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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
Many disease-susceptible SNPs exhibit significant disparity in ancestral and derived allele frequencies across worldwide populations . While previous studies have examined population differentiation of alleles at specific SNPs , global ethnic patterns of ensembles of disease risk alleles across human diseases are unexa...	We identified 12 risk alleles that had been validated to increase the risk of type 2 diabetes ( T2D ) in five or more different subpopulations . These risk alleles share a consistent pattern of decreasing frequencies in the human genomes from Sub-Saharan Africa and through Europe to East Asia regions . These differenti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "public", "health", "and", "epidemiology", "statistics", "population", "genetics", "algorithms", "genome", "analysis", "tools", "genome", "databases", "mathematics", "epidemiology", "biology", "metabolic", "disorders", "computer", "science", "genetics", "genom...	2012	Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases
CD4+ and CD8+ T cells are central players in immunity to helminth infections . However , the role of T cell subsets in human helminth infections is not well understood . In addition , the common γc cytokines , IL-2 , IL-4 , IL-7 , IL-9 and IL-15 play an important role in the maintenance of these CD4+ and CD8+ T cell su...	Strongyloides stercoralis ( Ss ) , an intestinal nematode , the causative agent of strongyloidiasis , infects 30–100 million people worldwide . Ss infection is often clinically asymptomatic and long lasting due , in large part , to the parasites auto-infective life cycle and their ability to modulate the host immune sy...	[ "Abstract", "Introduction", "Material", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "cytokines", "immunology", "parasitic", "diseases", "nematode", "infections", "developmental", "biology", "molecular", "development", "cyt...	2018	Altered levels of memory T cell subsets and common γc cytokines in Strongyloides stercoralis infection and partial reversal following anthelmintic treatment
Estrogen receptors ( ER ) are important regulators of metabolic diseases such as obesity and insulin resistance ( IR ) . While ERα seems to have a protective role in such diseases , the function of ERβ is not clear . To characterize the metabolic function of ERβ , we investigated its molecular interaction with a master...	In the present study , we demonstrate for the first time a pro-diabetogenic function of the ERβ . Our experiments indicate that ERβ impairs insulin sensitivity and glucose tolerance in mice challenged with a high fat diet ( HFD ) . Loss of ERβ , studied in ERβ -/- mice ( βERKO mice ) , results in increased body weight ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "cell", "biology/cell", "signaling", "physiology", "diabetes", "and", "endocrinology/obesity", "physiology/endocrinology", "pharmacology", "diabetes", "and", "endocrinology", "biochemistry/transcription", "and", "translation", "molecular", "biology", "cell", "bi...	2008	Metabolic Actions of Estrogen Receptor Beta (ERβ) are Mediated by a Negative Cross-Talk with PPARγ
Signaling pathways mediate the effect of external stimuli on gene expression in cells . The signaling proteins in these pathways interact with each other and their phosphorylation levels often serve as indicators for the activity of signaling pathways . Several signaling pathways have been identified in mammalian cells...	Cellular systems are dynamic in nature , perform various biological functions and can adapt to their environment through compositional and structural remodeling . This remodeling is initiated by the binding of external ligands to receptor proteins on the cell surface or other stimuli resulting in the activation of vari...	[ "Abstract", "Introduction", "Results", "Materials", "and", "Methods" ]	[ "molecular", "biology/bioinformatics", "mathematics/statistics", "computational", "biology/systems", "biology", "computational", "biology/signaling", "networks" ]	2010	Identification of Crosstalk between Phosphoprotein Signaling Pathways in RAW 264.7 Macrophage Cells
Single nucleotide polymorphisms ( SNPs ) on chromosome 9p21 are associated with coronary artery disease , diabetes , and multiple cancers . Risk SNPs are mainly non-coding , suggesting that they influence expression and may act in cis . We examined the association between 56 SNPs in this region and peripheral blood exp...	Genetic variants on chromosome 9p21 have been associated with several important diseases including coronary artery disease , diabetes , and multiple cancers . Most of the risk variants in this region do not alter any protein sequence and are therefore likely to act by influencing the expression of nearby genes . We inv...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cardiovascular", "disorders/coronary", "artery", "disease", "genetics", "and", "genomics/complex", "traits", "genetics", "and", "genomics/cancer", "genetics", "genetics", "and", "genomics/gene", "expression" ]	2010	Chromosome 9p21 SNPs Associated with Multiple Disease Phenotypes Correlate with ANRIL Expression
Outbreaks of H5N1 in poultry in Vietnam continue to threaten the livelihoods of those reliant on poultry production whilst simultaneously posing a severe public health risk given the high mortality associated with human infection . Authorities have invested significant resources in order to control these outbreaks . Of...	Highly pathogenic avian influenza H5N1 continues to spread rapidly between flocks of poultry in many parts of the world including areas in Southeast Asia and Africa where infection has become endemic . Meanwhile the number of human cases and fatalities are steadily accumulating . As a result , the control of outbreaks ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "public", "health", "and", "epidemiology/global", "health", "public", "health", "and", "epidemiology/infectious", "diseases", "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases" ]	2010	A Bayesian Approach to Quantifying the Effects of Mass Poultry Vaccination upon the Spatial and Temporal Dynamics of H5N1 in Northern Vietnam
Triggering receptor expressed on myeloid cells ( TREM ) -1 and TREM-2 are key regulators of the inflammatory response that are involved in the clearance of invading pathogens . Melioidosis , caused by the "Tier 1" biothreat agent Burkholderia pseudomallei , is a common form of community-acquired sepsis in Southeast-Asi...	Triggering receptor expressed on myeloid cells ( TREM ) -1 and -2 are receptors on immune cells that act as mediators of the innate immune response . It is thought that TREM-1 amplifies the immune response , while TREM-2 acts as a negative regulator . Previously , we found that TREM-1 is upregulated in melioidosis pati...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "body", "fluids", "immune", "cells", "pathology", "and", "laboratory", "medicine", "melioidosis", "immunology", "cell", "processes", "animal", "models", "bacterial", "diseases", "sepsis", "model", "organisms",...	2016	Triggering Receptor Expressed on Myeloid Cells (TREM)-2 Impairs Host Defense in Experimental Melioidosis
In the human neocortex , single excitatory pyramidal cells can elicit very large glutamatergic EPSPs ( VLEs ) in inhibitory GABAergic interneurons capable of triggering their firing with short ( 3–5 ms ) delay . Similar strong excitatory connections between two individual neurons have not been found in nonhuman cortice...	Many microscale features in the human neocortex—a part of the brain involved in higher functions such as sensory perception , generation of motor commands , spatial reasoning , and language—are closely similar to those reported in experimental animals commonly used in neuroscience , like mice . However , the human neoc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "action", "potentials", "nervous", "system", "membrane", "potential", "brain", "electrophysiology", "neuroscience", "synaptic", "plasticity", "nerve", "fibers", "interneurons", "excitatory", "postsynaptic", "potentials", "development...	2016	Plasticity in Single Axon Glutamatergic Connection to GABAergic Interneurons Regulates Complex Events in the Human Neocortex
Red light promotes germination after activating phytochrome phyB , which destabilizes the germination repressor PIF1 . Early upon seed imbibition , canopy light , unfavorable for photosynthesis , represses germination by stabilizing PIF1 after inactivating phyB . Paradoxically , later upon imbibition , canopy light sti...	Canopy light , unfavorable for photosynthesis , elicits paradoxical responses in seeds . Depending on the timing of irradiation upon seed imbibition , canopy light can either block or promote germination . The promotion effect is mediated by the light sensor phyA and , intriguingly , it is poorly efficient when compare...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "plant", "anatomy", "oxidative", "stress", "brassica", "light", "plant", "physiology", "electromagnetic", "radiation", "plant", "science", "model", "organisms", "experimental", "organism", "systems", "seedlings", "plants", "research", "and", "analysis", "methods", "arab...	2019	polyamine uptake transporter 2 (put2) and decaying seeds enhance phyA-mediated germination by overcoming PIF1 repression of germination
Mating-type switching in Schizosaccharomyces pombe entails programmed gene conversion events regulated by DNA replication , heterochromatin , and the HP1-like chromodomain protein Swi6 . The whole mechanism remains to be fully understood . Using a gene deletion library , we screened ~ 3400 mutants for defects in the do...	Effects of chromatin structure on recombination can be studied in the fission yeast S . pombe where two heterochromatic loci , mat2 and mat3 , are chosen in a cell-type specific manner to convert the expressed mat1 locus and switch the yeast mating-type . The system has previously revealed the determining role of heter...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "molecular", "probe", "techniques", "dna-binding", "proteins", "organisms", "fungi", "model", "organisms", "experimental", "organism", "systems", "molecular", "biology", "techniques", "epigenetics", "gel", "electrophoresis", "chromatin", "schizosaccharomyces", "heterochromati...	2018	New insights into donor directionality of mating-type switching in Schizosaccharomyces pombe
Countries have traditionally been split into two major groups: developed or industrialized ( “the North” ) and developing or underdeveloped ( “the South” ) . Several authors and organizations have challenged this classification to recognize countries that have reached an intermediate stage of social and economic develo...	Splitting countries into two groups—rich and poor; developed ( the “North” ) and developing ( the “South” ) ; leaders and followers—appears to us to be progressively more simplistic , unrealistic and a heritage from colonial times . Triggered by the first wave of globalization , the share of world income going to today...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "china", "economic", "analysis", "pathogens", "tropical", "diseases", "geographical", "locations", "microbiology", "social", "sciences", "viruses", "rna", "viruses", "network", "analy...	2018	Revisiting the concept of Innovative Developing Countries (IDCs) for its relevance to health innovation and neglected tropical diseases and for the prevention and control of epidemics
Chronic human immunodeficiency virus-1 ( HIV-1 ) infection in patients leads to multi-lineage hematopoietic abnormalities or pancytopenia . The deficiency in hematopoietic progenitor cells ( HPCs ) induced by HIV-1 infection has been proposed , but the relevant mechanisms are poorly understood . We report here that bot...	Multi-lineage hematopoietic abnormalities generally occur during chronic infection which results in a disorder of human leukocyte development and differentiation , contributing to human immunodeficiency virus-1 ( HIV-1 ) -infection induced immune-pathogenesis in AIDS patients . Although successful antiretroviral therap...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "flow", "cytometry", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "animal", "models", "of", "disease", "immunology", "microbiology", "retroviruses", "viruses", "immunodeficiency"...	2017	HIV-1 infection depletes human CD34+CD38- hematopoietic progenitor cells via pDC-dependent mechanisms
