016	Josephin Domain Structural Conformations Explored by Metadynamics in Essential Coordinates
Kato-Katz is a widely used method for the diagnosis of soil-transmitted helminth infection . Fecal samples cannot be preserved , and hence , should be processed on the day of collection and examined under a microscope within 60 min of slide preparation . Mini-FLOTAC is a technique that allows examining fixed fecal samp...	Soil-transmitted helminths are parasitic worms ( hookworm , roundworm , and whipworm ) that affect hundreds of millions of people . Kato-Katz is the most widely used technique for the diagnosis of soil-transmitted helminth infection . It requires the collection , processing , and microscopic examination of stool sample...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	How Long Can Stool Samples Be Fixed for an Accurate Diagnosis of Soil-Transmitted Helminth Infection Using Mini-FLOTAC?
Adipose tissue grows by two mechanisms: hyperplasia ( cell number increase ) and hypertrophy ( cell size increase ) . Genetics and diet affect the relative contributions of these two mechanisms to the growth of adipose tissue in obesity . In this study , the size distributions of epididymal adipose cells from two mouse...	Obesity is an enlargement of adipose tissue to store excess energy intake . Hyperplasia ( cell number increase ) and hypertrophy ( cell size increase ) are two possible growth mechanisms . The in vivo dynamic change of fat tissue cannot be monitored in real time due to current technical limitations . However , we can m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/cell", "growth", "and", "division", "genetics", "and", "genomics/complex", "traits", "biophysics/theory", "and", "simulation", "developmental", "biology/cell", "differentiation", "diabetes", "and", "endocrinology/obesity", "nutrition/obesity", "physiology/integ...	2009	Hypertrophy and/or Hyperplasia: Dynamics of Adipose Tissue Growth
The RIG-I like receptor pathway is stimulated during RNA virus infection by interaction between cytosolic RIG-I and viral RNA structures that contain short hairpin dsRNA and 5′ triphosphate ( 5′ppp ) terminal structure . In the present study , an RNA agonist of RIG-I was synthesized in vitro and shown to stimulate RIG-...	Development of safe and effective drugs that inhibit virus replication remains a challenge . Activation of natural host defense using interferon ( IFN ) therapy has proven an effective treatment of certain viral infections . As a distinct variation on this concept , we analyzed the capacity of small RNA molecules that ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "expression", "analysis", "medicine", "hiv", "prevention", "respiratory", "infections", "immune", "activation", "influenza", "immunity", "to", "infections", "immunology", "dengue", "pulmonology", "immune", "defense", "infectious", "disease", "control", "immunomo...	2013	Systems Analysis of a RIG-I Agonist Inducing Broad Spectrum Inhibition of Virus Infectivity
Genome-wide association studies ( GWAS ) have demonstrated the ability to identify the strongest causal common variants in complex human diseases . However , to date , the massive data generated from GWAS have not been maximally explored to identify true associations that fail to meet the stringent level of association...	Genome-wide association studies ( GWAS ) seek to identify loci in which changes in DNA are correlated with disease . However , GWAS do not necessarily lead directly to genes associated with disease , and they do not typically inform the broader context in which disease genes operate , thereby providing limited insights...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/disease", "models", "genetics", "and", "genomics/genetics", "of", "disease", "genetics", "and", "genomics/complex", "traits", "genetics", "and", "genomics/gene", "expression" ]	2010	Liver and Adipose Expression Associated SNPs Are Enriched for Association to Type 2 Diabetes
The influence of mono-ubiquitylation of histone H2B ( H2Bub ) on transcription via nucleosome reassembly has been widely documented . Recently , it has also been shown that H2Bub promotes recovery from replication stress; however , the underling molecular mechanism remains unclear . Here , we show that H2B ubiquitylati...	Eukaryotic DNA is organized into nucleosomes , which are the fundamental repeating units of chromatin . Coordination of chromatin structure is required for efficient and accurate DNA replication . Aberrant DNA replication results in mutations and chromosome rearrangements that may be associated with human disorders . T...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "genomics", "dna", "replication", "cell", "biology", "chromosome", "biology", "genome", "analysis", "genetics", "biology", "and", "life", "sciences", "dna", "epigenetics", "computational", "biology", "chromatin" ]	2014	H2B Mono-ubiquitylation Facilitates Fork Stalling and Recovery during Replication Stress by Coordinating Rad53 Activation and Chromatin Assembly
