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
Whether mechanically unfolded fibronectin ( Fn ) is present within native extracellular matrix fibrils is controversial . Fn extensibility under the influence of cell traction forces has been proposed to originate either from the force-induced lengthening of an initially compact , folded quaternary structure as is foun...	Cells are embedded within an extracellular matrix that regulates many cellular processes , including stem cell differentiation and cancer progression . Yet the underlying molecular mechanisms that mediate these processes remain unknown . Within the extracellular matrix of cells , super-molecular assemblies of fibronect...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biophysics", "cell", "biology" ]	2007	Force-Induced Unfolding of Fibronectin in the Extracellular Matrix of Living Cells
Apical–basal polarity is essential for the formation and function of epithelial tissues , whereas loss of polarity is a hallmark of tumours . Studies in Drosophila have identified conserved polarity factors that define the apical ( Crumbs , Stardust , Par-6 , atypical protein kinase C [aPKC] ) , junctional ( Bazooka [B...	The Drosophila midgut is lined by a single-layered epithelium that acts as a barrier to the environment while allowing for nutrient uptake and related physiological processes . To fulfil these roles , midgut epithelial cells are highly polarised , with a pronounced asymmetric distribution of cellular components . Previ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "physiology", "invertebrates", "septate", "junctions", "medicine", "and", "health", "sciences", "junctional", "complexes", "green", "fluorescent", "protein", "cloning", "vertebrates", "animals", "cell", "polarity", "animal", "models", "developmental", "biology", ...	2018	An alternative mode of epithelial polarity in the Drosophila midgut
Several organisms , including humans , display a deceleration in mortality rates at advanced ages . This mortality deceleration is sufficiently rapid to allow late-life mortality to plateau in old age in several species , causing the apparent cessation of biological ageing . Here , it is shown that late-life mortality ...	In diverse species , mortality rates increase with age at a relatively fixed rate within populations . However , recent discoveries have suggested this relationship breaks down in advanced old age , with mortality rate increases slowing and even reaching a plateau . This late-life mortality deceleration has initiated s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "death", "rates", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "statistics", "physiological", "processes", "developmental", "biology", "research", "design", "organism", "development", "forecasting", "mathematics", "cohort", "stud...	2018	Errors as a primary cause of late-life mortality deceleration and plateaus
Vibrio cholerae causes over 2 million cases of cholera and 90 , 000 deaths each year . Serosurveillance can be a useful tool for estimating the intensity of cholera transmission and prioritizing populations for cholera control interventions . Current methods involving venous blood draws and downstream specimen storage ...	Cholera remains a major public health issue among underprivileged populations in the developing world . Current methods of disease surveillance are inadequate for identifying key populations at highest risk of cholera . Serosurveillance can provide accurate measurements of an individual or population’s exposure to chol...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "enzyme-linked", "immunoassays", "pathogens", "vibrio", "immunology", "tropical", "diseases", "microbiology", "vaccines", "bacterial", "disease...	2018	Dried Blood Spots for Measuring Vibrio cholerae-specific Immune Responses
The identity of the specific molecules required for the process of retinal circuitry formation is largely unknown . Here we report a newly identified zebrafish mutant in which the absence of the atypical cadherin , Celsr3 , leads to a specific defect in the development of GABAergic signaling in the inner retina . This ...	Visual information is transmitted through the retina from photoreceptors to bipolars to ganglion cells , the output neurons connecting to the brain . This vertical transmission of information is modulated by inhibitory lateral interneurons . Normal vision requires the proper transmission and processing of these neurona...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cadherins", "medicine", "retinal", "disorders", "cell", "biology", "synapses", "cell", "adhesion", "ophthalmology", "biology", "molecular", "cell", "biology", "neuroscience", "neurophysiology" ]	2011	Celsr3 Is Required for Normal Development of GABA Circuits in the Inner Retina
Bartonella species are emerging infectious organisms transmitted by arthropods capable of causing long-lasting infection in mammalian hosts . Among over 30 species described from four continents to date , 15 are known to infect humans , with eight of these capable of infecting dogs as well . B . bacilliformis is the on...	Bartonella are bacteria transmitted by fleas , ticks , sandflies and other insects capable of infecting humans , domestic animals , livestock and wildlife , including marine mammals . In humans , they cause diseases such as trench fever , cat scratch disease , endocarditis , fever of unknown origin and have been recent...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "disease", "epidemiology", "bartonellosis", "bacterial", "diseases", "veterinary", "diagnostics", "neglected", "tropical", "diseases", "population", "biology", "small", "animal", "care", "veterinary", "science", "veterinary", "medicine", "infectiou...	2013	Infection of Domestic Dogs in Peru by Zoonotic Bartonella Species: A Cross-Sectional Prevalence Study of 219 Asymptomatic Dogs
miRNAs ( microRNAs ) are a class of endogenous small RNAs that are thought to negatively regulate protein production . Aberrant expression of many miRNAs is linked to cancer and other diseases . Little is known about the factors that regulate the expression of miRNAs . We have identified numerous regulatory elements up...	microRNAs ( miRNAs ) are unusually small RNAs that are thought to control the production of proteins in the cell . Recent studies have linked miRNAs to several types of cancers . Several studies strongly suggest that miRNAs could be useful as diagnostic and prognostic markers of various cancers . Thus , although miRNAs...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics", "mammals" ]	2007	Regulatory Circuit of Human MicroRNA Biogenesis
Hair follicles undergo recurrent cycling of controlled growth ( anagen ) , regression ( catagen ) , and relative quiescence ( telogen ) with a defined periodicity . Taking a genomics approach to study gene expression during synchronized mouse hair follicle cycling , we discovered that , in addition to circadian fluctua...	The hair follicle renews itself by repeatedly cycling among growth , regression , and rest phases . One function of hair follicle cycling is to allow seasonal changes in hair growth . Understanding the regulation of hair follicle cycling is also of interest because abnormal regulation of hair cycle control genes is res...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/bioinformatics", "cell", "biology/gene", "expression", "computational", "biology/transcriptional", "regulation" ]	2009	Circadian Clock Genes Contribute to the Regulation of Hair Follicle Cycling
Adhesion of the Trypanosoma cruzi trypomastigotes , the causative agent of Chagas' disease in humans , to components of the extracellular matrix ( ECM ) is an important step in host cell invasion . The signaling events triggered in the parasite upon binding to ECM are less explored and , to our knowledge , there is no ...	Interaction of Trypanosoma cruzi with the extracellular matrix ( ECM ) is an essential step in the invasion of mammalian cells . However , the nature of the signaling triggered in the parasite is poorly understood . Herein the key role of nitric oxide in T . cruzi signaling is described , using an ECM preparation , in ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Down Regulation of NO Signaling in Trypanosoma cruzi upon Parasite-Extracellular Matrix Interaction: Changes in Protein Modification by Nitrosylation and Nitration
Schistosomiasis in pregnancy may cause low birth weight , prematurity and stillbirth of the offspring . The placenta of pregnant women might be involved when schistosome ova are trapped in placental tissue . Standard histopathological methods only allow the examination of a limited amount of placental tissue and are th...	Schistosomiasis in pregnant women is associated with prematurity , low birth weight and stillbirth of the fetus . Schistosome eggs may be trapped in the placental tissue and , thus , contribute to fetal harm . As the placenta is a large organ , current microscopic histopathological examinations commonly lack sensitivit...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "medicine", "and", "health", "sciences", "reproductive", "system", "chemical", "compounds", "maternal", "health", "obstetrics", "and", "gynecology", "helminths", "tropical", "diseases", "parasitic", "diseases", "an...	2017	Improvement of a tissue maceration technique for the determination of placental involvement in schistosomiasis
A novel bunyavirus was recently found to cause severe febrile illness with high mortality in agricultural regions of China , Japan , and South Korea . This virus , named severe fever with thrombocytopenia syndrome virus ( SFTSV ) , represents a new group within the Phlebovirus genus of the Bunyaviridae . Little is know...	As obligate , intracellular parasites , viruses depend upon numerous host-derived factors to replicate . For many bunyaviruses , these pro-viral host factors are largely uncharacterized . In the present study , we used an unbiased genetic screening strategy to identify human genes that facilitate the entry process of a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "&", "methods" ]	[ "sv40", "medicine", "and", "health", "sciences", "rift", "valley", "fever", "virus", "vesicular", "stomatitis", "virus", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "pathogens", "microbiology", "viral", "structure", "viruses", "rna", "viruses",...	2017	A role for glycolipid biosynthesis in severe fever with thrombocytopenia syndrome virus entry