Transformation is an important mechanism of microbial evolution through which bacteria have been observed to rapidly adapt in response to clinical interventions; examples include facilitating vaccine evasion and the development of penicillin resistance in the major respiratory pathogen Streptococcus pneumoniae . To cha...	Transformation is the process by which cells take up DNA from the environment and integrate it into their genome . It was first observed in the bacterium Streptococcus pneumoniae , a common cause of pneumonia and meningitis . This ability has allowed S . pneumoniae to evolve resistance to penicillin and to change its s...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome", "sequencing", "genomics", "genome", "evolution", "chromosome", "biology", "genetics", "population", "genetics", "biology", "evolutionary", "biology", "genomic", "evolution", "evolutionary", "genetics", "genetics", "and", "genomics" ]	2012	A High-Resolution View of Genome-Wide Pneumococcal Transformation
Glucose is the main energy substrate in the adult brain under normal conditions . Accumulating evidence , however , indicates that lactate produced in astrocytes ( a type of glial cell ) can also fuel neuronal activity . The quantitative aspects of this so-called astrocyte-neuron lactate shuttle ( ANLS ) are still deba...	The brain has remarkable information processing capacity , yet is also very energy efficient . How this metabolic efficiency is achieved given the spatial and metabolic constraints inherent to the designs and energy requirements of brain cells is a fundamental question in neurobiology . The major cell classes in mammal...	[ "Abstract", "Introduction", "Methods", "Discussion" ]	[]	2015	Multi-timescale Modeling of Activity-Dependent Metabolic Coupling in the Neuron-Glia-Vasculature Ensemble
Members of the TRIpartite interaction Motif ( TRIM ) family of E3 ligases have been shown to exhibit antiviral activities . Here we report a near comprehensive screen for antiretroviral activities of 55 TRIM proteins ( 36 human , 19 mouse ) . We identified ∼20 TRIM proteins that , when transiently expressed in HEK293 c...	A lot of excitement in the field of innate immunity to retroviruses such as HIV has come from the discovery of TRIM5 as a key player in cross species restriction . TRIM5 belongs to a family of E3 ligases with over 70 members , a number of which have exhibited antiviral activity . These findings have led to the hypothes...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viruses", "mus", "virology", "in", "vitro", "microbiology", "homo" ]	2008	TRIM E3 Ligases Interfere with Early and Late Stages of the Retroviral Life Cycle
Computational prediction of nucleotide binding specificity for transcription factors remains a fundamental and largely unsolved problem . Determination of binding positions is a prerequisite for research in gene regulation , a major mechanism controlling phenotypic diversity . Furthermore , an accurate determination of...	A historically difficult problem in computational biology is the identification of transcription factor binding sites ( TFBS ) in the promoters of co-regulated genes . With increasing emphasis on research in transcriptional regulation , this problem is also uniquely relevant to emerging results from recent experiments ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mathematics", "saccharomyces", "genetics", "and", "genomics", "computational", "biology" ]	2007	Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites
Human hepatitis B virus ( HBV ) causes chronic hepatitis and is associated with the development of hepatocellular carcinoma . HBV infection alters mitochondrial metabolism . The selective removal of damaged mitochondria is essential for the maintenance of mitochondrial and cellular homeostasis . Here , we report that H...	Hepatitis B virus ( HBV ) chronic infections represent the common cause for the development of hepatocellular carcinoma . Mitochondrial liver injury has been long recognized as one of the consequences of HBV infection during chronic hepatitis . Mitochondria are dynamic organelles that undergo fission , fusion , and sel...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Hepatitis B Virus Disrupts Mitochondrial Dynamics: Induces Fission and Mitophagy to Attenuate Apoptosis
Leptospirosis is a zoonosis caused by highly motile , helically shaped bacteria that penetrate the skin and mucous membranes through lesions or abrasions , and rapidly disseminate throughout the body . Although the intraperitoneal route of infection is widely used to experimentally inoculate hamsters , this challenge r...	Leptospirosis is the most widespread bacterial infection transmitted from animals to man . Humans are exposed to infection when host animals that harbor the bacteria in their kidneys shed them in their urine . Human infections , caused by the bacterium Leptospira interrogans , frequently result in a life-threatening il...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "leptospira", "pathology", "and", "laboratory", "medicine", "medical", "microbiology", "microbial", "pathogens", "pathogens", "biology", "and", "life", "sciences", "leptospira", "interrogans", "microbiology", "bacteria", "bacterial...	2014	Kinetics of Leptospira interrogans Infection in Hamsters after Intradermal and Subcutaneous Challenge
Wolbachia pipientis is a ubiquitous , maternally transmitted bacterium that infects the germline of insect hosts . Estimates are that Wolbachia infect nearly 40% of insect species on the planet , making it the most prevalent infection on Earth . The bacterium , infamous for the reproductive phenotypes it induces in art...	The world’s most common intracellular infection , Wolbachia pipientis , infects 40% of insect species and is currently used to prevent transmission of Dengue by mosquitoes . The bacterium targets the germline of insects , where it is faithfully transmitted to the developing oocyte and the next generation . Here we iden...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Wolbachia Utilize Host Actin for Efficient Maternal Transmission in Drosophila melanogaster
Facioscapulohumeral dystrophy ( FSHD ) is caused by the mis-expression of DUX4 in skeletal muscle cells . DUX4 is a transcription factor that activates genes normally associated with stem cell biology and its mis-expression in FSHD cells results in apoptosis . To identify genes and pathways necessary for DUX4-mediated ...	Facioscapulohumeral dystrophy ( FSHD ) is a common form of muscular dystrophy which is currently untreatable . It is caused by the inappropriate expression in skeletal muscle of the gene DUX4 that encodes a transcription factor normally expressed in some stem cells . When DUX4 is expressed in cultured human or mouse sk...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "cell", "death", "medicine", "and", "health", "sciences", "muscle", "tissue", "gene", "regulation", "cell", "processes", "population", "genetics", "immunology", "gene", "pool", "non-coding", "rna", "stem", "cells", "population", "biology", "small", ...	2017	DUX4-induced dsRNA and MYC mRNA stabilization activate apoptotic pathways in human cell models of facioscapulohumeral dystrophy
Using robust , integrated analysis of multiple genomic datasets , we show that genes depleted for non-synonymous de novo mutations form a subnetwork of 72 members under strong selective constraint . We further show this subnetwork is preferentially expressed in the early development of the human hippocampus and is enri...	Some genes are extremely intolerant of mutations that alter their amino acid sequence . Such mutations are highly likely to drive disease , and previous reports have implicated these genes in multiple diseases . To better understand the function of these constrained genes and their place in cellular organization , we d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "genetic", "networks", "protein", "interactions", "protein", "interaction", "networks", "brain", "mutation", "mathematics", "network", "analysis", "genome", "analysis", "discrete", "mathematics", "combinatorics", "computer", "and",...	2016	Network Analysis of Genome-Wide Selective Constraint Reveals a Gene Network Active in Early Fetal Brain Intolerant of Mutation
The circadian regulatory network is organized in a hierarchical fashion , with a central oscillator in the suprachiasmatic nuclei ( SCN ) orchestrating circadian oscillations in peripheral tissues . The nature of the relationship between central and peripheral oscillators , however , is poorly understood . We used the ...	Circadian rhythms confer adaptive advantage by allowing organisms to anticipate daily rhythms in their environment , such as light and temperature cycles . In mammals , the central circadian time-keeping mechanism resides within the hypothalamus , integrating information from the retina and synchronizing circadian osci...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "biology", "genomics", "neuroscience", "genetics", "and", "genomics" ]	2012	Brain-Specific Rescue of Clock Reveals System-Driven Transcriptional Rhythms in Peripheral Tissue
There is increasing evidence for a connection between DNA replication and the expression of adjacent genes . Therefore , this study addressed the question of whether a herpesvirus origin of replication can be used to activate or increase the expression of adjacent genes . Cell lines carrying an episomal vector , in whi...	All herpesviruses show a precisely regulated gene expression profile , including true-late genes , which are turned on only after the onset of DNA replication . We used this intrinsic viral mechanism to generate a versatile conditional gene expression system that exploits the activity of the murine cytomegalovirus ( MC...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "biotechnology", "medicine", "infectious", "diseases", "model", "organisms", "genetics", "biology", "microbiology", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2012	Cytomegalovirus Replicon-Based Regulation of Gene Expression In Vitro and In Vivo
RNA silencing plays a critical role in plant resistance against viruses . To counteract host defense , plant viruses encode viral suppressors of RNA silencing ( VSRs ) that interfere with the cellular silencing machinery through various mechanisms not always well understood . We examined the role of Mungbean yellow mos...	Plants have developed small RNA ( siRNA ) -mediated post-transcriptional gene silencing as a defense mechanism against viruses . In response , plant viruses encode viral suppressors of RNA silencing ( VSRs ) that can interfere with various steps of the silencing pathway . Mungbean yellow mosaic virus ( MYMV ) is a plan...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "plant", "anatomy", "rna", "interference", "gene", "regulation", "membrane", "proteins", "plant", "science", "plant", "pathology", "epigenetics", "cellular", "structures", "and", "organelles", "small", "interfering", "rnas", "genetic", "interference", "proteins", "gene"...	2018	S‐acylation mediates Mungbean yellow mosaic virus AC4 localization to the plasma membrane and in turns gene silencing suppression