Seed dormancy is an important economic trait for agricultural production . Abscisic acid ( ABA ) and Gibberellins ( GA ) are the primary factors that regulate the transition from dormancy to germination , and they regulate this process antagonistically . The detailed regulatory mechanism involving crosstalk between ABA...	Seed dormancy prevents or delays germination in maturated seeds . The optimal level of seed dormancy is a valuable trait for agricultural production and post-harvest management . High ABA and low GA content in seeds promote seed dormancy . However , the precise molecular mechanisms controlling seed dormancy and germina...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "plant", "science", "plant", "growth", "and", "development", "plant", "genetics", "biology", "plant", "physiology" ]	2013	ABI4 Regulates Primary Seed Dormancy by Regulating the Biogenesis of Abscisic Acid and Gibberellins in Arabidopsis
Inference about the causal structure that induces correlations between two traits can be achieved by combining genetic associations with a mediation-based approach , as is done in the causal inference test ( CIT ) . However , we show that measurement error in the phenotypes can lead to the CIT inferring the wrong causa...	Understanding the causal relationships between pairs of traits is crucial for unravelling the causes of disease . To this end , results from genome-wide association studies are valuable because if a trait is known to be influenced by a genetic variant then this knowledge can be used to test the trait’s causal influence...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "infographics", "genome-wide", "association", "studies", "social", "sciences", "simulation", "and", "modeling", "mathematics", "statistics", "(mathematics)", "test", "statistics", "genome", "analysis", "epigenetics", "dna", "molecular", "genetics", "dna", "methylation", "...	2017	Orienting the causal relationship between imprecisely measured traits using GWAS summary data
Developmental constraints have been postulated to limit the space of feasible phenotypes and thus shape animal evolution . These constraints have been suggested to be the strongest during either early or mid-embryogenesis , which corresponds to the early conservation model or the hourglass model , respectively . Confli...	During development , vertebrate embryos pass through a “phylotypic” stage , during which their morphology is most similar between different species . This gave rise to the hourglass model , which predicts the highest developmental constraints during mid-embryogenesis . In the last decade , a large effort has been made ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome", "expression", "analysis", "microarrays", "developmental", "biology", "genomics", "genome", "evolution", "comparative", "genomics", "biology", "computational", "biology", "evolutionary", "biology", "genomic", "evolution", "evolutionary", "developmental", "biology" ]	2013	The Hourglass and the Early Conservation Models—Co-Existing Patterns of Developmental Constraints in Vertebrates
In nature , closely related species may hybridize while still retaining their distinctive identities . Chromosomal regions that experience reduced recombination in hybrids , such as within inversions , have been hypothesized to contribute to the maintenance of species integrity . Here , we examine genomic sequences fro...	The transformation of populations into distinct species depends on whether hybridization , recombination , and subsequent gene introgression can be suppressed between diverging species . We use partial genome sequences to reconstruct this evolutionary process in the Drosophila pseudoobscura species subgroup , which inc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/population", "genetics", "evolutionary", "biology/genomics", "genetics", "and", "genomics/comparative", "genomics", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics" ]	2009	The Genomics of Speciation in Drosophila: Diversity, Divergence, and Introgression Estimated Using Low-Coverage Genome Sequencing
RNA processing events that take place on the transcribed pre-mRNA include capping , splicing , editing , 3′ processing , and polyadenylation . Most of these processes occur co-transcriptionally while the RNA polymerase II ( Pol II ) enzyme is engaged in transcriptional elongation . How Pol II elongation rates are influ...	The pre-mRNA emerging from RNA polymerase II during eukaryotic transcription undergoes a series of processing events . These include 5′-capping , intron excision and exon ligation during splicing , 3′-end processing , and polyadenylation . Processing events occur co-transcriptionally , meaning that a variety of enzymes...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/gene", "expression", "cell", "biology/nuclear", "structure", "and", "function" ]	2011	The In Vivo Kinetics of RNA Polymerase II Elongation during Co-Transcriptional Splicing
The QT interval ( QT ) is heritable and its prolongation is a risk factor for ventricular tachyarrhythmias and sudden death . Most genetic studies of QT have examined European ancestral populations; however , the increased genetic diversity in African Americans provides opportunities to narrow association signals and i...	The QT interval ( QT ) provides a measure of a ventricular action potential , and its prolongation is associated with sudden death and ventricular arrhythmias . Genome-wide association studies performed in European populations have identified common genetic variants that influence QT . However , it is unclear whether t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "population", "genetics", "biology", "computational", "biology", "genetics", "and", "genomics", "human", "genetics" ]	2012	Fine-Mapping and Initial Characterization of QT Interval Loci in African Americans
