Split (3)

train · 24.8k rows

Search is not available for this dataset

article stringlengths 4.36k 149k	summary stringlengths 32 3.35k	section_headings listlengths 1 91	keywords listlengths 0 141	year stringclasses 13 values	title stringlengths 20 281
Impaired insulin secretion is a hallmark of type 2 diabetes ( T2D ) . Epigenetics may affect disease susceptibility . To describe the human methylome in pancreatic islets and determine the epigenetic basis of T2D , we analyzed DNA methylation of 479 , 927 CpG sites and the transcriptome in pancreatic islets from T2D an...	Epigenetic modifications such as DNA methylation are implicated in the development of human disease . However , genome-wide epigenetic analyses in patients with type 2 diabetes ( T2D ) remain scarce . In this study we aimed to unravel the epigenetic basis of T2D by analyzing DNA methylation of 479 , 927 CpG sites in hu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "genome", "analysis", "tools", "diabetes", "mellitus", "type", "2", "diabetic", "endocrinology", "gastroenterology", "and", "hepatology", "endocrinology", "gene", "expression", "genetics", "human", "genetics", "molecular", "genetics", "epigenetics", "biology",...	2014	Genome-Wide DNA Methylation Analysis of Human Pancreatic Islets from Type 2 Diabetic and Non-Diabetic Donors Identifies Candidate Genes That Influence Insulin Secretion
Arsenic contamination of drinking water is a major public health issue in many countries , increasing risk for a wide array of diseases , including cancer . There is inter-individual variation in arsenic metabolism efficiency and susceptibility to arsenic toxicity; however , the basis of this variation is not well unde...	Exposure to arsenic through drinking water is a serious public health issue in many countries , including Bangladesh and the United States . Although there is substantial inter-individual variation in arsenic metabolism and toxicity , the biological basis of this variation is not well understood . Here , we have conduc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "public", "health", "and", "epidemiology", "epidemiology", "global", "health", "public", "health", "toxicology" ]	2012	Genome-Wide Association Study Identifies Chromosome 10q24.32 Variants Associated with Arsenic Metabolism and Toxicity Phenotypes in Bangladesh
Diverse soil-resident bacteria can contribute to plant growth and health , but the molecular mechanisms enabling them to effectively colonize their plant hosts remain poorly understood . We used randomly barcoded transposon mutagenesis sequencing ( RB-TnSeq ) in Pseudomonas simiae , a model root-colonizing bacterium , ...	Plants fix carbon to create an abundance of sugars and amino acids , thus providing an enticing environment for microorganisms that reside in soil . Once these microorganisms have colonized the root environment , they can dramatically influence plant growth and development . We set out to identify a comprehensive set o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "methods", "and", "resources", "transposon", "mutagenesis", "brassica", "operons", "mutation", "model", "organisms", "materials", "science", "experimental", "organism", "systems", "dna", "molecular", "biology", "techniques", "mutagenesis", "and", "gene", "deletion", "te...	2017	Genome-wide identification of bacterial plant colonization genes
Animals living in groups make movement decisions that depend , among other factors , on social interactions with other group members . Our present understanding of social rules in animal collectives is mainly based on empirical fits to observations , with less emphasis in obtaining first-principles approaches that allo...	Animals need to act on uncertain data and with limited cognitive abilities to survive . It is well known that our sensory and sensorimotor processing uses probabilistic estimation as a means to counteract these limitations . Indeed , the way animals learn , forage or select mates is well explained by probabilistic esti...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "animal", "behavior", "theoretical", "biology", "ecology", "biology", "zoology", "neuroscience", "behavioral", "ecology" ]	2011	Collective Animal Behavior from Bayesian Estimation and Probability Matching
Comparisons between diverse vertebrate genomes have uncovered thousands of highly conserved non-coding sequences , an increasing number of which have been shown to function as enhancers during early development . Despite their extreme conservation over 500 million years from humans to cartilaginous fish , these element...	Recent comparative analyses of vertebrate genomes has resulted in the identification of highly conserved non-coding sequences near genes that coordinate early development . Many of these sequences can activate gene expression and are thought to be important regulatory elements . Surprisingly , a large set of these long...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/genomics", "genetics", "and", "genomics/functional", "genomics", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics", "developmental", "biology/developmental", "evolution", "computational", "biology/genomics", "evolutionary", "bio...	2009	Early Evolution of Conserved Regulatory Sequences Associated with Development in Vertebrates
The human gut harbours a large and genetically diverse population of symbiotic microbes that both feed and protect the host . Evolutionary theory , however , predicts that such genetic diversity can destabilise mutualistic partnerships . How then can the mutualism of the human microbiota be explained ? Here we develop ...	The cells of our bodies are greatly outnumbered by the bacteria that live on us and , in particular , in our gut . It is now clear that many gut bacteria are highly beneficial , protecting us from pathogens and helping us with digestion . But what prevents beneficial bacteria from going bad ? Why don't bacteria evolve ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology", "microbiology", "microbial", "evolution", "theoretical", "biology", "evolutionary", "modeling", "biology", "evolutionary", "theory", "microbial", "ecology", "systems", "biology", "ecosystem", "modeling", "immunity", "innate", "immunity", "computational", "biol...	2012	The Evolution of Mutualism in Gut Microbiota Via Host Epithelial Selection
We previously developed a panel of neutralizing monoclonal antibodies against Dengue virus ( DENV ) -1 , of which few exhibited inhibitory activity against all DENV-1 genotypes . This finding is consistent with reports observing variable neutralization of different DENV strains and genotypes using serum from individual...	Within each Dengue virus ( DENV ) serotype , viruses are subdivided into genotypes based upon the protein sequence variation . Infection with a given serotype is believed to induce neutralizing antibodies that provide long-term immunity against secondary infection by a strain of the same serotype . However , recent stu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "virology", "biology", "microbiology", "viral", "structure", "viral", "diseases" ]	2012	Structural Basis of Differential Neutralization of DENV-1 Genotypes by an Antibody that Recognizes a Cryptic Epitope
Polycomb group proteins are transcriptional repressors that play a central role in the establishment and maintenance of gene expression patterns during development . Using mice with an N-ethyl-N-nitrosourea ( ENU ) -induced mutation in Suppressor of Zeste 12 ( Suz12 ) , a core component of Polycomb Repressive Complex 2...	The chromatin environment that surrounds a gene heavily influences the gene's transcriptional activity . Specific modifications on histone tails serve as signposts for the basal transcriptional machinery , reflecting a cell's developmental history and identifying genes that should be actively transcribed and those that...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "molecular", "biology", "genetics", "and", "genomics", "hematology" ]	2008	Polycomb Repressive Complex 2 (PRC2) Restricts Hematopoietic Stem Cell Activity
Functional oocytes are produced through complex molecular and cellular processes . In particular , the contribution of post-transcriptional gene regulation mediated by RNA-binding proteins ( RBPs ) is crucial for controlling proper gene expression during this process . DAZL ( deleted in azoospermia-like ) is one of the...	Evolutionarily conserved DAZ family genes are indispensably involved in germline development . Dazl ( deleted in azoospermia-like ) is a member of the mammalian DAZ family of genes , and plays crucial roles in the sexual differentiation of primordial germ cells and spermatogenesis , and is implicated in the progression...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "rna-binding", "proteins", "medicine", "and", "health", "sciences", "reproductive", "system", "vertebrates", "animals", "xenopus", "germ", "cells", "animal", "models", "zygotes", "developmental", "biology", "oocytes", "model", "organisms", "amphibians", "experimental", ...	2018	Requirement of the 3′-UTR-dependent suppression of DAZL in oocytes for pre-implantation mouse development
The mature human brain is organized into a collection of specialized functional networks that flexibly interact to support various cognitive functions . Studies of development often attempt to identify the organizing principles that guide the maturation of these functional networks . In this report , we combine resting...	The first two decades of life represent a period of extraordinary developmental change in sensory , motor , and cognitive abilities . One of the ultimate goals of developmental cognitive neuroscience is to link the complex behavioral milestones that occur throughout this time period with the equally intricate functiona...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience/neurodevelopment", "neuroscience/cognitive", "neuroscience" ]	2009	Functional Brain Networks Develop from a “Local to Distributed” Organization
Future HIV vaccines are expected to induce effective Th1 cell-mediated and Env-specific antibody responses that are necessary to offer protective immunity to HIV infection . However , HIV infections are highly prevalent in helminth endemic areas . Helminth infections induce polarised Th2 responses that may impair HIV v...	Chronic parasitic worm infections are thought to reduce the efficacy of vaccines . Given that HIV and worm infections are common in sub-Saharan Africa ( SSA ) and their geographical distribution vastly overlaps , it is likely that future HIV vaccines in SSA will be administered to a large proportion of people with chro...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "viral", "vaccines", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "physiology", "immune", "cells", "immunology", "microbiology", "vaccines", "preventive", "medicine", "animal", "models", "model", "organisms", "exp...	2018	Chronic schistosomiasis suppresses HIV-specific responses to DNA-MVA and MVA-gp140 Env vaccine regimens despite antihelminthic treatment and increases helminth-associated pathology in a mouse model
As we move forward from the current generation of genome-wide association ( GWA ) studies , additional cohorts of different ancestries will be studied to increase power , fine map association signals , and generalize association results to additional populations . Knowledge of genetic ancestry as well as population sub...	Many association studies have been published looking for genetic variants contributing to a variety of human traits such as obesity , diabetes , and height . Because the frequency of genetic variants can differ across populations , it is important to have estimates of genetic ancestry in the individuals being studied ....	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/medical", "genetics", "genetics", "and", "genomics/population", "genetics" ]	2010	Rapid Assessment of Genetic Ancestry in Populations of Unknown Origin by Genome-Wide Genotyping of Pooled Samples