It is widely accepted that transcriptional regulation of eukaryotic genes is intimately coupled to covalent modifications of the underlying chromatin template , and in certain cases the functional consequences of these modifications have been characterized . Here we present evidence that gene activation in the silent h...	The proper regulation of gene expression is of fundamental importance in the maintenance of normal growth and development . Misregulation of genes can lead to such outcomes as cancer , diabetes and neurodegenerative disease . A key step in gene regulation occurs during the transcription of the chromosomal DNA into mess...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology", "chromosome", "biology", "gene", "expression", "genetics", "biology", "and", "life", "sciences", "epigenetics", "chromatin", "dna", "transcription" ]	2014	Uncoupling Transcription from Covalent Histone Modification
Many cellular processes pertinent for viral infection are regulated by the addition of small ubiquitin-like modifiers ( SUMO ) to key regulatory proteins , making SUMOylation an important mechanism by which viruses can commandeer cellular pathways . Epstein-Barr virus ( EBV ) is a master at manipulating of cellular pro...	The functions of many cellular proteins important for anti-viral responses and oncogenesis are controlled by modifications by small ubiquitin-like modifiers ( SUMOs ) . Here we present the first screen of Epstein-Barr virus ( EBV ) proteins for those that can globally alter SUMO modifications of cellular proteins . We ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "293t", "cells", "enzymes", "pathogens", "biological", "cultures", "enzymology", "dna-binding", "proteins", "microbiology", "viral", "structure", "plasmid", "construction", "viruses", ...	2018	A genome-wide screen of Epstein-Barr virus proteins that modulate host SUMOylation identifies a SUMO E3 ligase conserved in herpesviruses
RIG-I-Like Receptors ( RLRs ) sense cytosolic viral RNA to transiently activate type I IFN production . Here , we report that a type I IFN inducible DExD/H helicase , DDX24 , exerts a negative-regulatory effect on RLR function . Expression of DDX24 specifically suppressed RLR activity , while DDX24 loss , which caused ...	Innate immunity is the first and most rapid host defense against virus infection . Viral RNAs , which are generated during RNA virus replication in host cells , can be recognized through RIG-I-Like Receptors ( RLRs ) to transiently produce type I interferon , which further induce abundant interferon stimulated genes ( ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	DDX24 Negatively Regulates Cytosolic RNA-Mediated Innate Immune Signaling
While some evidence supports the beneficial effects of integrating neglected tropical disease ( NTD ) programs to optimize coverage and reduce costs , there is minimal information regarding when or how to effectively operationalize program integration . The lack of systematic analyses of integration experiences and of ...	Neglected tropical diseases are a group of parasitic , viral , and bacterial diseases that are often co-endemic in low resource settings . Five of these diseases ( lymphatic filariasis , onchocerciasis , schistosomiasis , soil transmitted helminths , and trachoma ) are addressed specifically through a method called mas...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "research", "funding", "medicine", "and", "health", "sciences", "tropical", "diseases", "parasitic", "diseases", "health", "care", "bacterial", "diseases", "pharmaceutics", "eye", "diseases", "neglected", "tropical", "diseases", "onchocerciasis", "public", "and", "occup...	2016	Integrated Healthcare Delivery: A Qualitative Research Approach to Identifying and Harmonizing Perspectives of Integrated Neglected Tropical Disease Programs
Various studies showed that chemotherapy can control schistosomiasis morbidity , but association of measures ( water supply , sewage disposal and increase of socioeconomic conditions ) is necessary for transmission control . A survey dealing with socioeconomic conditions , snail survey , contact with natural waters , a...	A clinical-epidemiological reevaluation on schistosomiasis mansoni was performed in 2005 , in the urban area of a little town , Comercinho , MG , specifically focusing on the inhabitants of the same area in 1981 , when a first survey and treatment with oxamniquine were carried out . The surveys included: identification...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology/epidemiology", "infectious", "diseases/helminth", "infections", "public", "health", "and", "epidemiology/infectious", "diseases" ]	2011	Evaluation of a 25-Year-Program for the Control of Schistosomiasis Mansoni in an Endemic Area in Brazil
Sequencing of whole tumor genomes holds the promise of revealing functional somatic regulatory mutations , such as those described in the TERT promoter . Recurrent promoter mutations have been identified in many additional genes and appear to be particularly common in melanoma , but convincing functional data such as i...	Cancer is caused by somatic mutations that alter cell behavior . While such mutations typically occur in protein-coding genes , recent studies describe individual positions in gene regulatory regions ( promoters ) that are recurrently mutated in many independent tumors . This suggests that positive selection could be a...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "&", "methods" ]	[ "cancer", "genomics", "medicine", "and", "health", "sciences", "computational", "biology", "cancers", "and", "neoplasms", "basic", "cancer", "research", "oncology", "mutation", "genome", "analysis", "sequence", "motif", "analysis", "mutation", "databases", "frameshift",...	2017	Recurrent promoter mutations in melanoma are defined by an extended context-specific mutational signature
The contemporary proteinogenic repertoire contains 20 amino acids with diverse functional groups and side chain geometries . Primordial proteins , in contrast , were presumably constructed from a subset of these building blocks . Subsequent expansion of the proteinogenic alphabet would have enhanced their capabilities ...	Proteins are linear polymers of a set of typically 20 different amino acid building blocks . The amino acid sequence—encoded by a genetic template—directs the folding of newly synthesized proteins into compact 3D structures and dictates the function of the protein product . Monomers containing distinct physico-chemical...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry", "forms", "of", "evolution", "directed", "evolution", "evolutionary", "biology", "chemical", "biology", "biology" ]	2013	Directed Evolution of a Model Primordial Enzyme Provides Insights into the Development of the Genetic Code
Regulatory networks have evolved to allow gene expression to rapidly track changes in the environment as well as to buffer perturbations and maintain cellular homeostasis in the absence of change . Theoretical work and empirical investigation in Escherichia coli have shown that negative autoregulation confers both rapi...	All genes have to deal with intrinsic noise , and a variety of mechanisms have evolved to reduce it . One important mechanism of noise reduction for transcription factors is negative autoregulation , in which a gene product represses its own rate of transcription . Negative auotregulation occurs frequently in E . coli ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biology", "evolutionary", "biology" ]	2013	Under-Dominance Constrains the Evolution of Negative Autoregulation in Diploids
Herpesvirus latency is generally thought to be governed by epigenetic modifications , but the dynamics of viral chromatin at early timepoints of latent infection are poorly understood . Here , we report a comprehensive spatial and temporal analysis of DNA methylation and histone modifications during latent infection wi...	A characteristic feature of herpesviruses is their ability to establish a latent infection during which most of the viral genes are silenced . As a consequence , no viral progeny is produced and the host cell remains viable . While the viral genome may persist in the nucleus of such cells indefinitely , it retains the ...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "virology/persistence", "and", "latency", "virology/viral", "replication", "and", "gene", "regulation", "genetics", "and", "genomics/gene", "expression", "virology/viruses", "and", "cancer", "genetics", "and", "genomics/epigenetics" ]	2010	The Epigenetic Landscape of Latent Kaposi Sarcoma-Associated Herpesvirus Genomes
Thiamine deficiency is thought to be an issue in Cambodia and throughout Southeast Asia due to frequent clinical reports of infantile beriberi . However the extent of this public health issue is currently unknown due to a lack of population-representative data . Therefore we assessed the thiamine status ( measured as e...	Thiamine is an often-overlooked micronutrient of concern in Cambodia and throughout Southeast Asia , where reports of beriberi are not uncommon due to a diet of thiamine-poor , white , polished rice . Thiamine plays a critical role in cellular energy generation , and also modulates neuronal and neuromuscular transmissi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "b", "vitamins", "children", "medicine", "and", "health", "sciences", "body", "fluids", "chemical", "compounds", "geographical", "locations", "beriberi", "organic", "compounds", "age", "groups", "nutrition", "infants", "families", "chemistry", "vitamins", "nutritional",...	2017	High prevalence of thiamine (vitamin B1) deficiency in early childhood among a nationally representative sample of Cambodian women of childbearing age and their children
There is growing evidence that population-level brain activity is often organized into propagating waves that are structured in both space and time . Such spatiotemporal patterns have been linked to brain function and observed across multiple recording methodologies and scales . The ability to detect and analyze these ...	Structured activity such as propagating wave patterns at the level of neural circuits can arise from highly variable firing activity of individual neurons . This property makes the brain , a quintessential example of a complex system , analogous to other complex physical systems such as turbulent fluids , in which stru...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "and", "materials" ]	[ "velocity", "classical", "mechanics", "engineering", "and", "technology", "statistics", "signal", "processing", "marmosets", "vertebrates", "social", "sciences", "neuroscience", "animals", "mammals", "signal", "filtering", "animal", "models", "primates", "multivariate", "...	2018	Detection and analysis of spatiotemporal patterns in brain activity
Nitric oxide ( NO• ) is generated by the innate immune response to neutralize pathogens . NO• and its autoxidation products have an extensive biochemical reaction network that includes reactions with iron-sulfur clusters , DNA , and thiols . The fate of NO• inside a pathogen depends on a kinetic competition among its m...	Nitric oxide ( NO• ) is a highly reactive metabolite used by immune cells to combat pathogens . Since the biological effects of NO• are governed by its broad reactivity , it is desirable to determine how NO• distributes among its many targets inside a cell . A quantitative understanding of this distribution and how it ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "microbial", "metabolism", "neurochemistry", "small", "molecules", "enzymes", "metabolic", "networks", "microbiology", "host-pathogen", "interaction", "bacterial", "biochemistry", "escherichia", "coli", "biological", "systems", "engineering", "prokaryotic", "m...	2013	A Kinetic Platform to Determine the Fate of Nitric Oxide in Escherichia coli
Japanese encephalitis virus ( JEV ) is the causative agent of Japanese encephalitis , the leading cause of viral encephalitis in Asia . JEV transmission cycle involves mosquitoes and vertebrate hosts . The detection of JEV RNA in a pool of Culex pipiens caught in 2010 in Italy raised the concern of a putative emergence...	Japanese encephalitis virus ( JEV ) is the leading cause of viral encephalitis in Asia . JEV is maintained in a cycle involving mosquitoes and vertebrate hosts , mainly pigs and wading birds . Humans can be infected when bitten by an infected mosquito . Culex tritaeniorhynchus is the main vector of the disease in tropi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "animal", "models", "of", "disease", "geographical", "locations", "microbiology", "saliva", "animals", "animal", "models", "physiological", "processes", "model", "organisms", "salivation", "expe...	2017	European Aedes albopictus and Culex pipiens Are Competent Vectors for Japanese Encephalitis Virus