Cattle and other ruminants produce large quantities of methane ( ~110 million metric tonnes per annum ) , which is a potent greenhouse gas affecting global climate change . Methane ( CH4 ) is a natural by-product of gastro-enteric microbial fermentation of feedstuffs in the rumen and contributes to 6% of total CH4 emis...	Methane is a potent greenhouse gas and ruminant livestock contribute a substantial amount of total methane from human activities . Variation between cows’ methane production has been found partly due to their genetics ( heritable ) , making genetic selection a promising strategy for breeding low methane emitting cows ....	[ "Abstract", "Introduction", "Results", "Discussion", "Conclusions", "Materials", "and", "methods" ]	[ "taxonomy", "livestock", "ecology", "and", "environmental", "sciences", "archaeal", "taxonomy", "microbiome", "chemical", "compounds", "community", "structure", "atmospheric", "science", "microbiology", "data", "management", "archaea", "bacteria", "methane", "microbial", ...	2018	Host genetics and the rumen microbiome jointly associate with methane emissions in dairy cows
Many bacterial pathogens utilize a type III secretion system to deliver multiple effector proteins into host cells . Here we found that the type III effectors , NleE from enteropathogenic E . coli ( EPEC ) and OspZ from Shigella , blocked translocation of the p65 subunit of the transcription factor , NF-κB , to the hos...	Bacterial intestinal pathogens have evolved distinct ways of colonizing the gut and causing disease . Enteropathogenic E . coli ( EPEC ) and its close relative enterohemorrhagic E . coli O157:H7 ( EHEC ) are extracellular pathogens that cause a characteristic lesion on the intestinal mucosa known as an attaching and ef...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "biology/cell", "signaling", "microbiology/innate", "immunity", "immunology/innate", "immunity", "microbiology/cellular", "microbiology", "and", "pathogenesis", "infectious", "diseases/gastrointestinal", "infections" ]	2010	The Type III Effectors NleE and NleB from Enteropathogenic E. coli and OspZ from Shigella Block Nuclear Translocation of NF-κB p65
Scrub typhus is a febrile infection caused by the obligate intracellular bacterium Orientia tsutsugamushi , which causes significant morbidity and mortality across the Asia-Pacific region . The control of this vector-borne disease is challenging due to humans being dead-end hosts , vertical maintenance of the pathogen ...	Scrub typhus is a disease caused by bacteria that invade cells in our immune system and blood vessels . It is transmitted by mites and is treatable with antibiotics . Unfortunately diagnosis is difficult and requires techniques that are not easily accessible everywhere . Currently , there is no scrub typhus vaccine ava...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "typhus", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "vertebrates", "animals", "mammals", "primates", "animal", "...	2017	Strong interferon-gamma mediated cellular immunity to scrub typhus demonstrated using a novel whole cell antigen ELISpot assay in rhesus macaques and humans
Trypanosoma cruzi is the causal agent of Chagas Disease that is endemic in Latin American , afflicting more than ten million people approximately . This disease has two phases , acute and chronic . The acute phase is often asymptomatic , but with time it progresses to the chronic phase , affecting the heart and gastroi...	Chagas disease , caused by the protozoan Trypanosoma cruzi , affects more than 10 million people in Latin America . In the chronic phase , a lethal complication may develop: Chronic Chagasic Cardiomyopathy . In this condition the vascular lining , the endothelium , is involved and participates in disease progression . ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Simvastatin and Benznidazole-Mediated Prevention of Trypanosoma cruzi-Induced Endothelial Activation: Role of 15-epi-lipoxin A4 in the Action of Simvastatin
Over long timescales , neuronal dynamics can be robust to quite large perturbations , such as changes in white matter connectivity and grey matter structure through processes including learning , aging , development and certain disease processes . One possible explanation is that robust dynamics are facilitated by home...	Recently there has been much interest in investigating the role of synaptic plasticity in supporting healthy brain activity . In particular , the balance between excitation and inhibition in the brain is believed to play a critical role in brain dynamics , and it is likely that this balance is regulated by homeostatic ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "diagnostic", "radiology", "functional", "magnetic", "resonance", "imaging", "neural", "networks", "nervous", "system", "homeostatic", "mechanisms", "neuroscience", "magnetic", "resonance", "imaging", "simulation", "and", "modeling...	2018	A biophysical model of dynamic balancing of excitation and inhibition in fast oscillatory large-scale networks
Studies of the 1918 H1N1 influenza pandemic , the H5N1 avian influenza outbreak , and the 2009 H1N1 pandemic illustrate that sex and pregnancy contribute to severe outcome from infection , suggesting a role for sex steroids . To test the hypothesis that the sexes respond differently to influenza , the pathogenesis of i...	Sex and pregnancy affect the outcome of infection with seasonal , avian , and pandemic influenza viruses among young adults . Males and females are biologically different , yet the implications of these differences on influenza A virus pathogenesis are not well characterized . Generally , females mount more robust immu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunopathology", "virology", "immunology", "biology", "microbiology", "immune", "response" ]	2011	Elevated 17β-Estradiol Protects Females from Influenza A Virus Pathogenesis by Suppressing Inflammatory Responses