Homologous recombination is essential for crossover ( CO ) formation and accurate chromosome segregation during meiosis . It is of considerable importance to work out how recombination intermediates are processed , leading to CO and non-crossover ( NCO ) outcome . Genetic analysis in budding yeast and Caenorhabditis el...	Meiotic recombination is required for genetic diversity and for proper chromosome segregation . Recombination intermediates , such as Holliday junctions ( HJs ) , are generated and eventually resolved to produce crossover ( CO ) and non-crossover ( NCO ) . While an excess of meiotic double-strand breaks is generated , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "meiosis", "cell", "death", "nuclear", "staining", "nucleases", "caenorhabditis", "enzymes", "cell", "cycle", "and", "cell", "division", "cell", "processes", "dna-binding", "proteins", "enzymology", "animals", "animal", "models", "germ", "cells", "cae...	2018	The conserved LEM-3/Ankle1 nuclease is involved in the combinatorial regulation of meiotic recombination repair and chromosome segregation in Caenorhabditis elegans
Human mesenchymal stem cell ( hMSC ) delivery has demonstrated promise in preclinical and clinical trials for myocardial infarction therapy; however , broad acceptance is hindered by limited understanding of hMSC-human cardiomyocyte ( hCM ) interactions . To better understand the electrophysiological consequences of di...	Myocardial infarction—better known as a heart attack—strikes on average every 43 seconds in America . An emerging approach to treat myocardial infarction patients involves the delivery of human mesenchymal stem cells ( hMSCs ) to the damaged heart . While clinical trials of this therapeutic approach have yet to report ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "cell", "physiology", "action", "potentials", "medicine", "and", "health", "sciences", "muscle", "tissue", "cardiovascular", "anatomy", "membrane", "potential", "electrophysiology", "neuroscience", "ion", "channels", "bioassays", "and", "physiological", "analysis", "resea...	2016	Modeling Electrophysiological Coupling and Fusion between Human Mesenchymal Stem Cells and Cardiomyocytes
Soluble ICAM-1 ( sICAM-1 ) is an endothelium-derived inflammatory marker that has been associated with diverse conditions such as myocardial infarction , diabetes , stroke , and malaria . Despite evidence for a heritable component to sICAM-1 levels , few genetic loci have been identified so far . To comprehensively add...	Soluble Intercellular Adhesion Molecule 1 ( sICAM-1 ) is an inflammatory marker that has been associated with several common diseases such as diabetes , heart disease , stroke , and malaria . While it is known that blood concentrations of sICAM-1 are at least partially genetically determined , our current knowledge of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cardiovascular", "disorders/coronary", "artery", "disease", "immunology/genetics", "of", "the", "immune", "system", "genetics", "and", "genomics/complex", "traits" ]	2011	Genome-Wide Association Analysis of Soluble ICAM-1 Concentration Reveals Novel Associations at the NFKBIK, PNPLA3, RELA, and SH2B3 Loci
The current reference test for the detection of S . mansoni in endemic areas is stool microscopy based on one or more Kato-Katz stool smears . However , stool microscopy has several shortcomings that greatly affect the efficacy of current schistosomiasis control programs . A highly specific multiplex real-time polymera...	In the developing world , over 207 million people are infected with parasitic Schistosoma worms . Schistosoma mansoni is one of the most widespread species , and its routine diagnosis is based on microscopic detection of parasite eggs in stool samples . This technique is , however , highly observer-dependent and has su...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion", "Conclusion" ]	[]	2015	Is PCR the Next Reference Standard for the Diagnosis of Schistosoma in Stool? A Comparison with Microscopy in Senegal and Kenya
Epithelial stem cells reside in specific niches that regulate their self-renewal and differentiation , and are responsible for the continuous regeneration of tissues such as hair , skin , and gut . Although the regenerative potential of mammalian teeth is limited , mouse incisors grow continuously throughout life and c...	Stem cells reside in specific niches that regulate their self-renewal and differentiation , and are responsible for the continuous regeneration of tissues . Although the regenerative potential of mammalian teeth is limited , mouse incisors grow continuously throughout life and contain stem cells at their proximal ends ...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "mus", "(mouse)" ]	2007	An Integrated Gene Regulatory Network Controls Stem Cell Proliferation in Teeth
The study of the effect of large-scale drivers ( e . g . , climate ) of human diseases typically relies on aggregate disease data collected by the government surveillance network . The usual approach to analyze these data , however , often ignores a ) changes in the total number of individuals examined , b ) the bias t...	Disease data collected by the government surveillance system are frequently used to understand the influence of large-scale phenomena ( e . g . , climate ) on human health because these data often have a large temporal and/or geographical span . The down side is that a ) these data are often biased towards individuals ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2013	Improving the Modeling of Disease Data from the Government Surveillance System: A Case Study on Malaria in the Brazilian Amazon
As fundamental processes in mitochondrial dynamics , mitochondrial fusion , fission and transport are regulated by several core components , including Miro . As an atypical Rho-like small GTPase with high molecular mass , the exchange of GDP/GTP in Miro may require assistance from a guanine nucleotide exchange factor (...	Mitochondrial dynamics including fusion , fission and transport are essential for energy supply in eukaryotic cells; and defects in mitochondrial dynamics often result in premature aging and diseases such as Parkinson's disease ( PD ) . In mitochondrial transport machinery , the Miro/Milton complex loads mitochondria o...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "invertebrates", "cell", "death", "medicine", "and", "health", "sciences", "rna", "interference", "pathology", "and", "laboratory", "medicine", "enzymes", "neurodegenerative", "diseases", "cell", "processes", "enzymology", "animals", "animal", "models", "guanine", "nucl...	2016	Vimar Is a Novel Regulator of Mitochondrial Fission through Miro
Many viruses subvert the host cell's ability to mount and complete various DNA damage responses ( DDRs ) after infection . HCMV infection of permissive fibroblasts activates host DDRs at the time of viral deposition and during replication , but the DDRs remain uncompleted without arrest or apoptosis . We believe this w...	Human cytomegalovirus ( HCMV ) is a leading cause of birth defects . This may be due in part to this virus' ability to inflict specific damage to its host's DNA , combined with the disruption of an infected cell's ability to repair damage . Earlier studies found that components of the cell's repair machinery were diffe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "microbiology", "molecular", "cell", "biology" ]	2012	HCMV-Infected Cells Maintain Efficient Nucleotide Excision Repair of the Viral Genome while Abrogating Repair of the Host Genome
Placebo response in the clinical trial setting is poorly understood and alleged to be driven by statistical confounds , and its biological underpinnings are questioned . Here we identified and validated that clinical placebo response is predictable from resting-state functional magnetic-resonance-imaging ( fMRI ) brain...	Placebo response is extensively studied in healthy subjects and for experimental manipulations . However , in the clinical setting it has been primarily relegated to statistical confounds . Here , for the first time we examine the predictability of future placebo response in the clinical setting in patients with chroni...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "knees", "rheumatology", "medicine", "and", "health", "sciences", "legs", "diagnostic", "radiology", "functional", "magnetic", "resonance", "imaging", "limbs", "(anatomy)", "neuroscience", "magnetic", "resonance", "imaging", "clinical", "medicine", "pharmaceutics", "brain...	2016	Brain Connectivity Predicts Placebo Response across Chronic Pain Clinical Trials
Neglected Tropical Diseases ( NTDs ) are a group of several communicable diseases prevalent in the tropical and subtropical areas . The co-endemicity of these diseases , the similarity of the clinical signs , and need to maximize limited financial and human resources have necessitated implementation of integrated appro...	Neglected Tropical Diseases are a group of several communicable diseases prevalent in the tropical and subtropical areas . The co-endemicity of these diseases , the similarity of the clinical signs , need to maximize limited financial and human resources have necessitated the integrated approach . Our study aims to sha...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "dermatology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "tropical", "diseases", "geographical", "locations", "treponematoses", "bacterial", "diseases", "skin", "infections", "signs", "and", "symptoms", "benin", "neglected", ...	2018	Integrated approach in the control and management of skin neglected tropical diseases in Lalo, Benin
In BALB/c mice , susceptibility to infection with the intracellular parasite Leishmania major is driven largely by the development of T helper 2 ( Th2 ) responses and the production of interleukin ( IL ) -4 and IL-13 , which share a common receptor subunit , the IL-4 receptor alpha chain ( IL-4Rα ) . While IL-4 is the ...	Leishmaniasis is a parasitic infection caused by protozoan parasites of Leishmania species and is transmitted by the sandfly . Disease in humans ranges from localized cutaneous lesions to disseminated visceral Leishmaniasis . Mouse models of Leishmania major infection have demonstrated that a “healing” response in C57B...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Deletion of IL-4 Receptor Alpha on Dendritic Cells Renders BALB/c Mice Hypersusceptible to Leishmania major Infection
Errors in sample annotation or labeling often occur in large-scale genetic or genomic studies and are difficult to avoid completely during data generation and management . For integrative genomic studies , it is critical to identify and correct these errors . Different types of genetic and genomic data are inter-connec...	Many human diseases are complex with multiple genetic and environmental causal factors interacting together to give rise to disease phenotypes . Such factors affect biological systems through many layers of regulations , including transcriptional and epigenetic regulation , and protein changes . To fully understand the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "biology", "and", "life", "sciences", "genomics", "computational", "biology" ]	2014	MODMatcher: Multi-Omics Data Matcher for Integrative Genomic Analysis
The asparagine hydroxylase , factor inhibiting HIF ( FIH ) , confers oxygen-dependence upon the hypoxia-inducible factor ( HIF ) , a master regulator of the cellular adaptive response to hypoxia . Studies investigating whether asparagine hydroxylation is a general regulatory oxygen-dependent modification have identifie...	Hypoxia is a commonly encountered physiologic and pathophysiologic stress to which mammalian cells have evolved an effective adaptive response . This response is governed by a transcription factor termed the hypoxia-inducible factor ( HIF ) . The mechanisms linking the cellular sensing of oxygen levels to HIF activatio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2016	FIH Regulates Cellular Metabolism through Hydroxylation of the Deubiquitinase OTUB1