The circadian clock integrates temporal information with environmental cues in regulating plant development and physiology . Recently , the circadian clock has been shown to affect plant responses to biotic cues . To further examine this role of the circadian clock , we tested disease resistance in mutants disrupted in...	Plants are frequently challenged by various pathogens . The circadian clock , which is the internal time measuring machinery , has been implicated in regulating plant responses to biotic cues . To better understand the role of the circadian clock in defense control , we tested disease resistance with Arabidopsis mutant...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2013	Crosstalk between the Circadian Clock and Innate Immunity in Arabidopsis
The nosocomial pathogen Acinetobacter baumannii is a significant threat due to its ability to cause infections refractory to a broad range of antibiotic treatments . We show here that a highly conserved sensory-transduction system , BfmRS , mediates the coordinate development of both enhanced virulence and resistance i...	Infections with the hospital-acquired bacterium Acinetobacter baumannii are highly difficult to treat . The pathogen has evolved multiple lines of defense against antimicrobial stress , including a barrier-forming cell envelope as well as control systems that respond to antimicrobial stresses by enhancing antibiotic re...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "antimicrobials", "cell", "walls", "medicine", "and", "health", "sciences", "cell", "cycle", "and", "cell", "division", "drugs", "cell", "processes", "immunology", "microbiology", "dna", "transcription", "antibiotic", "resistance", "clinical", "medicine", "antibiotics",...	2018	A global regulatory system links virulence and antibiotic resistance to envelope homeostasis in Acinetobacter baumannii
Genetics is believed to have an important role in intellectual disability ( ID ) . Recent studies have emphasized the involvement of de novo mutations ( DNMs ) in ID but the extent to which they contribute to its pathogenesis and the identity of the corresponding genes remain largely unknown . Here , we report a screen...	Intellectual disability ( ID ) is the most frequent severe handicap of childhood . Several observations indicate that genetic factors explain a large fraction of cases with ID . We and others have recently found that de novo mutations ( DNMs; genetic changes not transmitted from the parents ) represent a common cause o...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences", "medicine", "and", "health", "sciences" ]	2014	De Novo Mutations in Moderate or Severe Intellectual Disability
The virulence regulator ToxR initiates and coordinates gene expression needed by Vibrio cholerae to colonize the small intestine and cause disease . Despite its prominence in V . cholerae virulence , our understanding of the direct ToxR regulon is limited to four genes: toxT , ompT , ompU and ctxA . Here , we determine...	The transcription factor ToxR initiates a virulence regulatory cascade required for V . cholerae to express essential host colonization factors and cause disease . Genome-wide expression studies suggest that ToxR regulates many genes important for V . cholerae pathogenesis , yet our knowledge of the direct regulon cont...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biofilms", "sequencing", "techniques", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "pathogens", "vibrio", "regulatory", "proteins", "microbiology", "dna-binding", "proteins", "regulator", "genes", "vibrio",...	2016	ToxR Antagonizes H-NS Regulation of Horizontally Acquired Genes to Drive Host Colonization
Metagenome analysis of the gut symbionts of three different insects was conducted as a means of comparing taxonomic and metabolic diversity of gut microbiomes to diet and life history of the insect hosts . A second goal was the discovery of novel biocatalysts for biorefinery applications . Grasshopper and cutworm gut s...	The symbiotic gut microbiome of herbivorous insects is vital for their ability to utilize and specialize on plants with very different nutrient qualities . Moreover , the gut microbiome is a significant resource for the discovery of biocatalysts and microbes with applications to various biotechnologies . We compared th...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "biofuels", "biology", "genomics", "microbiology", "agricultural", "biotechnology", "genetics", "and", "genomics", "agriculture" ]	2013	Comparative Genomic Analysis of the Endosymbionts of Herbivorous Insects Reveals Eco-Environmental Adaptations: Biotechnology Applications
The rod-shaped bacterium Escherichia coli selects the cell center as site of division with the help of the proteins MinC , MinD , and MinE . This protein system collectively oscillates between the two cell poles by alternately binding to the membrane in one of the two cell halves . This dynamic behavior , which emerges...	Cellular protein structures have long been suggested to form by protein self-organization . A particularly clear example is provided by the proteins MinC , MinD , and MinE selecting the center as site of cell division in the rod-shaped bacterium Escherichia coli . Based on binding of MinD to the cytoplasmic membrane an...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Membrane Binding of MinE Allows for a Comprehensive Description of Min-Protein Pattern Formation
In bacterial genomes , gene order is not random . This is most evident when looking at operons , these often encoding enzymes involved in the same metabolic pathway or proteins from the same complex . Is gene order within operons nonrandom , however , and if so why ? We examine this issue using metabolic operons as a c...	In bacteria , different enzymes from the same metabolic pathway are often encoded within one transcriptional unit , an operon . There is also , we show , a tendency for the enzymes that are needed earlier in the pathway to feature earlier in the operon , so-called colinearity . Why might this be ? We test three ideas ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/chromosome", "biology", "evolutionary", "biology/genomics", "evolutionary", "biology/bioinformatics" ]	2009	Stochasticity in Protein Levels Drives Colinearity of Gene Order in Metabolic Operons of Escherichia coli
Voltage-gated ion channels are essential for electrical signaling in neurons and other excitable cells . Among them , voltage-gated sodium and calcium channels are four-domain proteins , and ion selectivity is strongly influenced by a ring of amino acids in the pore regions of these channels . Sodium channels contain a...	Voltage-gated sodium and calcium channels are four-domain proteins that are essential for electrical signaling in neurons and other excitable cells . Recent genomic and functional analyses reveal a novel family of four-domain , Ca2+-selective cation channels in a variety of invertebrates , from sea anemones to insects ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "agriculture", "biology" ]	2013	Role of the DSC1 Channel in Regulating Neuronal Excitability in Drosophila melanogaster: Extending Nervous System Stability under Stress
The Eukaryotic RecA-like proteins Rad51 and Dmc1 cooperate during meiosis to promote recombination between homologous chromosomes by repairing programmed DNA double strand breaks ( DSBs ) . Previous studies showed that Rad51 and Dmc1 form partially overlapping co-foci . Here we show these Rad51-Dmc1 co-foci are often a...	During meiosis , a specialized form of chromosome segregation ensures that gametes contain only one copy of the parental chromosome complement . Accurate segregation of maternal and paternal chromosomes requires them to first become connected in pairs . Homologous recombination forms these needed connections . Connecti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Small Rad51 and Dmc1 Complexes Often Co-occupy Both Ends of a Meiotic DNA Double Strand Break
Schizosaccharomyces pombe Rad3 checkpoint kinase and its human ortholog ATR are essential for maintaining genome integrity in cells treated with genotoxins that damage DNA or arrest replication forks . Rad3 and ATR also function during unperturbed growth , although the events triggering their activation and their criti...	Eukaryotic genomes , which range in size from ∼107 to ∼1011 base pairs , are replicated with nearly absolute fidelity every cell cycle . This amazing feat happens despite the frequent stalling or collapse of replication forks . The checkpoint kinase ATR is activated by replication fork stalling and phosphorylates histo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/dna", "replication", "molecular", "biology/histone", "modification", "molecular", "biology/recombination", "molecular", "biology/centromeres", "molecular", "biology/chromosome", "structure", "molecular", "biology/dna", "repair" ]	2010	Rad3ATR Decorates Critical Chromosomal Domains with γH2A to Protect Genome Integrity during S-Phase in Fission Yeast
Russell’s viper envenoming is a major problem in South Asia and causes venom induced consumption coagulopathy . This study aimed to investigate the kinetics and dynamics of venom and clotting function in Russell’s viper envenoming . In a prospective cohort of 146 patients with Russell’s viper envenoming , we measured v...	Snake envenoming is an important health issue in many parts of the world and coagulopathy is one of the commonest manifestations . Russell’s viper envenoming occurs throughout south-east and south Asia and most commonly causes a venom induced consumption coagulopathy which may be complicated by bleeding . There is a li...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Venom Concentrations and Clotting Factor Levels in a Prospective Cohort of Russell’s Viper Bites with Coagulopathy
IFI16 ( gamma-interferon-inducible protein 16 ) , a predominantly nuclear protein involved in transcriptional regulation , also functions as an innate immune response DNA sensor and induces the IL-1β and antiviral type-1 interferon-β ( IFN-β ) cytokines . We have shown that IFI16 , in association with BRCA1 , functions...	Eukaryotic cells elicit innate immune responses against invading microbes including viruses . IFI16 , a predominantly nuclear protein , has emerged as an innate response nuclear DNA sensor . Recognition of nuclear KSHV , HSV-1 and EBV dsDNA genomes by IFI16-BRCA1 leads to IFI16 acetylation , cytoplasmic translocation o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "viruses", "immunoprecipitation", "dna", "viruses", "viral", "genome", "inflammasomes", "mammalian", "genomics", "anti...	2016	Histone H2B-IFI16 Recognition of Nuclear Herpesviral Genome Induces Cytoplasmic Interferon-β Responses
Chromosomal inversions have been an enduring interest of population geneticists since their discovery in Drosophila melanogaster . Numerous lines of evidence suggest powerful selective pressures govern the distributions of polymorphic inversions , and these observations have spurred the development of many explanatory ...	Chromosomal inversions are known to respond to powerful natural selection in many species . Despite this evidence , little progress has been made towards understanding the nature of selection that affects inversions . Here , we utilize two recently released population-resequencing projects from D . melanogaster to addr...	[ "Abstract", "Introduction", "Results/Discussion", "Conclusion", "and", "Prospects", "Methods" ]	[ "population", "genetics", "biology", "population", "biology", "genetics", "and", "genomics" ]	2012	Population Genomics of Inversion Polymorphisms in Drosophila melanogaster