miRNAs participate in the regulation of apoptosis . However , it remains largely unknown as to how miRNAs are integrated into the apoptotic program . Mitochondrial fission is involved in the initiation of apoptosis . It is not yet clear whether miRNAs are able to regulate mitochondrial fission . Here we report that miR...	Apoptosis is related to the pathogenesis of many diseases such as tumors and neurodegenerative and cardiovascular disorders . Apoptosis is controlled by a variety of genes , and among them a protein called “p53” has been taken as a “death star” and is involved in the initiation of apoptosis . The upstream and downstrea...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/post-translational", "regulation", "of", "gene", "expression", "molecular", "biology/rna-protein", "interactions", "molecular", "biology/translation", "mechanisms", "physiology/cell", "signaling", "biochemistry/transcription", "and", "translation" ]	2010	miR-30 Regulates Mitochondrial Fission through Targeting p53 and the Dynamin-Related Protein-1 Pathway
The specificities of transcription factors are most commonly represented with probabilistic models . These models provide a probability for each base occurring at each position within the binding site and the positions are assumed to contribute independently . The model is simple and intuitive and is the basis for many...	Transcription factors ( TFs ) , a class of DNA-binding proteins , play a central role in the regulation of gene expression . TFs control the rate of transcription by binding to the genome in a sequence-specific manner . Thus , one important aspect in the study of gene regulation mechanism is to model the binding specif...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "protein", "interactions", "applied", "mathematics", "dna-binding", "proteins", "simulation", "and", "modeling", "algorithms", "mathematics", "sequence", "motif", "analysis", "research", "and", "analysis", "methods", "sequence", "analysis", "bioinformatics", "proteins", "...	2017	Inherent limitations of probabilistic models for protein-DNA binding specificity
Macroautophagy has been shown to be important for the cellular remodelling required for Leishmania differentiation . We now demonstrate that L . major contains a functional ATG12-ATG5 conjugation system , which is required for ATG8-dependent autophagosome formation . Nascent autophagosomes were found commonly associate...	Leishmaniasis is a disease of humans that is of major significance throughout many parts of the world . It is caused by the protozoan parasite Leishmania and mammals are infected through the bite of a sand fly in which the parasite develops . Parasite remodelling crucial for generation of the human-infective forms is a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biochemistry", "infectious", "diseases", "veterinary", "microbiology", "biology", "microbiology", "molecular", "cell", "biology", "veterinary", "science" ]	2012	ATG5 Is Essential for ATG8-Dependent Autophagy and Mitochondrial Homeostasis in Leishmania major
It has been hypothesized that HIV-1 viral load set-point is a surrogate measure of HIV-1 viral virulence , and that it may be subject to natural selection in the human host population . A key test of this hypothesis is whether viral load set-points are correlated between transmitting individuals and those acquiring inf...	During the long period of asymptomatic infection with HIV-1 there is considerable variability in viral load set-point between infected individuals . Higher viral load set-points increase infectivity and decrease survival . Previous work has shown that the most commonly observed viral load set-points are those intermedi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/hiv", "infection", "and", "aids", "evolutionary", "biology/microbial", "evolution", "and", "genomics" ]	2010	HIV-1 Transmitting Couples Have Similar Viral Load Set-Points in Rakai, Uganda
Knowledge of spatial chromosomal organizations is critical for the study of transcriptional regulation and other nuclear processes in the cell . Recently , chromosome conformation capture ( 3C ) based technologies , such as Hi-C and TCC , have been developed to provide a genome-wide , three-dimensional ( 3D ) view of c...	Understanding how chromosomes fold provides insights into the complex relationship among chromatin structure , gene activity and the functional state of the cell . Recently , chromosome conformation capture based technologies , such as Hi-C and TCC , have been developed to provide a genome-wide , high resolution and th...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genomics", "chromosome", "biology", "biology", "computational", "biology", "structural", "genomics", "genetics", "and", "genomics" ]	2013	Bayesian Inference of Spatial Organizations of Chromosomes
Leptospirosis is a neglected zoonosis affecting animals and humans caused by infection with Leptospira . The bacteria can survive outside of hosts for long periods of time in soil and water . While identification of Leptospira species from human cases and animal reservoirs are increasingly reported , little is known ab...	Leptospirosis is a zoonotic disease that is caused by either direct contact with the urine of animals infected with pathogenic forms of Leptospira , or indirectly , through contact with contaminated water or soil . Because many people become infected through the environment , where the bacteria can live for many months...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion", "Conclusion" ]	[ "livestock", "medicine", "and", "health", "sciences", "surface", "water", "leptospira", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "vertebrates", "animals", "mammals", "farms", "molecular", "biology", "techniques", "bacteria", "bacterial", ...	2016	Distribution and Diversity of Pathogenic Leptospira Species in Peri-domestic Surface Waters from South Central Chile
Candida albicans is a major invasive fungal pathogen in humans . An important virulence factor is its ability to switch between the yeast and hyphal forms , and these filamentous forms are important in tissue penetration and invasion . A common feature for filamentous growth is the ability to inhibit cell separation af...	Candida albicans is a major fungal pathogen in immunologically compromised patients . A key virulence trait is its ability to switch between the yeast and hyphal forms . Whereas yeast cells are required for dissemination , the filamentous forms are important in tissue penetration and invasion . In order to make a hypha...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	A Single Nucleotide Polymorphism Uncovers a Novel Function for the Transcription Factor Ace2 during Candida albicans Hyphal Development
As part of a prospective study of leptospirosis and biodiversity of Leptospira in the Peruvian Amazon , a new Leptospira species was isolated from humans with acute febrile illness . Field trapping identified this leptospire in peridomestic rats ( Rattus norvegicus , six isolates; R . rattus , two isolates ) obtained i...	Leptospirosis has emerged as a globally important infectious disease . Its impact on public health is often difficult to determine , sometimes because of low clinical suspicion , or , as is more common , difficulty in laboratory diagnosis . Gold-standard serology-based diagnosis has a number of important limitations , ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "microbiology/environmental", "microbiology", "microbiology/immunity", "to", "infections", "infectious", "diseases/neglected", "tropical", "diseases", "microbiology/microbial", "evolution", "and", "genomics", "infectious", "diseases/bacterial", "infections", "infectious", "diseases...	2008	Human Leptospirosis Caused by a New, Antigenically Unique Leptospira Associated with a Rattus Species Reservoir in the Peruvian Amazon
Soil-transmitted helminths and intestinal protozoa infection are widespread in developing countries , yet an accurate diagnosis is rarely performed . The aim of this study was to evaluate the recently developed mini–FLOTAC method and to compare with currently more widely used techniques for the diagnosis of intestinal ...	The mini-FLOTAC has been recently developed as a novel direct method for the diagnosis of intestinal parasitic infections . Mini-FLOTAC attempts to address the challenge of using modern technology matched with high sensitivity , affordability , and appropriateness of diagnosis in resource-limited settings where intesti...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "taeniasis", "medicine", "infectious", "diseases", "amebiasis", "schistosomiasis", "soil-transmitted", "helminths", "parasitic", "intestinal", "diseases", "trichuriasis", "giardiasis", "hookworm", "infection", "strongyloidiasis", "neglected", "tropical", "diseases", "enterobias...	2013	Mini-FLOTAC, an Innovative Direct Diagnostic Technique for Intestinal Parasitic Infections: Experience from the Field
Infertility affects about one in six couples attempting pregnancy , with the man responsible in approximately half of the cases . Because the pathophysiology underlying azoospermia is not elucidated , most male infertility is diagnosed as idiopathic . Genome-wide gene expression analyses with microarray on testis speci...	Worldwide , approximately 15% of couples attempting pregnancy meet with failure . Male factors are thought to be responsible in 20%–50% of all infertility cases . Azoospermia , the absence of sperm in the ejaculate due to defects in its production or delivery is common in male infertility . In this study , we focused o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "primates", "urology", "mammals", "homo", "(human)", "genetics", "and", "genomics" ]	2008	Genome-Wide Expression of Azoospermia Testes Demonstrates a Specific Profile and Implicates ART3 in Genetic Susceptibility
Tay-Sachs and Sandhoff diseases are lethal inborn errors of acid β-N-acetylhexosaminidase activity , characterized by lysosomal storage of GM2 ganglioside and related glycoconjugates in the nervous system . The molecular events that lead to irreversible neuronal injury accompanied by gliosis are unknown; but gene trans...	Sandhoff and Tay-Sachs disease are devastating neurological diseases associated with developmental regression , blindness , seizures , and death in infants and young children . These disorders are caused by mutations in β-hexosaminidase genes , which result in neuronal accumulation of certain lipids , glycosphingolipid...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "histology", "model", "organisms", "genetics", "genetics", "and", "genomics", "biology", "neuroscience", "metabolic", "disorders" ]	2012	Characterization of Inducible Models of Tay-Sachs and Related Disease