Previous work in Arabidopsis showed that after an ancient tetraploidy event , genes were preferentially removed from one of the two homeologs , a process known as fractionation . The mechanism of fractionation is unknown . We sought to determine whether such preferential , or biased , fractionation exists in maize and ...	All genomes can accumulate dispensable DNA in the form of duplications of individual genes or even partial or whole genome duplications . Genomes also can accumulate selfish DNA elements . Duplication events specifically are often followed by extensive gene loss . The maize genome is particularly extreme , having becom...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/plant", "genomes", "and", "evolution", "genetics", "and", "genomics", "genetics", "and", "genomics/comparative", "genomics" ]	2010	Following Tetraploidy in Maize, a Short Deletion Mechanism Removed Genes Preferentially from One of the Two Homeologs
Evolutionary conflict permeates biological systems . In sexually reproducing organisms , sex-specific optima mean that the same allele can have sexually antagonistic expression , i . e . beneficial in one sex and detrimental in the other , a phenomenon known as intralocus sexual conflict . Intralocus sexual conflict is...	Males and females are markedly different in many features , meaning that a trait that is beneficial for one sex may be detrimental for the other . Recent studies show that this type of sexual antagonism is abundant in natural populations; however , no study has tested the evolutionary fate of a sexually antagonistic al...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "sexual", "selection", "sexual", "conflict", "population", "genetics", "biology", "evolutionary", "biology", "evolutionary", "processes", "evolutionary", "genetics", "evolutionary", "theory" ]	2012	Experimental Evolution of a Novel Sexually Antagonistic Allele
FBW7 is a crucial component of an SCF-type E3 ubiquitin ligase , which mediates degradation of an array of different target proteins . The Fbw7 locus comprises three different isoforms , each with its own promoter and each suspected to have a distinct set of substrates . Most FBW7 targets have important functions in de...	The Notch signalling pathway is a highly conserved system that controls cell differentiation decisions in a wide range of animal species and cell types , and at different steps during cell lineage progression . An important function of the Notch pathway is in lateral inhibition—an interaction between equal adjacent cel...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "cell", "fate", "determination", "neural", "stem", "cells", "stem", "cells", "signaling", "molecular", "development", "gene", "expression", "biology", "molecular", "cell", "biology", "cell", "differentiation", "dna", "transcription", "adult",...	2013	Fbw7 Repression by Hes5 Creates a Feedback Loop That Modulates Notch-Mediated Intestinal and Neural Stem Cell Fate Decisions
Lipids are constantly shuttled through the body to redistribute energy and metabolites between sites of absorption , storage , and catabolism in a complex homeostatic equilibrium . In Drosophila , lipids are transported through the hemolymph in the form of lipoprotein particles , known as lipophorins . The mechanisms b...	Understanding the complex mechanisms that regulate the storage of caloric surpluses in the form of fat is critical in view of the public health problems caused by the continuous rise of obesity and diabetes . Important advances in the field have been obtained from studies using simple animal models like worms or flies ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "developmental", "biology/cell", "differentiation", "genetics", "and", "genomics/gene", "function", "cell", "biology" ]	2011	Drosophila Lipophorin Receptors Mediate the Uptake of Neutral Lipids in Oocytes and Imaginal Disc Cells by an Endocytosis-Independent Mechanism
Chagas disease caused by Trypanosoma cruzi is a neglected disease that affects about 7 million people in Latin America , recently emerging on other continents due to migration . As infection in mice is characterized by depletion of plasma L-arginine , the effect on infection outcome was tested in mice with or without L...	Trypanosoma cruzi is the causative agent of the neglected Chagas disease in humans . During infection in mice , depletion of plasma L-arginine is correlated with mortality . L-arginine is a semi-essential amino acid needed for cell proliferation , and is the substrate of arginase 1 ( Arg-1 ) and inducible nitric oxide ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "neurochemistry", "body", "fluids", "parasite", "replication", "cardiovascular", "anatomy", "neuroscience", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "organisms", "parasitemia", "electrocardiography", "protozo...	2018	L-arginine supplementation reduces mortality and improves disease outcome in mice infected with Trypanosoma cruzi
One of the simplest organisms to divide asymmetrically is the bacterium Caulobacter crescentus . The DivL pseudo-histidine kinase , positioned at one cell pole , regulates cell-fate by controlling the activation of the global transcription factor CtrA via an interaction with the response regulator ( RR ) DivK . DivL un...	Across all kingdoms of life the generation of cell-type diversity is the consequence of asymmetry at the point of cell division . The bacterium Caulobacter crescentus divides asymmetrically to produce daughter cells that have distinct morphology and behavior . As in eukaryotes , an unequal distribution of signaling pro...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "crystal", "structure", "caulobacter", "condensed", "matter", "physics", "microbiology", "bacterial", "biochemistry", "signaling", "complexes", "prokaryotic", "models", "model", "organisms", "crystallography", "cellular", "structures", "and", "organelles", "...	2014	Cell Fate Regulation Governed by a Repurposed Bacterial Histidine Kinase
Understanding the etiology of metastasis is very important in clinical perspective , since it is estimated that metastasis accounts for 90% of cancer patient mortality . Metastasis results from a sequence of multiple steps including invasion and migration . The early stages of metastasis are tightly controlled in norma...	We provide here a logical model that proposes gene/pathway candidates that could abrogate metastasis . The model explores the mechanisms and interplays between pathways that are involved in the process , identifies the main players in these mechanisms and gives some insight on how the pathways could be altered . The mo...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration
An increasing number of small RNAs ( sRNAs ) have been shown to regulate critical pathways in prokaryotes and eukaryotes . In bacteria , regulation by trans-encoded sRNAs is predominantly found in the coordination of intricate stress responses . The mechanisms by which sRNAs modulate expression of its targets are diver...	The activation of stress response programs , while crucial for the survival of a bacterial cell under stressful conditions , is costly in terms of energy and substrates and risky to the normal functions of the cell . Stress response is therefore tightly regulated . A recently discovered layer of regulation involves sma...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "microbiology", "computational", "biology", "biophysics", "molecular", "biology", "eubacteria" ]	2007	Quantitative Characteristics of Gene Regulation by Small RNA
This paper introduces the concept of phase-locking analysis of oscillatory cellular signaling systems to elucidate biochemical circuit architecture . Phase-locking is a physical phenomenon that refers to a response mode in which system output is synchronized to a periodic stimulus; in some instances , the number of res...	Key to robust discernment of cell circuit architecture is to have as many distinct response features as possible for comparison and evaluation . One under-appreciated characteristic of oscillatory circuits is that under periodic stimulation , these systems will exhibit responses synchronized to this stimulatory input ,...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biotechnology/chemical", "biology", "of", "the", "cell", "computational", "biology/systems", "biology", "biotechnology/bioengineering", "computational", "biology/signaling", "networks" ]	2010	Phase-Locked Signals Elucidate Circuit Architecture of an Oscillatory Pathway
Intracellular protozoan parasites are causative agents of infectious diseases that constitute major health problems for developing countries . Leishmania sp . , Trypanosoma cruzi or Toxoplasma gondii are all obligate intracellular protozoan parasites that reside and multiply within the host cells of mammals , including...	Research on intracellular parasites require using non-invasive technologies to follow up parasite proliferation inside their natural host cells by staying in the more physiological conditions as possible . High Content Screening ( HCS ) technology has recently emerged as a powerful image-based approach to screen new an...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "engineering", "and", "technology", "signal", "processing", "tropical", "diseases", "microbiology", "parasitic", "diseases", "parasitology", "neglected", "tropical", "diseases", "veteri...	2014	INsPECT, an Open-Source and Versatile Software for Automated Quantification of (Leishmania) Intracellular Parasites
Pathogenic fungi must extend filamentous hyphae across solid surfaces to cause diseases of plants . However , the full inventory of genes which support this is incomplete and many may be currently concealed due to their essentiality for the hyphal growth form . During a random T-DNA mutagenesis screen performed on the ...	All plant-pathogenic fungi must grow hyphae across host tissues and cells to establish diseases . We have identified a single glycosyltransferase enzyme from the pleomorphic wheat pathogen Zymoseptoria tritici which functions specifically to enable hyphal growth on solid surfaces , and is therefore essential for fungal...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Conclusions", "Methods" ]	[ "fungal", "spores", "plant", "anatomy", "medicine", "and", "health", "sciences", "fungal", "genetics", "fungi", "plant", "science", "plant", "pathology", "fungal", "diseases", "plants", "fungal", "reproduction", "infectious", "diseases", "mycology", "grasses", "leaves...	2017	A conserved fungal glycosyltransferase facilitates pathogenesis of plants by enabling hyphal growth on solid surfaces
Children under two years of age are in the most critical window for growth and development . As mobility increases , this time period also coincides with first exposure to soil-transmitted helminth ( STH ) infections in tropical and sub-tropical environments . The association between malnutrition and STH infection , ho...	Malnutrition , including stunting and underweight , is one of the leading causes of morbidity and mortality in preschool-age children . Children under two years of age are at a particularly critical period for growth and development , and for first exposure to worm infections in tropical and subtropical environments . ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "helminth", "infections", "medicine", "and", "health", "sciences", "nutrition", "epidemiology", "biology", "and", "life", "sciences", "soil-transmitted", "helminthiases", "parasitic", "diseases", "malnutrition" ]	2014	Risk Factors Associated with Malnutrition in One-Year-Old Children Living in the Peruvian Amazon
Chromosome segregation requires sister chromatid resolution . Condensins are essential for this process since they organize an axial structure where topoisomerase II can work . How sister chromatid separation is coordinated with chromosome condensation and decatenation activity remains unknown . We combined four-dimens...	Successful cell division requires that chromosomes are properly condensed and that each sister chromatid is self-contained by the time the sister pairs are segregated into separate daughter cells . It is also essential that the kinetochores at the centromeres of each pair of sister chromatids bind microtubules from opp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology" ]	2008	Dual Role of Topoisomerase II in Centromere Resolution and Aurora B Activity
