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
Schistosomiasis , one of the most prevalent neglected tropical diseases , is a life-threatening public health problem in Yemen especially in rural communities . This cross-sectional study aims to determine the prevalence and associated risk factors of schistosomiasis among children in rural Yemen . Urine and faecal sam...	Schistosomiasis remains one of the most serious and prevalent diseases worldwide . Despite intensive control efforts by the government and international bodies , schistosomiasis is the second cause of death , after malaria , in Yemen , with an estimated 3 million cases . We screened 400 children in rural areas of five ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "schistosomiasis", "neglected", "tropical", "diseases", "parasitic", "diseases" ]	2013	Prevalence and Associated Factors of Schistosomiasis among Children in Yemen: Implications for an Effective Control Programme
Despite comparable levels of virus replication , simian immunodeficiency viruses ( SIV ) infection is non-pathogenic in natural hosts , such as sooty mangabeys ( SM ) , whereas it is pathogenic in non-natural hosts , such as rhesus macaques ( RM ) . Comparative studies of pathogenic and non-pathogenic SIV infection can...	Simian immunodeficiency viruses ( SIV ) are typically non-pathogenic in their natural hosts . However , if the same virus infects a non-natural host it often leads to AIDS-like symptoms . Therefore , comparing SIV infections in these two types of host might help explain the pathogenesis of SIV in non-natural hosts and ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "infectious", "diseases/hiv", "infection", "and", "aids", "immunology/immune", "response", "infectious", "diseases/viral", "infections" ]	2010	Similar Impact of CD8+ T Cell Responses on Early Virus Dynamics during SIV Infections of Rhesus Macaques and Sooty Mangabeys
Epstein-Barr virus ( EBV ) is a human herpesvirus that causes acute infectious mononucleosis and is associated with cancer and autoimmune disease . While many studies have been performed examining acute disease in adults following primary infection , little is known about the virological and immunological events during...	Chronic viral infections are ubiquitous in the human population . Many of these viruses persist in spite of the host immune response . Epstein-Barr virus ( EBV ) is a human herpesvirus and the primary causative agent of acute infectious mononucleosis . The virus is primarily transmitted through salivary exchange yet th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Incubation Period of Primary Epstein-Barr Virus Infection: Viral Dynamics and Immunologic Events
Nef is the viral gene product employed by the majority of primate lentiviruses to overcome restriction by tetherin ( BST-2 or CD317 ) , an interferon-inducible transmembrane protein that inhibits the detachment of enveloped viruses from infected cells . Although the mechanisms of tetherin antagonism by HIV-1 Vpu and HI...	Tetherin ( BST-2 , CD317 or HM1 . 24 ) is an interferon-inducible cellular restriction factor that prevents the release of enveloped viruses from infected cells . Human and simian immunodeficiency viruses have evolved to use different viral proteins to overcome the anti-viral effects of tetherin . Whereas HIV-1 Vpu and...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "immunology", "biology", "microbiology", "molecular", "cell", "biology" ]	2013	Tetherin/BST-2 Antagonism by Nef Depends on a Direct Physical Interaction between Nef and Tetherin, and on Clathrin-mediated Endocytosis
Macrophages display flexible activation states that range between pro-inflammatory ( classical activation ) and anti-inflammatory ( alternative activation ) . These macrophage polarization states contribute to a variety of organismal phenotypes such as tissue remodeling and susceptibility to infectious and inflammatory...	Macrophages provide a first line of defense against invading pathogens and play an important role in the initiation and resolution of immune responses . When in contact with pathogens or immune factors , such as cytokines , macrophages assume activation states that range between pro-inflammatory ( classical activation ...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[]	2015	Transcriptional and Linkage Analyses Identify Loci that Mediate the Differential Macrophage Response to Inflammatory Stimuli and Infection
Human Endogenous Retrovirus type K ( HERV-K ) is the only HERV known to be insertionally polymorphic; not all individuals have a retrovirus at a specific genomic location . It is possible that HERV-Ks contribute to human disease because people differ in both number and genomic location of these retroviruses . Indeed vi...	Human Endogenous Retrovirus type K ( HERV-K ) is the youngest of retrovirus families in the human genome and is the only group of endogenous retroviruses that has polymorphic members; a locus containing a HERV-K can be occupied in one individual but empty in others . HERV-Ks could contribute to disease risk or pathogen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "linear", "discriminant", "analysis", "statistics", "human", "genomics", "data", "mining", "genomic", "databases", "mathematics", "genome", "analysis", "mammalian", "genomics", "information", "technology", "research", "and", "analysis", "methods", "sequence", "analysis", ...	2019	A computational framework to assess genome-wide distribution of polymorphic human endogenous retrovirus-K In human populations
During microbial evolution , genome rearrangement increases with increasing sequence divergence . If the relationship between synteny and sequence divergence can be modeled , gene clusters in genomes of distantly related organisms exhibiting anomalous synteny can be identified and used to infer functional conservation ...	Based on trends between gene sequence divergence and gene order divergence over time , we developed a new synteny-based method to refine functional annotation . This method uses these trends to determine the probability that any two syntenous genes ( genes that are sequential in two organisms ) are functionally related...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genomics", "biology", "computational", "biology", "microbiology", "genetics", "and", "genomics" ]	2011	A Semi-Quantitative, Synteny-Based Method to Improve Functional Predictions for Hypothetical and Poorly Annotated Bacterial and Archaeal Genes
Substitutions that disrupt pre-mRNA splicing are a common cause of genetic disease . On average , 13 . 4% of all hereditary disease alleles are classified as splicing mutations mapping to the canonical 5′ and 3′ splice sites . However , splicing mutations present in exons and deeper intronic positions are vastly underr...	To understand the extent to which disrupted pre-mRNA splicing causes human disease , we re-analyzed coding mutations in MLH1 , one of the causal genes of Lynch Syndrome . We found that a high fraction of the MLH1 coding mutations resulted in disrupted splicing . To further investigate a more general role of defective s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "genetic", "diseases", "mutation", "hereditary", "nonpolyposis", "colorectal", "cancer", "forecasting", "mathematics", "statistics", "(mathematics)", "genome", "analysis", "nonsense", "mutation", "molecular", "biology", "techniques",...	2018	Hereditary cancer genes are highly susceptible to splicing mutations
Chagas cardiomyopathy , caused by the protozoan Trypanosoma cruzi , is characterized by alterations in intracellular ion , heart failure and arrhythmias . Arrhythmias have been related to sudden death , even in asymptomatic patients , and their molecular mechanisms have not been fully elucidated . The aim of this study...	Chagas disease , caused by the parasite Trypanosoma cruzi , is an endemic disease of Latin-American countries , affecting an estimated 8 million people in 21 countries . It is spread by the bite of triatomine reduvid bug . Due to immigration towards non-endemic regions , the disease can spread and affect people around ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Evidence of Reversible Bradycardia and Arrhythmias Caused by Immunogenic Proteins Secreted by T. cruzi in Isolated Rat Hearts
Genome-wide association ( GWA ) analyses have generally been used to detect individual loci contributing to the phenotypic diversity in a population by the effects of these loci on the trait mean . More rarely , loci have also been detected based on variance differences between genotypes . Several hypotheses have been ...	Most biological traits vary in natural populations , and understanding the genetic basis of this variation remains an important challenge . Genome-wide association ( GWA ) studies have emerged as a powerful tool to address this challenge by dissecting the genetic architecture of trait variation into the contribution of...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Multi-allelic Genetic Architecture of a Variance-Heterogeneity Locus for Molybdenum Concentration in Leaves Acts as a Source of Unexplained Additive Genetic Variance
Mathematical modelling has become an established tool for studying the dynamics of biological systems . Current applications range from building models that reproduce quantitative data to identifying systems with predefined qualitative features , such as switching behaviour , bistability or oscillations . Mathematicall...	Mathematical modelling has become an important tool in biology . As modelling requires separating the essential from the ordinary , there is never just one model but a collection thereof . To understand biology through modelling it is therefore crucial to be able to tell which of these models are capable of reproducing...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "phosphorylation", "chemical", "compounds", "applied", "mathematics", "reactants", "organic", "compounds", "dna", "transcription", "simulation", "and", "modeling", "algorithms", "systems", "science", "mathematics", "chemical", "equilibrium", "algebra", "basic", "amino", "...	2017	Identifying parameter regions for multistationarity
Dynamics can provide deep insights into the functional mechanisms of proteins and protein complexes . For large protein complexes such as GroEL/GroES with more than 8 , 000 residues , obtaining a fine-grained all-atom description of its normal mode motions can be computationally prohibitive and is often unnecessary . F...	Proteins and other biomolecules are not static but are constantly in motion . Moreover , they possess intrinsic collective motion patterns that are tightly linked to their functions . Thus , an accurate and detailed description of their motions can provide deep insights into their functional mechanisms . For large prot...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models
Germline stem cells in the Drosophila ovary are maintained by a somatic niche . The niche is structurally and functionally complex and contains four cell types , the escort , cap , and terminal filament cells and the newly identified transition cell . We find that the large Maf transcription factor Traffic jam ( Tj ) i...	Establishment and maintenance of stem cells often depends on associated niche cells . The germline stem cell niche of the Drosophila ovary has been a long-standing model for the analysis of the interactions between stem cells and niche cells . Surprisingly little is known , however , about the mechanisms that pattern t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "physiology", "invertebrates", "medicine", "and", "health", "sciences", "reproductive", "system", "animals", "cell", "differentiation", "cell", "formation", "germ", "cells", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "...	2017	Specification and spatial arrangement of cells in the germline stem cell niche of the Drosophila ovary depend on the Maf transcription factor Traffic jam