Bacterial chemotaxis is one of the best studied signal transduction pathways . CheW is a scaffold protein that mediates the association of the chemoreceptors and the CheA kinase in a ternary signaling complex . The effects of replacing conserved Arg62 of CheW with other residues suggested that the scaffold protein play...	Signal transduction is a universal biological process and a common target of drug design . The chemotaxis machinery in Escherichia coli is a model signal transduction system , and the CheW protein is one of its core components . CheW is thought to work as a scaffold protein that mediates the formation of the signaling ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2013	Conformational Coupling between Receptor and Kinase Binding Sites through a Conserved Salt Bridge in a Signaling Complex Scaffold Protein
SH3 domains are peptide recognition modules that mediate the assembly of diverse biological complexes . We scanned billions of phage-displayed peptides to map the binding specificities of the SH3 domain family in the budding yeast , Saccharomyces cerevisiae . Although most of the SH3 domains fall into the canonical cla...	Significant diversity exists in protein structure and function , yet certain structural domains are used repeatedly across species to execute similar functions . The SH3 domain is one such common structural domain . It is found in signaling proteins and mediates protein–protein interactions by binding to short peptide ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "computational", "biology/sequence", "motif", "analysis", "biotechnology/protein", "chemistry", "and", "proteomics", "cell", "biology", "computational", "biology/genomics", "computational", "biology", "computational", "biology/systems", "biology" ]	2009	Bayesian Modeling of the Yeast SH3 Domain Interactome Predicts Spatiotemporal Dynamics of Endocytosis Proteins
The HMT3522 progression series of human breast cells have been used to discover how tissue architecture , microenvironment and signaling molecules affect breast cell growth and behaviors . However , much remains to be elucidated about malignant and phenotypic reversion behaviors of the HMT3522-T4-2 cells of this series...	The HMT3522 isogenic human breast cancer progression series has been used to study the effect of various drugs on the reversion of the breast cancer cells . Despite significant efforts to delineate key signaling events responsible for phenotypic reversion of the malignant HMT3522-T4-2 ( T4-2 ) breast cells in this seri...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computer", "applications", "algorithms", "systems", "biology", "computer", "and", "information", "sciences", "computer", "modeling", "mathematics", "cell", "biology", "applied", "mathematics", "biology", "and", "life", "sciences", "physical", "sciences", "computational",...	2014	Network Analysis of Breast Cancer Progression and Reversal Using a Tree-Evolving Network Algorithm
Genetic association studies , in particular the genome-wide association study ( GWAS ) design , have provided a wealth of novel insights into the aetiology of a wide range of human diseases and traits , in particular cardiovascular diseases and lipid biomarkers . The next challenge consists of understanding the molecul...	Genome-wide association studies ( GWAS ) have found a large number of genetic regions ( “loci” ) affecting clinical end-points and phenotypes , many outside coding intervals . One approach to understanding the biological basis of these associations has been to explore whether GWAS signals from intermediate cellular phe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computer", "applications", "computer", "and", "information", "sciences", "web-based", "applications", "medicine", "and", "health", "sciences", "clinical", "medicine", "genetics", "biology", "and", "life", "sciences", "population", "biology", "cardiology" ]	2014	Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics
New systems genetics approaches are needed to rapidly identify host genes and genetic networks that regulate complex disease outcomes . Using genetically diverse animals from incipient lines of the Collaborative Cross mouse panel , we demonstrate a greatly expanded range of phenotypes relative to classical mouse models...	New emerging pathogens are a significant threat to human health with at least six highly pathogenic viruses , including four respiratory viruses , having spread from animal hosts into the human population within the past 15 years . With the emergence of new pathogens , new and better animal models are needed in order t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Genome Wide Identification of SARS-CoV Susceptibility Loci Using the Collaborative Cross