Replication of arboviruses in their arthropod vectors is controlled by innate immune responses . The RNA sequence-specific break down mechanism , RNA interference ( RNAi ) , has been shown to be an important innate antiviral response in mosquitoes . In addition , immune signaling pathways have been reported to mediate ...	Chikungunya virus ( CHIKV ) is a mosquito-borne human-pathogenic arbovirus of the Togaviridae family , genus Alphavirus . Arbovirus replication in vectors , such as mosquitoes , is not passively tolerated but leads to immune responses , that control virus infection . These responses therefore represent interesting targ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "epidemiology", "virology", "vector", "biology", "biology", "and", "life", "sciences", "microbiology", "disease", "vectors" ]	2014	Characterization of Aedes aegypti Innate-Immune Pathways that Limit Chikungunya Virus Replication
PRP4 encodes the only kinase among the spliceosome components . Although it is an essential gene in the fission yeast and other eukaryotic organisms , the Fgprp4 mutant was viable in the wheat scab fungus Fusarium graminearum . Deletion of FgPRP4 did not block intron splicing but affected intron splicing efficiency in ...	In eukaryotic organisms , many genes containing introns that need to be spliced by the spliceosome after transcription . Among all the spliceosome components , Prp4 is the only protein kinase . Unlike other organisms , deletion of the FgPRP4 kinase gene was not lethal in the wheat scab fungus Fusarium graminearum . In ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "phosphorylation", "sequencing", "techniques", "suppressor", "genes", "cereal", "crops", "fungi", "model", "organisms", "crops", "gene", "types", "molecular", "biology", "techniques", "plants", "schizosaccharomyces", "research", "and", "analysis", "methods", "saccharomyce...	2016	FgPrp4 Kinase Is Important for Spliceosome B-Complex Activation and Splicing Efficiency in Fusarium graminearum
The double-stranded RNA-activated protein kinase R ( PKR ) is a key regulator of the innate immune response . Activation of PKR during viral infection culminates in phosphorylation of the α subunit of the eukaryotic translation initiation factor 2 ( eIF2α ) to inhibit protein translation . A broad range of regulatory f...	Our manuscript explores the immune response to viral infection by investigating events triggered by the protein kinase PKR . This sentinel kinase is constitutively expressed in all cells as an inactive protein that is subsequently activated by viral RNA produced during an infection . The active kinase perturbs viral re...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/host", "antiviral", "responses", "molecular", "biology/rna-protein", "interactions", "immunology/innate", "immunity", "cell", "biology/cell", "signaling" ]	2009	An Antiviral Response Directed by PKR Phosphorylation of the RNA Helicase A
Asthma is a complex phenotype influenced by genetic and environmental factors . We conducted a genome-wide association study ( GWAS ) with 938 Japanese pediatric asthma patients and 2 , 376 controls . Single-nucleotide polymorphisms ( SNPs ) showing strong associations ( P<1×10−8 ) in GWAS were further genotyped in an ...	Asthma is the most common chronic disorder in children , and asthma exacerbation is an important cause of childhood morbidity and hospitalization . Here , taking advantage of recent technological advances in human genetics , we performed a genome-wide association study and follow-up validation studies to identify genet...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "genetics", "of", "the", "immune", "system", "clinical", "immunology", "genetics", "genetics", "and", "genomics", "biology", "human", "genetics", "immunology", "respiratory", "medicine", "pulmonology", "asthma" ]	2011	Genome-Wide Association Study Identifies HLA-DP as a Susceptibility Gene for Pediatric Asthma in Asian Populations
The leaves of angiosperms contain highly complex venation networks consisting of recursively nested , hierarchically organized loops . We describe a new phenotypic trait of reticulate vascular networks based on the topology of the nested loops . This phenotypic trait encodes information orthogonal to widely used geomet...	Planar reticular networks are ubiquitous in nature and engineering , formed for instance by the arterial vasculature in the mammalian neocortex , urban street grids or the vascular network of plant leaves . We use a topological metric to characterize the way loops are nested in such networks and analyze a large databas...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Topological Phenotypes Constitute a New Dimension in the Phenotypic Space of Leaf Venation Networks
Viruses often encode proteins with multiple functions due to their compact genomes . Existing approaches to identify functional residues largely rely on sequence conservation analysis . Inferring functional residues from sequence conservation can produce false positives , in which the conserved residues are functionall...	The analysis of sequence conservation is a common approach to identify functional residues within a protein . However , not all functional residues are conserved as natural evolution and species diversification permit continuous innovation of protein functionality through the retention of advantageous mutations . Non-c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Functional Constraint Profiling of a Viral Protein Reveals Discordance of Evolutionary Conservation and Functionality
Myotonic dystrophy type 1 ( DM1 ) is associated with one of the most highly unstable CTG•CAG repeat expansions . The formation of further repeat expansions in transgenic mice carrying expanded CTG•CAG tracts requires the mismatch repair ( MMR ) proteins MSH2 and MSH3 , forming the MutSβ complex . It has been proposed t...	Myotonic dystrophy type 1 is a neuromuscular disease characterized by highly variable clinical manifestations , including muscular and neuropsychological symptoms . DM1 results from the dramatic expansion of an unstable CTG repeat in the DMPK gene . Longer CTG repeats cause a more severe form of the disease and an earl...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neurological", "disorders/neuromuscular", "diseases", "genetics", "and", "genomics/genetics", "of", "disease", "molecular", "biology/dna", "repair" ]	2009	MSH2 ATPase Domain Mutation Affects CTG•CAG Repeat Instability in Transgenic Mice
Ambitious projects aim to record the activity of ever larger and denser neuronal populations in vivo . Correlations in neural activity measured in such recordings can reveal important aspects of neural circuit organization . However , estimating and interpreting large correlation matrices is statistically challenging ....	It is now possible to record the spiking activity of hundreds of neurons at the same time . A meaningful statistical description of the collective activity of these neural populations—their ‘functional connectivity’—is a forefront challenge in neuroscience . We addressed this problem by identifying statistically effici...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Improved Estimation and Interpretation of Correlations in Neural Circuits
A new approach for dengue control has been proposed that relies on life-shortening strains of the obligate intracellular bacterium Wolbachia pipientis to modify mosquito population age structure and reduce pathogen transmission . Previously we reported the stable transinfection of the major dengue vector Aedes aegypti ...	A virulent strain of the vertically-inherited bacterium Wolbachia pipientis ( wMelPop-CLA ) from the vinegar fly Drosophila melanogaster has been established in the dengue vector Aedes aegypti as part of a biological strategy for dengue control . In this medically important disease vector , wMelPop-CLA infection shorte...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "ecology/environmental", "microbiology", "infectious", "diseases/viral", "infections", "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases" ]	2010	A Virulent Wolbachia Infection Decreases the Viability of the Dengue Vector Aedes aegypti during Periods of Embryonic Quiescence
Cancer driving genes have been identified as recurrently affected by variants that alter protein-coding sequences . However , a majority of cancer variants arise in noncoding regions , and some of them are thought to play a critical role through transcriptional perturbation . Here we identified putative transcriptional...	Identifying driver variants is a current challenge facing cancer genomics . A well-established and robust method for this is to find recurrence in large cohorts of samples . Recurrence patterns of amino acid-changing variants can reveal oncogenes and tumor suppressor genes . However , such single-gene approaches have l...	[ "Abstract", "Introduction", "Results/Discussion", "Material", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "breast", "tumors", "genetic", "networks", "gene", "regulation", "protein", "interaction", "networks", "carcinomas", "cancers", "and", "neoplasms", "gastrointestinal", "tumors", "liver", "diseases", "dna", "transcription", "oncol...	2017	Network perturbation by recurrent regulatory variants in cancer
The specific binding of regulatory proteins to DNA sequences exhibits no clear patterns of association between amino acids ( AAs ) and nucleotides ( NTs ) . This complexity of protein-DNA interactions raises the question of whether a simple set of wide-coverage recognition rules can ever be identified . Here , we analy...	Transcriptional factors ( TF ) are proteins that bind specific short DNA sequences adjacent to the genes whose transcription they regulate . Although the nucleotide sequence recognized by a given regulator depends on the amino acids contacting the DNA , the mode in which amino acids and nucleotides interact is strongly...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "computational", "biology/synthetic", "biology", "computational", "biology/transcriptional", "regulation" ]	2010	Local Gene Regulation Details a Recognition Code within the LacI Transcriptional Factor Family
Cooperation and competition between human players in repeated microeconomic games offer a window onto social phenomena such as the establishment , breakdown and repair of trust . However , although a suitable starting point for the quantitative analysis of such games exists , namely the Interactive Partially Observable...	In multi-round games in which players can benefit by trusting each other , swift and catastrophic breakdowns can arise amidst otherwise efficient cooperation . We present a model that quantifies this as a form of anger , and we exploit novel algorithmic improvements in inference based on the model to examine exchanges ...	[ "Abstract", "Introduction", "Results", "Materials", "and", "methods", "Discussion" ]	[ "recreation", "learning", "medicine", "and", "health", "sciences", "decision", "making", "applied", "mathematics", "social", "sciences", "neuroscience", "theory", "of", "mind", "learning", "and", "memory", "health", "care", "cognitive", "psychology", "mathematics", "c...	2018	A model of risk and mental state shifts during social interaction