Virtually every molecular biologist has searched a protein or DNA sequence database to find sequences that are evolutionarily related to a given query . Pairwise sequence comparison methods—i . e . , measures of similarity between query and target sequences—provide the engine for sequence database search and have been ...	Searching a protein or DNA sequence database to find sequences that are evolutionarily related to a query is one of the foundational problems in computational biology . These database searches rely on pairwise comparisons of sequence similarity between the query and targets , but despite years of method refinements , p...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "computational", "biology/protein", "homology", "detection" ]	2011	Detecting Remote Evolutionary Relationships among Proteins by Large-Scale Semantic Embedding
As nascent polypeptide chains are synthesized , they pass through a tunnel in the large ribosomal subunit . Interaction between specific nascent chains and the ribosomal tunnel is used to induce translational stalling for the regulation of gene expression . One well-characterized example is the Escherichia coli SecM ( ...	In all cells , ribosomes perform the job of making proteins . As the proteins are synthesized they pass through a tunnel in the ribosome , and some growing proteins interact with the tunnel , leading to stalling of protein synthesis . Here , we used cryo-electron microscopy to determine the structure of a ribosome stal...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biophysics/macromolecular", "assemblies", "and", "machines", "biochemistry/rna", "structure", "molecular", "biology/rna-protein", "interactions", "molecular", "biology/translation", "mechanisms", "molecular", "biology/translational", "regulation", "biophysics/rna", "structure", "b...	2011	SecM-Stalled Ribosomes Adopt an Altered Geometry at the Peptidyl Transferase Center
Drosophila telomeres are sequence-independent structures that are maintained by transposition to chromosome ends of three specialized retroelements ( HeT-A , TART and TAHRE; collectively designated as HTT ) rather than telomerase activity . Fly telomeres are protected by the terminin complex ( HOAP-HipHop-Moi-Ver ) tha...	Telomeres are specialized structures that protect chromosome ends from incomplete replication , degradation and end-to-end fusion . Abnormalities in telomere structure or maintenance can promote a variety of human diseases including premature aging and cancer . Although all human telomeres contain the same DNA sequence...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Analysis of Pendolino (peo) Mutants Reveals Differences in the Fusigenic Potential among Drosophila Telomeres
Men who have sex with men ( MSM ) were found to be one of the high-risk populations for Entamoeba histolytica ( E . histolytica ) infection . Accompanied by the prevalence of human immunodeficiency virus ( HIV ) among MSM , invasive amebiasis caused by E . histolytica has been paid attention to as an opportunistic para...	Entamoeba histolytica ( E . histolytica ) is a very common human gastrointestinal parasitic disease which affects 50 million people worldwide . Men who have sex with men ( MSM ) have already been found to be one of the high-risk populations with E . histolytica infection . Previous studies have reported an increased ri...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "amebiasis", "infectious", "disease", "epidemiology", "epidemiology", "neglected", "tropical", "diseases" ]	2013	Seroprevalence of Entamoeba histolytica Infection among Chinese Men Who Have Sex with Men
The first identified Chikungunya outbreak occurred in Bangladesh in 2008 . In late October 2011 , a local health official from Dohar Sub-district , Dhaka District , reported an outbreak of undiagnosed fever and joint pain . We investigated the outbreak to confirm the etiology , describe the clinical presentation , and ...	Chikungunya virus is transmitted through bites from Aedes mosquitoes and causes outbreaks of fever and polyarthralgia; the geographic range of infection is expanding . An outbreak of fever with prolonged joint pain was investigated in Bangladesh in 2011 , where house-to-house surveys were carried out to identify suspec...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	An Outbreak of Chikungunya in Rural Bangladesh, 2011
There is significant heterogeneity in reported sensitivities and specificities of diagnostic serological assays for Chagas disease , as might be expected from studies that vary widely according to setting , research design , antigens employed , and reference standard . The purpose of this study is to summarize the repo...	Chagas disease , an infectious disease endemic to Latin America , is caused by the protozoan parasite Trypanosoma cruzi . T . cruzi can be transmitted through blood transfusions , organ transplants , or from mother to fetus , although it is most commonly transmitted through insect vectors . Infections can remain silent...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "biology" ]	2012	A Systematic Review of High Quality Diagnostic Tests for Chagas Disease
Although systemic immunity is critical to the process of tumor rejection , cancer research has largely focused on immune cells in the tumor microenvironment . To understand molecular changes in the patient systemic response ( SR ) to the presence of BC , we profiled RNA in blood and matched tumor from 173 patients . We...	We present a novel system ( MIxT ) to identify genes and pathways in the primary tumor that are tightly linked to genes and pathways in the patient systemic response ( SR ) . These results suggest new ways to tackle and monitor the disease by looking outside the tumor and exploiting the patient SR .	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "genetic", "networks", "body", "fluids", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "immune", "cells", "immunology", "signs", "and", "symptoms", "network", "analysis", "immune", "s...	2017	Interactions between the tumor and the blood systemic response of breast cancer patients
Many collective phenomena in Nature emerge from the -partial- synchronisation of the units comprising a system . In the case of the brain , this self-organised process allows groups of neurons to fire in highly intricate partially synchronised patterns and eventually lead to high level cognitive outputs and control ove...	Synchronisation plays an important role in most of the neuronal activities and in particular in the control of the motor system . However , due to biochemical dysfunction in the brain activity , an abnormal and excessive synchronisation may occur being responsible for severe symptoms of several neurological diseases . ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "control", "theory", "medicine", "and", "health", "sciences", "neural", "networks", "engineering", "and", "technology", "electronics", "neurodegenerative", "diseases", "signal", "processing", "neuroscience", "epileptic", "seizures", "control", "engineering", "systems", "s...	2018	A minimally invasive neurostimulation method for controlling abnormal synchronisation in the neuronal activity
Since 2003 , the tropical arthritogenic chikungunya ( CHIK ) virus has become an increasingly medical and economic burden in affected areas as it can often result in long-term disabilities . The clinical spectrum of post-CHIK ( pCHIK ) rheumatic disorders is wide . Evidence-based recommendations are needed to help phys...	With a 6-year insight , we extensively and retrospectively describe clinical profiles and specific treatments of mechanical and inflammatory post-chikungunya rheumatic disorders . In the current context of chikungunya’s global spread , we provide the first diagnostic and therapeutic algorithm to guide physicians accord...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Specific Management of Post-Chikungunya Rheumatic Disorders: A Retrospective Study of 159 Cases in Reunion Island from 2006-2012
Information sampling is often biased towards seeking evidence that confirms one’s prior beliefs . Despite such biases being a pervasive feature of human behavior , their underlying causes remain unclear . Many accounts of these biases appeal to limitations of human hypothesis testing and cognition , de facto evoking no...	Human decision-making often appears irrational . A major challenge is to explain why apparently irrational behavior occurs and what potential benefits it might have conferred for our evolutionary ancestors . A well-studied behavior in experimental psychology is “confirmation bias , ” where we sample information that si...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "recreation", "education", "decision", "making", "engineering", "and", "technology", "demography", "sociology", "social", "sciences", "neuroscience", "cell", "phones", "experimental", "psychology", "cognition", "games", "behavior", "educational", "attainment", "communicatio...	2016	Approach-Induced Biases in Human Information Sampling
The number of child deaths is a potential indicator to assess the health condition of a country , and represents a major health challenge in Bangladesh . Although the country has performed exceptionally well in decreasing the mortality rate among children under five over the last few decades , mortality still remains r...	Children are a significant asset of a country . Child deaths are an important way to determine the health sector development . The effectiveness of the interventions is required to prevent child deaths . The purpose of this study is to identify the prevalence and risk factors of child deaths in Bangladesh . Data were c...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusion" ]	[]	2015	Prevalence and Determinants of the Gender Differentials Risk Factors of Child Deaths in Bangladesh: Evidence from the Bangladesh Demographic and Health Survey, 2011
Here we present the first global functional analysis of cellular responses to pore-forming toxins ( PFTs ) . PFTs are uniquely important bacterial virulence factors , comprising the single largest class of bacterial protein toxins and being important for the pathogenesis in humans of many Gram positive and Gram negativ...	The plasma membrane surrounds cells and protects their interior from the environment and from attack by disease-causing agents like bacteria and viruses . Bacteria that cause disease have discovered that an effective way to attack cells is to secrete proteins ( pore-forming toxins ) that breach , i . e . , form holes i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "genetics", "and", "genomics/functional", "genomics", "immunology/innate", "immunity", "immunology", "infectious", "diseases/bacterial", "infections", "genetics", "and", "genomics" ]	2011	Global Functional Analyses of Cellular Responses to Pore-Forming Toxins
The acquisition and analysis of datasets including multi-level omics and physiology from non-model species , sampled from field populations , is a formidable challenge , which so far has prevented the application of systems biology approaches . If successful , these could contribute enormously to improving our understa...	Understanding how living organisms adapt to changes in their natural habitats is of paramount importance particularly in respect to environmental stressors , such as pollution or climate . Computational models integrating the multi-level molecular responses with organism physiology are likely to be indispensable tools ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome", "expression", "analysis", "functional", "genomics", "environmental", "sciences", "marine", "monitoring", "marine", "biology", "toxicology", "environmental", "protection", "marine", "and", "aquatic", "sciences", "regulatory", "networks", "biology", "microarrays", ...	2011	Towards a System Level Understanding of Non-Model Organisms Sampled from the Environment: A Network Biology Approach