Increased rates for failure in leishmaniasis antimony treatment have been recently recognized worldwide . Although several risk factors have been identified there is no clinical score to predict antimony therapy failure of cutaneous leishmaniasis . A case control study was conducted in Peru from 2001 to 2004 . 171 pati...	The manuscript is relevant because of the finding of a new risk factor for chemotherapy failure and the development of a prognosis score for cutaneous leishmaniasis . The proportion of patients that have multiple lesions in American Tegumentary Leishmaniasis ( ATL ) is considerable . Publications and our experience per...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "epidemiology", "infectious", "disease", "epidemiology", "leishmaniasis", "neglected", "tropical", "diseases", "infectious", "disease", "control" ]	2012	Prediction Score for Antimony Treatment Failure in Patients with Ulcerative Leishmaniasis Lesions
The failure of current strategies to provide an explanation for controversial findings on the pattern of pathophysiological changes in Alzheimer's Disease ( AD ) motivates the necessity to develop new integrative approaches based on multi-modal neuroimaging data that captures various aspects of disease pathology . Prev...	Establishing an accurate diagnosis of Alzheimer's disease has been a major challenge in the past decades . With an increasing amount of studies aiming at detection and validation of imaging biomarkers for this disease , many apparently controversial findings have been reported over the time . The failure of current str...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "radiology", "and", "medical", "imaging", "pet", "imaging", "mental", "health", "diagnostic", "radiology", "neurological", "disorders", "neurology", "dementia", "alzheimer", "disease", "nuclear", "medicine", "neuroimaging", "radiology", "psychiatry" ]	2013	Generative FDG-PET and MRI Model of Aging and Disease Progression in Alzheimer's Disease
Pancreatobiliary cancers have among the highest mortality rates of any cancer type . Discovering the full spectrum of molecular genetic alterations may suggest new avenues for therapy . To catalogue genomic alterations , we carried out array-based genomic profiling of 31 exocrine pancreatic cancers and 6 distal bile du...	Pancreatic cancer is a devastating disease , having among the lowest survival rates of any cancer . A better understanding of the molecular basis of pancreatic cancer may lead to improved rationale therapies . We report here the discovery of amplification ( i . e . extra copies ) of the GATA6 gene in many human pancrea...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "genetics", "and", "genomics/gene", "discovery", "gastroenterology", "and", "hepatology/biliary", "tract", "genetics", "and", "genomics/gene", "function", "oncology/gastrointestinal", "cancers", "genetics", "and", "genomics/cancer", "ge...	2008	Genomic Profiling Identifies GATA6 as a Candidate Oncogene Amplified in Pancreatobiliary Cancer
Because no dengue vaccine or antiviral therapy is commercially available , controlling the primary mosquito vector , Aedes aegypti , is currently the only means to prevent dengue outbreaks . Traditional models of Ae . aegypti assume that population dynamics are regulated by density-dependent larval competition for food...	Controlling the mosquito Aedes aegypti is of public health importance because , at present , it is the only means to stop dengue virus transmission . Implementing successful mosquito control programs requires understanding what factors regulate population abundance , as well as anticipating how mosquitoes may adapt to ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "global", "health", "neglected", "tropical", "diseases", "infectious", "diseases", "disease", "ecology", "dengue", "fever", "biology", "vectors", "and", "hosts", "population", "ecology", "public", "health", "behav...	2011	Oviposition Site Selection by the Dengue Vector Aedes aegypti and Its Implications for Dengue Control
Simian virus 40 ( SV40 ) and cellular DNA replication rely on host ATM and ATR DNA damage signaling kinases to facilitate DNA repair and elicit cell cycle arrest following DNA damage . During SV40 DNA replication , ATM kinase activity prevents concatemerization of the viral genome whereas ATR activity prevents accumula...	Viruses from both Polyomaviridae and Papillomaviridae families share several characteristics . These include common modes of DNA replication and an accumulation of DNA damage signaling and repair proteins at replicating viral DNA . Several DNA repair proteins , with unknown functions during viral DNA replication , asso...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "non-homologous", "end", "joining", "dna", "replication", "cell", "biology", "virology", "biology", "and", "life", "sciences", "dna", "dna", "repair", "dna", "recombination", "microbiology", "viral", "replication", "viral", "replication", "complex", "m...	2014	SV40 Utilizes ATM Kinase Activity to Prevent Non-homologous End Joining of Broken Viral DNA Replication Products
IL-4Rα-dependent responses are essential for granuloma formation and host survival during acute schistosomiasis . Previously , we demonstrated that mice deficient for macrophage-specific IL-4Rα ( LysMcreIl4ra−/lox ) developed increased hepatotoxicity and gut inflammation; whereas inflammation was restricted to the live...	Schistosomiasis is a tropical disease caused by one of the species of the parasitic worm Schistosoma which infects over 200 million people worldwide . Signalling via the IL-4 receptor alpha ( IL-4Rα ) , which is the common receptor chain for the ligands IL-4 and IL-13 , is essential for inducing protective Type 2 immun...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "cell", "biology/leukocyte", "signaling", "and", "gene", "expression", "immunology/immune", "response", "infectious", "diseases/helminth", "infections", "immunology/immunity", "to", "infections", "immunology/leukocyte", "activation" ]	2010	IL-4Rα-Independent Expression of Mannose Receptor and Ym1 by Macrophages Depends on their IL-10 Responsiveness
A number of neurological disorders arise from perturbations in biochemical signaling and protein complex formation within neurons . Normally , proteins form networks that when activated produce persistent changes in a synapse’s molecular composition . In hippocampal neurons , calcium ion ( Ca2+ ) flux through N-methyl-...	Learning and memory formation are likely associated with dynamic fluctuations in the connective strength of neuronal synapses . These fluctuations , called synaptic plasticity , are regulated by calcium ion ( Ca2+ ) influx through ion channels localized to the post-synaptic membrane . Within the post-synapse , the domi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "neurochemistry", "enzymology", "brain", "neuroscience", "simulation", "and", "modeling", "ganglion", "cells", "chemical", "dissociation", "enzyme", "chemistry", "neuronal", "tuning", "research", "and", "analysis", "methods", "an...	2017	Competitive tuning: Competition's role in setting the frequency-dependence of Ca2+-dependent proteins
Immune correlates of protection against intracellular bacterial pathogens are largely thought to be cell-mediated , although a reasonable amount of data supports a role for antibody-mediated protection . To define a role for antibody-mediated immunity against an intracellular pathogen , Rhodococcus equi , that causes g...	Development of effective vaccines for diseases such as tuberculosis , brucellosis and others caused by intracellular pathogens has proved challenging , as data exist supporting both antibody and cellular immune effectors as mediators of protection . To address this problem against an important , and representative , eq...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "complement", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "body", "fluids", "pathology", "and", "laboratory", "medicine", "intracellular", "pathogens", "pathogens", "immunology", "vertebrates", "animals", "pulmonology", "mammals", "pneumonia...	2018	Antibody to Poly-N-acetyl glucosamine provides protection against intracellular pathogens: Mechanism of action and validation in horse foals challenged with Rhodococcus equi
The respiratory mucosa is a major site for pathogen invasion and , hence , a site requiring constant immune surveillance . The type I , semi-invariant natural killer T ( NKT ) cells are enriched within the lung vasculature . Despite optimal positioning , the role of NKT cells in respiratory infectious diseases remains ...	NKT cells are innate-like lymphocytes with a demonstrated role in a wide range of diseases . Often cited for their ability to rapidly produce a variety of cytokines upon activation , they have long been appreciated for their ability to “jump-start” the immune system and to shape the quality of both the innate and adapt...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Border Patrol Gone Awry: Lung NKT Cell Activation by Francisella tularensis Exacerbates Tularemia-Like Disease
Staphylococcus aureus nasal colonization is an important risk factor for community and nosocomial infection . Despite the importance of S . aureus to human health , molecular mechanisms and host factors influencing nasal colonization are not well understood . To identify host factors contributing to nasal colonization ...	Staphylococcus aureus is a medically important human pathogen that is found in the nasal passages of approximately 1/3 of the population . The nose serves as a reservoir for spread of this pathogen and predisposes the host to potential infection . Factors contributing to S . aureus nasal colonization are only beginning...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "biology", "microbiology", "otorhinolaryngology", "otolaryngology" ]	2011	Hemoglobin Promotes Staphylococcus aureus Nasal Colonization