Glucocorticoids are essential for life , but are also implicated in disease pathogenesis and may produce unwanted effects when given in high doses . Glucocorticoid receptor ( GR ) transcriptional activity and clinical outcome have been linked to its oligomerization state . Although a point mutation within the GR DNA-bi...	The powerful anti-inflammatory and immunosuppressive action of glucocorticoids have made them one of the most prescribed drugs worldwide . Unfortunately , acute or chronic treatment may have severe side-effects . Glucocorticoids bind to the glucocorticoid receptor ( GR ) , a ligand-dependent transcription factor . GR r...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "signal", "transduction", "cell", "biology", "nucleic", "acids", "biology", "and", "life", "sciences", "dna", "nuclear", "receptor", "signaling", "molecular", "cell", "biology", "cell", "signaling" ]	2014	Live Cell Imaging Unveils Multiple Domain Requirements for In Vivo Dimerization of the Glucocorticoid Receptor
The oral polio vaccine ( OPV ) contains live-attenuated polioviruses that induce immunity by causing low virulence infections in vaccine recipients and their close contacts . Widespread immunization with OPV has reduced the annual global burden of paralytic poliomyelitis by a factor of 10 , 000 or more and has driven w...	Oral polio vaccine ( OPV ) has played an essential role in the elimination of wild poliovirus ( WPV ) . OPV contains attenuated ( weakened ) yet transmissible viruses that can spread from person to person . In its attenuated form , this spread is beneficial as it generates population immunity . However , the attenuatio...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "infectious", "disease", "epidemiology", "pathogens", "immunology", "microbiology", "viruses", "preventive", "medicine", "physiological", "processes", "vaccines", ...	2018	Assessing the stability of polio eradication after the withdrawal of oral polio vaccine
Obtaining informed consent for clinical trials is especially challenging when working in rural , resource-limited areas , where there are often high levels of illiteracy and lack of experience with clinical research . Such an area , a remote field site in the northeastern part of the state of Minas Gerais , Brazil , is...	Conducting clinical trials of new vaccines in rural , resource-limited areas can be challenging since the people living in these areas often have high levels of illiteracy , little experience with clinical research , and limited access to routine health care . Especially difficult is obtaining informed consent for part...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "non-clinical", "medicine/sociology", "infectious", "diseases/helminth", "infections", "non-clinical", "medicine/bioethics", "infectious", "diseases/neglected", "tropical", "diseases" ]	2010	Health Education through Analogies: Preparation of a Community for Clinical Trials of a Vaccine against Hookworm in an Endemic Area of Brazil
Pathogenic microbes employ a variety of methods to overcome host defenses , including the production and dispersal of molecules that are toxic to their hosts . Pseudomonas aeruginosa , a Gram-negative bacterium , is a pathogen of a diverse variety of hosts including mammals and the nematode Caenorhabditis elegans . In ...	The bacterium Pseudomonas aeruginosa is a pathogen of a wide variety of organisms . It has been shown that P . aeruginosa factors that are critical for its toxicity to the nematode worm Caenorhabditis elegans are also important for its pathogenicity in mammals . In this report we show that phenazines , a class of small...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "biochemistry", "gram", "negative", "microbial", "pathogens", "biology", "microbiology", "host-pathogen", "interaction", "toxic", "agents", "bacterial", "biochemistry", "bacterial", "pathogens", "toxicology", "pathogenesis" ]	2013	Identification of Pseudomonas aeruginosa Phenazines that Kill Caenorhabditis elegans
By applying REMD simulations we have performed comparative analysis of the conformational ensembles of amino-truncated Aβ10-40 peptide produced with five force fields , which combine four protein parameterizations ( CHARMM36 , CHARMM22* , CHARMM22/cmap , and OPLS-AA ) and two water models ( standard and modified TIP3P ...	Dependence of protein conformational ensembles on force field parameterizations limits the predictive power of molecular dynamics simulations . To address this problem , we evaluated five all-atom force fields for their consistency in reproducing the conformational ensemble of Alzheimer’s Aβ10-40 peptide . To generate ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "geometry", "simulation", "and", "modeling", "probability", "distribution", "mathematics", "protein", "structure", "prediction", "protein", "structure", "research", "and", "analysis", "methods", "proteins", "peptide", "mapping", "salt", "bridges", "chemistry", "proteomics...	2017	Is the Conformational Ensemble of Alzheimer’s Aβ10-40 Peptide Force Field Dependent?
Genome-wide association studies ( GWAS ) have identified more than 90 susceptibility loci for breast cancer , but the underlying biology of those associations needs to be further elucidated . More genetic factors for breast cancer are yet to be identified but sample size constraints preclude the identification of indiv...	Although individual genetic variant-based genome-wide association studies have greatly increased our understanding of the genetic susceptibility to breast cancer , the genetic variants identified to date account for a relatively small proportion of the heritability . Shifting the focus of analysis from individual genet...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "genome-wide", "association", "studies", "body", "weight", "medicine", "and", "health", "sciences", "breast", "tumors", "body", "fluids", "cancers", "and", "neoplasms", "oncology", "mathematics", "forecasting", "statistics", "(mathematics)", "physiological", "parameters",...	2017	Trans-ethnic predicted expression genome-wide association analysis identifies a gene for estrogen receptor-negative breast cancer
Third-generation cephalosporins are a class of β-lactam antibiotics that are often used for the treatment of human infections caused by Gram-negative bacteria , especially Escherichia coli . Worryingly , the incidence of human infections caused by third-generation cephalosporin-resistant E . coli is increasing worldwid...	The rapid global rise of infections caused by Escherichia coli that are resistant to clinically relevant antimicrobials , including third-generation cephalosporins , is cause for concern . The intestinal tract of livestock , in particular poultry , is an important reservoir for drug resistant E . coli , but it is unkno...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "antimicrobials", "gram", "negative", "bacteria", "medicine", "and", "health", "sciences", "genome", "evolution", "evolutionary", "biology", "food", "chains", "infectious", "disease", "epidemiology", "plasmids", "population", "genetics", "microbiology", "g...	2014	Dissemination of Cephalosporin Resistance Genes between Escherichia coli Strains from Farm Animals and Humans by Specific Plasmid Lineages
During a blood meal , Lutzomyia intermedia sand flies transmit Leishmania braziliensis , a parasite causing tegumentary leishmaniasis . In experimental leishmaniasis , pre-exposure to saliva of most blood-feeding sand flies results in parasite establishment in absence of any skin damages in mice challenged with dermotr...	Leishmaniasis is a vector-borne parasitic disease of serious public health importance . No efficient vaccine is currently available . Parasites are transmitted to mammalian hosts during sand fly bites . During this process , both parasites and sand fly salivary products are delivered into the skin . Immunization with s...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immunizations", "immunity", "host-pathogen", "interaction", "biology", "microbiology", "parasitology" ]	2014	Repeated Exposure to Lutzomyia intermedia Sand Fly Saliva Induces Local Expression of Interferon-Inducible Genes Both at the Site of Injection in Mice and in Human Blood
During embryonic development , pattern formation must be tightly synchronized with tissue morphogenesis to coordinate the establishment of the spatial identities of cells with their movements . In the vertebrate retina , patterning along the dorsal-ventral and nasal-temporal ( anterior-posterior ) axes is required for ...	The vertebrate brain contains a point-to-point representation of sensory input from the eye . This visual map forms during embryonic development , by neuronal cells of the retina sending targeted axon projections to the brain . Since the projection needs to wire up neighboring cell positions in the retina to neighborin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/embryology", "genetics", "and", "genomics/animal", "genetics", "neuroscience/sensory", "systems", "developmental", "biology/morphogenesis", "and", "cell", "biology", "cell", "biology/cell", "signaling", "cell", "biology/morphogenesis", "and", "cell", ...	2009	Dynamic Coupling of Pattern Formation and Morphogenesis in the Developing Vertebrate Retina
We describe here the Drosophila gene hydra that appears to have originated de novo in the melanogaster subgroup and subsequently evolved in both structure and expression level in Drosophila melanogaster and its sibling species . D . melanogaster hydra encodes a predicted protein of ~300 amino acids with no apparent sim...	Similar groups of animals have similar numbers of genes , but not all of these genes are the same . While some genes are highly conserved and can be easily and uniquely identified in species ranging from yeast to plants to humans , other genes are sometimes found in only a small number or even in a single species . Suc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "arthropods", "eukaryotes", "evolutionary", "biology", "drosophila", "animals", "insects" ]	2007	Evolution of hydra, a Recently Evolved Testis-Expressed Gene with Nine Alternative First Exons in Drosophila melanogaster
The concept of robustness of regulatory networks has received much attention in the last decade . One measure of robustness has been associated with the volume of the feasible region , namely , the region in the parameter space in which the system is functional . In this paper , we show that , in addition to volume , t...	Developing models with a large number of parameters for describing the dynamics of a biochemical network is a common exercise today . The dependence of predictions of such a network model on the choice of parameters is important to understand for two reasons . For the purpose of fitting biological data and making predi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Acknowledgments" ]	[ "computational", "biology/systems", "biology" ]	2009	Shape, Size, and Robustness: Feasible Regions in the Parameter Space of Biochemical Networks
When chromosomal DNA is damaged , progression through the cell cycle is halted to provide the cells with time to repair the genetic material before it is distributed between the mother and daughter cells . In Saccharomyces cerevisiae , this cell cycle arrest occurs at the G2/M transition . However , it is also necessar...	A key aspect of the division of cells is that the genomic material must be carefully duplicated , protected from damage , and correctly distributed during this process . When the cells detect problems that affect the integrity or the proper distribution of the genome , they trigger different surveillance mechanisms to ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Inhibition of the Mitotic Exit Network in Response to Damaged Telomeres