We present a computational model of spatial navigation comprising different learning mechanisms in mammals , i . e . , associative , cognitive mapping and parallel systems . This model is able to reproduce a large number of experimental results in different variants of the Morris water maze task , including standard as...	We present a computational model of navigation that successfully reproduces a set of different experiments involving cognitive mapping and associative phenomena during spatial learning . The key ingredients of the model that are responsible for this achievement are ( i ) the coordination of different navigation strateg...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "learning", "medicine", "and", "health", "sciences", "brain", "social", "sciences", "neuroscience", "learning", "and", "memory", "simulation", "and", "modeling", "cognitive", "psychology", "animal", "behavior", "animal", "management", "zoology", "animal", "performance",...	2018	Interactions of spatial strategies producing generalization gradient and blocking: A computational approach
The Drosophila protocadherins Dachsous and Fat regulate growth and tissue polarity by modulating the levels , membrane localization and polarity of the atypical myosin Dachs . Localization to the apical junctional membrane is critical for Dachs function , and the adapter protein Vamana/Dlish and palmitoyl transferase A...	During development , organs grow to achieve a consistent final size . The evolutionarily conserved Hippo signaling network plays a central role in organ size control , and when dysregulated can be associated with cancer and other diseases . Fat signaling is one of several upstream pathways that impinge on Hippo signali...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "rna", "interference", "developmental", "biology", "immunoprecipitation", "epigenetics", "co-immunoprecipitation", "morphogenesis", "cellular", "structures", "and", "organelles", "research", "and", "analysis", "methods", "lipids", "genetic", "interference", "proteins", "fats"...	2019	Early girl is a novel component of the Fat signaling pathway
RecQ helicases , including Saccharomyces cerevisiae Sgs1p and the human Werner syndrome protein , are important for telomere maintenance in cells lacking telomerase activity . How maintenance is accomplished is only partly understood , although there is evidence that RecQ helicases function in telomere replication and ...	Because telomeres are situated at the ends of chromosomes , they are both essential for chromosome integrity and particularly susceptible to processes that lead to loss of their own DNA sequences . The enzyme telomerase can counter these losses , but there are also other means of telomere maintenance , some of which de...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "cell", "biology", "yeast", "and", "fungi", "geriatrics", "genetics", "and", "genomics", "saccharomyces" ]	2007	Evidence That a RecQ Helicase Slows Senescence by Resolving Recombining Telomeres
Estimates suggest that more than 25 , 000 to 125 , 000 people die annually from snakebite envenomation worldwide . In contrast to this major disease burden , thorough bibliometric studies do not exist so far that illustrate the overall research activity over a long time span . Therefore , the NewQIS-platform conducted ...	Snakebite injury is a neglected tropical disease and lead to an enormous burden of disease in many parts of the world with about 25 , 000–125 , 000 estimated deaths . Therefore , research on this area of medicine is crucial since new diagnostic and therapeutic pathways may help to diminish disease burden . This study p...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusions" ]	[ "medicine", "and", "health", "sciences", "toxins", "pathology", "and", "laboratory", "medicine", "japan", "bibliometrics", "tropical", "diseases", "geographical", "locations", "vertebrates", "animals", "toxic", "agents", "toxicology", "reptiles", "scientometrics", "neglec...	2016	Snakebite Envenoming – A Combined Density Equalizing Mapping and Scientometric Analysis of the Publication History
The development of high-throughput biotechnologies allows the collection of omics data to study the biological mechanisms underlying complex diseases at different levels , such as genomics , epigenomics , and transcriptomics . However , each technology is designed to collect a specific type of omics data . Thus , the a...	In this research , we developed a statistical approach using a modified Fisher’s method ( denoted as Omnibus-Fisher ) to combine separate p-values of association testing for a trait and SNPs , DNA methylation markers , and RNA sequencing , calculated by kernel machine regression into an overall gene-level p-value to ac...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "sequencing", "techniques", "medicine", "and", "health", "sciences", "pulmonology", "simulation", "and", "modeling", "methylation", "epigenetics", "dna", "molecular", "biology", "techniques", "rna", "sequencing", "dna", "methylation", "chromatin", "asthma", "research", ...	2019	An integrative association method for omics data based on a modified Fisher’s method with application to childhood asthma
Progress in modern neuroscience critically depends on our ability to observe the activity of large neuronal populations with cellular spatial and high temporal resolution . However , two bottlenecks constrain efforts towards fast imaging of large populations . First , the resulting large video data is challenging to an...	The voxel rate of imaging systems ultimately sets the limit on the speed of data acquisition . These limits often mean that only a small fraction of the activity of large neuronal populations can be observed at high spatio-temporal resolution . For imaging of very large populations with single cell resolution , tempora...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "fluorescence", "imaging", "statistical", "noise", "applied", "mathematics", "neuroscience", "simulation", "and", "modeling", "algorithms", "mathematics", "statistics", "(mathematics)", "computational", "neuroscience", "neuroimaging", "research", "and", "analysis", "methods",...	2017	Multi-scale approaches for high-speed imaging and analysis of large neural populations
Understanding the genetic basis of adaption is a central task in biology . Populations of the honey bee Apis mellifera that inhabit the mountain forests of East Africa differ in behavior and morphology from those inhabiting the surrounding lowland savannahs , which likely reflects adaptation to these habitats . We perf...	Identifying the genes and genetic changes responsible for environmental adaptation is an important step towards understanding how species evolve . The honey bee Apis mellifera has adapted to a variety of habitats across its worldwide geographical distribution . Here we aim to identify the genetic basis of adaptation in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "ecology", "and", "environmental", "sciences", "honey", "bees", "population", "genetics", "invertebrate", "genomics", "animals", "genetic", "mapping", "evolutionary", "adaptation", "population", "biology", "bees", "hymenoptera", "ecosystems", "animal", "g...	2017	Two extended haplotype blocks are associated with adaptation to high altitude habitats in East African honey bees
Epithelial-mesenchymal-transition promotes intra-tumoral heterogeneity , by enhancing tumor cell invasiveness and promoting drug resistance . We integrated transcriptomic data for two clonal subpopulations from a prostate cancer cell line ( PC-3 ) into a genome-scale metabolic network model to explore their metabolic d...	The coexistence within the same tumor of a variety of subpopulations , featuring different phenotypes ( intra-tumoral heterogeneity ) represents a challenge for diagnosis , prognosis and targeted therapies . In this work , we have explored the metabolic differences underlying tumor heterogeneity by building cell-type-s...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "physiology", "medicine", "and", "health", "sciences", "neurochemistry", "eicosanoids", "metabolic", "networks", "cell", "metabolism", "neuroscience", "metabolites", "network", "analysis", "genome", "analysis", "pharmacology", "drug", "metabolism", "computer", "an...	2018	Model-driven discovery of long-chain fatty acid metabolic reprogramming in heterogeneous prostate cancer cells
The 16p11 . 2 600 kb BP4-BP5 deletion and duplication syndromes have been associated with developmental delay; autism spectrum disorders; and reciprocal effects on the body mass index , head circumference and brain volumes . Here , we explored these relationships using novel engineered mouse models carrying a deletion ...	The 16p11 . 2 BP4-BP5 deletion and duplication syndromes are frequent copy number variants in humans , and are associated with developmental delay and autism spectrum disorders , with a reciprocal effect on head circumference and body mass index . Here we explored gene dosage effect in mouse models and found that the d...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "vertebrates", "social", "sciences", "mice", "neuroscience", "animals", "mammals", "learning", "and", "memory", "diet", "biological", "locomotion", "animal", "models", "perception", "model", "organisms", "cognitive", "psychology"...	2016	Reciprocal Effects on Neurocognitive and Metabolic Phenotypes in Mouse Models of 16p11.2 Deletion and Duplication Syndromes
The increasing burden of dengue fever ( DF ) in the Americas , and the current epidemic in previously unaffected countries , generate major costs for national healthcare systems . There is a need to quantify the average cost per DF case . In Mexico , few data are available on costs , despite DF being endemic in some ar...	Dengue fever ( DF ) is caused by infection with the dengue virus , which is spread by the Aedes aegypti mosquito . Although the effects of DF are usually mild , in some cases serious illness and even death may result . The average costs per case when extrapolated to society may therefore be high , particularly given th...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infographics", "medicine", "and", "health", "sciences", "public", "policy", "geographical", "locations", "tropical", "diseases", "social", "sciences", "indirect", "costs", "sociology", "charts", "health", "care", "ethnicities", "north", "america", "political", "science...	2016	Calculation of the Average Cost per Case of Dengue Fever in Mexico Using a Micro-Costing Approach
To investigate the stability and functional role of long-residence water molecules in the Q61H variant of the signaling protein K-ras , we analyzed all available Ras crystal structures and conformers derived from a series of independent explicit solvent molecular dynamics ( MD ) simulations totaling 1 . 76 µs . We show...	K-ras belongs to the Ras family of G-proteins that regulate cell proliferation and development . To execute its function , K-ras adopts different conformational states when it is active and inactive . In addition to these two states , it samples many transient intermediate conformations as it makes the transition from ...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "biology", "computational", "biology", "biophysics" ]	2012	The Role of Conserved Waters in Conformational Transitions of Q61H K-ras
Clonorchiasis is prevalent in the Far East , and a major health problem in endemic areas . Infected persons may experience , if not treated , serious complications such as bile stone formation , pyogenic cholangitis , and even cholangiocarcinoma . Early diagnosis and treatment are important to prevent serious complicat...	Clonorchiasis , a parasitic infection by Clonorchis sinensis , is one of the major public health problems in eastern Asian countries , including China , Korea , and Vietnam , causing cholangiocarcinoma if not treated . The definitive diagnosis is important for successful treatment and prevention of the infection in end...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "helminths", "tropical", "diseases", "geographical", "locations", "parasitic", "diseases", "animals", "invertebrate", "genomics", "trematodes", "organisms", "clonorchis", "sinensis", "foodborne", "trematodiases", "ne...	2017	Application of a loop-mediated isothermal amplification (LAMP) assay targeting cox1 gene for the detection of Clonorchis sinensis in human fecal samples