St . Louis encephalitis virus ( SLEV , Flavivirus , Flaviviridae ) is an emerging mosquito-borne pathogen in South America , with human SLEV encephalitis cases reported in Argentina and Brazil . Genotype III strains of SLEV were isolated from Culex quinquefasciatus mosquitoes in Cordoba , Argentina in 2005 , during the...	St . Louis encephalitis virus ( SLEV , Flavivirus , Flaviviridae ) is an emerging arbovirus in South America , with human SLEV encephalitis cases reported in Argentina and Brazil . Genotype III strains of SLEV were isolated from mosquitoes during the largest SLEV outbreak ever reported in South America ( Córdoba , Arge...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "zoonoses", "neglected", "tropical", "diseases", "arboviral", "infections", "viral", "diseases", "vectors", "and", "hosts" ]	2011	Comparison of Argentinean Saint Louis Encephalitis Virus Non-Epidemic and Epidemic Strain Infections in an Avian Model
Mayaro virus ( MAYV ) , an alphavirus similar to chikungunya virus ( CHIKV ) , causes an acute debilitating disease which results in the development of long-term arthralgia in more than 50% of infected individuals . Currently , the immune response and its role in the development of MAYV-induced persistent arthralgia re...	Mayaro virus ( MAYV ) causes an acute debilitating disease which results in the development of long-term arthralgia in more than 50% of infected individuals , similarly to what has been described with CHIKV . In this study , we evaluated the immune response of individuals with confirmed MAYV infection in a one-year lon...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Long-Term Arthralgia after Mayaro Virus Infection Correlates with Sustained Pro-inflammatory Cytokine Response
Toxoplasma gondii is an intracellular parasite that transitions from acute infection to a chronic infective state in its intermediate host via encystation , which enables the parasite to evade immune detection and clearance . It is widely accepted that the tissue cyst perimeter is highly and specifically decorated with...	The Toxoplasma tissue cyst is essential to the persistence of the parasite during the chronic infection of an immunocompetent host . While significant efforts have been made to identify molecular factors that trigger and sustain parasite encystation , the role of the glycoconjugates that decorate the cyst wall has rece...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "host-pathogen", "interaction", "biology", "microbiology", "glycobiology", "parasitology" ]	2013	A Nucleotide Sugar Transporter Involved in Glycosylation of the Toxoplasma Tissue Cyst Wall Is Required for Efficient Persistence of Bradyzoites
Dengue is an arboviral disease that imposes substantial health and economic burdens across the globe . Vector control remains a key strategy in settings where Dengvaxia ( a dengue vaccine ) has not been licenced due to safety concerns and where mass immunization programmes are not cost-effective . Though inspections ar...	Dengue is a disease that is transmitted by Aedes mosquitoes . In areas where the use of a dengue vaccine has not been authorized due to safety concerns and is not cost-effective , reducing the population of Aedes mosquitoes remains the key method in controlling the disease . One approach to mosquito population control ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "geographical", "locations", "social", "sciences", "animals", "singapore", "vaccines", "habitats", "infectious", "disease", "control", "insect", "vectors", "zoology", ...	2019	The effectiveness of inspections on reported mosquito larval habitats in households: A case-control study
Human immunodeficiency virus type 1 ( HIV-1 ) exploits a diverse array of host cell functions in order to replicate . This is mediated through a network of virus-host interactions . A variety of recent studies have catalogued this information . In particular the HIV-1 , Human Protein Interaction Database ( HHPID ) has ...	HIV-1 is responsible for millions of deaths every year by causing acquired immunodeficiency syndrome ( AIDS ) . Therefore , research is ongoing in order to better understand and counter HIV-1 infection . Like any virus , HIV-1 must enter host cells and use cellular machinery to replicate . To do this , proteins of the ...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "virology/viral", "replication", "and", "gene", "regulation", "infectious", "diseases/hiv", "infection", "and", "aids", "infectious", "diseases/viral", "infections", "computational", "biology", "virology/effects", "of", "virus", "infection", "on", "host", "gene", "express...	2010	Patterns of HIV-1 Protein Interaction Identify Perturbed Host-Cellular Subsystems
Pro-inflammatory cytokinemia is a hallmark of highly pathogenic H5N1 influenza virus ( IAV ) disease yet little is known about the role of host proteins in modulating a pathogenic innate immune response . The host Interferon Induced Protein 35 ( Ifi35 ) has been implicated in increased susceptibility to H5N1-IAV infect...	Highly pathogenic influenza A viruses ( IAV ) are an important human pathogen that cause high mortality and can acquire the ability to cause pandemics . Following highly pathogenic H5N1-IAV infection , exaggerated inflammatory responses are detrimental to the host and lead to more disease; tipping the balance between p...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "inflammatory", "diseases", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "orthomyxoviruses", "viruses", "animal", "model...	2018	Interferon induced protein 35 exacerbates H5N1 influenza disease through the expression of IL-12p40 homodimer
Alveolar echinococcosis is a worldwide zoonosis of great public health concern . Analysis of genome data for Echinococcus multilocularis has identified antigen families that can be used in diagnostic assays and vaccine development . However , little gene expression data is available for antigens of the egg and early la...	Humans become infected with E . multilocularis through oral ingestion of the eggs . Untreated alveolar echinococcosis has a fatality rate of >90% in humans , causing great public health concern in the northern hemisphere . The genome databases of E . multilocularis have been recently published , but still there is no a...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "medicine", "and", "health", "sciences", "vesicles", "pathology", "and", "laboratory", "medicine", "immunology", "tropical", "diseases", "parasitic", "diseases", "parasitology", "vaccines", "preventive", "medicine", "developmental", "biology", "genome", "analysis", "negle...	2016	Analysis on Gene Expression Profile in Oncospheres and Early Stage Metacestodes from Echinococcus multilocularis
Candida albicans is frequently detected with heavy infection by Streptococcus mutans in plaque-biofilms from children with early-childhood caries ( ECC ) . This cross-kingdom biofilm contains an extensive matrix of extracellular α-glucans that is produced by an exoenzyme ( GtfB ) secreted by S . mutans . Here , we repo...	Early childhood caries is a severe form of tooth decay that affects toddlers and is clinically distinct from other forms of the disease . It is characterized by the frequent isolation of the commensal yeast Candida albicans and the bacterial pathogen Streptococcus mutans within caries-associated biofilms . This mixed-k...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "biofilms", "bacteriology", "exopolysaccharides", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "fungal", "structure", "mutation", "fungi", "experimental", "organism", "systems", "fungal", "pathogens", ...	2017	Candida albicans mannans mediate Streptococcus mutans exoenzyme GtfB binding to modulate cross-kingdom biofilm development in vivo
Recursive splicing , a process by which a single intron is removed from pre-mRNA transcripts in multiple distinct segments , has been observed in a small subset of Drosophila melanogaster introns . However , detection of recursive splicing requires observation of splicing intermediates that are inherently unstable , ma...	The splicing of RNA transcripts is an essential step in the production of mature mRNA molecules , involving removal of intron sequences and joining of flanking exon sequences . Introns are usually removed as a single unit in a two-step catalytic reaction . However , a small subset of introns in flies are removed via sp...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing", "techniques", "invertebrates", "animals", "invertebrate", "genomics", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "experimental", "organism", "systems", "genome", "analysis", "sequence", "motif", "analysis", "molecular", "biology", ...	2018	Numerous recursive sites contribute to accuracy of splicing in long introns in flies
Multi-scale computational modeling is a major branch of computational biology as evidenced by the US federal interagency Multi-Scale Modeling Consortium and major international projects . It invariably involves specific and detailed sequences of data analysis and simulation , often with multiple tools and datasets , an...	We present a computational workflow as a proof of concept for integration and implementation of a reusable and reproducible cardiac multi-scale electrophysiology model that is expandable , modular and portable . This framework enables scientists to create intuitive , user-friendly and flexible end-to-end automated scie...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "graphical", "user", "interfaces", "action", "potentials", "medicine", "and", "health", "sciences", "engineering", "and", "technology", "membrane", "potential", "electrophysiology", "neuroscience", "simulation", "and", "modeling", "human", "factors", "engineering", "scien...	2019	A demonstration of modularity, reuse, reproducibility, portability and scalability for modeling and simulation of cardiac electrophysiology using Kepler Workflows
Cys-loop ligand-gated ion channels ( LGICs ) mediate fast ionotropic neurotransmission . They are proven drug targets in nematodes and arthropods , but are poorly characterized in flatworms . In this study , we characterized the anion-selective , non-acetylcholine-gated Cys-loop LGICs from Schistosoma mansoni . Full-le...	Schistosomiasis is a debilitating disease caused by blood flukes in the genus Schistosoma that afflicts over 200 million people worldwide . Treatment relies almost exclusively on a single drug , praziquantel . Reports of sub-optimal efficacy of praziquantel raise concerns about the prospect of drug resistance and highl...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "biomacromolecule-ligand", "interactions", "molecular", "neuroscience", "neurochemistry", "parasite", "evolution", "microbiology", "neuroscience", "parasitology", "parasite", "physiology", "ion", "channels", "molecular", "genetics", "neurotransmitters", "proteins", "neurochemical...	2013	Molecular Cloning and Characterization of Novel Glutamate-Gated Chloride Channel Subunits from Schistosoma mansoni