Topoisomerase inhibitors such as camptothecin and etoposide are used as anti-cancer drugs and induce double-strand breaks ( DSBs ) in genomic DNA in cycling cells . These DSBs are often covalently bound with polypeptides at the 3′ and 5′ ends . Such modifications must be eliminated before DSB repair can take place , bu...	Induction of double-strand breaks ( DSBs ) in chromosomal DNA effectively activates a program of cellular suicide and is widely used for chemotherapy on malignant cancer cells . Cells resist such therapies by quickly repairing the DSBs . Repair is carried out by two major DSB repair pathways , homologous recombination ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/dna", "repair", "genetics", "and", "genomics/gene", "function", "genetics", "and", "genomics/chromosome", "biology" ]	2010	Collaborative Action of Brca1 and CtIP in Elimination of Covalent Modifications from Double-Strand Breaks to Facilitate Subsequent Break Repair
Constraint-based models of metabolism are a widely used framework for predicting flux distributions in genome-scale biochemical networks . The number of published methods for integration of transcriptomic data into constraint-based models has been rapidly increasing . So far the predictive capability of these methods h...	Constraint-based modeling has become one of the most successful approaches for modeling large-scale biochemical networks . There are nowadays hundreds of genome-scale reconstructions of metabolic networks available for a wide variety of organisms ranging from bacteria to human cells . One of the limitations of the cons...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "systems", "biology", "biochemistry", "biochemical", "simulations", "computer", "and", "information", "sciences", "network", "analysis", "biology", "and", "life", "sciences", "metabolic", "networks", "computational", "biology" ]	2014	Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism
Despite the crucial role of the liver in glucose homeostasis , a detailed mathematical model of human hepatic glucose metabolism is lacking so far . Here we present a detailed kinetic model of glycolysis , gluconeogenesis and glycogen metabolism in human hepatocytes integrated with the hormonal control of these pathway...	Glucose is an indispensable fuel for all cells and organs , but at the same time leads to problems at high concentrations . As a consequence , blood glucose is controlled in a narrow range to guarantee constant supply and on the other hand avoid damages associated with elevated glucose levels . The liver is the main or...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "metabolic", "networks", "anatomy", "and", "physiology", "hormones", "endocrine", "physiology", "physiological", "processes", "homeostasis", "insulin", "endocrinology", "diabetes", "and", "endocrinology", "biology", "systems", "biology", "biochemical", "simulati...	2012	Quantifying the Contribution of the Liver to Glucose Homeostasis: A Detailed Kinetic Model of Human Hepatic Glucose Metabolism
Many targets of plant microRNAs ( miRNAs ) are thought to play important roles in plant physiology and development . However , because plant miRNAs are typically encoded by medium-size gene families , it has often been difficult to assess their precise function . We report the generation of a large-scale collection of ...	MiRNAs are small RNA molecules that play an important role in regulating gene function , both in animals and in plants . In plants , miRNA target mimicry is an endogenous mechanism used to negatively regulate the activity of a specific miRNA family , through the production of a false target transcript that cannot be cl...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "discovery", "genetics", "and", "genomics/functional", "genomics", "plant", "biology/plant", "growth", "and", "development", "genetics", "and", "genomics/plant", "genetics", "and", "gene", "expression" ]	2010	A Collection of Target Mimics for Comprehensive Analysis of MicroRNA Function in Arabidopsis thaliana
Modulation of interactions among neurons can manifest as dramatic changes in the state of population dynamics in cerebral cortex . How such transitions in cortical state impact the information processing performed by cortical circuits is not clear . Here we performed experiments and computational modeling to determine ...	When many simple parts interact , the collective behavior of the whole can be astonishingly complex . A particularly striking example is our capacity for sensory perception , which results from the collective interactions of billions of relatively simple neurons . Another example is found in physical systems which unde...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Maximizing Sensory Dynamic Range by Tuning the Cortical State to Criticality
Ebola and Marburg viruses ( family Filoviridae , genera Ebolavirus and Marburgvirus ) cause haemorrhagic fevers in humans , often associated with high mortality rates . The presence of antibodies to Ebola virus ( EBOV ) and Marburg virus ( MARV ) has been reported in some African countries in individuals without a hist...	Ebola and Marburg viruses cause haemorrhagic fevers often fatal to humans . Here , we looked for antibodies to Ebola and Marburg viruses ( i . e . , markers of previous contact with these viruses ) in Congolese blood donors with no previous history of haemorrhagic fever . We found serologic evidence for contact with Ma...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Risk Factors Associated with Ebola and Marburg Viruses Seroprevalence in Blood Donors in the Republic of Congo
DNA polymerase ν ( pol ν ) , encoded by the POLN gene , is an A-family DNA polymerase in vertebrates and some other animal lineages . Here we report an in-depth analysis of pol ν–defective mice and human cells . POLN is very weakly expressed in most tissues , with the highest relative expression in testis . We construc...	The work described here fills a current gap in the study of the 16 known DNA polymerases in vertebrate genomes . Until now , experiments with genetically disrupted mice have been reported for all but pol ν , encoded by the POLN gene . To intensively analyze the role of mammalian pol ν we generated multiple Poln-deficie...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "gene", "regulation", "dna-binding", "proteins", "animal", "models", "dna", "damage", "model", "organisms", "polymerases", "experimental", "organism", "systems", "sequence", "motif", "analysis", "dna", "molecular", "biology", "techniques", "mammalian", "genomics", "homo...	2017	Analysis of DNA polymerase ν function in meiotic recombination, immunoglobulin class-switching, and DNA damage tolerance
A single-tube one-step real-time reverse transcription loop-mediated isothermal amplification ( RT-LAMP ) assay for rapid detection of chikungunya virus ( CHIKV ) targeting the conserved 6K-E1 target region was developed . The assay was validated with sera collected from a CHIKV outbreak in Senegal in 2015 . A novel de...	Current chikungunya virus ( CHIKV ) outbreaks highlight the necessity of sensitive techniques to allow the virus detection even at an early stage ( before the onset of clinical symptoms ) . In addition , CHIKV sometimes is misdiagnosed with other pathogens ( i . e . , dengue virus or malaria ) , which implies that spec...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "annealing", "(genetics)", "pathogens", "tropical", "diseases", "microbiology", "rna", "extraction", "alphaviruses", "viruses", "chikungunya", ...	2018	Development of a single-tube one-step RT-LAMP assay to detect the Chikungunya virus genome
The multidimensional computations performed by many biological systems are often characterized with limited information about the correlations between inputs and outputs . Given this limitation , our approach is to construct the maximum noise entropy response function of the system , leading to a closed-form and minima...	Biological systems across many scales , from molecules to ecosystems , can all be considered information processors , detecting important events in their environment and transforming them into actions . Detecting events of interest in the presence of noise and other overlapping events often necessitates the use of nonl...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "physics", "neuroscience/sensory", "systems", "computational", "biology/computational", "neuroscience", "computational", "biology", "neuroscience/theoretical", "neuroscience" ]	2011	Minimal Models of Multidimensional Computations
Increased pain sensitivity is a comorbidity associated with many clinical diseases , though the underlying causes are poorly understood . Recently , chronic pain hypersensitivity in rodents treated to induce chronic inflammation in peripheral tissues was linked to enhanced tryptophan catabolism in brain mediated by ind...	Chronic pain is a factor in diseases that afflict many people , yet the underlying causes of pain are poorly understood . Here we assess the effects of virus infections on pain sensitivity in mice . Infecting mice with two different viruses , influenza and mouse leukemia virus ( MuLV ) increased pain sensitivity . Infl...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "somatosensory", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "immune", "cells", "pathology", "and", "laboratory", "medicine", "respiratory", "infections", "nervous", "system", "spleen", "pathogens", "immunology", "microbi...	2016	Virus Infections Incite Pain Hypersensitivity by Inducing Indoleamine 2,3 Dioxygenase
The importance of host-specialization to speciation processes in obligate host-associated bacteria is well known , as is also the ability of recombination to generate cohesion in bacterial populations . However , whether divergent strains of highly recombining intracellular bacteria , such as Wolbachia , can maintain t...	Speciation in sexual organisms is defined as the inability of two populations to get viable offspring . Speciation in asexual , obligate endosymbionts is thought to be an indirect consequence of host-specialization . An important question is if divergent endosymbionts would start blending if the host barrier isolating ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome", "sequencing", "genome", "evolution", "microbial", "evolution", "comparative", "genomics", "biology", "genomics", "evolutionary", "biology", "genomic", "evolution", "microbiology", "evolutionary", "processes", "host-pathogen", "interaction" ]	2013	Comparative Genomics of Wolbachia and the Bacterial Species Concept
Replicative DNA helicases expose the two strands of the double helix to the replication apparatus , but accessory helicases are often needed to help forks move past naturally occurring hard-to-replicate sites , such as tightly bound proteins , RNA/DNA hybrids , and DNA secondary structures . Although the Schizosaccharo...	Progression of the DNA replication machinery is challenged in every S phase by active transcription , tightly bound protein complexes , and formation of stable DNA secondary structures . Using genome-wide analyses , we show that the evolutionarily conserved fission yeast Pfh1 DNA helicase promotes fork progression and ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "transfer", "rna", "enzymes", "cell", "cycle", "and", "cell", "division", "cell", "processes", "dna-binding", "proteins", "enzymology", "dna", "damage", "fungi", "model", "organisms", "polymerases", "dna", "replication", "dna", "synthesis", "phase", "schizosaccharomyc...	2016	Pfh1 Is an Accessory Replicative Helicase that Interacts with the Replisome to Facilitate Fork Progression and Preserve Genome Integrity
Mycetoma is a neglected tropical disease , endemic in many tropical and subtropical regions , characterised by massive deformity and disability and can be fatal if untreated early and appropriately . Interleukins ( IL ) -35 and IL-37 are newly discovered cytokines that play an important role in suppressing the immune s...	Mycetoma is a progressive chronic granulomatous fungal or bacterial infection that may result in massive destruction of subcutaneous tissues , muscles and bones . Mycetoma is a neglected disease which is endemic in many tropical and subtropical areas . If the disease is not treated properly , eventually it ends up with...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[]	2019	The Role of Interleukin-1 cytokine family (IL-1β, IL-37) and interleukin-12 cytokine family (IL-12, IL-35) in eumycetoma infection pathogenesis