Malaria parasites elude eradication attempts both within the human host and across nations . At the individual level , parasites evade the host immune responses through antigenic variation . At the global level , parasites escape drug pressure through single nucleotide variants and gene copy amplification events confer...	Malaria is one of the six diseases that together are responsible for 90% of all infectious disease deaths throughout the world . The five species of Plasmodium that cause human malaria take over 655 , 000 lives each year . Parasites evade the immune response through antigenic variation and develop resistance to anti-ma...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetic", "mutation", "genome", "evolution", "mitosis", "telomeres", "molecular", "genetics", "chromosome", "biology", "biology", "evolutionary", "genetics", "mutagenesis", "genetics", "gene", "duplication", "genomics", "evolutionary", "biology", "genomic", "evolution", ...	2013	Mitotic Evolution of Plasmodium falciparum Shows a Stable Core Genome but Recombination in Antigen Families
The bromodomain protein Brd4 promotes HIV-1 latency by competitively inhibiting P-TEFb-mediated transcription induced by the virus-encoded Tat protein . Brd4 is recruited to the HIV LTR by interactions with acetyl-histones3 ( AcH3 ) and AcH4 . However , the precise modification pattern that it reads and the writer for ...	A major impediment to the cure of HIV/AIDS is the viral latency . Previous studies have identified the bromodomain protein Brd4 as a promoter of HIV latency by binding to the viral LTR to inhibit Tat-induced transcription . Here , we discover that the LTR of latent HIV has low acetylated histone H3 ( AcH3 ) but high Ac...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "flow", "cytometry", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "evolutionary", "biology", "pathogens", "immunology", "population", "genetics", "microbiology", "dna-binding", "proteins", "g...	2018	The KAT5-Acetyl-Histone4-Brd4 axis silences HIV-1 transcription and promotes viral latency
Reorganization of the microtubule network is important for the fast isodiametric expansion of giant-feeding cells induced by root-knot nematodes . The efficiency of microtubule reorganization depends on the nucleation of new microtubules , their elongation rate and activity of microtubule severing factors . New microtu...	Among plant pathogens , sedentary endoparasitic nematodes are one of the most damaging pests in global agriculture . Nematodes are greatly resistant due to a broad physiological variability , consequently difficult to fight against . The use of pesticides is highly pollutant to the environment and therefore new strateg...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "transgenic", "plants", "plant", "biology", "botany", "anatomy", "and", "physiology", "histology", "plant", "science", "plant", "morphology", "plant", "pathology", "genetically", "modified", "organisms", "biology", "agriculture", "physiology", "plant", ...	2011	Feeding Cells Induced by Phytoparasitic Nematodes Require γ-Tubulin Ring Complex for Microtubule Reorganization
B-Lymphotropic Polyomavirus ( LPyV ) serves as a paradigm of virus receptor binding and tropism , and is the closest relative of the recently discovered Human Polyomavirus 9 ( HPyV9 ) . LPyV infection depends on sialic acid on host cells , but the molecular interactions underlying LPyV-receptor binding were unknown . W...	Viruses must engage specific receptors on host cells in order to initiate infection . The type of receptor and its concentration on cells determine viral spread and tropism , but for many viruses , the receptor and the mode of recognition by the virus are not known . We have characterized the structural requirements fo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Structures of B-Lymphotropic Polyomavirus VP1 in Complex with Oligosaccharide Ligands
Since the major outbreak in 2007 in the Yap Island , Zika virus ( ZIKV ) causing dengue-like syndromes has affected multiple islands of the South Pacific region . In May 2015 , the virus was detected in Brazil and then spread through South and Central America . In December 2015 , ZIKV was detected in French Guiana and ...	Zika virus ( ZIKV ) is an emerging mosquito-borne arbovirus causing dengue-like symptoms . This virus was commonly detected in Africa and Asia . Since its emergence in Yap Island in Micronesia in 2007 , ZIKV reemerged in the South Pacific region in 2013 and ultimately reached the American continent in 2015 . The human ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "united", "states", "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "chikungunya", "infection", "geographical", "locations", "saliva", "animals", "north", "america", "caribbean", "insect", "vectors", "guadeloupe", "infectious", "diseases", "s...	2016	Differential Susceptibilities of Aedes aegypti and Aedes albopictus from the Americas to Zika Virus
Nuclear pore complexes ( NPCs ) form gateways for material transfer across the nuclear envelope of eukaryotic cells . Disordered proteins , rich in phenylalanine-glycine repeat motifs ( FG-nups ) , form the central transport channel . Understanding how nups are arranged in the interior of the NPC may explain how NPC fu...	Cells of higher life forms separate their genomes from the rest of the cell in a nucleus that surrounds the genome by a nuclear envelope . Hundreds of pores , each a complex made of many proteins , assure traffic into and out of the nucleus through highly selective transport: small biomolecules can pass unhindered , wh...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biophysics", "biology", "computational", "biology" ]	2014	Assembly of Nsp1 Nucleoporins Provides Insight into Nuclear Pore Complex Gating
Since 2011 , cohorts of schoolchildren in regions bordering Lake Victoria in Kenya and Tanzania have been investigated for morbidity caused by Schistosoma mansoni infection . Despite being neighbouring countries with similar lifestyles and ecological environments , Tanzanian schoolchildren had lower S . mansoni prevale...	Millions of school-age children in Kenya and Tanzania are at risk for infection with Schistosoma mansoni , which has an impact on their physical health . A total of 490 schoolchildren ( 163 from Kenya and 327 from Tanzania ) aged 9–11 years living along the shores of Lake Victoria in Kenya and Tanzania provided data on...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "schoolchildren", "medicine", "and", "health", "sciences", "education", "helminths", "sociology", "tropical", "diseases", "social", "sciences", "diet", "parasitic", "diseases", "physical", "activity", "animals", "h...	2018	Diet and hygiene practices influence morbidity in schoolchildren living in Schistosomiasis endemic areas along Lake Victoria in Kenya and Tanzania—A cross-sectional study
Trachomatous trichiasis significantly reduces vision and health related quality of life ( QoL ) . Although trichiasis surgery is widely performed to treat trichiasis , there is little data on the effect of surgery on QoL . We measured the impact of trichiasis surgery on vision and health related QoL in a longitudinal s...	We previously reported that Trachomatous Trichiasis ( TT ) has a profound impact on vision and heath related quality of life ( QoL ) , even when vision is not impaired . The World Health Organization ( WHO ) recommends corrective eyelid surgery for trichiasis to reduce the risk of vision loss . However , trichiasis sur...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "social", "sciences", "neuroscience", "surgical", "and", "invasive", "medical", "procedures", "visual", "acuity", "health", "care", "regression", "analysis", "optical", "properties", "mathematics", "statistics", "(mathematics)", ...	2016	Impact of Trichiasis Surgery on Quality of Life: A Longitudinal Study in Ethiopia
The packaging of DNA inside a nucleus shows complex structure stabilized by a host of DNA-bound factors . Both the distribution of these factors and the contacts between different genomic locations of the DNA can now be measured on a genome-wide scale . This has advanced the development of models aimed at predicting th...	The three-dimensional folding of DNA inside the nucleus into specific conformations is necessary for the proper functioning of cells . These structures can be measured by chromosome conformation capture methods ( Hi-C ) that report the number of times that each pair of genomic sites are found in proximal location in a ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "invertebrate", "genomics", "animals", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "mathematics", "materials", "science", "experimental", "organism", "systems", "epigenetics", "dna", "dna", "structure", "macromolecules", "structu...	2018	A maximum-entropy model for predicting chromatin contacts
Ciliopathies are human disorders caused by dysfunction of primary cilia , ubiquitous organelles involved in transduction of environmental signals such as light sensation in photoreceptors . Concentration of signal detection proteins such as opsins in the ciliary membrane is achieved by RabGTPase-regulated polarized ves...	Ciliopathies are human disorders caused by dysfunction of primary cilia , ubiquitous organelles involved in transduction of environmental signals to the cells . Concentration and regulation of signal detection proteins in the ciliary membrane is therefore tightly regulated through polarized vesicle trafficking and thro...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "physiology", "fish", "medicine", "and", "health", "sciences", "vesicles", "ocular", "anatomy", "vertebrates", "social", "sciences", "neuroscience", "animals", "animal", "models", "osteichthyes", "membrane", "fusion", "model", "organisms", "experimental", "organ...	2017	Loss-of-function of the ciliopathy protein Cc2d2a disorganizes the vesicle fusion machinery at the periciliary membrane and indirectly affects Rab8-trafficking in zebrafish photoreceptors
Simultaneous spike-counts of neural populations are typically modeled by a Gaussian distribution . On short time scales , however , this distribution is too restrictive to describe and analyze multivariate distributions of discrete spike-counts . We present an alternative that is based on copulas and can account for ar...	The brain has an enormous number of neurons that do not work alone but in an ensemble . Yet , mostly individual neurons were measured in the past and therefore models were restricted to independent neurons . With the advent of new multi-electrode techniques , however , it becomes possible to measure a great number of n...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "neuroscience/theoretical", "neuroscience", "neuroscience/sensory", "systems" ]	2009	Analyzing Short-Term Noise Dependencies of Spike-Counts in Macaque Prefrontal Cortex Using Copulas and the Flashlight Transformation
Recent genome-wide analyses have uncovered a high accumulation of RNA polymerase II ( Pol II ) at the 5′ end of genes . This elevated Pol II presence at promoters , referred to here as Poll II poising , is mainly ( but not exclusively ) attributed to temporal pausing of transcription during early elongation which , in ...	Accumulation of RNA polymerase II ( Pol II ) in the promoter proximal region has been proposed to be important for rapid gene activation , but the full regulatory role of Pol II dynamics is yet to be delineated . Defining polymerase poising as a significant enrichment of accumulation of Pol II near the promoter , and c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "sequencing", "techniques", "medicine", "and", "health", "sciences", "immune", "cells", "gene", "regulation", "metabolic", "processes", "immediate", "early", "genes", "immunology", "dna", "transcription", "gene", "types", "sequence", "motif", "analys...	2016	Ups and Downs of Poised RNA Polymerase II in B-Cells