During central nervous system ( CNS ) development , genetic programs establish neural stem cells and drive both stem and daughter cell proliferation . However , the prominent anterior expansion of the CNS implies anterior–posterior ( A–P ) modulation of these programs . In Drosophila , a set of neural stem cell factors...	The central nervous system displays a pronounced anterior expansion that forms the brain . In the fruit fly Drosophila melanogaster , this expansion is driven by enhanced anterior cell proliferation . Recent studies reveal that cell proliferation in the brain is promoted by the Polycomb Group Complex , a key epigenetic...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "nervous", "system", "cell", "cycle", "and", "cell", "division", "cell", "processes", "neuroscience", "animals", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms",...	2019	Brain expansion promoted by polycomb-mediated anterior enhancement of a neural stem cell proliferation program
HIV-1 Tat is a key regulator of viral transcription , however little is known about the mechanisms that control its turnover in T cells . Here we use a novel proteomics technique , called DiffPOP , to identify the molecular target of JIB-04 , a small molecule compound that potently and selectively blocks HIV-1 Tat expr...	The HIV-1 Tat protein is critical for virus expression and replication , but little is known about the factors that control its expression level in T cells . Here , we have investigated a small molecule compound , JIB-04 , which induces the rapid and selective destruction of the HIV-1 Tat protein in HeLa and T cells , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "cell", "death", "medicine", "and", "health", "sciences", "autophagic", "cell", "death", "immune", "cells", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "hela", "cells", "molecular", "probe", "technique...	2018	SHMT2 and the BRCC36/BRISC deubiquitinase regulate HIV-1 Tat K63-ubiquitylation and destruction by autophagy
A virus’ mutational robustness is described in terms of the strength and distribution of the mutational fitness effects , or MFE . The distribution of MFE is central to many questions in evolutionary theory and is a key parameter in models of molecular evolution . Here we define the mutational fitness effects in influe...	Like other RNA viruses , influenza virus has a very high mutation rate . While high mutation rates may increase the rate at which influenza virus will adapt to a new host , acquire a new route of transmission , or escape from host immune surveillance , data from model systems suggest that most new viral mutations are e...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "transfection", "microbial", "mutation", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "orthomyxoviruses", "viruses", "mutation", "substitution", "mutation", "rna", "viruses", "genome", "analysis", "mol...	2016	The Mutational Robustness of Influenza A Virus
Monomethyl branched-chain fatty acids ( mmBCFAs ) are essential for Caenorhabditis elegans growth and development . To identify factors acting downstream of mmBCFAs for their function in growth regulation , we conducted a genetic screen for suppressors of the L1 arrest that occurs in animals depleted of the 17-carbon m...	Fatty acids serve diverse functions in organisms , including roles at the cell membrane to coordinate cell signaling processes . Monomethyl branched-chain fatty acids ( mmBCFAs ) are a special type of fatty acid that is commonly present in animals . Because mmBCFAs are a small component of the total fatty acid pool , t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "function", "developmental", "biology/developmental", "molecular", "mechanisms", "cell", "biology/cell", "signaling" ]	2009	P-Type ATPase TAT-2 Negatively Regulates Monomethyl Branched-Chain Fatty Acid Mediated Function in Post-Embryonic Growth and Development in C. elegans
Klebsiella pneumoniae ( Kp ) , one of the most common causes of healthcare-associated infections , increases patient morbidity , mortality , and hospitalization costs . Kp must acquire nutrients from the host for successful infection; however , the host is able to prevent bacterial nutrient acquisition through multiple...	The bacteria Klebsiella pneumoniae ( Kp ) is an important cause of infection in healthcare settings . These infections can be difficult to treat , as they frequently occur in chronically ill patients and the bacteria have the ability to acquire multiple antibiotic resistance markers . Kp is a common colonizer of the in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "neurochemistry", "pathology", "and", "laboratory", "medicine", "pathogens", "animal", "models", "of", "disease", "metabolic", "processes", "dna-binding", "proteins", "microbiology", "neuroscience", "animal", "models", "model", "...	2019	The Klebsiella pneumoniae citrate synthase gene, gltA, influences site specific fitness during infection
The 2018 outbreak of Nipah virus in Kerala , India , highlights the need for global surveillance of henipaviruses in bats , which are the reservoir hosts for this and other viruses . Nipah virus , an emerging paramyxovirus in the genus Henipavirus , causes severe disease and stuttering chains of transmission in humans ...	Nipah virus is an emerging zoonotic virus that spills over from bats to humans causing severe disease and chains of transmission in humans . In May 2018 , in Kerala , India , Nipah virus infected 23 people , killing 21 . We reviewed and analyzed published records of Nipah virus surveillance in bats and identified eleve...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Data", "availability" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "henipavirus", "pathogens", "geographical", "locations", "microbiology", "vertebrates", "india", "australia", "animals", "mammals", "viruses", "rna", "viruses", "infectious", "disease",...	2019	Prioritizing surveillance of Nipah virus in India
A well-known histopathological feature of diseased skin in Buruli ulcer ( BU ) is coagulative necrosis caused by the Mycobacterium ulcerans macrolide exotoxin mycolactone . Since the underlying mechanism is not known , we have investigated the effect of mycolactone on endothelial cells , focussing on the expression of ...	Buruli ulcer ( BU ) is a neglected tropical disease that is most common in West Africa and parts of Australia , but has been reported from over 30 countries worldwide . The symptoms are painless ulcers of the skin caused by a bacterial infection . The bacteria , Mycobacterium ulcerans , produce a macrolide toxin called...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Mycolactone-Dependent Depletion of Endothelial Cell Thrombomodulin Is Strongly Associated with Fibrin Deposition in Buruli Ulcer Lesions
Transmission is a matter of life or death for pathogen lineages and can therefore be considered as the main motor of their evolution . Gammaherpesviruses are archetypal pathogenic persistent viruses which have evolved to be transmitted in presence of specific immune response . Identifying their mode of transmission and...	Epstein-Barr virus and the Kaposi's Sarcoma-associated Herpesvirus are two human gammaherpesviruses which are linked to the development of several cancers . Efficient control of these infections is therefore of major interest , particularly in some epidemiological circumstances . These viruses are however host-specific...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "animal", "models", "of", "infection", "model", "organisms", "viral", "transmission", "and", "infection", "virology", "biology", "microbiology", "mouse" ]	2013	Illumination of Murine Gammaherpesvirus-68 Cycle Reveals a Sexual Transmission Route from Females to Males in Laboratory Mice
Inbreeding has long been recognized as a primary cause of fitness reduction in both wild and domesticated populations . Consanguineous matings cause inheritance of haplotypes that are identical by descent ( IBD ) and result in homozygous stretches along the genome of the offspring . Size and position of regions of homo...	Small populations have an increased risk of inbreeding depression due to a higher expression of deleterious alleles . This can have major consequences for the viability of these populations . In domesticated species like the pig that are artificially selected in breeding populations , but also in wild populations that ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biogeography", "population", "genetics", "genome", "sequencing", "genome", "analysis", "tools", "effective", "population", "size", "zoology", "structural", "genomics", "genetic", "polymorphism", "chromosome", "biology", "comparative", "genomics", "biology", "population", ...	2012	Regions of Homozygosity in the Porcine Genome: Consequence of Demography and the Recombination Landscape
Rearrangements of about 2 . 5 kilobases of regulatory DNA located 5′ of the transcription start site of the Drosophila even-skipped locus generate large-scale changes in the expression of even-skipped stripes 2 , 3 , and 7 . The most radical effects are generated by juxtaposing the minimal stripe enhancers MSE2 and MSE...	Metazoan genes , including those of humans , contain large noncoding regions that are required for viability . Sequence variations in these regions are statistically associated with human disease , but the mechanisms underlying these associations are not well understood . These regions regulate transcription and are fr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "biochemistry", "developmental", "biology", "computer", "science", "genomics", "computer", "modeling", "mathematics", "genetics", "applied", "mathematics", "biology", "computational", "biology", "evolutionary", "biology", "genetics", "and", "genomics" ...	2013	Rearrangements of 2.5 Kilobases of Noncoding DNA from the Drosophila even-skipped Locus Define Predictive Rules of Genomic cis-Regulatory Logic