How do adapting populations navigate the tensions between the costs of gene expression and the benefits of gene products to optimize the levels of many genes at once ? Here we combined independently-arising beneficial mutations that altered enzyme levels in the central metabolism of Methylobacterium extorquens to uncov...	The pace and outcome of a series of adaptive steps in an evolving lineage depends upon how well different beneficial mutations stack on top of each other . We found that independent beneficial mutations that affected gene expression for a metabolic pathway did not work well together , and were often jointly deleterious...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "microbial", "metabolism", "microbial", "mutation", "population", "genetics", "metabolic", "networks", "microbiology", "bacterial", "biochemistry", "microbial", "evolution", "molecular", "genetics", "forms", "of", "evolution", "microbial", "physiology", "met...	2014	Mapping the Fitness Landscape of Gene Expression Uncovers the Cause of Antagonism and Sign Epistasis between Adaptive Mutations
Experimental leishmaniasis is an excellent model system for analyzing Th1/Th2 differentiation . Resistance to Leishmania ( L . ) major depends on the development of a L . major specific Th1 response , while Th2 differentiation results in susceptibility . There is growing evidence that the microenvironment of the early ...	To clear skin infections with the parasite Leishmania major , a specific T-helper ( Th ) -cell immune response has to be generated . The type of Th-cell response is determined early after infection by yet unknown mechanisms . In resistant mice a Th1-pattern is generated . A Th2-pattern in BALB/c mice , however , result...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/immune", "response", "immunology/innate", "immunity", "dermatology/skin", "infections", "infectious", "diseases/skin", "infections", "immunology/immunity", "to", "infections" ]	2010	Keratinocytes Determine Th1 Immunity during Early Experimental Leishmaniasis
The identification of genes essential for bacterial growth and survival represents a promising strategy for the discovery of antimicrobial targets . Essential genes can be identified on a genome-scale using transposon mutagenesis approaches; however , variability between screens and challenges with interpretation of es...	With the rise of antibiotic resistance , there is a growing need to discover new therapeutic targets to treat bacterial infections . One attractive strategy is to target genes that are essential for growth and survival . Essential genes can be identified with transposon mutagenesis approaches; however , variability bet...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2019	Reconciling high-throughput gene essentiality data with metabolic network reconstructions
Respiratory syncytial virus ( RSV ) is the most frequent cause of lower respiratory disease in infants , but no vaccine or effective therapy is available . The initiation of RSV infection of immortalized cells is largely dependent on cell surface heparan sulfate ( HS ) , a receptor for the RSV attachment ( G ) glycopro...	Respiratory syncytial virus ( RSV ) is the second most common infectious cause of infant death worldwide . Despite this great clinical impact , no effective antivirals or vaccines against RSV are available . Here we find that the RSV attachment ( G ) glycoprotein uses CX3CR1 as a receptor on primary human airway epithe...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Respiratory Syncytial Virus Uses CX3CR1 as a Receptor on Primary Human Airway Epithelial Cultures
Understanding the relationship between external stimuli and the spiking activity of cortical populations is a central problem in neuroscience . Dense recurrent connectivity in local cortical circuits can lead to counterintuitive response properties , raising the question of whether there are simple arithmetical rules f...	Understanding how the brain represents and processes stimuli requires a quantitative understanding of how signals propagate through networks of neurons . Developing such an understanding is made difficult by the dense interconnectivity of neurons , especially in the cerebral cortex . One approach to quantifying neural ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "action", "potentials", "medicine", "and", "health", "sciences", "optogenetics", "neural", "networks", "membrane", "potential", "electrophysiology", "neuroscience", "simulation", "and", "modeling", "network", "analysis", "brain", "mapping", "convolution", "bioassays", "an...	2018	Imbalanced amplification: A mechanism of amplification and suppression from local imbalance of excitation and inhibition in cortical circuits
A few studies investigated the relationship between toxoplasmosis and mental disorders , such as obsessive compulsive disorder ( OCD ) . However , the specific nature of the association between Toxoplasma gondii ( T . gondii ) infection and OCD is not yet clear . The aim of this study was to collect information on the ...	Toxoplasma gondii ( T . gondii ) is an obligate neurotropic parasite that infected about 25–30% of the total human population in the developed and developing countries . The obsessive compulsive disorder ( OCD ) is a psychiatric disease that affects the income and quality of life . Some studies confirmed an association...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "neuropsychiatric", "disorders", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "anxiety", "disorders", "toxoplasma", "gondii", "statistics", "obsessive-compulsive", "disorder", "metaanalysis", "database", "searching", "parasitic", "diseases", "para...	2019	Relationship between toxoplasmosis and obsessive compulsive disorder: A systematic review and meta-analysis
Maximum growth rate per individual ( r ) and carrying capacity ( K ) are key life-history traits that together characterize the density-dependent population growth and therefore are crucial parameters of many ecological and evolutionary theories such as r/K selection . Although r and K are generally thought to correlat...	Two parameters are widely used to describe density-dependent population growth: the maximum growth rate per individual ( r ) and the maximum population size or carrying capacity ( K ) . The relationship between these parameters is the subject of many fundamental theories and debates in ecology and evolutionary biology ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "organismal", "evolution", "ecology", "and", "environmental", "sciences", "quantitative", "trait", "loci", "microbiology", "fungi", "model", "organisms", "experimental", "organism", "systems", "microbial", "evolution", "molecular", "genetics", "population", "biology", "sa...	2019	Environment-dependent pleiotropic effects of mutations on the maximum growth rate r and carrying capacity K of population growth
The centrosome is a non–membrane-bound cellular compartment consisting of 2 centrioles surrounded by a protein coat termed the pericentriolar material ( PCM ) . Centrioles generally remain physically associated together ( a phenomenon called centrosome cohesion ) , yet how this occurs in the absence of a bounding lipid...	Many subcellular organelles are not enclosed by a lipid membrane but instead exist freely in the cellular interior . How the number and position of such non–membrane-bound organelles are maintained is a general unanswered question . Here , I study this problem by focusing on the centrosome—an organelle that nucleates m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "centrosomes", "gene", "regulation", "cell", "cycle", "and", "cell", "division", "cell", "processes", "green", "fluorescent", "protein", "light", "microscopy", "mitosis", "luminescent", "proteins", "microscopy", "centrioles", "cellular", "structures", "and", "organelles...	2018	Stable centrosomal roots disentangle to allow interphase centriole independence
HIV-1 infection begins with the binding of trimeric viral envelope glycoproteins ( Env ) to CD4 and a co-receptor on target T-cells . Understanding how these ligands influence the structure of Env is of fundamental interest for HIV vaccine development . Using cryo-electron microscopy , we describe the contrasting struc...	HIV infection occurs following the binding of viral envelope glycoproteins ( Env ) to receptors on target cell surfaces . Binding to these molecules induces conformational changes in Env , ultimately leading to the exposure of a viral fusion peptide and fusion of viral and cellular membranes . Understanding the structu...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "hiv", "viral", "diseases" ]	2012	Structural Mechanism of Trimeric HIV-1 Envelope Glycoprotein Activation
In 1980 , human diploid cell vaccine ( HDCV , Imovax Rabies , Sanofi Pasteur ) , was licensed for use in the United States . To assess adverse events ( AEs ) after HDCV reported to the US Vaccine Adverse Event Reporting System ( VAERS ) , a spontaneous reporting surveillance system . We searched VAERS for US reports af...	In 1980 , human diploid cell rabies vaccine ( HDCV , Imovax Rabies , Sanofi Pasteur ) , was licensed for use in the United States . To assess adverse events ( AEs ) after HDCV reported to the US Vaccine Adverse Event Reporting System ( VAERS ) , a spontaneous reporting surveillance system . We searched VAERS for US rep...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "clinical", "research", "design", "pathogens", "immunology", "tropical", "diseases", "microbiology", "data", "mining", "vaccines", "preventive", "medicine", "research", "design", "vir...	2016	Post-Marketing Surveillance of Human Rabies Diploid Cell Vaccine (Imovax) in the Vaccine Adverse Event Reporting System (VAERS) in the United States, 1990‒2015
Circadian oscillator networks rely on a transcriptional activator called CLOCK/CYCLE ( CLK/CYC ) in insects and CLOCK/BMAL1 or NPAS2/BMAL1 in mammals . Identifying the targets of this heterodimeric basic-helix-loop-helix ( bHLH ) transcription factor poses challenges and it has been difficult to decipher its specific s...	Life on earth is subject to daily light/dark and temperature cycles that reflect the earth rotation about its own axis . Under such conditions , organisms ranging from bacteria to human have evolved molecularly geared circadian clocks that resonate with the environmental cycles . These clocks serve as internal timing d...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry", "fish", "computational", "biology", "drosophila", "mammals" ]	2008	Modeling an Evolutionary Conserved Circadian Cis-Element
Sequencing projects have identified large numbers of rare stop-gain and frameshift variants in the human genome . As most of these are observed in the heterozygous state , they test a gene’s tolerance to haploinsufficiency and dominant loss of function . We analyzed the distribution of truncating variants across 16 , 2...	Genome sequencing provides evidence for large numbers of putative protein truncating variants in humans . Most truncating variants are only observed in few individuals but are collectively prevalent and widely distributed across the coding genome . Most of the truncating variants are so rare that they are only observed...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome
Malaria infection begins when a female Anopheles mosquito injects Plasmodium sporozoites into the skin of its host during blood feeding . Skin-deposited sporozoites may enter the bloodstream and infect the liver , reside and develop in the skin , or migrate to the draining lymph nodes ( DLNs ) . Importantly , the DLN i...	Malaria is responsible for the deaths of 0 . 5–2 million people each year . A safe and effective vaccine is likely needed for the control or eradication of malaria . Immunization with irradiated sporozoites , the infectious stage of the parasite transmitted by mosquitoes , protects people against malaria through the ac...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Lymph-Node Resident CD8α+ Dendritic Cells Capture Antigens from Migratory Malaria Sporozoites and Induce CD8+ T Cell Responses