A novel microduplication syndrome involving various-sized contiguous duplications in 17p13 . 3 has recently been described , suggesting that increased copy number of genes in 17p13 . 3 , particularly PAFAH1B1 , is associated with clinical features including facial dysmorphism , developmental delay , and autism spectrum...	The widespread use of genomic array technology has lead to the identification of a plethora of novel human genomic disorders . These complex conditions occur as a consequence of structural genomic alterations ( deletions , amplifications , complex rearrangements ) . Understanding the specific consequences of such alter...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "nucleic", "acids", "dna", "biology", "dna", "repair" ]	2011	Increased RPA1 Gene Dosage Affects Genomic Stability Potentially Contributing to 17p13.3 Duplication Syndrome
The major histocompatibility complex ( MHC ) of immunity genes has been reported to influence mate choice in vertebrates , and a recent study presented genetic evidence for this effect in humans . Specifically , greater dissimilarity at the MHC locus was reported for European-American mates ( parents in HapMap Phase 2 ...	There is evidence in numerous species that genes involved in immunity influence mate choice . Factors like body odor may subconsciously favor partners with different immunity alleles , to avoid inbreeding and/or endow offspring with broad resistance to pathogens . A previous study , based on HapMap genotypes , reported...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "computational", "biology/population", "genetics", "genetics", "and", "genomics/genetics", "of", "the", "immune", "system", "evolutionary", "biology/human", "evolution", "immunology/genetics", "of", "the", "immune", "system", "genetics", "and", "genomics/population", "genet...	2010	Absence of Evidence for MHC–Dependent Mate Selection within HapMap Populations
Despite a broad cell-type tropism , cytomegalovirus ( CMV ) is an evidentially pulmonary pathogen . Predilection for the lungs is of medical relevance in immunocompromised recipients of hematopoietic cell transplantation , in whom interstitial CMV pneumonia is a frequent and , if left untreated , fatal clinical manifes...	From an epidemiological perspective , natural host-to-host transmission of human CMV mostly occurs in early childhood through saliva from virus-shedding intimate contact persons , such as family members or peers . The oronasal route of transmission involves also the airway mucosa and airway-draining lymph nodes . Almos...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "t", "helper", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "respiratory", "infections", "immunology", "cloning", "pulmonology", "animal", "models", ...	2019	Coincident airway exposure to low-potency allergen and cytomegalovirus sensitizes for allergic airway disease by viral activation of migratory dendritic cells
Changes in higher order chromatin organisation have been linked to transcriptional regulation; however , little is known about how such organisation alters during embryonic development or how it is regulated by extrinsic signals . Here we analyse changes in chromatin organisation as neural differentiation progresses , ...	Changes in the position of genes within the nucleus and in their local organisation frequently correlate with whether or not genes are turned on . However , little is known about how such nuclear organisation is controlled and whether this can be separated from the mechanisms that promote transcription . We show here t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "gene", "expression", "genetics", "epigenetics", "biology", "molecular", "cell", "biology" ]	2013	FGF Signalling Regulates Chromatin Organisation during Neural Differentiation via Mechanisms that Can Be Uncoupled from Transcription
Fusarium graminearum , the causal agent of Fusarium head blight in cereal crops , produces sexual progeny ( ascospore ) as an important overwintering and dissemination strategy for completing the disease cycle . This homothallic ascomycetous species does not require a partner for sexual mating; instead , it carries two...	The production of sexual propagules via a self-fertile mating strategy in Fusarium graminearum , an important cereal pathogen , is essential for overwintering and dissemination during the recurrent disease cycle caused by this fungus . Genome-wide microarray analyses allow the identification of gene sets that are regul...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	A Large-Scale Functional Analysis of Putative Target Genes of Mating-Type Loci Provides Insight into the Regulation of Sexual Development of the Cereal Pathogen Fusarium graminearum
Activated Cdc42 kinases ( Acks ) are evolutionarily conserved non-receptor tyrosine kinases . Activating somatic mutations and increased ACK1 protein levels have been found in many types of human cancers and correlate with a poor prognosis . ACK1 is activated by epidermal growth factor ( EGF ) receptor signaling and fu...	A number of recent studies have uncovered an involvement of Ack family members in human cancer . The majority of these studies focus on human ACK1 and suggest that ACK1 regulates diverse cancer-relevant biological functions , including stimulation of proliferation , blocking programmed cell death , and enhancing metast...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "cell", "death", "basic", "cancer", "research", "signaling", "in", "selected", "disciplines", "gene", "function", "oncology", "tyrosine", "kinase", "signaling", "cascade", "signaling", "in", "cellular", "processes", "oncogenic", "signaling", "ras", "signal...	2012	Drosophila Activated Cdc42 Kinase Has an Anti-Apoptotic Function
The ever-increasing availability of transcriptomic and metabolomic data can be used to deeply analyze and make ever-expanding predictions about biological processes , as changes in the reaction fluxes through genome-wide pathways can now be tracked . Currently , constraint-based metabolic modeling approaches , such as ...	The recent advances in omics technologies have provided us with an unprecedented abundance of data spanning genomes , global gene expression , and metabolomes . Though these advancements in high-throughput data collection offer an excellent opportunity for a more thorough understanding of metabolic capacities of a wide...	[ "Abstract", "Introduction", "Results", "Materials", "and", "methods", "Discussion" ]	[ "cell", "physiology", "enzymes", "metabolic", "networks", "enzymology", "cell", "metabolism", "phosphatases", "metabolomics", "metabolites", "network", "analysis", "thermodynamics", "computer", "and", "information", "sciences", "proteins", "metabolic", "pathways", "gene", ...	2019	Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models
To uncover the processes and mechanisms of cellular physiology , it first necessary to gain an understanding of the underlying metabolic dynamics . Recent studies using a constraint-based approach succeeded in predicting the steady states of cellular metabolic systems by utilizing conserved quantities in the metabolic ...	Although a metabolic shift is essential for the adaptation of cells or organisms to environmental changes , the transient behaviors of metabolic systems are poorly understood . When describing the time development of metabolic systems , there are several conserved quantities to consider due to balances of metabolic rea...	[ "Abstract", "Introduction", "Results", "Discussion", "Models", "and", "methods" ]	[ "relaxation", "time", "coenzymes", "enzymes", "metabolic", "networks", "enzymology", "systems", "science", "mathematics", "metabolites", "network", "analysis", "enzyme", "metabolism", "enzyme", "chemistry", "relaxation", "(physics)", "computer", "and", "information", "sci...	2017	Metabolic dynamics restricted by conserved carriers: Jamming and feedback
Many choice situations require imagining potential outcomes , a capacity that was shown to involve memory brain regions such as the hippocampus . We reasoned that the quality of hippocampus-mediated simulation might therefore condition the subjective value assigned to imagined outcomes . We developed a novel paradigm t...	Economic theory assumes that we assign some sort of value to options that are presented to us in order to choose between them . In neuroscience , evidence suggests that memory brain regions , such as the hippocampus , are involved in imagining novel situations . We therefore hypothesized that the hippocampus might be c...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[]	2013	A Critical Role for the Hippocampus in the Valuation of Imagined Outcomes
Filamentous fungi produce diverse secondary metabolites ( SMs ) essential to their ecology and adaptation . Although each SM is typically produced by only a handful of species , global SM production is governed by widely conserved transcriptional regulators in conjunction with other cellular processes , such as develop...	Filamentous fungi produce a highly diverse cadre of secondary metabolites , small molecules whose potent toxic activities are integral to the fungal lifestyle . Most secondary metabolites are narrowly taxonomically distributed , whereas the transcriptional regulators that control their production , alongside with contr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Examining the Evolution of the Regulatory Circuit Controlling Secondary Metabolism and Development in the Fungal Genus Aspergillus
Piwi-interacting RNAs are a diverse class of small non-coding RNAs implicated in the silencing of transposable elements and the safeguarding of genome integrity . In mammals , male germ cells express two genetically and developmentally distinct populations of piRNAs at the pre-pachytene and pachytene stages of meiosis ...	Small non-coding RNAs play critical roles during development and in disease . The integrity of the germline genome is of paramount importance to the wellbeing of offspring and the survival of species . Piwi-interacting RNAs ( piRNAs ) are a class of small non-coding RNAs abundantly expressed in the gonad . Compared to ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "biology" ]	2012	Blockade of Pachytene piRNA Biogenesis Reveals a Novel Requirement for Maintaining Post-Meiotic Germline Genome Integrity
Recent advances in top-down mass spectrometry enabled identification of intact proteins , but this technology still faces challenges . For example , top-down mass spectrometry suffers from a lack of sensitivity since the ion counts for a single fragmentation event are often low . In contrast , nanopore technology is ex...	Protein identification is the key step in many proteomics studies . Currently , the most popular technique for intact protein analysis is top-down mass spectrometry which recently enabled high-throughput identification of many proteins and their proteoforms . However , this approach requires large amounts of materials ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "protein", "transport", "sequencing", "techniques", "cell", "processes", "dna-binding", "proteins", "materials", "science", "molecular", "biology", "techniques", "materials", "by", "structure", "research", "and", "analysis", "methods", "amino", "acid", "analysis", "prot...	2017	Single-molecule protein identification by sub-nanopore sensors