Carcinogenesis is a complex process with multiple genetic and environmental factors contributing to the development of one or more tumors . Understanding the underlying mechanism of this process and identifying related markers to assess the outcome of this process would lead to more directed treatment and thus signific...	It is widely known that cancer is a complex process in which a large number of genes appear to be involved . Through experimental approaches , some oncogenes and tumor suppressors have been identified as playing important roles in the signaling and the regulatory pathways . However , we have not fully understood the co...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology/breast", "cancer", "computational", "biology/systems", "biology", "computational", "biology/genomics" ]	2011	CAERUS: Predicting CAncER oUtcomeS Using Relationship between Protein Structural Information, Protein Networks, Gene Expression Data, and Mutation Data
The control of RNA stability is a key determinant in cellular gene expression . The stability of any transcript is modulated through the activity of cis- or trans-acting regulatory factors as well as cellular quality control systems that ensure the integrity of a transcript . As a result , invading viral pathogens must...	In order to replicate efficiently , a virus must ensure that its genes are properly expressed in the context of an infected host cell . Recent work has demonstrated that eukaryotic cells have RNA quality control pathways that degrade improperly processed , aberrant RNAs . Our published findings using an unusual Kaposi'...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/post-translational", "regulation", "of", "gene", "expression", "molecular", "biology/rna-protein", "interactions", "virology/viral", "replication", "and", "gene", "regulation", "molecular", "biology/mrna", "stability", "molecular", "biology/mrna", "transpo...	2010	Kaposi's Sarcoma-Associated Herpesvirus ORF57 Protein Binds and Protects a Nuclear Noncoding RNA from Cellular RNA Decay Pathways
Down-regulation of GABAergic inhibition may result in the generation of epileptiform activities . Besides spike-triggered synchronous GABA release , changes in asynchronous release ( AR ) following high-frequency discharges may further regulate epileptiform activities . In brain slices obtained from surgically removed ...	The balance between excitation and inhibition in the cerebral cortex is important for multiple brain functions . Down-regulation of GABA-induced inhibition disrupts this balance and may lead to epileptic seizures . Asynchronous release of GABA is known to occur at certain GABAergic synapses and represents release of in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "epilepsy", "synapses", "neurological", "disorders", "neurology", "biology", "neuroscience", "neurophysiology" ]	2012	Enhancement of Asynchronous Release from Fast-Spiking Interneuron in Human and Rat Epileptic Neocortex
A major challenge in the control of human African trypanosomiasis ( HAT ) is lack of reliable diagnostic tests that are rapid and easy to use in remote areas where the disease occurs . In Trypanosoma brucei gambiense HAT , the Card Agglutination Test for Trypanosomiasis ( CATT ) has been the reference screening test si...	Early diagnosis and treatment of human African trypanosomiasis is essential for safe and effective treatment . The tests used to screen suspected patients and populations at risk are difficult to implement in remote rural settings where the disease occurs . Availability of simple , easy to use , instrument-free rapid d...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "engineering", "and", "technology", "african", "trypanosomiasis", "angola", "tropical", "diseases", "geographical", "locations", "parasitic", "diseases", "parasitology", "neglected", "tropical", "diseases", "afric...	2016	Sensitivity and Specificity of a Prototype Rapid Diagnostic Test for the Detection of Trypanosoma brucei gambiense Infection: A Multi-centric Prospective Study
α-Actinin is an actin crosslinking molecule that can serve as a scaffold and maintain dynamic actin filament networks . As a crosslinker in the stressed cytoskeleton , α-actinin can retain conformation , function , and strength . α-Actinin has an actin binding domain and a calmodulin homology domain separated by a long...	The cell interacts with its environment in both biochemical and mechanical ways . In this study we explore one of the ways in which the cell interacts mechanically with its environment . α-Actinin is a cytoskeletal crosslinker: it functions to scaffold the cytoskeletal actin filaments that provide mechanical reinforcem...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biophysics/theory", "and", "simulation", "cell", "biology/cytoskeleton" ]	2009	Molecular Mechanics of the α-Actinin Rod Domain: Bending, Torsional, and Extensional Behavior
Spatially and temporally regulated membrane trafficking events incorporate membrane and cell wall materials into the pollen tube apex and are believed to underlie the rapid pollen tube growth . In plants , the molecular mechanisms and physiological functions of intra-Golgi transport and Golgi integrity maintenance rema...	In the pistils of flowering plants , pollen tubes elongate at the tips to deliver the male gametes to the egg cells for fertilization . The tip growth of pollen tube is due to the deposition of cell membranes and wall materials at a restricted tip area of the plasma membrane . Vesicle trafficking events occurred at the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "walls", "plant", "anatomy", "vesicles", "plant", "cell", "biology", "cell", "processes", "brassica", "pollen", "membrane", "proteins", "plant", "cell", "walls", "plant", "science", "model", "organisms", "golgi", "apparatus", "plants", "cellular", "structure...	2016	Arabidopsis COG Complex Subunits COG3 and COG8 Modulate Golgi Morphology, Vesicle Trafficking Homeostasis and Are Essential for Pollen Tube Growth
Coordination of the cell cycle with developmental events is crucial for generation of tissues during development and their maintenance in adults . Defects in that coordination can shift the balance of cell fates with devastating clinical effects . Yet our understanding of the molecular mechanisms integrating core cell ...	How are cell cycle regulators coordinated with cell fate and patterning regulators during development ? Several studies suggest that core cell cycle regulators can influence development , but molecular mechanisms remain unknown for the most part . We have tackled this question in the nematode Caenorhabditis elegans . S...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/germ", "cells", "molecular", "biology/post-translational", "regulation", "of", "gene", "expression", "developmental", "biology/stem", "cells", "cell", "biology/cell", "growth", "and", "division", "cell", "biology/developmental", "molecular", "mechani...	2011	Cyclin E and Cdk2 Control GLD-1, the Mitosis/Meiosis Decision, and Germline Stem Cells in Caenorhabditis elegans
The disease state of amebiasis , caused by Entamoeba histolytica , varies from asymptomatic to severe manifestations that include dysentery and extraintestinal abscesses . The virulence factors of the pathogen , and host defense mechanisms , contribute to the outcomes of infection; however , the underlying genetic fact...	Comparative genomic analysis of pathogens is used to identify genes associated with disease manifestations . In the present study , this approach was used to identify genes , present in a strain of Entamoeba histolytica isolated from dysenteric patients , but absent in strains isolated from asymptomatic infected indivi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "taxonomy", "trophozoites", "parasite", "groups", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "vertebrates", "parasitic", "protozoans", "animals", "parasitology", "mammals", "apicomplexa", "phylogenetics", "data", "management", "...	2018	AIG1 affects in vitro and in vivo virulence in clinical isolates of Entamoeba histolytica
Comprehensive mapping of environmental microbiomes in terms of their compositional features remains a great challenge in understanding the microbial biosphere of the Earth . It bears promise to identify the driving forces behind the observed community patterns and whether community assembly happens deterministically . ...	We here set out to map the entirety of available environmental microbiomes in order to discover the underlying compositional characteristics . For us it is intriguing to see which environmental factors influence the assembly of microbiomes . We collected many diverse environmental samples and annotated them with a rest...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Comprehensive Meta-analysis of Ontology Annotated 16S rRNA Profiles Identifies Beta Diversity Clusters of Environmental Bacterial Communities
In 2015 , Zika virus ( ZIKV; Flaviviridae; Flavivirus ) emerged in the Americas , causing millions of infections in dozens of countries . The rapid spread of the virus and the association with disease outcomes such as Guillain-Barré syndrome and microcephaly make understanding transmission dynamics essential . Currentl...	The mechanisms contributing to the explosive nature of the current ZIKV outbreak in the Americas are poorly understood . Therefore , we characterized the replication of three strains , one from each phylogenetic clade of ZIKV and evaluated virus strain differences in transmission efficiency by American mosquitoes . Our...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "invertebrates", "vero", "cells", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "pathogens", "biological", "cultures", "vector-borne", "diseases", "microbiology", "sa...	2016	Vector Competence of American Mosquitoes for Three Strains of Zika Virus
Cortical oscillations are thought to be involved in many cognitive functions and processes . Several mechanisms have been proposed to regulate oscillations . One prominent but understudied mechanism is gap junction coupling . Gap junctions are ubiquitous in cortex between GABAergic interneurons . Moreover , recent expe...	Oscillations of neural activity emerge when many neurons repeatedly activate together and are observed in many brain regions , particularly during sleep and attention . Their functional role is still debated , but could be associated with normal cognitive processes such as memory formation or with pathologies such as s...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "physiology", "resonance", "frequency", "medicine", "and", "health", "sciences", "action", "potentials", "neural", "networks", "nervous", "system", "membrane", "potential", "junctional", "complexes", "electrophysiology", "neuroscience", "gap", "junctions", "neuron...	2018	Gap junction plasticity as a mechanism to regulate network-wide oscillations