The human immune system depends on a highly diverse collection of antibody-making B cells . B cell receptor sequence diversity is generated by a random recombination process called “rearrangement” forming progenitor B cells , then a Darwinian process of lineage diversification and selection called “affinity maturation ...	Antibodies must recognize a great diversity of antigens to protect us from infectious disease . The binding properties of antibodies are determined by the DNA sequences of their corresponding B cell receptors ( BCRs ) . These BCR sequences are created in naive form by VDJ recombination , which randomly selects and trim...	[ "Abstract", "Introduction", "Results", "Methods" ]	[ "blood", "cells", "sequencing", "techniques", "medicine", "and", "health", "sciences", "immune", "cells", "markov", "models", "insertion", "mutation", "applied", "mathematics", "immunology", "simulation", "and", "modeling", "algorithms", "mutation", "mathematics", "phyl...	2016	Likelihood-Based Inference of B Cell Clonal Families
Antigenic variation in African trypanosomes requires monoallelic transcription and switching of variant surface glycoprotein ( VSG ) genes . The transcribed VSG , always flanked by ‘70 bp’-repeats and telomeric-repeats , is either replaced through DNA double-strand break ( DSB ) repair or transcriptionally inactivated ...	Previous studies on antigenic variation in African trypanosomes relied upon positive or negative selection , yielding only cells that underwent variation . This made it difficult to define individual switched clones as independent , potentially introduced bias in the relative contribution of each switching mechanism an...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "biology", "microbiology", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2013	DNA Break Site at Fragile Subtelomeres Determines Probability and Mechanism of Antigenic Variation in African Trypanosomes
A critical question in biology is the identification of functionally important amino acid sites in proteins . Because functionally important sites are under stronger purifying selection , site-specific substitution rates tend to be lower than usual at these sites . A large number of phylogenetic models have been develo...	To understand how a protein functions , a critical step is to know which regions in its protein tertiary structure may be functionally important . Functionally important protein regions are typically more conserved than other regions because mutations in these regions are more likely to be deleterious . A number of phy...	[ "Abstract", "Introduction", "Results", "Discussion", "Models" ]	[ "evolutionary", "modeling", "sequence", "analysis", "biology", "computational", "biology" ]	2014	Phylogenetic Gaussian Process Model for the Inference of Functionally Important Regions in Protein Tertiary Structures
Defective viral genomes of the copy-back type ( cbDVGs ) are the primary initiators of the antiviral immune response during infection with respiratory syncytial virus ( RSV ) both in vitro and in vivo . However , the mechanism governing cbDVG generation remains unknown , thereby limiting our ability to manipulate cbDVG...	Copy-back defective viral genomes ( cbDVGs ) regulate infection and pathogenesis of Mononegavirales . cbDVGs are believed to arise from random errors that occur during virus replication and the predominant hypothesis is that the viral polymerase is the main driver of cbDVG generation . Here we describe a specific genom...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "flow", "cytometry", "medicine", "and", "health", "sciences", "respiratory", "infections", "rna", "extraction", "dna-binding", "proteins", "microbiology", "pulmonology", "pediatrics", "polymerases", "viral", "genome", "pediatric", "infections", "extraction", "techniques", ...	2019	A specific sequence in the genome of respiratory syncytial virus regulates the generation of copy-back defective viral genomes
We seek to characterize the motility of mouse fibroblasts on 2D substrates . Utilizing automated tracking techniques , we find that cell trajectories are super-diffusive , where displacements scale faster than t1/2 in all directions . Two mechanisms have been proposed to explain such statistics in other cell types: run...	Cells must move through their environment in many different biological processes , from wound healing to cancer invasion to the development of an embryo . There are different ways for cells to explore the physical space around them—ranging from moving along a straight path at constant speed to executing a random walk w...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "cell", "motility", "medicine", "and", "health", "sciences", "ballistics", "immune", "cells", "classical", "mechanics", "immunology", "vertebrates", "mathematical", "models", "mice", "animals", "fibroblasts", "mammals", "probability", "distribution", "...	2019	Identifying the mechanism for superdiffusivity in mouse fibroblast motility
Stress response networks frequently have a single upstream regulator that controls many downstream genes . However , the downstream targets are often diverse , therefore it remains unclear how their expression is specialized when under the command of a common regulator . To address this , we focused on a stress respons...	Bacteria can sense and respond to stress in their environment . This process is often coordinated by a master regulator that turns on or off many downstream genes , allowing the cell to survive the stress . However , individual genes encode products that are diverse and optimal expression for each gene may differ . Her...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "channel", "capacity", "cellular", "stress", "responses", "engineering", "and", "technology", "gene", "regulation", "signal", "processing", "cell", "processes", "green", "fluorescent", "protein", "signal", "filtering", "regulator", "genes", "luminescent", "proteins", "g...	2017	Customized Regulation of Diverse Stress Response Genes by the Multiple Antibiotic Resistance Activator MarA
Tardigrada , a phylum of meiofaunal organisms , have been at the center of discussions of the evolution of Metazoa , the biology of survival in extreme environments , and the role of horizontal gene transfer in animal evolution . Tardigrada are placed as sisters to Arthropoda and Onychophora ( velvet worms ) in the sup...	Tardigrades are justly famous for their abilities to withstand environmental extremes . Many freshwater and terrestrial species can undergo anhydrobiosis—life without water—and thereby withstand desiccation , freezing , and other insults . We explored the comparative biology of anhydrobiosis in 2 species of tardigrade ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "taxonomy", "horizontal", "gene", "transfer", "invertebrates", "ecology", "and", "environmental", "sciences", "computational", "biology", "extremophiles", "invertebrate", "genomics", "animals", "gene", "transfer", "genomic", "databases", "phylogenetics", "data", "management...	2017	Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus
Mathematical models predict an exponential distribution of infection prevalence across communities where a disease is disappearing . Trachoma control programs offer an opportunity to test this hypothesis , as the World Health Organization has targeted trachoma for elimination as a public health concern by the year 2020...	Trachoma is the leading infectious cause of blindness and the World Health Organization plans to eliminate it as a public health concern worldwide by the year 2020 . It can be difficult for local trachoma programs to assess whether disease is headed towards elimination in their area . Mathematical infectious disease mo...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	The Distribution of Ocular Chlamydia Prevalence across Tanzanian Communities Where Trachoma Is Declining
Microscopy-based identification of eggs in stool offers simple , reliable and economical options for assessing the prevalence and intensity of hookworm infections , and for monitoring the success of helminth control programs . This study was conducted to evaluate and compare the diagnostic parameters of the Kato-Katz (...	Hookworm infection is widespread in resource-poor countries worldwide . Detection of hookworm eggs in human feces can be done by the Kato Katz technique ( KK ) , sodium nitrate flotation technique ( SNF ) or PCR . This study was conducted to evaluate and compare the diagnostic parameters of the KK and simple SNF in ter...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "veterinary", "parasitology", "parasitology", "biology", "and", "life", "sciences", "intestinal", "parasites", "veterinary", "science" ]	2014	Simple Fecal Flotation Is a Superior Alternative to Guadruple Kato Katz Smear Examination for the Detection of Hookworm Eggs in Human Stool
Clostridium difficile is the etiological agent of antibiotic-associated diarrhoea ( AAD ) and pseudomembranous colitis in humans . The role of the surface layer proteins ( SLPs ) in this disease has not yet been fully explored . The aim of this study was to investigate a role for SLPs in the recognition of C . difficil...	Clostridium difficile is the leading cause of antibiotic-associated diarrhoea among hospital patients and in severe cases can cause pseudomembranous colitis and even death . There is currently limited information regarding how this pathogen is recognised by the immune system and the key mechanisms necessary for clearan...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immune", "cells", "immune", "activation", "antigen-presenting", "cells", "immunology", "microbiology", "host-pathogen", "interaction", "adaptive", "immunity", "bacterial", "pathogens", "t", "cells", "biology", "pathogenesis", "gram", "positive", "immunity", "innate", "im...	2011	A Role for TLR4 in Clostridium difficile Infection and the Recognition of Surface Layer Proteins
African animal trypanosomosis is a major obstacle to the development of more efficient and sustainable livestock production systems in West Africa . Riverine tsetse species such as Glossina palpalis gambiensis Vanderplank and Glossina tachinoides Westwood are the major vectors . A wide variety of control tactics is ava...	Tsetse flies are insects that transmit trypanosomes to humans ( sleeping sickness ) and animals ( nagana ) . Controlling these vectors is a very efficient way to control these diseases . In Burkina Faso , a tsetse eradication campaign is presently targeting the northern part of the Mouhoun River Basin . To attain this ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "veterinary", "diseases", "pest", "control", "african", "trypanosomiasis", "zoonotic", "diseases", "neglected", "tropical", "diseases", "veterinary", "science", "integrated", "control", "agriculture", "trypanosomiasis" ]	2011	Contrasting Population Structures of Two Vectors of African Trypanosomoses in Burkina Faso: Consequences for Control
The basic unit of genome packaging is the nucleosome , and nucleosomes have long been proposed to restrict DNA accessibility both to damage and to transcription . Nucleosome number in cells was considered fixed , but recently aging yeast and mammalian cells were shown to contain fewer nucleosomes . We show here that ma...	The accurate preservation and correct retrieval of genetic information is crucial for all living organisms . In eukaryotes , whether single-celled yeast or complex mammals , the DNA containing the genetic information is wrapped around beads of histone proteins to form structures called nucleosomes along the length of t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "expression", "analysis", "protein", "abundance", "dna", "transcription", "genome", "sequencing", "chromatin", "chromosome", "biology", "gene", "expression", "biology", "proteomics", "molecular", "biology", "biochemistry", "cell", "biology", "genomics", "molecul...	2011	Substantial Histone Reduction Modulates Genomewide Nucleosomal Occupancy and Global Transcriptional Output