Quantitative trait locus ( QTL ) analysis is a powerful tool for mapping genes for complex traits in mice , but its utility is limited by poor resolution . A promising mapping approach is association analysis in outbred stocks or different inbred strains . As a proof of concept for the association approach , we applied...	In rodents , as in humans , traits such as obesity or diabetes are under the influence of many genes spread throughout the genome . Using linkage analysis , the locations of the major contributing genes can be mapped only to very large regions of chromosomes , usually encompassing hundreds of genes . This has made it d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "genetics", "and", "genomics/animal", "genetics", "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/genome", "projects", "genetics", "and", "genomics" ]	2008	High-Resolution Mapping of Gene Expression Using Association in an Outbred Mouse Stock
Interactions between an organism and its environment can significantly influence phenotypic evolution . A first step toward understanding this process is to characterize phenotypic diversity within and between populations . We explored the phenotypic variation in stress sensitivity and genomic expression in a large pan...	Much attention has been given to the ways in which organisms evolve new phenotypes and the influence of the environment on this process . A major focus of study is defining the genetic basis for phenotypes important for organismal fitness . As a first step toward this goal , we surveyed phenotypic variation in diverse ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "genetics", "and", "genomics/comparative", "genomics", "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/functional", "genomics" ]	2008	Variations in Stress Sensitivity and Genomic Expression in Diverse S. cerevisiae Isolates
Severe acute respiratory syndrome coronavirus ( SARS-CoV ) encodes a papain-like protease ( PLpro ) with both deubiquitinating ( DUB ) and deISGylating activities that are proposed to counteract the post-translational modification of signaling molecules that activate the innate immune response . Here we examine the str...	All coronaviruses such as the SARS virus and the recently identified Middle East Respiratory Syndrome ( MERS ) virus encode in their genomes at least one papain-like protease ( PLpro ) enzyme that has two distinct functions in viral pathogenesis . The first function is to process the viral polyprotein into individual p...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biomacromolecule-ligand", "interactions", "biochemistry", "enzyme", "structure", "proteins", "enzymes", "biology", "and", "life", "sciences", "enzymology", "biophysics" ]	2014	Structural Basis for the Ubiquitin-Linkage Specificity and deISGylating Activity of SARS-CoV Papain-Like Protease
In addition to modulating the function and stability of cellular mRNAs , microRNAs can profoundly affect the life cycles of viruses bearing sequence complementary targets , a finding recently exploited to ameliorate toxicities of vaccines and oncolytic viruses . To elucidate the mechanisms underlying microRNA-mediated ...	Virus host range is shaped by cellular determinants such as transcription factors and receptor expression . In addition , we have previously shown that tissue-specific microRNAs can be utilized to direct the specificity of a replication competent picornavirus , Coxsackievirus A21 . In this report , we demonstrate the m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/viral", "replication", "and", "gene", "regulation", "molecular", "biology/translation", "mechanisms", "molecular", "biology/mrna", "stability", "oncology/myelomas", "and", "lymphoproliferative", "diseases", "virology/mechanisms", "of", "resistance", "and", "susceptibi...	2010	MicroRNA Antagonism of the Picornaviral Life Cycle: Alternative Mechanisms of Interference
Evidence is mounting that mutation rates are sufficiently high for deleterious alleles to be a major evolutionary force affecting the evolution of sex , the maintenance of genetic variation , and many other evolutionary phenomena . Though point estimates of mutation rates are improving , we remain largely ignorant of t...	A variety of evolutionary phenomena are affected by the rate at which mutations enter a population and how those mutations are distributed amongst individuals . Although it is typically assumed that mutations occur randomly among individuals , this may not be the case . Individuals in poor condition may experience elev...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology" ]	2008	Increased Transmission of Mutations by Low-Condition Females: Evidence for Condition-Dependent DNA Repair
Human T-lymphotropic virus type 1 ( HTLV-1 ) has been discovered in 1980 and has been linked to tropical spastic paraparesis ( HAM/TSP ) in 1985 in Martinique . There is no data on HAM/TSP incidence trends . We report , in the present work , the temporal trends incidence of HAM/TSP in Martinique over 25 years . Martini...	Human T-lymphotropic virus type 1 ( HTLV-1 ) was discovered in 1980 and HTLV-1-associated myelopathy/tropical spastic paraparesis ( HAM/TSP ) was described five years later in 1985 . HAM/TSP is a progressive disabling disorder characterized by spastic paraparesis with bladder and bowel dysfunction that constitutes a si...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "geomorphology", "medicine", "and", "health", "sciences", "clinical", "laboratory", "sciences", "pathology", "and", "laboratory", "medicine", "landforms", "pathogens", "topography", "geographical", "locations", "microbiology", "neurorehabilitation", "census", "health", "car...	2018	Temporal trends in Human T-Lymphotropic virus 1 (HTLV-1) associated myelopathy/tropical spastic paraparesis (HAM/TSP) incidence in Martinique over 25 years (1986-2010)
Pulmonary adenoma susceptibility 1 ( Pas1 ) is the major locus responsible for lung tumor susceptibility in mice; among the six genes mapping in this locus , Kras is considered the best candidate for Pas1 function although how it determines tumor susceptibility remains unknown . In an ( A/J×C57BL/6 ) F4 intercross popu...	A person's risk of developing cancer depends on both genetic and environmental factors . To study the genetic predisposition to cancer without the influence of environmental variables , scientists study mice treated with urethane , a chemical carcinogen that induces lung tumors . By crossing inbred ( genetically identi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "cancer", "genetics", "model", "organisms", "genetic", "polymorphism", "gene", "expression", "genetics", "gene", "regulation", "biology", "and", "life", "sciences", "population", "genetics", "molecular", "genetics", "genomics", "evolutionary", "biolo...	2014	Mouse Pulmonary Adenoma Susceptibility 1 Locus Is an Expression QTL Modulating Kras-4A
Yeast two-hybrid screens are an important method for mapping pairwise physical interactions between proteins . The fraction of interactions detected in independent screens can be very small , and an outstanding challenge is to determine the reason for the low overlap . Low overlap can arise from either a high false-dis...	The genome sequence of an organism provides a parts list of proteins , but not an instruction manual for assembling the parts into a cell . Assembly instructions now come from experiments such as two-hybrid screens that detect physical interactions between pairs of proteins . Defining the resources required for generat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mathematics", "caenorhabditis", "computational", "biology", "drosophila", "saccharomyces" ]	2007	Where Have All the Interactions Gone? Estimating the Coverage of Two-Hybrid Protein Interaction Maps
Data-driven models of functional magnetic resonance imaging ( fMRI ) activity can elucidate dependencies that involve the combination of multiple brain regions . Activity in some regions during resting-state fMRI can be predicted with high accuracy from the activities of other regions . However , it remains unclear in ...	Models of fMRI activity can elucidate underlying dependencies that involve the combination of multiple brain regions . However , it remains unclear in which regions activity depends on unique integration of multiple predictor regions . To address this question , sparse ( parsimonious ) models could serve to better dete...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cingulate", "cortex", "medicine", "and", "health", "sciences", "diagnostic", "radiology", "functional", "magnetic", "resonance", "imaging", "data", "acquisition", "engineering", "and", "technology", "signal", "processing", "brain", "neuroscience", "magnetic", "resonance"...	2017	Multiregional integration in the brain during resting-state fMRI activity
The lion Panthera leo is one of the world's most charismatic carnivores and is one of Africa's key predators . Here , we used a large dataset from 357 lions comprehending 1 . 13 megabases of sequence data and genotypes from 22 microsatellite loci to characterize its recent evolutionary history . Patterns of molecular g...	The lion Panthera leo , a formidable carnivore with a complex cooperative social system , has fascinated humanity since pre-historical times , inspiring hundreds of religious and cultural allusions . Here , we use a comprehensive sample of 357 individuals from most of the major lion populations in Africa and Asia . We ...	[ "Abstract", "Introduction", "Results/Discussion", "Material", "and", "Methods" ]	[ "evolutionary", "biology", "genetics", "and", "genomics/population", "genetics" ]	2008	The Evolutionary Dynamics of the Lion Panthera leo Revealed by Host and Viral Population Genomics
The level of susceptibility to tuberculosis ( TB ) infection depends upon allelic variations in numerous interacting genes . In our mouse model system , the whole-genome quantitative trait loci ( QTLs ) scan revealed three QTLs involved in TB control on chromosomes 3 , 9 , and in the vicinity of the H2 complex on chrom...	Many genes of the host regulate interactions with Mycobacterium tuberculosis and determine the level of susceptibility to , and severity of , tuberculosis ( TB ) . Identification of these genes and their alleles is continuing and contributes new knowledge about the host-pathogen interactions . So far , forward genetic ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The QTL within the H2 Complex Involved in the Control of Tuberculosis Infection in Mice Is the Classical Class II H2-Ab1 Gene
Chinese Erhualian is the most prolific pig breed in the world . The breed exhibits exceptionally large and floppy ears . To identify genes underlying this typical feature , we previously performed a genome scan in a large scale White Duroc × Erhualian cross and mapped a major QTL for ear size to a 2-cM region on chromo...	A central but challenging objective in current biology is to dissect the genetic basis of quantitative traits . Numerous quantitative trait loci ( QTL ) have been uncovered in model and farm animals , providing unexpected insights into the biology of complex traits . However , only a few causal variants underlying the ...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "animal", "genetics", "heredity", "genetics", "animal", "management", "biology", "quantitative", "traits", "genetic", "determinism", "genetics", "and", "genomics", "agriculture" ]	2011	A Missense Mutation in PPARD Causes a Major QTL Effect on Ear Size in Pigs
Among animal models of schistosomiasis , the rhesus macaque is unique in that an infection establishes but egg excretion rapidly diminishes , potentially due to loss of adult worms from the portal system via shunts or death by immune attack . To investigate this , six rhesus macaques were exposed to Schistosoma mansoni...	Infection with blood-dwelling schistosome worms is a major cause of human disease in many tropical countries . Despite intensive efforts a vaccine has proved elusive , not least because the chronic nature of the infection provides few pointers for vaccine development . The rhesus macaque appears unique among animal mod...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/helminth", "infections", "immunology/immunity", "to", "infections", "immunology/immune", "response", "pathology/histopathology" ]	2008	Elimination of Schistosoma mansoni Adult Worms by Rhesus Macaques: Basis for a Therapeutic Vaccine?