It is well known that , in order to preserve its structure and function , a protein cannot change its sequence at random , but only by mutations occurring preferentially at specific locations . We here investigate quantitatively the amount of variability that is allowed in protein sequence evolution , by computing the ...	Protein sequence evolution is an extremely complex process , whose roles are ultimately determined by the necessity of living organisms to adapt to changes in the environment . We here address a fundamental question related with this process: in how many independent directions can a sequence evolve , without compromisi...	[ "Abstract", "Introduction", "Methods", "Results", "and", "discussion" ]	[ "sequencing", "techniques", "taxonomy", "split-decomposition", "method", "multiple", "alignment", "calculation", "phylogenetics", "data", "management", "protein", "structure", "molecular", "biology", "techniques", "research", "and", "analysis", "methods", "sequence", "analy...	2019	The intrinsic dimension of protein sequence evolution
Integrative and conjugative elements ( ICEs ) are widespread mobile genetic elements that are usually found integrated in bacterial chromosomes . They are important agents of evolution and contribute to the acquisition of new traits , including antibiotic resistances . ICEs can excise from the chromosome and transfer t...	Integrative and conjugative elements ( ICEs ) are mobile genetic elements that transfer DNA between bacteria , driving bacterial evolution and the acquisition of new traits , including antibiotic resistances . ICEs normally reside integrated in a host genome , but can excise and transfer to recipient cells . Many ICEs ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2013	Selective Pressures to Maintain Attachment Site Specificity of Integrative and Conjugative Elements
The 5' untranslated region ( 5' UTR ) of the enterovirus 71 ( EV71 ) RNA genome contains an internal ribosome entry site ( IRES ) that is indispensable for viral protein translation . Due to the limited coding capacity of their RNA genomes , EV71 and other picornaviruses typically recruit host factors , known as IRES t...	Many RNA viruses utilize internal ribosome entry sites ( IRES ) located in the 5’ untranslated region of genomic RNA to translate viral proteins in a cap-independent manner . Host proteins that are recruited to assist in viral IRES-driven translation are known as ITAFs ( IRES trans-acting factors ) , of which far upstr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "probe", "techniques", "enzymes", "messenger", "rna", "rna", "extraction", "microbiology", "enzymology", "immunoblotting", "plasmid", "construction", "untranslated", "regions", "dna", "construction", "molecular", "biology", "techniques", "extraction", "techniqu...	2016	Additive Promotion of Viral Internal Ribosome Entry Site-Mediated Translation by Far Upstream Element-Binding Protein 1 and an Enterovirus 71-Induced Cleavage Product
This study reports on in vitro and in vivo tests that sought to assess the antifungal activity of a newly developed magnetic carrier system comprising amphotericin B loaded onto the surface of pre-coated ( with a double-layer of lauric acid ) magnetite nanoparticles . The in vitro tests compared two drugs; i . e . , th...	Lung fungal infections are caused by pathogens inhaled as spores which convert into invasive yeast forms in the lungs . This type of infection can spread to other sites in the body through the blood and lymphatic systems , sometimes leading to ulcerations and skin lesions . The drug of choice for treatment is Amphoteri...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "antimicrobials", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "engineering", "and", "technology", "pathogens", "drugs", "immunology", "tropical", "diseases", "microbiology", "antifungals", "...	2016	Antifungal Activity of Amphotericin B Conjugated to Nanosized Magnetite in the Treatment of Paracoccidioidomycosis
T . vaginalis , a human-infective parasite , causes the most common nonviral sexually transmitted infection ( STI ) worldwide and contributes to adverse inflammatory disorders . The immune response to T . vaginalis is poorly understood . Neutrophils ( polymorphonuclear cells [PMNs] ) are the major immune cell present a...	The human parasite Trichomonas vaginalis is a large unicellular , motile eukaryote that causes a highly prevalent sexually transmitted infection in humans: trichomoniasis . While harmful effects of trichomoniasis are associated with inflammation , the immune response to the parasite is sorely under-characterized . Neut...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "flow", "cytometry", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "enzymes", "cytotoxicity", "assay", "cell", "processes", "enzymology", "immunology", "parasitic", "diseases", "toxicology", ...	2018	Neutrophils kill the parasite Trichomonas vaginalis using trogocytosis
Characterization of the length dependence of end-to-end loop-closure kinetics in unfolded polypeptide chains provides an understanding of early steps in protein folding . Here , loop-closure in poly-glycine-serine peptides is investigated by combining single-molecule fluorescence spectroscopy with molecular dynamics si...	In studies of protein folding evidence exists for early compaction in the unfolded state , although it is unclear whether these compact conformations contain specific secondary structures ( through hydrophilic interactions ) or whether compaction is a non-specific hydrophobic-driven effect . Here we combine single-mole...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "biochemistry", "biophysics/protein", "folding", "biophysics/experimental", "biophysical", "methods", "biochemistry/protein", "folding", "biophysics/theory", "and", "simulation", "computational", "biology/molecular", "dynamics", "biochemistry/theory", "and", "simulation", "computat...	2010	Hydrogen-Bond Driven Loop-Closure Kinetics in Unfolded Polypeptide Chains
Trichinella spiralis is a muscle-specific parasitic worm that is uniquely intracellular . T . spiralis reprograms terminally differentiated skeletal muscle cells causing them to de-differentiate and re-enter the cell cycle , a process that cannot occur naturally in mammalian skeletal muscle cells , but one that holds g...	Parasitic worms often establish long-lasting infections in their hosts; tightly regulating their surroundings to strike a delicate balance between host cell modulation and protection that will ensure their replication . This is accomplished via the active secretion of parasite glycolipids and glycoproteins into the hos...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "enzymes", "skeletal", "muscles", "enzymology", "parasitic", "diseases", "muscle", "proteins", "molecular", "motors", "molecular", "biology", "techniques", ...	2016	Ubiquitin-Dependent Modification of Skeletal Muscle by the Parasitic Nematode, Trichinella spiralis
Giardiasis is an intestinal infection correlated with poverty and poor drinking water quality , and treatment options are limited . According to the Center for Disease Control and Prevention , Giardia infections afflict nearly 33% of people in developing countries , and 2% of the adult population in the developed world...	Cellular signaling by the cyclic nucleotides cAMP and cGMP is ubiquitously found in organisms from human to unicellular parasites . Cyclic nucleotide-specific phosphodiesterases ( PDEs ) are pivotal regulators of these signaling processes and these enzymes represent important drug targets for a variety of diseases . El...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "trophozoites", "parasite", "groups", "markov", "models", "giardia", "parasitic", "protozoans", "parasitology", "apicomplexa", "fungi", "model", "organisms", "protozoans", "mathematics", "experimental", "organism", "systems", "saccharomyces", "giardia", "lamblia", "research...	2017	The single cyclic nucleotide-specific phosphodiesterase of the intestinal parasite Giardia lamblia represents a potential drug target
Recently it has been observed that cancer tissue is characterised by an increased variability in DNA methylation patterns . However , how the correlative patterns in genome-wide DNA methylation change during the carcinogenic progress has not yet been explored . Here we study genome-wide inter-CpG correlations in DNA me...	DNA methylation is a covalent modification of DNA which can regulate how active genes are . DNA methylation is altered at many genomic loci in cancer cells , leading to widespread functional disruption . Importantly , DNA methylation alterations across the genome are seen even in early carcinogenesis . Although the pat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "cancer", "detection", "and", "diagnosis", "biochemistry", "carcinogenesis", "physics", "medicine", "and", "health", "sciences", "statistical", "mechanics", "genetics", "biology", "and", "life", "sciences", "dna", "computational", "biology", "dna", "modifica...	2014	The Dynamics of DNA Methylation Covariation Patterns in Carcinogenesis
Live attenuated vaccines are used to combat tropical theileriosis in North Africa , the Middle East , India , and China . The attenuation process is empirical and occurs only after many months , sometimes years , of in vitro culture of virulent clinical isolates . During this extensive culturing , attenuated lines lose...	Tropical theileriosis is a leukaemia-like disease of cattle caused by the Apicomplexa parasite Theileria annulata . Live attenuated vaccines are used to control the mortality and morbidity of tropical theileriosis and each endemic country produces its own vaccine by isolating a virulent clinical isolate and then growin...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biotechnology", "biochemistry", "infectious", "diseases", "medicine", "and", "health", "sciences", "cell", "biology", "biology", "and", "life", "sciences", "immunology", "microbiology", "tropical", "diseases", "parasitic", "diseases", "veterinary", "science", "parasitolo...	2014	Engineering Attenuated Virulence of a Theileria annulata–Infected Macrophage