Discrete clusters of circadian clock neurons temporally organize daily behaviors such as sleep and wake . In Drosophila , a network of just 150 neurons drives two peaks of timed activity in the morning and evening . A subset of these neurons expresses the neuropeptide pigment dispersing factor ( PDF ) , which is import...	Animals depend on being awake at the right time of day to find food and mates and fend off predators . Circadian pacemaker neurons in the brain play a crucial role in timing of specific behaviors to the appropriate times of day . These neurons are further specialized to those primarily responsible for morning and eveni...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/neuronal", "and", "glial", "cell", "biology", "genetics", "and", "genomics/animal", "genetics", "neuroscience", "mental", "health/sleep", "disorders", "cell", "biology/gene", "expression" ]	2009	The Neuropeptide PDF Acts Directly on Evening Pacemaker Neurons to Regulate Multiple Features of Circadian Behavior
Vasopressin neurons generate distinctive phasic patterned spike activity in response to elevated extracellular osmotic pressure . These spikes are generated in the cell body and are conducted down the axon to the axonal terminals where they trigger Ca2+ entry and subsequent exocytosis of hormone-containing vesicles and...	Vasopressin is a hormone that is secreted from specialised brain cells into the bloodstream; it acts at the kidneys to control water excretion , and thereby help to maintain a stable ‘osmotic pressure’ . Specialised cells in the brain sense osmotic pressure , and generate electrical signals which the thousands of vasop...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "neurophysiology", "homeostatic", "mechanisms", "computational", "neuroscience", "single", "neuron", "function", "endocrine", "system", "biology", "anatomy", "and", "physiology", "neuroendocrinology", "neuroscience", "computational", "biology", "coding", "mechanisms", "endocr...	2013	Spike Triggered Hormone Secretion in Vasopressin Cells; a Model Investigation of Mechanism and Heterogeneous Population Function
Complex traits such as obesity are manifestations of intricate interactions of multiple genetic factors . However , such relationships are difficult to identify . Thanks to the recent advance in high-throughput technology , a large amount of data has been collected for various complex traits , including obesity . These...	Obesity has become a perilous global epidemic that can lead to complex diseases , such as diabetes and cardiovascular diseases . Much effort has been devoted to the studies of the genetic mechanisms that pillow the manifestation of obesity . Although a large quantity of experimental data has been accumulated lately usi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "biology", "computational", "biology" ]	2013	Integrative Analysis Using Module-Guided Random Forests Reveals Correlated Genetic Factors Related to Mouse Weight
While some human-specific protein-coding genes have been proposed to originate from ancestral lncRNAs , the transition process remains poorly understood . Here we identified 64 hominoid-specific de novo genes and report a mechanism for the origination of functional de novo proteins from ancestral lncRNAs with precise s...	Although gene duplication has been believed as a predominant mechanism for creating new genes , recent reports suggested that new proteins could evolve “de novo” from non-coding DNA regions . These de novo genes are also named as “motherless” genes due to their lack of ancestral proteins as precursors , while recently ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Emergence, Retention and Selection: A Trilogy of Origination for Functional De Novo Proteins from Ancestral LncRNAs in Primates
The study aimed to determine costs to the state government of implementing different interventions for controlling rabies among the entire human and animal populations of Tamil Nadu . This built upon an earlier assessment of Tamil Nadu's efforts to control rabies . Anti-rabies vaccines were made available at all health...	Rabies is a fatal viral disease . It is transmitted mostly through dog bites in greater parts of Asia and Africa . It is primarily a disease of the poorer population groups with children being the most vulnerable . Control of rabies among humans therefore requires interventions in the animal as well as the human sector...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "rabies", "socioeconomic", "aspects", "of", "health", "disease", "ecology", "social", "and", "behavioral", "sciences", "economic", "models", "health", "economics", "veterinary", "diseases", "cost", "models", "global", "health", "z...	2014	Costs Analysis of a Population Level Rabies Control Programme in Tamil Nadu, India
Previous studies have demonstrated that Marburg viruses ( MARV ) and Ebola viruses ( EBOV ) inhibit interferon ( IFN ) -α/β signaling but utilize different mechanisms . EBOV inhibits IFN signaling via its VP24 protein which blocks the nuclear accumulation of tyrosine phosphorylated STAT1 . In contrast , MARV infection ...	The closely related members of the filovirus family , Ebola virus ( EBOV ) and Marburg virus ( MARV ) , cause severe hemorrhagic disease in humans with high fatality rates . Infected individuals exhibit dysregulated immune responses which appear to result from several factors , including virus-mediated impairment of in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/emerging", "viral", "diseases", "virology", "infectious", "diseases/viral", "infections", "immunology/innate", "immunity", "virology/immune", "evasion", "virology/host", "antiviral", "responses" ]	2010	Marburg Virus Evades Interferon Responses by a Mechanism Distinct from Ebola Virus