In the yeast Saccharomyces cerevisiae and most other eukaryotes , mitotic recombination is important for the repair of double-stranded DNA breaks ( DSBs ) . Mitotic recombination between homologous chromosomes can result in loss of heterozygosity ( LOH ) . In this study , LOH events induced by ultraviolet ( UV ) light ...	Nearly every living organism has to cope with DNA damage caused by ultraviolet ( UV ) exposure from the sun . UV causes various types of DNA damage . Defects in the repair of these DNA lesions are associated with the human disease xeroderma pigmentosum , one symptom of which is predisposition to skin cancer . The DNA d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Genome-Wide High-Resolution Mapping of UV-Induced Mitotic Recombination Events in Saccharomyces cerevisiae
Control of rabies requires a consistent supply of dependable resources , constructive cooperation between veterinary and public health authorities , and systematic surveillance . These are challenging in any circumstances , but particularly during conflict . Here we describe available human rabies surveillance data fro...	Control of rabies requires cooperation between government departments , consistent funding , and an understanding of the epidemiology of the disease obtained through surveillance . Here we describe human rabies surveillance data from Iraq and the results of renewed sampling for rabies in animals . In Iraq , it is oblig...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "social", "and", "behavioral", "sciences", "microbiology", "political", "science", "rabies", "neglected", "tropical", "diseases", "infectious", "disease", "control", "veterinary", "science", "war", "and", "civil", ...	2013	Rabies in Iraq: Trends in Human Cases 2001–2010 and Characterisation of Animal Rabies Strains from Baghdad
Many natural prion diseases of humans and animals are considered to be acquired through oral consumption of contaminated food or pasture . Determining the route by which prions establish host infection will identify the important factors that influence oral prion disease susceptibility and to which intervention strateg...	Prion diseases are infectious neurodegenerative disorders that affect humans and animals . Many natural prion diseases are orally acquired through consumption of contaminated food or pasture . An understanding of how prions infect the intestine will help identify factors that influence disease susceptibility and allow ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "diseases", "medicine", "and", "health", "sciences", "immune", "physiology", "spleen", "animal", "prion", "diseases", "lymphatic", "system", "zoology", "digestive", "system", "research", "and", "analysis", "methods", "specimen", "preparation", "and", "treatm...	2016	Increased Abundance of M Cells in the Gut Epithelium Dramatically Enhances Oral Prion Disease Susceptibility
Iron is an essential cofactor , but it is also toxic at high levels . In Schizosaccharomyces pombe , the sensor glutaredoxin Grx4 guides the activity of the repressors Php4 and Fep1 to mediate a complex transcriptional response to iron deprivation: activation of Php4 and inactivation of Fep1 leads to inhibition of iron...	Iron is an essential biometal but it is also toxic , and therefore its intracellular availability from disposable iron pools is tightly regulated . From bacteria to higher eukaryotes , iron starvation triggers complex genetic responses to exacerbate the otherwise limited iron uptake and decrease intracellular iron stor...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	A Cascade of Iron-Containing Proteins Governs the Genetic Iron Starvation Response to Promote Iron Uptake and Inhibit Iron Storage in Fission Yeast
The innate immune system of plants consists of two layers . The first layer , called basal resistance , governs recognition of conserved microbial molecules and fends off most attempted invasions . The second layer is based on Resistance ( R ) genes that mediate recognition of effectors , proteins secreted by pathogens...	In agriculture , the most environmentally friendly way to combat plant diseases is to make use of the innate immune system of plants , for instance by crossing into crop varieties polymorphic resistance genes that occur in natural populations of the crop plant or its close relatives . Plant pathogens , however , have c...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "plant", "biology/plant-biotic", "interactions" ]	2008	Suppression of Plant Resistance Gene-Based Immunity by a Fungal Effector
We use high-density single nucleotide polymorphism ( SNP ) genotyping microarrays to demonstrate the ability to accurately and robustly determine whether individuals are in a complex genomic DNA mixture . We first develop a theoretical framework for detecting an individual's presence within a mixture , then show , thro...	In this report we describe a framework for accurately and robustly resolving whether individuals are in a complex genomic DNA mixture using high-density single nucleotide polymorphism ( SNP ) genotyping microarrays . We develop a theoretical framework for detecting an individual's presence within a mixture , show its l...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "genetics", "and", "genomics/genomics", "genetics", "and", "genomics", "genetics", "and", "genomics/bioinformatics", "genetics", "and", "genomics/medical", "genetics", "genetics", "and", "genomics/population", "genetics" ]	2008	Resolving Individuals Contributing Trace Amounts of DNA to Highly Complex Mixtures Using High-Density SNP Genotyping Microarrays
Leishmaniasis is one of the most diverse and complex of all vector-borne diseases worldwide . It is caused by parasites of the genus Leishmania , obligate intramacrophage protists characterised by diversity and complexity . Its most severe form is visceral leishmaniasis ( VL ) , a systemic disease that is fatal if left...	Leishmaniasis is a vector-borne disease with a complex ecology and epidemiology . It has three main clinical forms of which visceral leishmaniasis ( VL ) is the most severe , as it is fatal if untreated . It is caused by a protist parasite , Leishmania spp . , and is transmitted to humans by phlebotomine sandflies . Th...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "biota", "microbiology", "metagenomics", "neglected", "tropical", "diseases", "infectious", "disease", "control", "environmental", "protection", "infectious", "diseases", "biology", "vectors", "and", "hosts", "ecology", "vector", "biology", "leishmaniasis", "g...	2011	Metagenomic Analysis of Taxa Associated with Lutzomyia longipalpis, Vector of Visceral Leishmaniasis, Using an Unbiased High-Throughput Approach
Trinucleotide repeat expansion is the genetic basis for a sizeable group of inherited neurological and neuromuscular disorders . Friedreich ataxia ( FRDA ) is a relentlessly progressive neurodegenerative disorder caused by GAA·TTC repeat expansion in the first intron of the FXN gene . The expanded repeat reduces FXN mR...	The human genome is comprised of the DNA base sequences used by the cell as a blueprint to direct proper cellular function . Changes in this sequence , known as genomic instability , often interfere with vital cellular functions , resulting in genetic disorders . Repetitive DNA sequences are particularly susceptible to...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/disease", "models", "molecular", "biology/transcription", "elongation", "neurological", "disorders/neuromuscular", "diseases", "genetics", "and", "genomics/gene", "expression" ]	2009	Progressive GAA·TTC Repeat Expansion in Human Cell Lines
JC polyomavirus ( JCV ) carriers with a compromised immune system , such as in HIV , or subjects on immune-modulating therapies , such as anti VLA-4 therapy may develop progressive multifocal leukoencephalopathy ( PML ) which is a lytic infection of oligodendrocytes in the brain . Serum antibodies to JCV mark infection...	JC virus infection can lead to progressive multifocal leukoencephalopathy in individuals with a compromised immune system , such as during HIV infections or when treated with immunosuppressive or immunomodulating therapies . Progressive multifocal leukoencephalopathy is a rare but potentially fatal disease characterize...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "progressive", "multifocal", "leukoencephalopathy", "infectious", "diseases", "medicine", "and", "health", "sciences", "major", "histocompatibility", "complex", "clinical", "immunology", "multiple", "sclerosis", "autoimmune", "diseases", "biology", "and", "life", "sciences"...	2014	JC Polyomavirus Infection Is Strongly Controlled by Human Leucocyte Antigen Class II Variants
A SNP upstream of the INSIG2 gene , rs7566605 , was recently found to be associated with obesity as measured by body mass index ( BMI ) by Herbert and colleagues . The association between increased BMI and homozygosity for the minor allele was first observed in data from a genome-wide association scan of 86 , 604 SNPs ...	Obesity is an epidemic in the United States of America and developing world , portending an epidemic of related diseases such as diabetes and heart disease . While diet and lifestyle contribute to obesity , half of the population variation in body mass index , a common measure of obesity , is determined by inherited fa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "homo", "(human)", "genetics", "and", "genomics", "diabetes", "and", "endocrinology", "public", "health", "and", "epidemiology" ]	2007	The Association of a SNP Upstream of INSIG2 with Body Mass Index is Reproduced in Several but Not All Cohorts
To assess the effectiveness of community-wide deployment of insecticide–impregnated collars for dogs- the reservoir of Leishmania infantum–to reduce infantile clinical visceral leishmaniasis ( VL ) . A pair matched–cluster randomised controlled trial involving 40 collared and 40 uncollared control villages ( 161 [95% C...	Zoonotic visceral leishmaniasis is a sand fly-borne disease of humans and dogs caused by the intracellular parasite Leishmania infantum . Dogs are the proven reservoir . The disease is of global health significance , and usually fatal unless treated . There are limited options to reduce transmission . Insecticide-treat...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "kala-azar", "children", "medicine", "and", "health", "sciences", "tropical", "diseases", "geographical", "locations", "vertebrates", "sand", "flies", "parasitic", "diseases", "dogs", "animals", "mammals", "age", "groups", "neglected", "tropical", "diseases", "insect", ...	2019	Insecticide–impregnated dog collars reduce infantile clinical visceral leishmaniasis under operational conditions in NW Iran: A community–wide cluster randomised trial
During development of the vertebrate body axis , Hox genes are transcribed sequentially , in both time and space , following their relative positions within their genomic clusters . Analyses of animal genomes support the idea that Hox gene clustering is essential for coordinating the various times of gene activations ....	Hox genes encode proteins that control embryonic development along the head-to-tail axis . These genes are clustered in one site on the chromosome and their respective positions within the cluster determine their time and place of activation . Here , by using a large set of targeted mutations disturbing the integrity o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/animal", "genetics", "genetics", "and", "genomics/gene", "expression", "developmental", "biology/pattern", "formation", "genetics", "and", "genomics/chromosome", "biology", "developmental", "biology/molecular", "development", "evolutionary", "biolog...	2009	Uncoupling Time and Space in the Collinear Regulation of Hox Genes

Subsets and Splits

No community queries yet

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