Interferon regulatory factor ( IRF ) -1 is an immunomodulatory transcription factor that functions downstream of pathogen recognition receptor signaling and has been implicated as a regulator of type I interferon ( IFN ) -αβ expression and the immune response to virus infections . However , this role for IRF-1 remains ...	Interferon regulatory factor ( IRF ) -1 is a transcription factor that has been implicated in immune regulation and induction of type I IFN gene expression . To better understand the contribution of IRF-1 to antiviral immunity , we infected cells and mice lacking IRF-1 with West Nile virus ( WNV ) , an encephalitic fla...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viral", "classification", "immunology", "microbiology", "host-pathogen", "interaction", "adaptive", "immunity", "rna", "viruses", "emerging", "infectious", "diseases", "animal", "models", "of", "infection", "biology", "pathogenesis", "viral", "replication", "immune", "re...	2011	Interferon Regulatory Factor-1 (IRF-1) Shapes Both Innate and CD8+ T Cell Immune Responses against West Nile Virus Infection
An essential component of genome function is the syntax of genomic regulatory elements that determine how diverse transcription factors interact to orchestrate a program of regulatory control . A precise characterization of in vivo spacing constraints between key transcription factors would reveal key aspects of this g...	The letters in our genome spell words and phrases that control when each gene is activated . To understand how these words and phrases function in health and disease , we have developed a new computational method to determine what word positions in our genomic text are used by each genome regulatory protein , and how t...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "sequence", "analysis", "genomics", "functional", "genomics", "regulatory", "networks", "biology", "computational", "biology", "genetics", "and", "genomics" ]	2012	High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints
Persistent activity and match effects are widely regarded as neuronal correlates of short-term storage and manipulation of information , with the first serving active maintenance and the latter supporting the comparison between memory contents and incoming sensory information . The mechanistic and functional relationsh...	Over short time periods , memories are stored by sustained patterns of spiking activity which , once initiated by the stimulus , persist over the entire retention interval . How the information stored by such persistent activity is later retrieved is presently unclear . Here we propose that , besides temporarily storin...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Modulation of Network Excitability by Persistent Activity: How Working Memory Affects the Response to Incoming Stimuli
Chikungunya virus ( CHIKV ) is a mosquito-borne virus currently transmitted in about 60 countries . CHIKV causes acute flu-like symptoms and in many cases prolonged musculoskeletal and joint pain . Detection of the infection is mostly done using RT-RCR or ELISA , which are not suitable for point-of-care diagnosis . In ...	CHIKV is transmitted to humans via mosquitos . CHIKV induces clinical signs similar to Influenza , Dengue , and Zika viruses . We have developed a molecular assay for the detection of CHIKV genome based on isothermal„recombinase polymerase amplification ( RPA ) assay”performed at 42°C . The result was obtained in maxim...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "reverse", "transcriptase-polymerase", "chain", "reaction", "dengue", "virus", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "pathogens", "immunology", "tropical", "diseases", "microbiology"...	2016	A Field-Deployable Reverse Transcription Recombinase Polymerase Amplification Assay for Rapid Detection of the Chikungunya Virus
Rickettsia bacteria are responsible for diseases in humans and animals around the world , however few details are available regarding its ecology and circulation among wild animals and human populations at high transmission risk in Brazil . The aim of this study was to investigate the occurrence of ticks and Rickettsia...	The present study reported serological findings and molecular assays of Rickettsia spp and ticks of wild boars , simultaneous to their correspondent hunting dogs and hunters . Seropositivity for Rickettsia spp . was higher in wild boars when compared to dogs and humans but was similar between dogs and humans . Despite ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "ixodes", "pathology", "and", "laboratory", "medicine", "pathogens", "geographical", "locations", "microbiology", "vertebrates", "dogs", "animals", "mammals", "rickett...	2019	Ticks and serosurvey of anti-Rickettsia spp. antibodies in wild boars (Sus scrofa), hunting dogs and hunters of Brazil
For the last three decades , evolutionary biologists have sought to understand which factors modulate the evolution of parasite virulence . Although theory has identified several of these modulators , their effect has seldom been analysed experimentally . We investigated the role of two such major factors—the mode of t...	Virulence is a key property of parasites , and is linked to the emergence of new diseases and to the reduction of ecosystem biodiversity . Consequently , scientists have devoted a great effort to build theoretical models that predict which factors may modulate virulence evolution . However , whether ( and how ) these f...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "organismal", "evolution", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "evolutionary", "biology", "host-pathogen", "interactions", "coevolution", "microbial", "evolution", "virology", "viral", "transmission", "and", "infection", ...	2014	Vertical Transmission Selects for Reduced Virulence in a Plant Virus and for Increased Resistance in the Host
The major DNA repair pathways operate on damage in double-strand DNA because they use the intact strand as a template after damage removal . Therefore , lesions in transient single-strand stretches of chromosomal DNA are expected to be especially threatening to genome stability . To test this hypothesis , we designed s...	A variety of error avoidance mechanisms assure low mutation rates across the genome . Genetic defects in DNA replication or repair can lead to genome-wide increase in mutation frequency that may result in cancer predisposition and genetic disease . Transient localized hypermutability drastically differs in its biologic...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "molecular", "biology/dna", "repair" ]	2008	Hypermutability of Damaged Single-Strand DNA Formed at Double-Strand Breaks and Uncapped Telomeres in Yeast Saccharomyces cerevisiae
Organogenesis is controlled by gene networks activated by upstream selector genes . During development the gene network is activated stepwise , with a sequential deployment of successive transcription factors and signalling molecules that modify the interaction of the elements of the network as the organ forms . Very l...	Organogenesis is controlled by gene networks activated by upstream selector genes . To address how the network organization changes during development and how the target genes integrate the genetic information it provides , we analyze in Drosophila the induction of posterior spiracle organogenesis by the Hox gene Abdom...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	JAK/STAT and Hox Dynamic Interactions in an Organogenetic Gene Cascade
Dengue virus ( DENV ) and Zika virus ( ZIKV ) are members of the Flaviviridae and are predominantly transmitted via mosquito bites . Both viruses are responsible for a growing number of infections in tropical and subtropical regions . DENV infection can cause lethargy with severe morbidity and dengue shock syndrome lea...	Dengue virus ( DENV ) and Zika virus ( ZIKV ) are responsible for a growing number of infections in tropical and subtropical regions . DENV infection can cause dengue shock syndrome leading to death in some cases , while ZIKV is now linked with Guillain-Barré syndrome and congenital anomalies including microcephaly . T...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "dengue", "virus", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "cloning", "viruses", "bacterial", "diseases", "rna", "viruses", "molecular", "bio...	2018	MAIT cells are activated in acute Dengue virus infection and after in vitro Zika virus infection
Systemic , life-threatening infections in humans are often caused by bacterial or fungal species that normally inhabit a different locale in our body , particularly mucosal surfaces . A hallmark of these opportunistic pathogens , therefore , is their ability to thrive in disparate niches within the host . In this work ...	Our skin and mouth , as well as our genital and gastrointestinal tracts , are laden with microorganisms belonging to all three domains of life ( bacteria , archaea , and eukaryotes ) . Much of the time these commensal microorganisms are not only harmless but provide advantages to us . However , when the host's defenses...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "biology", "microbiology", "genetics", "and", "genomics" ]	2013	Candida albicans Commensalism and Pathogenicity Are Intertwined Traits Directed by a Tightly Knit Transcriptional Regulatory Circuit
Persistently low white blood cell count ( WBC ) and neutrophil count is a well-described phenomenon in persons of African ancestry , whose etiology remains unknown . We recently used admixture mapping to identify an approximately 1-megabase region on chromosome 1 , where ancestry status ( African or European ) almost e...	Many African Americans have white blood cell counts ( WBC ) that are persistently below the normal range for people of European descent , a condition called “benign ethnic neutropenia . ” Because most African Americans have both African and European ancestors , selected genetic variants can be analyzed to assign probab...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "discovery", "genetics", "and", "genomics", "genetics", "and", "genomics/population", "genetics" ]	2009	Reduced Neutrophil Count in People of African Descent Is Due To a Regulatory Variant in the Duffy Antigen Receptor for Chemokines Gene
Axonal growth and guidance rely on correct growth cone responses to guidance cues . Unlike the signaling cascades that link axonal growth to cytoskeletal dynamics , little is known about the crosstalk mechanisms between guidance and membrane dynamics and turnover . Recent studies indicate that whereas axonal attraction...	Syntaxin-1 is a core factor in tethering synaptic vesicles and mediating their fusion to the cell membrane at the synapse . Thus , Syntaxin-1 mediates neurotransmission in the adult nervous system . Here we show that this protein is also involved in axonal guidance in the CNS of vertebrates and invertebrates during the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "nervous", "system", "neuroscience", "animals", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "experimental", "organism", "systems", "nerve", "fibers", "embryos...	2018	A conserved role for Syntaxin-1 in pre- and post-commissural midline axonal guidance in fly, chick, and mouse
Chemotherapy continues to have a major impact on reducing the burden of disease caused by trypanosomatids . Unfortunately though , the mode-of-action ( MoA ) of antitrypanosomal drugs typically remains unclear or only partially characterised . This is the case for four of five current drugs used to treat Human African ...	African trypanosomes cause devastating and lethal diseases in humans and livestock . These parasites are transmitted among mammals by tsetse flies and circulate and grow in blood and tissue fluids . There are several drugs available to treat patients but , despite their use for many decades , we know relatively little ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "cell", "cycle", "and", "cell", "division", "cell", "processes", "membrane", "potential", "electrophysiology", "parasitic", "protozoans", "mitosis", "trypanosoma", "brucei", "trypanosoma", "brucei", "gambiense", "protozoans", "dn...	2018	Insights into antitrypanosomal drug mode-of-action from cytology-based profiling