Overexpression of the xenotoxin transporter P-glycoprotein ( P-gp ) represents one major reason for the development of multidrug resistance ( MDR ) , leading to the failure of antibiotic and cancer therapies . Inhibitors of P-gp have thus been advocated as promising candidates for overcoming the problem of MDR . Howeve...	A major reason for the failure of cancer , antibiotic and antiviral therapies is the development of multidrug resistance ( MDR ) . P-glycoprotein ( P-gp ) , an ATP-dependent transport protein located in the membrane of epithelial cells of the kidney , liver , pancreas , colon and the blood-brain barrier , has been link...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computer", "applications", "medicine", "medicinal", "chemistry", "drugs", "and", "devices", "small", "molecules", "computer-aided", "design", "protein", "structure", "pharmacology", "proteins", "chemistry", "biology", "drug", "discovery", "biochemistry", "computer", "sci...	2011	Exhaustive Sampling of Docking Poses Reveals Binding Hypotheses for Propafenone Type Inhibitors of P-Glycoprotein
Borrelia burgdorferi , the bacterial pathogen of Lyme borreliosis , differentially expresses select genes in vivo , likely contributing to microbial persistence and disease . Expression analysis of spirochete genes encoding potential membrane proteins showed that surface-located membrane protein 1 ( lmp1 ) transcripts ...	The pathogen of Lyme borreliosis , Borrelia burgdorferi , causes disease in many parts of the world , resulting in multi-system complications in infected humans and animals . The microbe produces certain antigens in response to host environments that potentially allow it to persist and cause disease . Here , we analyze...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/immunity", "to", "infections", "microbiology", "infectious", "diseases/bacterial", "infections", "molecular", "biology", "microbiology/cellular", "microbiology", "and", "pathogenesis" ]	2009	A Chromosomally Encoded Virulence Factor Protects the Lyme Disease Pathogen against Host-Adaptive Immunity
Once considered a phenotypically monomorphic bacterium , there is a growing body of work demonstrating heterogeneity among Mycobacterium tuberculosis ( Mtb ) strains in clinically relevant characteristics , including virulence and response to antibiotics . However , the genetic and molecular basis for most phenotypic d...	Tuberculosis , caused by the bacterium Mycobacterium tuberculosis ( Mtb ) , remains a serious global health problem , causing ~1 . 5 million deaths a year world-wide . Like other bacterial pathogens , diversity among strains of Mtb contributes to differences in infection outcomes , vaccine efficacy , and response to an...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "transposon", "mutagenesis", "drugs", "microbiology", "antibiotic", "resistance", "antibiotics", "genome", "analysis", "genetic", "elements", "pharmacology", "molecular", "biology", "techniques", "mutagenesis", "and...	2018	TnSeq of Mycobacterium tuberculosis clinical isolates reveals strain-specific antibiotic liabilities
Identification of dengue patients at risk for progressing to severe disease is difficult . Significant plasma leakage is a hallmark of severe dengue infection which can suddenly lead to hypovolemic shock around the time of defervescence . We hypothesized that the detection of subclinical plasma leakage may identify tho...	Dengue virus infection ranges from a mild febrile illness to severe illness . Severe dengue is mainly characterized by transient plasma leakage , which may lead to a sudden onset of shock around the time of defervescence . Severe bleeding and organ impairment are less common features of severe dengue . In clinical prac...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "neglected", "tropical", "diseases", "infectious", "diseases", "dengue", "fever" ]	2013	The Predictive Diagnostic Value of Serial Daily Bedside Ultrasonography for Severe Dengue in Indonesian Adults
The dynamics of the memory CD8 T cell receptor ( TCR ) repertoire upon virus re-exposure and factors governing the selection of TCR clonotypes conferring protective immunity in real life settings are poorly understood . Here , we examined the dynamics and functionality of the virus-specific memory CD8 TCR repertoire be...	In this study we examined the diversity and dynamics of the repertoire of receptors of CD8 T cells that are selected and enriched upon real-life multiple exposures to viral infections . Using hepatitis C virus ( HCV ) infection in a cohort of high risk people who inject drugs , we demonstrate that protection upon two s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "hepacivirus", "pathogens", "immunology", "microbiology", "cloning", "viruses", "rna", "viruses", "cytotoxic", "t", "cells", "molecular", "biolo...	2017	Selective expansion of high functional avidity memory CD8 T cell clonotypes during hepatitis C virus reinfection and clearance
Aedes aegypti , the ‘yellow fever mosquito’ , is the primary vector to humans of dengue and yellow fever flaviviruses ( DENV , YFV ) , and is a known vector of the chikungunya alphavirus ( CV ) . Because vaccines are not yet available for DENV or CV or are inadequately distributed in developing countries ( YFV ) , mana...	Pyrethroid insecticides prolong the opening of voltage-dependent sodium channels in insect nerves to produce instant paralysis and “knock-down . ” Many insects have evolved knock-down resistance through nonsynonymous mutations that reduce pyrethroid binding in the channels . In 2006 we discovered one such mutation in t...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/viral", "infections", "genetics", "and", "genomics/gene", "function", "public", "health", "and", "epidemiology/infectious", "diseases", "infectious", "diseases/tropical", "and", "travel-associated", "diseases", "genetics", "and", "genomics/population", ...	2009	Recent Rapid Rise of a Permethrin Knock Down Resistance Allele in Aedes aegypti in México