Postzygotic reproductive isolation is characterized by two striking empirical patterns . The first is Haldane's rule—the preferential inviability or sterility of species hybrids of the heterogametic ( XY ) sex . The second is the so-called large X effect—substitution of one species's X chromosome for another's has a di...	The evolution of reproductive isolation is a fundamental step in the origin of species . One kind of reproductive isolation , the sterility and inviability of species hybrids , is characterized by two of the strongest rules in evolutionary biology . The first is Haldane's rule: for species crosses in which just one hyb...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "arthropods", "eukaryotes", "evolutionary", "biology", "drosophila", "animals", "insects" ]	2007	High-Resolution Genome-Wide Dissection of the Two Rules of Speciation in Drosophila
A fundamental question in evolutionary genetics concerns the extent to which adaptive phenotypic convergence is attributable to convergent or parallel changes at the molecular sequence level . Here we report a comparative analysis of hemoglobin ( Hb ) function in eight phylogenetically replicated pairs of high- and low...	The convergent evolution of similar traits in different species could be due to repeated changes at the genetic level or different changes that produce the same phenotypic effect . To investigate the extent to which convergence in phenotype is caused by repeated mutations , we investigated the molecular basis of conver...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[]	2015	Convergent Evolution of Hemoglobin Function in High-Altitude Andean Waterfowl Involves Limited Parallelism at the Molecular Sequence Level
The goal of human genome re-sequencing is obtaining an accurate assembly of an individual's genome . Recently , there has been great excitement in the development of many technologies for this ( e . g . medium and short read sequencing from companies such as 454 and SOLiD , and high-density oligo-arrays from Affymetrix...	In recent years , the development of high throughput sequencing and array technologies has enabled the accurate re-sequencing of individual genomes , especially in identifying and reconstructing the variants in an individual's genome compared to a “reference” . The costs and sensitivities of these technologies differ c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "molecular", "biology/bioinformatics", "computer", "science", "computational", "biology/genomics" ]	2009	Integrating Sequencing Technologies in Personal Genomics: Optimal Low Cost Reconstruction of Structural Variants
Kinetoplastid parasites—trypanosomes and leishmanias—infect millions of humans and cause economically devastating diseases of livestock , and the few existing drugs have serious deficiencies . Benzoxaborole-based compounds are very promising potential novel anti-trypanosomal therapies , with candidates already in human...	Trypanosomes and leishmanias infect millions of humans and cause economically devastating diseases of livestock; the few existing drugs have serious deficiencies . Trypanosomosis of cattle caused by Trypanosoma congolense and Trypanosoma vivax , is a serious problem in Africa because cattle are used not only for food b...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "messenger", "rna", "parasitic", "protozoans", "parasitology", "trypanosoma", "brucei", "protozoans", "methylation", "pharmacology", "drug", "metabolism", "veterinary", "science", "veterinary", "parasitology", "gene", "expression", ...	2018	The trypanocidal benzoxaborole AN7973 inhibits trypanosome mRNA processing
Synaptic activity can boost neuroprotection through a mechanism that requires synapse-to-nucleus communication and calcium signals in the cell nucleus . Here we show that in hippocampal neurons nuclear calcium is one of the most potent signals in neuronal gene expression . The induction or repression of 185 neuronal ac...	The dialogue between the synapse and the nucleus plays an important role in the physiology of neurons because it links brief changes in the membrane potential to the transcriptional regulation of genes critical for neuronal survival and long-term memory . The propagation of activity-induced calcium signals to the cell ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience/neuronal", "signaling", "mechanisms", "neuroscience/neurobiology", "of", "disease", "and", "regeneration", "cell", "biology/gene", "expression", "cell", "biology/neuronal", "signaling", "mechanisms" ]	2009	Nuclear Calcium Signaling Controls Expression of a Large Gene Pool: Identification of a Gene Program for Acquired Neuroprotection Induced by Synaptic Activity
There is a growing recognition for the importance of proteins with large intrinsically disordered ( ID ) segments in cell signaling and regulation . ID segments in these proteins often harbor regions that mediate molecular recognition . Coupled folding and binding of the recognition regions has been proposed to confer ...	Protein-protein interactions are essential to communication and signal integration in cells . For these processes to be precise , interactions between proteins have to be specific and well coordinated . In order to understand the specificity in protein interactions , researches have focused on interfaces between two or...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "macromolecular", "complex", "analysis", "biochemistry", "protein", "chemistry", "protein", "interactions", "proteins", "biology", "computational", "biology", "biophysics", "macromolecular", "structure", "analysis" ]	2013	On the Importance of Polar Interactions for Complexes Containing Intrinsically Disordered Proteins
Type 2 diabetes ( T2D ) is more prevalent in African Americans than in Europeans . However , little is known about the genetic risk in African Americans despite the recent identification of more than 70 T2D loci primarily by genome-wide association studies ( GWAS ) in individuals of European ancestry . In order to inve...	Despite the higher prevalence of type 2 diabetes ( T2D ) in African Americans than in Europeans , recent genome-wide association studies ( GWAS ) were examined primarily in individuals of European ancestry . In this study , we performed meta-analysis of 17 GWAS in 8 , 284 cases and 15 , 543 controls to explore the gene...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "diabetes", "mellitus", "medicine", "and", "health", "sciences", "diabetic", "endocrinology", "epidemiology", "endocrinology", "genetics", "biology", "and", "life", "sciences", "genetics", "of", "disease", "type", "2", "diabetes", "metabolic", "disorders", "genetic", ...	2014	Meta-Analysis of Genome-Wide Association Studies in African Americans Provides Insights into the Genetic Architecture of Type 2 Diabetes
Fibrinogen is an essential part of the blood coagulation cascade and a major component of the extracellular matrix in mammals . The interface between fibrinogen and bacterial pathogens is an important determinant of the outcome of infection . Here , we demonstrate that a canine host-restricted skin pathogen , Staphyloc...	Many bacterial pathogens are specialized for a single host-species and rarely cause infections of other hosts . Our understanding of the bacterial factors underpinning host-specificity are limited . Here we demonstrate that a canine host-restricted bacterial pathogen , Staphylococcus pseudintermedius , produces a surfa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "bacteriology", "biofilms", "cell", "physiology", "cell", "binding", "medicine", "and", "health", "sciences", "chemical", "characterization", "pathology", "and", "laboratory", "medicine", "fibrinogen", "pathogens", "microbiology", "staphylococcus", "aureus", "glycoproteins"...	2019	Host-specialized fibrinogen-binding by a bacterial surface protein promotes biofilm formation and innate immune evasion
Computational approaches to tune the activation of intracellular signal transduction pathways both predictably and selectively will enable researchers to explore and interrogate cell biology with unprecedented precision . Techniques to control complex nonlinear systems typically involve the application of control theor...	Most cell behavior arises as a response to external forces . Signals from the extracellular environment are passed to the cell's nucleus through a complex network of interacting proteins . Perturbing these pathways can change the strength or outcome of the signals , which could be used to treat or prevent a pathologica...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "bioengineering", "biomedical", "engineering", "systems", "biology", "computer", "and", "information", "sciences", "network", "analysis", "engineering", "and", "technology", "biology", "and", "life", "sciences", "signaling", "networks", "computational", "...	2014	Multiple Model-Informed Open-Loop Control of Uncertain Intracellular Signaling Dynamics
The spatial arrangement of Ca2+ channels and vesicles remains unknown for most CNS synapses , despite of the crucial importance of this geometrical parameter for the Ca2+ control of transmitter release . At a large model synapse , the calyx of Held , transmitter release is controlled by several Ca2+ channels in a "doma...	Ca2+ channels provide the rise in intracellular Ca2+ concentration necessary to initiate the membrane fusion of transmitter—filled vesicles at synapses . Because Ca2+ diffuses away from Ca2+ channels , the distance between Ca2+ channels and vesicles on the range of tens of nanometers is a crucial determinant of the ves...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	An Exclusion Zone for Ca2+ Channels around Docked Vesicles Explains Release Control by Multiple Channels at a CNS Synapse
Hematogenous dissemination is important for infection by many bacterial pathogens , but is poorly understood because of the inability to directly observe this process in living hosts at the single cell level . All disseminating pathogens must tether to the host endothelium despite significant shear forces caused by blo...	Many bacterial pathogens can cause systemic illness by disseminating through the blood to distant target sites . However , hematogenous dissemination is still poorly understood , in part because of an inability to directly observe this process in living hosts in real time and at the level of individual pathogens . We r...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/bacterial", "infections", "microbiology/cellular", "microbiology", "and", "pathogenesis", "microbiology/medical", "microbiology" ]	2008	Molecular Mechanisms Involved in Vascular Interactions of the Lyme Disease Pathogen in a Living Host
There has been much effort to prioritize genomic variants with respect to their impact on “function” . However , function is often not precisely defined: sometimes it is the disease association of a variant; on other occasions , it reflects a molecular effect on transcription or epigenetics . Here , we coupled multiple...	With advances in sequencing technologies , a deluge of genomic data is available; however , only a fraction of non-coding genomic variants are functionally relevant . Sifting through this data to prioritize genomic variants with respect to function is an important but challenging task . In this study , we built GRAM , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "binding", "cell", "physiology", "genome-wide", "association", "studies", "luciferase", "assay", "luciferase", "chemical", "characterization", "enzymes", "enzymology", "biochemical", "analysis", "enzyme", "assays", "genome", "analysis", "bioassays", "and", "physio...	2019	GRAM: A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell-type specific manner
The chemical-genetic profile can be defined as quantitative values of deletion strains' growth defects under exposure to chemicals . In yeast , the compendium of chemical-genetic profiles of genomewide deletion strains under many different chemicals has been used for identifying direct target proteins and a common mode...	Finding the specific targets of chemicals and deciphering how drugs work in our body is important for the effective development of new drugs . Growth profiles of yeast genomewide deletion strains under many different chemicals have been used for identifying target proteins and a common mode-of-action of drugs . In this...	[ "Abstract", "Introduction", "Results/Discussion", "Method" ]	[ "computational", "biology/systems", "biology", "computational", "biology/genomics" ]	2008	Inference of Protein Complex Activities from Chemical-Genetic Profile and Its Applications: Predicting Drug-Target Pathways