Paragonimiasis is a food-borne trematodiasis leading to lung disease . Worldwide , an estimated 21 million people are infected . Foci of ongoing transmission remain often unnoticed . We evaluated a simple questionnaire approach using lay-informants at the village level to identify paragonimiasis foci and suspected para...	Paragonimiasis is a neglected pulmonary disease provoked by a food-borne trematode parasite . The infection may develop into severe pulmonary disease , often diagnosed with delay and confused with tuberculosis . Globally an estimated 21 millions people are infected . Human infection is acquired through consumption of r...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "public", "health", "and", "epidemiology/epidemiology", "infectious", "diseases/helminth", "infections", "public", "health", "and", "epidemiology/infectious", "diseases", "infectious", "diseases/respiratory", "infections...	2009	Rapid Identification of Paragonimiasis Foci by Lay Informants in Lao People's Democratic Republic
Zika virus ( ZIKV ) , an emerging flavivirus , has recently spread explosively through the Western hemisphere . In addition to symptoms including fever , rash , arthralgia , and conjunctivitis , ZIKV infection of pregnant women can cause microcephaly and other developmental abnormalities in the fetus . We report herein...	Although it was first identified almost 70 years ago , Zika virus had rarely been associated with pathology in humans until the 21st century . Recent outbreaks in the South Pacific and the Americas have been characterized by numerous confirmed cases , some involving neurologic sequelae and , of most concern , birth def...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "body", "fluids", "immune", "physiology", "pathogens", "immunology", "microbiology", "viruses", "urine", "lymph",...	2017	Zika Virus infection of rhesus macaques leads to viral persistence in multiple tissues
Coordinated cell migration during development is crucial for morphogenesis and largely relies on cells of the neural crest lineage that migrate over long distances to give rise to organs and tissues throughout the body . Recent studies of protein arginylation implicated this poorly understood posttranslational modifica...	Formation of many organs during development depends on the coordinated migration of individual cells and cell layers throughout the embryo . The majority of migrating cells originate from the neural crest lineage that gives rise to peripheral neurons , ganglia , pigment cells , and craniofacial structures , as well as ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/pattern", "formation", "cell", "biology/morphogenesis", "and", "cell", "biology", "developmental", "biology/organogenesis", "developmental", "biology/morphogenesis", "and", "cell", "biology" ]	2010	Arginylation-Dependent Neural Crest Cell Migration Is Essential for Mouse Development
Although many methods are available to test sequence variants for association with complex diseases and traits , methods that specifically seek to identify causal variants are less developed . Here we develop and evaluate a Bayesian hierarchical regression method that incorporates prior information on the likelihood of...	The decline in DNA sequencing cost permits the interrogation of potentially all variants across the entire allele frequency spectrum for their associations with complex human diseases and traits . However , the identification of causal variants remains challenging . Existing single variant tests do not distinguish betw...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "genetics", "biology", "computational", "biology" ]	2013	Leveraging Prior Information to Detect Causal Variants via Multi-Variant Regression
Ebola virus ( EBOV ) causes acute hemorrhagic fever in humans and non-human primates with mortality rates up to 90% . So far there are no effective treatments available . This study evaluates the protective efficacy of 8 monoclonal antibodies ( MAbs ) against Ebola glycoprotein in mice and guinea pigs . Immunocompetent...	Ebola virus ( EBOV ) causes acute hemorrhagic fever in humans and non-human primates with mortality rates up to 90% . So far there are no effective treatments available . This study evaluates the protective efficacy of 8 monoclonal antibodies ( MAbs ) against the Ebola virus surface glycoprotein , in mice and guinea pi...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "immunology", "biology" ]	2012	Ebola GP-Specific Monoclonal Antibodies Protect Mice and Guinea Pigs from Lethal Ebola Virus Infection
Long non-coding RNAs ( lncRNAs ) have been recognized as key players in transcriptional regulation . We show that the lncRNA steroid receptor RNA activator ( SRA ) participates in regulation through complex formation with trithorax group ( TrxG ) and polycomb repressive complex 2 ( PRC2 ) complexes . Binding of the SRA...	Long non-coding RNAs ( lncRNAs ) can play an important role in regulation of gene expression . In a number of cases , individual lncRNAs have been shown to interact with either the trithorax group ( TrxG ) or polycomb repressive complex 2 ( PRC2 ) protein complexes , which deliver histone modifications associated respe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Association of the Long Non-coding RNA Steroid Receptor RNA Activator (SRA) with TrxG and PRC2 Complexes
The central terminals of primary afferent fibers experience depolarization upon activation of GABAA receptors ( GABAAR ) because their intracellular chloride concentration is maintained above electrochemical equilibrium . Primary afferent depolarization ( PAD ) normally mediates inhibition via sodium channel inactivati...	Postsynaptic GABAAR mediate inhibition by causing hyperpolarization or by preventing ( shunting ) the depolarization caused by concurrent excitatory input . Presynaptic GABAAR work differently , in the spinal cord at least . Because of their higher-than-equilibrium intracellular chloride concentration , the central ter...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "action", "potentials", "medicine", "and", "health", "sciences", "neurochemistry", "chemical", "compounds", "depolarization", "membrane", "potential", "electrophysiology", "neuroscience", "ion", "channels", "nerve", "fibers", "neurotransmitters", "sodium", "channels", "anim...	2016	Combined Changes in Chloride Regulation and Neuronal Excitability Enable Primary Afferent Depolarization to Elicit Spiking without Compromising its Inhibitory Effects
Giardia trophozoites attach to the intestinal microvilli ( or inert surfaces ) using an undefined “suction-based” mechanism , and remain attached during cell division to avoid peristalsis . Flagellar motility is a key factor in Giardia's pathogenesis and colonization of the host small intestine . Specifically , the bea...	Giardia is a widespread , single-celled , intestinal parasite that infects millions of people and animals each year . Colonization of the small intestine is a critical part of Giardia's life cycle in any host . This colonization is initiated when cells attach to the intestinal wall via a specialized suction cup-like st...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "molecular", "cell", "biology", "cell", "biology", "cell", "adhesion", "microbial", "pathogens", "biology", "microbiology", "quantitative", "parasitology", "parasitology" ]	2011	Giardia Flagellar Motility Is Not Directly Required to Maintain Attachment to Surfaces
The co-evolution of myxoma virus ( MYXV ) and the European rabbit occurred independently in Australia and Europe from different progenitor viruses . Although this is the canonical study of the evolution of virulence , whether the genomic and phenotypic outcomes of MYXV evolution in Europe mirror those observed in Austr...	Species jumps and subsequent pathogen evolution are of increasing importance in a globally connected world . The co-evolution of myxoma virus and the European rabbit following the introduction of the virus into Australia in 1950 is the canonical case of host jumping and host-pathogen co-evolution on a continental scale...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "organismal", "evolution", "medicine", "and", "health", "sciences", "microbial", "mutation", "poxviruses", "myxoma", "virus", "pathology", "and", "laboratory", "medicine", "genome", "evolution", "insertion", "mutation", "pathogens", "microbiology", "vertebrates", "rabbits...	2017	Genomic and phenotypic characterization of myxoma virus from Great Britain reveals multiple evolutionary pathways distinct from those in Australia
Cysteine-rich receptor-like kinases ( CRKs ) are transmembrane proteins characterized by the presence of two domains of unknown function 26 ( DUF26 ) in their ectodomain . The CRKs form one of the largest groups of receptor-like protein kinases in plants , but their biological functions have so far remained largely unc...	Receptor-like kinases ( RLKs ) are important regulators in signal transduction in plants . However , the large number of RLKs and their high sequence similarity has hampered the analysis of RLKs . One of the largest subgroups of RLKs , the cysteine-rich receptor-like kinases ( CRKs ) , has been suggested to be involved...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Large-Scale Phenomics Identifies Primary and Fine-Tuning Roles for CRKs in Responses Related to Oxidative Stress
Although genome-wide association studies ( GWAS ) have identified hundreds of complex trait loci , the pathomechanisms of most remain elusive . Studying the genetics of risk factors predisposing to disease is an attractive approach to identify targets for functional studies . Intracranial aneurysms ( IA ) are rupture-p...	When multiple genes or genetic regions contribute to the inherited risk of a disease , it is referred to as a complex disease . Genome-wide association studies ( GWAS ) aim to detect common genetic variations that associate with complex traits or diseases . Although GWAS have been successful in identifying strongly ass...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "neurological", "disorders", "neurology", "genetics", "biology", "genetics", "and", "genomics", "cardiovascular" ]	2012	Intracranial Aneurysm Risk Locus 5q23.2 Is Associated with Elevated Systolic Blood Pressure
Gram-negative pathogens express fibrous adhesive organelles that mediate targeting to sites of infection . The major class of these organelles is assembled via the classical , alternative and archaic chaperone-usher pathways . Although non-classical systems share a wider phylogenetic distribution and are associated wit...	Gram-negative pathogens depend on fibrous adhesive organelles to attach to target tissues and establish infection . The major class of these organelles is assembled via the classical , alternative and archaic chaperone-usher ( CU ) pathways . CU pathways are recognized as promising new targets for the next generation o...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Structural Insight into Archaic and Alternative Chaperone-Usher Pathways Reveals a Novel Mechanism of Pilus Biogenesis
γ-herpesviruses ( γHVs ) have developed an interaction with their hosts wherein they establish a life-long persistent infection and are associated with the onset of various malignancies . One critical virulence factor involved in the persistency of murine γ-herpesvirus 68 ( γHV68 ) is the viral homolog of the Bcl-2 pro...	Autophagy ( ‘self-eating’ , lysosome-dependent degradation and recycling of the intracellular components in response to stress ) and apoptosis ( ‘self-killing’ , cells commit suicide in response to stress ) are important host defense mechanisms against viral infections . γ-herpesvirus 68 ( γHV68 ) encodes a Bcl-2 famil...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology", "virology", "microbiology", "molecular", "biology" ]	2009	Viral Bcl-2-Mediated Evasion of Autophagy Aids Chronic Infection of γHerpesvirus 68