Integrative and conjugative elements ( ICEs ) are agents of horizontal gene transfer and have major roles in evolution and acquisition of new traits , including antibiotic resistances . ICEs are found integrated in a host chromosome and can excise and transfer to recipient bacteria via conjugation . Conjugation involve...	Integrative and conjugative elements ( ICEs ) are mobile DNA elements that transfer genetic material between bacteria , driving bacterial evolution and the acquisition of new traits , including the spread of antibiotic resistances . ICEs typically reside integrated in a bacterial chromosome and are passively propagated...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2013	A Conserved Helicase Processivity Factor Is Needed for Conjugation and Replication of an Integrative and Conjugative Element
Chikungunya virus ( CHIKV ) is the most common alphavirus infecting humans worldwide , causing acute and chronically debilitating arthralgia at a great economic expense . To facilitate our study of CHIKV , we generated a mCherry tagged replication-competent chimeric virus , CHIKV 37997-mCherry . Single particle cryoEM ...	Chikungunya virus ( CHIKV ) is an alphavirus capable of causing long term debilitating joint and muscle pain at a great economic expense . Currently there are no licensed vaccines or treatment for CHIKV infection . We generated a modified version of the virus , termed CHIKV 37997-mCherry , stably expressing a fluoresce...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "pathogens", "immunology", "tropical", "diseases", "microbiology", "alphaviruses", "vir...	2018	An attenuated replication-competent chikungunya virus with a fluorescently tagged envelope
In this study , a Burkholderia mallei tonB mutant ( TMM001 ) deficient in iron acquisition was constructed , characterized , and evaluated for its protective properties in acute inhalational infection models of murine glanders and melioidosis . Compared to the wild-type , TMM001 exhibits slower growth kinetics , sidero...	Burkholderia mallei and B . pseudomallei are the causative agents of glanders and melioidosis , respectively . In addition to the recent rise in cases of glanders and the endemicity of melioidosis worldwide , these pathogens have gained attention as potential bioweapons . Further , these pathogens have huge potential f...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Characterization of the Burkholderia mallei tonB Mutant and Its Potential as a Backbone Strain for Vaccine Development
Type IV pili are expressed by a wide range of prokaryotes , including the opportunistic pathogen Pseudomonas aeruginosa . These flexible fibres mediate twitching motility , biofilm maturation , surface adhesion , and virulence . The pilus is composed mainly of major pilin subunits while the low abundance minor pilins F...	Pseudomonas aeruginosa causes dangerous infections , including chronic lung infections in cystic fibrosis patients . It uses many strategies to infect its hosts , including deployment of grappling hook-like fibres called type IV pili . Among the components involved in assembly and function of the pilus are five protein...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "bacteriology", "biofilms", "invertebrates", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "caenorhabditis", "pathogens", "microbiology", "operons", "animals", "pseudomonas", "aeruginosa", "animal", "models", "caenorhabditis", "elega...	2018	Pseudomonas aeruginosa type IV minor pilins and PilY1 regulate virulence by modulating FimS-AlgR activity
Many everyday estimation tasks have an inherently discrete nature , whether the task is counting objects ( e . g . , a number of paint buckets ) or estimating discretized continuous variables ( e . g . , the number of paint buckets needed to paint a room ) . While Bayesian inference is often used for modeling estimates...	Studies of human perception and decision making have traditionally focused on scenarios where participants have to make estimates about continuous variables . However discrete variables are also common in our environment , potentially requiring different theoretical models . We describe ways to model such scenarios wit...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "learning", "decision", "theory", "statistical", "noise", "decision", "making", "applied", "mathematics", "social", "sciences", "neuroscience", "learning", "and", "memory", "kernel", "functions", "cognitive", "psychology", "mathematics", "probability", "distribution", "st...	2016	Fast and Accurate Learning When Making Discrete Numerical Estimates