Diverse ion channels and their dynamics endow single neurons with complex biophysical properties . These properties determine the heterogeneity of cell types that make up the brain , as constituents of neural circuits tuned to perform highly specific computations . How do biophysical properties of single neurons impact...	Differences in ion channel composition endow different neuronal types with distinct computational properties . Understanding how these biophysical differences affect network-level computation is an important frontier . We focus on a set of biophysical properties , experimentally observed in developing cortical neurons ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "neuroscience", "single", "neuron", "function", "biology", "and", "life", "sciences", "computational", "biology", "neuroscience", "artificial", "neural", "networks" ]	2014	Intrinsic Neuronal Properties Switch the Mode of Information Transmission in Networks
The pathogenic yeast Cryptococcus neoformans causes fungal meningitis in immune-compromised patients . Cell proliferation in the budding yeast form is required for C . neoformans to infect human hosts , and virulence factors such as capsule formation and melanin production are affected by cell-cycle perturbation . Thus...	The opportunistic fungal pathogen Cryptococcus neoformans infects immune-compromised humans and causes fungal meningitis by proliferating in the central nervous system . The cell cycle has not been studied at the whole transcriptome level in C . neoformans . Here , we present the expression dynamics of all genes from a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cryptococcus", "neoformans", "medicine", "and", "health", "sciences", "genetic", "networks", "cryptococcus", "pathology", "and", "laboratory", "medicine", "pathogens", "cell", "cycle", "and", "cell", "division", "cell", "processes", "microbiology", "fungi", "model", ...	2016	Investigating Conservation of the Cell-Cycle-Regulated Transcriptional Program in the Fungal Pathogen, Cryptococcus neoformans
Crumbs family proteins are apical transmembrane proteins with ancient roles in cell polarity . Mouse Crumbs2 mutants arrest at midgestation with abnormal neural plate morphology and a deficit of mesoderm caused by defects in gastrulation . We identified an ENU-induced mutation , wsnp , that phenocopies the Crumbs2 null...	Post-translational addition of sugar chains is essential for normal activity of many secreted and transmembrane proteins and dozens of human genetic diseases are associated with congenital disorders of glycosylation . Protein O-glucosyltransferase 1 ( POGLUT1 ) , which is essential for early mouse development , catalyz...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Protein O-Glucosyltransferase 1 (POGLUT1) Promotes Mouse Gastrulation through Modification of the Apical Polarity Protein CRUMBS2
Stochastic fluctuations in signaling and gene expression limit the ability of cells to sense the state of their environment , transfer this information along cellular pathways , and respond to it with high precision . Mutual information is now often used to quantify the fidelity with which information is transmitted al...	This work demonstrates how different sources of variability within biochemical networks impact the interpretation of information transmission . These sources are the intrinsic noise generated within the pathway of a single cell , variability due to initial conditions and/or global parameters across the population . A t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Impact of Different Sources of Fluctuations on Mutual Information in Biochemical Networks
Pch2 is a widely conserved protein that is required in baker's yeast for the organization of meiotic chromosome axes into specific domains . We provide four lines of evidence suggesting that it regulates the formation and distribution of crossover events required to promote chromosome segregation at Meiosis I . First ,...	During meiosis , cells that ultimately become gametes ( such as eggs or sperm ) undergo a single round of DNA replication followed by two consecutive divisions . In most organisms , the segregation of chromosomes at the first meiotic division is dependent upon genetic exchange , or crossing over , at homologous sites a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/nuclear", "structure", "and", "function", "molecular", "biology/recombination", "genetics", "and", "genomics/nuclear", "structure", "and", "function", "molecular", "biology/chromosome", "structure", "genetics", "and", "genomics/chromosome", "biology", "molecu...	2009	The pch2Δ Mutation in Baker's Yeast Alters Meiotic Crossover Levels and Confers a Defect in Crossover Interference
The generation of distinct neuronal subtypes at different axial levels relies upon both anteroposterior and temporal cues . However , the integration between these cues is poorly understood . In the Drosophila central nervous system , the segmentally repeated neuroblast 5–6 generates a unique group of neurons , the Apt...	An animal's nervous system contains a wide variety of neuronal subtypes generated from neural progenitor ( “stem” ) cells , which generate different types of neurons at different axial positions and time points . Hence , the generation and specification of unique neuronal subtypes is dependent upon the integration of b...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "developmental", "biology", "developmental", "biology/stem", "cells", "developmental", "biology/cell", "differentiation", "neuroscience/neurodevelopment", "developmental", "biology/neurodevelopment", "developmental", "biology/molecular", "development", "developmental", "biology/develop...	2010	Segment-Specific Neuronal Subtype Specification by the Integration of Anteroposterior and Temporal Cues
Starvation of cells for the DNA building block dTTP is strikingly lethal ( thymineless death , TLD ) , and this effect is observed in all organisms . The phenomenon , discovered some 60 years ago , is widely used to kill cells in anticancer therapies , but many questions regarding the precise underlying mechanisms have...	Starvation of cells for DNA precursor dTTP is strikingly lethal in many organisms , like bacteria , yeast , and human cells . This type of death is unusual in that starvation for other nutritional requirements generally results in growth arrest , but not in death . The phenomenon is called thymineless death ( TLD ) , b...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "death", "cellular", "stress", "responses", "cell", "cycle", "and", "cell", "division", "cell", "processes", "microbiology", "nucleotides", "escherichia", "coli", "mutation", "prokaryotic", "models", "model", "organisms", "nucleic", "acid", "components", "dna"...	2014	dGTP Starvation in Escherichia coli Provides New Insights into the Thymineless-Death Phenomenon
Influenza A virus ( IAV ) infection is normally controlled by adaptive immune responses initiated by dendritic cells ( DCs ) . We investigated the consequences of IAV infection of human primary DCs on their ability to function as antigen-presenting cells . IAV was internalized by both myeloid DCs ( mDCs ) and plasmacyt...	Although the interactions between viruses and dendritic cells ( DCs ) have been studied for many years , surprisingly little is known on the functional relationship between infection and antigen presentation in primary human DCs . Here , we asked specifically whether Influenza A virus ( IAV ) infection of human primary...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "immune", "cells", "clinical", "immunology", "immunity", "virology", "viral", "transmission", "and", "infection", "immunology", "biology", "immunologic", "techniques", "microbiology", "viral", "diseases" ]	2012	Influenza A Virus Infection of Human Primary Dendritic Cells Impairs Their Ability to Cross-Present Antigen to CD8 T Cells
The unconventional prefoldin URI/RMP , in humans , and its orthologue in yeast , Bud27 , have been proposed to participate in the biogenesis of the RNA polymerases . However , this role of Bud27 has not been confirmed and is poorly elucidated . Our data help clarify the mechanisms governing biogenesis of the three euka...	The mechanisms governing the assembly and the transport of the three eukaryotic RNA polymerases to the nucleus are in discussion . Interesting papers have demonstrated the participation of some proteins in the assembly of the nuclear RNA polymerases and in their transport to the nucleus , but the mechanisms involved ar...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "spectrometric", "identification", "of", "proteins", "cellular", "structures", "protein", "interactions", "macromolecular", "assemblies", "microbiology", "gene", "function", "immunochemistry", "model", "organisms", "chaperone", "proteins", "cell", "nucleus", "proteins", "bi...	2013	The Prefoldin Bud27 Mediates the Assembly of the Eukaryotic RNA Polymerases in an Rpb5-Dependent Manner
Mutations that alter signaling of RAS/MAPK-family proteins give rise to a group of Mendelian diseases known as RASopathies . However , among RASopathies , the matrix of genotype-phenotype relationships is still incomplete , in part because there are many RAS-related proteins and in part because the phenotypic consequen...	While many causes of developmental disabilities have been identified , a large number of affected children cannot be diagnosed despite extensive medical testing . Previously unknown genetic factors are likely to be the culprits in many of these cases . Using DNA sequencing , and by sharing information among many doctor...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "sequencing", "techniques", "medicine", "and", "health", "sciences", "face", "disabilities", "enzymes", "enzymology", "alleles", "genome", "sequencing", "molecular", "biology", "techniques", "research", "and", "analysis", "methods", "public", "and", "occupational", "hea...	2018	De novo mutations in the GTP/GDP-binding region of RALA, a RAS-like small GTPase, cause intellectual disability and developmental delay
Gene expression can be highly heterogeneous in isogenic cell populations . An extreme type of heterogeneity is the so-called bistable or bimodal expression , whereby a cell can differentiate into two alternative expression states . Stochastic fluctuations of protein levels , also referred to as noise , provide the nece...	Gene expression can be highly heterogeneous in clonal cell populations . An extreme type of heterogeneity is the so-called bistable or bimodal expression , whereby a cell can differentiate into two alternative expression states , and consequently a population will be composed of cells that are ‘ON’ and cells that are ‘...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	A Novel Feedback Loop That Controls Bimodal Expression of Genetic Competence
Mitochondrial translation , essential for synthesis of the electron transport chain complexes in the mitochondria , is governed by nuclear encoded genes . Polymorphisms within these genes are increasingly being implicated in disease and may also trigger adverse drug reactions . Statins , a class of HMG-CoA reductase in...	The mitochondria are responsible for producing the cell's energy . Energy production is the result of carefully orchestrated interactions between proteins encoded by the mitochondrial DNA and by nuclear DNA . Sequence variations in genes encoding these proteins have been shown to cause disease and adverse drug reaction...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "cellular", "structures", "subcellular", "organelles", "rna", "interference", "microbiology", "model", "organisms", "mitochondrial", "myopathy", "genetics", "and", "genomics", "mitochondrial", "diseases", "gene", "expression", "biology", "molecular", "biolo...	2012	Polymorphisms in the Mitochondrial Ribosome Recycling Factor EF-G2mt/MEF2 Compromise Cell Respiratory Function and Increase Atorvastatin Toxicity

Subsets and Splits

No community queries yet

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