Caspase-dependent cleavage of antigens associated with apoptotic cells plays a prominent role in the generation of CD8+ T cell responses in various infectious diseases . We found that the emergence of a large population of autoreactive CD8+ T effector cells specific for apoptotic T cell-associated self-epitopes exceeds...	The emergence of a large population of mixed polyfunctional ( type-1 , -2 , -17 ) CD8+ T cell effector responses specific for apoptotic T cell-associated self-epitopes rather than the dysfunction or altered quality of virus-specific CD8+ T cells is associated with the progression toward chronic disease in the human mod...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "immune", "cells", "immune", "activation", "antigen-presenting", "cells", "immunity", "to", "infections", "immunology", "adaptive", "immunity", "hepatitis", "immune", "defense", "hepatitis", "c", "infectious", "diseases", "hiv", "t", "cells", "biology", "i...	2012	Polyfunctional Type-1, -2, and -17 CD8+ T Cell Responses to Apoptotic Self-Antigens Correlate with the Chronic Evolution of Hepatitis C Virus Infection
Distribution networks—from vasculature to urban transportation pathways—are spatially embedded networks that must route resources efficiently in the face of pressures induced by the costs of building and maintaining network infrastructure . Such requirements are thought to constrain the topological and spatial organiza...	Distribution networks such as vasculature systems or urban transportation pathways are prevalent in our world . Understanding how different kinds of transport systems are organized to allow for efficient function in their environments and in the presence of constraints on material costs is currently an open area of inv...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "neural", "networks", "mathematical", "models", "neuroscience", "fungal", "structure", "fungi", "mycelium", "network", "analysis", "biological", "transport", "research", "and", "analysis", "methods", "computer", "and", "information", "sciences", "mycology", "mathematical"...	2018	Comparing two classes of biological distribution systems using network analysis
Arbovirus vector dynamics and spread are influenced by climatic , environmental and geographic factors . Major Chikungunya and Dengue fever outbreaks occurring the last 10 years have coincided with the expansion of the mosquito vector Aedes albopictus to nearly all the continents . We characterized the ecological ( lar...	The objective of our research was to study the movements the mosquito Aedes albopictus . This mosquito transmits more than 20 viruses to humans throughout the world and is the vector of the recent major epidemics of Dengue and Chikungunya on Reunion Island and the Indian Ocean Region and is , therefore , of great inter...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "ecology", "genetics", "neglected", "tropical", "diseases", "arboviral", "infections", "biology", "genetics", "and", "genomics" ]	2013	Evidence of Habitat Structuring Aedes albopictus Populations in Réunion Island
Entamoeba histolytica is a pathogen that during its infective process confronts the host defenses , which damages the amoebic plasma membrane ( PM ) , resulting in the loss of viability . However , it is unknown whether amoebic trophozoites are able to repair their PM when it is damaged . Acid sphingomyelinases ( aSMas...	The host-amoeba relationship is based on a series of interplays between host defense mechanisms and parasite survival strategies . While host cells elaborate diverse mechanisms for pathogen elimination , Entamoeba histolytica trophozoites have also developed complex strategies to counteract host immune response and fac...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "trophozoites", "parasite", "groups", "lysosomes", "medicine", "and", "health", "sciences", "vesicles", "parasitic", "protozoans", "parasitology", "physiological", "processes", "apicomplexa", "protozoans", "cellular", "structures", "and", "organelles", "endosomes", "entamoe...	2019	Plasma membrane damage repair is mediated by an acid sphingomyelinase in Entamoeba histolytica
Despite a growing appreciation of their vast diversity in nature , mechanisms of speciation are poorly understood in Bacteria and Archaea . Here we use high-throughput genome sequencing to identify ongoing speciation in the thermoacidophilic Archaeon Sulfolobus islandicus . Patterns of homologous gene flow among genome...	Microorganisms from the bacterial and archaeal domains of the tree of life comprise the greatest breadth of biodiversity on earth . Yet the essential evolutionary process of speciation ( through which biodiversity is generated ) is poorly understood in microbes . At issue is the fundamental question of whether gene flo...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Material", "and", "Methods" ]	[ "biology", "genomics", "evolutionary", "biology", "microbiology", "population", "biology", "genetics", "and", "genomics" ]	2012	Patterns of Gene Flow Define Species of Thermophilic Archaea
Arthropod-borne pathogens are transmitted into a unique intradermal microenvironment that includes the saliva of their vectors . Immunomodulatory factors in the saliva can enhance infectivity; however , in some cases the immune response that develops to saliva from prior uninfected bites can inhibit infectivity . Most ...	The saliva of blood-feeding arthropods contains a variety of components that prevent blood clotting and interfere with the immune system of the vertebrate host . These properties have been shown to enhance or inhibit the transmission of different pathogens transmitted by arthropods . Yersinia pestis , the bacterial age...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "immune", "cells", "immunology", "microbiology", "parasitology", "disease", "susceptibility", "neutrophils", "bacterial", "pathogens", "antibody", "response", "white", "blood", "cells", "inflammation", "animal", "cells", "medical", "microbiology", "micro...	2014	Evaluation of the Murine Immune Response to Xenopsylla cheopis Flea Saliva and Its Effect on Transmission of Yersinia pestis
European liver fluke Opisthorchis felineus , causing opisthorchiasis disease , is widespread in Russia , Ukraine , Kazakhstan and sporadically detected in the EU countries . O . felineus infection leads to hepatobiliary pathological changes , cholangitis , fibrosis and , in severe cases , malignant transformation of bi...	Opisthorchiasis caused by Opisthorchis felineus is a fish-borne parasitic worm infection spread in Russia and some European countries . The morbidities provoked by O . felineus infection are cholangitis and bile duct fibrosis . Long-term infection is associated with high risk of developing cholangiocarcinoma , a genera...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion", "Conclusion" ]	[ "biliary", "system", "medicine", "and", "health", "sciences", "liver", "diagnostic", "radiology", "fibrosis", "vertebrates", "animals", "mammals", "liver", "diseases", "magnetic", "resonance", "imaging", "developmental", "biology", "gastroenterology", "and", "hepatology",...	2017	Magnetic resonance imaging and spectroscopy for differential assessment of liver abnormalities induced by Opisthorchis felineus in an animal model
Adenosine is a constituent of many molecules of life; increased free extracellular adenosine indicates cell damage or metabolic stress . The importance of adenosine signaling in basal physiology , as opposed to adaptive responses to danger/damage situations , is unclear . We generated mice lacking all four adenosine re...	Elevated extracellular adenosine generally indicates metabolic stress or cell damage and regulates many aspects of physiology . We studied “QKO” mice lacking all four adenosine receptors . Young QKO mice do not appear obviously ill , but do show decreased survival later in life . QKO mice demonstrate that adenosine rec...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "caffeine", "glycosylamines", "medicine", "and", "health", "sciences", "alkaloids", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "physiological", "parameters", "signs", "and", "symptoms", "body", "temperature", "inosine", "adenosine", "cardiology...	2019	Physiology and effects of nucleosides in mice lacking all four adenosine receptors
Trypanosomes , protozoan parasites of medical importance , essentially rely on post-transcriptional mechanisms to regulate gene expression in insect vectors and vertebrate hosts . RNA binding proteins ( RBPs ) that associate to the 3’-UTR of mature mRNAs are thought to orchestrate master developmental programs for thes...	Trypanosoma cruzi epimastigotes proliferate in the midgut of the hematophagous insect vector . Insect vectors can spend long periods of time without feeding , during which epimastigotes differentiate to infective metacyclic trypomastigotes in a process termed metacyclogenesis . This metamorphosis involves multiple phen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "messenger", "rna", "microbiology", "parasitic", "diseases", "parasitic", "protozoans", "protozoan", "life", "cycles", "developmental", "biology", "trypomastigotes", "protozoans", "epimastigotes", "cellular", "structures", "and", "...	2018	Translational repression by an RNA-binding protein promotes differentiation to infective forms in Trypanosoma cruzi
Both linear mixed models ( LMMs ) and sparse regression models are widely used in genetics applications , including , recently , polygenic modeling in genome-wide association studies . These two approaches make very different assumptions , so are expected to perform well in different situations . However , in practice ...	The goal of polygenic modeling is to better understand the relationship between genetic variation and variation in observed characteristics , including variation in quantitative traits ( e . g . cholesterol level in humans , milk production in cattle ) and disease susceptibility . Improvements in polygenic modeling wil...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "genome-wide", "association", "studies", "animal", "genetics", "statistics", "quantitative", "traits", "mathematics", "biostatistics", "biology", "heredity", "genetic", "association", "studies", "genetics", "human", "genetics", "genetics", "of", "disease", "statistical", ...	2013	Polygenic Modeling with Bayesian Sparse Linear Mixed Models
In plants and fungi , small RNAs silence gene expression in the nucleus by establishing repressive chromatin states . The role of endogenous small RNAs in metazoan nuclei is largely unknown . Here we show that endogenous small interfering RNAs ( endo-siRNAs ) direct Histone H3 Lysine 9 methylation ( H3K9me ) in Caenorh...	Chromatin consists of DNA and proteins . Chromatin can exist in many different states . The state of chromatin in highly regulated in order to ensure that genes are expressed correctly . RNAs play an important role in the regulation of chromatin . For example , in plants and fungi small RNAs drive the formation of hete...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "model", "organisms", "genetics", "biology", "genetics", "and", "genomics" ]	2011	A Pre-mRNA–Associating Factor Links Endogenous siRNAs to Chromatin Regulation
A fundamental challenge in the post-genome era is to understand and annotate the consequences of genetic variation , particularly within the context of human tissues . We present a set of integrated experiments that investigate the effects of common genetic variability on DNA methylation and mRNA expression in four hum...	In this paper , we describe a comprehensive assessment of the correlation between common genetic variability across the human genome , gene expression , and DNA methylation , within human brain . We studied the cerebellum , frontal cortex , temporal cortex , and pons regions of 150 individuals ( 600 tissue samples ) . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/epigenetics", "genetics", "and", "genomics/bioinformatics", "genetics", "and", "genomics/gene", "expression" ]	2010	Abundant Quantitative Trait Loci Exist for DNA Methylation and Gene Expression in Human Brain

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