The host response to dengue virus infection is characterized by the production of numerous cytokines , but the overall picture appears to be complex . It has been suggested that a balance may be involved between protective and pathologic immune responses . This study aimed to define differential immune responses in ass...	Dengue virus infection is an impressively emerging disease that can be fatal in severe cases . It is not precisely clear why some patients progress to severe disease whereas most patients only suffer from a mild infection . In severe disease , a “cytokine storm” is induced , which indicates the release of a great numbe...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "critical", "care", "and", "emergency", "medicine/pediatric", "critical", "care", "pediatrics", "and", "child", "health/pediatric", "critical", "care", "microbiology/immunity", "to", "infections", "genetics", "and", "genomics/gene", "expression", "infectious", "diseases/neg...	2008	Differential Gene Expression Changes in Children with Severe Dengue Virus Infections
Helminth parasites can cause considerable damage when migrating through host tissues , thus making rapid tissue repair imperative to prevent bleeding and bacterial dissemination particularly during enteric infection . However , how protective type 2 responses targeted against these tissue-disruptive multicellular paras...	To complete their lifecycles , helminth parasites have to migrate through tissues such as the skin , lung , liver and intestine . This migration causes severe tissue damage , resulting in the need for rapid repair to restore the integrity and function of damaged tissues . Protective type 2 immune responses against helm...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Immune Antibodies and Helminth Products Drive CXCR2-Dependent Macrophage-Myofibroblast Crosstalk to Promote Intestinal Repair
HIV virions assemble on the plasma membrane and bud out of infected cells using interactions with endosomal sorting complexes required for transport ( ESCRTs ) . HIV protease activation is essential for maturation and infectivity of progeny virions , however , the precise timing of protease activation and its relations...	ESCRTs are implicated in cellular processes which require fission of budding membranes . Likely the most studied of these processes is the HIV-ESCRT interactions . The canonical view is that interference with ESCRT recruitment results in a late budding arrest of virions at the plasma membrane and this mechanistic view ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "transfection", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "enzymes", "pathogens", "293t", "cells", "biological", "cultures", "microbiology", "enzymology", "viral", "structure", "retroviruses", "viruses", "immunodeficiency", "vi...	2016	The Race against Protease Activation Defines the Role of ESCRTs in HIV Budding
Actin is an abundant protein that constitutes a main component of the eukaryotic cytoskeleton . Its polymerization and depolymerization are regulated by a variety of actin-binding proteins . Their functions range from nucleation of actin polymerization to sequestering G-actin in 1∶1 complexes . The kinetics of forming ...	Actin polymerization and depolymerization drive cell motility and are regulated by a variety of actin-binding proteins . The widely-varying rate constants ( ka ) of the actin-binding proteins associating with G-actin , spanning at least three orders of magnitude , appear to be tuned for their distinct regulatory functi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biomacromolecule-ligand", "interactions", "cell", "motility", "macromolecular", "assemblies", "biophysics", "theory", "biology", "biophysics", "simulations", "biophysics" ]	2012	Prediction and Dissection of Widely-Varying Association Rate Constants of Actin-Binding Proteins
Rift Valley fever virus ( RVFV ) , a Phlebovirus with a genome consisting of three single-stranded RNA segments , is spread by infected mosquitoes and causes large viral outbreaks in Africa . RVFV encodes a nucleoprotein ( N ) that encapsidates the viral RNA . The N protein is the major component of the ribonucleoprote...	The Rift Valley fever virus ( RVFV ) , a negative strand RNA virus spread by infected mosquitoes , affects livestock and humans who can develop a severe disease . We studied the structure of its nucleoprotein ( N ) , which forms a filamentous coat that protects the viral RNA genome and is also required for RNA replicat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biomacromolecule-ligand", "interactions", "medicine", "macromolecular", "assemblies", "microbiology", "protein", "folding", "protein", "structure", "infectious", "diseases", "biology", "biophysics", "macromolecular", "complex", "analysis", "virology", "viral", "diseases", "c...	2011	The Hexamer Structure of the Rift Valley Fever Virus Nucleoprotein Suggests a Mechanism for its Assembly into Ribonucleoprotein Complexes
The somatic genome of the ciliated protist Tetrahymena undergoes DNA elimination of defined sequences called internal eliminated sequences ( IESs ) , which account for ∼30% of the germline genome . During DNA elimination , IES regions are heterochromatinized and assembled into heterochromatin bodies in the developing s...	Transposons are not just threats to genome integrity but also potentially contribute to the evolution of the host . Therefore , host organisms must evolve by balancing the harmfulness and usefulness of transposons . An evolutional product likely created by such a balance is the programmed DNA elimination in the ciliate...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	A Domesticated PiggyBac Transposase Interacts with Heterochromatin and Catalyzes Reproducible DNA Elimination in Tetrahymena

Subsets and Splits

No community queries yet

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