•NO is considered to be a key macrophage-derived cytotoxic effector during Trypanosoma cruzi infection . On the other hand , the microbicidal properties of reactive oxygen species ( ROS ) are well recognized , but little importance has been attributed to them during in vivo infection with T . cruzi . In order to invest...	When pathogens enter their hosts , they are fought by several resistance strategies , including capture by phagocytes and the production of pathogen-toxic molecules . Nitric oxide , a free radical , has been extensively studied as one of these toxic molecules that successfully mediates intracellular parasite killing , ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "biology" ]	2012	NADPH Phagocyte Oxidase Knockout Mice Control Trypanosoma cruzi Proliferation, but Develop Circulatory Collapse and Succumb to Infection
Latent infection by Epstein-Barr virus ( EBV ) is highly associated with the endemic form of Burkitt lymphoma ( eBL ) , which typically limits expression of EBV proteins to EBNA-1 ( Latency I ) . Interestingly , a subset of eBLs maintain a variant program of EBV latency - Wp-restricted latency ( Wp-R ) - that includes ...	Epstein-Barr virus ( EBV ) infects over 98% of the population worldwide and is associated with a variety of human cancers . In the healthy host , the virus represses expression of its proteins to avoid detection by the immune system to enable it to remain in the body for the lifetime of its host , a situation known as ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "medicine", "and", "health", "sciences", "cell", "biology", "viral", "persistence", "and", "latency", "pathology", "and", "laboratory", "medicine", "host-pathogen", "interactions", "cell", "growth", "virology", "virulence", "factors", "pathogen...	2014	Epstein-Barr Virus Nuclear Antigen 3A Promotes Cellular Proliferation by Repression of the Cyclin-Dependent Kinase Inhibitor p21WAF1/CIP1
People with spinal cord injury ( SCI ) are predisposed to pressure ulcers ( PU ) . PU remain a significant burden in cost of care and quality of life despite improved mechanistic understanding and advanced interventions . An agent-based model ( ABM ) of ischemia/reperfusion-induced inflammation and PU ( the PUABM ) was...	A virtual pressure ulcer was created as a platform to test therapies and determine the mechanisms most correlated with unfavorable outcomes . A layer of tissue fed with oxygen and diffusible molecules via blood vessels could develop an ulcer if pressure was applied , by simulating constriction of blood vessels in a cir...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	A Computational, Tissue-Realistic Model of Pressure Ulcer Formation in Individuals with Spinal Cord Injury
Most genes along the male single X chromosome in Drosophila are hypertranscribed about two-fold relative to each of the two female X chromosomes . This is accomplished by the MSL ( male-specific lethal ) complex that acetylates histone H4 at lysine 16 . The MSL complex contains two large noncoding RNAs , roX1 ( RNA on ...	In fruit flies , the male undergoes dosage compensation to increase the transcriptional output of its single X chromosome to match that of the females' two copies . A large ribonucleoprotein complex that consists of two large noncoding RNA , roX1 and roX2 , and at least five MSL ( male specific lethal ) chromatin-modif...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "model", "organisms", "gene", "expression", "genetics", "epigenetics", "biology", "molecular", "genetics", "genetics", "and", "genomics" ]	2012	Autoregulation of the Drosophila Noncoding roX1 RNA Gene
Body size is a classic quantitative trait with evolutionarily significant variation within many species . Locating the alleles responsible for this variation would help understand the maintenance of variation in body size in particular , as well as quantitative traits in general . However , successful genome-wide assoc...	Understanding the causes and consequences of natural genetic variation is crucial to the characterization of biological evolution . Moreover , natural genetic variation is comprised of millions of perturbations , which are partially randomized across genotypes such that a small number of individuals can be used to comb...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/genomics", "genetics", "and", "genomics/functional", "genomics", "evolutionary", "biology/genomics", "evolutionary", "biology", "genetics", "and", "genomics", "genetics", "and", "genomics/population", "genetics" ]	2011	Population-Based Resequencing of Experimentally Evolved Populations Reveals the Genetic Basis of Body Size Variation in Drosophila melanogaster
Asymptomatic persons infected with the parasites causing visceral leishmaniasis ( VL ) usually outnumber clinically apparent cases by a ratio of 4–10 to 1 . We describe patterns of markers of Leishmania donovani infection and clinical VL in relation to age in Bihar , India . We selected eleven villages highly endemic f...	In this study we assessed trends with age in the probability of being sero-positive or sero-converting for two serological markers of visceral leishmaniasis ( VL ) among asymptomatic residents of high incidence villages . As markers we used Direct Agglutination Test ( DAT ) and rK39 ELISA . We also compared titers amon...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion", "Conclusion" ]	[ "medicine", "infectious", "diseases", "leishmaniasis", "neglected", "tropical", "diseases" ]	2013	Latent Infection with Leishmania donovani in Highly Endemic Villages in Bihar, India
People learn modality-independent , conceptual representations from modality-specific sensory signals . Here , we hypothesize that any system that accomplishes this feat will include three components: a representational language for characterizing modality-independent representations , a set of sensory-specific forward...	When viewing an object , people perceive the object’s shape . Similarly , when grasping the same object , they also perceive its shape . In general , the perceived shape is identical in these two scenarios , illustrating modality invariance , an important type of perceptual constancy . Modality invariance suggests that...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	From Sensory Signals to Modality-Independent Conceptual Representations: A Probabilistic Language of Thought Approach
Bacillus subtilis possesses three essential enzymes thought to be involved in mRNA decay to varying degrees , namely RNase Y , RNase J1 , and RNase III . Using recently developed high-resolution tiling arrays , we examined the effect of depletion of each of these enzymes on RNA abundance over the whole genome . The dat...	RNA turnover is an important way of controlling gene expression . While the characterization of the pathways and enzymes for RNA degradation are well-advanced in Escherichia coli and yeast , studies in Gram-positive bacteria have lagged behind . This tiling array study shows that two essential enzymes , the single-stra...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "analysis", "tools", "prokaryotic", "models", "model", "organisms", "gene", "expression", "genetics", "molecular", "genetics", "biology", "genomics", "microbiology", "genetics", "and", "genomics" ]	2012	Three Essential Ribonucleases—RNase Y, J1, and III—Control the Abundance of a Majority of Bacillus subtilis mRNAs
Recent studies in vitro have reported that the Methoprene-tolerant ( Met ) and Taiman ( Tai ) complex is the functional receptor of juvenile hormone ( JH ) . Experiments in vivo of Met depletion have confirmed this factor's role in JH signal transduction , however , there is no equivalent data regarding Tai because its...	Insect metamorphosis is one of the most fascinating processes of animal development . However , the mechanisms governing metamorphosis only started to be unveiled in the last century , when physiological research revealed that the main factor involved is juvenile hormone ( JH ) , which represses metamorphosis in juveni...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "zoology", "biology", "and", "life", "sciences", "developmental", "biology" ]	2014	A Role for Taiman in Insect Metamorphosis
Group B Streptococcus ( GBS ) is a leading cause of invasive bacterial infections in human newborns and immune-compromised adults . The pore-forming toxin ( PFT ) β hemolysin/cytolysin ( βh/c ) is a major virulence factor for GBS , which is generally attributed to its cytolytic functions . Here we show βh/c has immunom...	Our studies show β hemolysin/cytolysin ( βh/c ) from Group B Streptococcus ( GBS ) , inhibits the activation of macrophages and the innate immune response to GBS . We show that βh/c triggers activation of mitogen activated protein kinase ( MAPK ) in GBS-infected macrophages leading to expression of the anti-inflammator...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "bacterial", "diseases", "infectious", "diseases", "group", "b", "streptococcal", "infection", "immunology", "biology", "immune", "response" ]	2012	The Pore-Forming Toxin β hemolysin/cytolysin Triggers p38 MAPK-Dependent IL-10 Production in Macrophages and Inhibits Innate Immunity
Horizontal gene transfer ( HGT ) has changed the way we regard evolution . Instead of waiting for the next generation to establish new traits , especially bacteria are able to take a shortcut via HGT that enables them to pass on genes from one individual to another , even across species boundaries . The tool Daisy offe...	Evolution is traditionally viewed as a process where changes are only vertically inherited from parent to offspring across generations . Many principles such as phylogenetic trees and even the “tree of life” are based on that doctrine . The concept of horizontal gene transfer changed the way we regard evolution complet...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "horizontal", "gene", "transfer", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "computational", "biology", "microbiology", "staphylococcus", "aureus", "gene", "transfer", "methicillin-resistant", "staphylococcus", "aure...	2019	Where did you come from, where did you go: Refining metagenomic analysis tools for horizontal gene transfer characterisation
Red blood cells ( RBCs ) infected by a Plasmodium parasite in malaria may lose their membrane deformability with a relative membrane stiffening more than ten-fold in comparison with healthy RBCs leading to potential capillary occlusions . Moreover , infected RBCs are able to adhere to other healthy and parasitized cell...	One of the most severe forms of cerebral malaria is caused by the parasite Plasmodium falciparum . During its development inside the host red blood cell it causes major mechanical and biochemical changes to the cell and can even alter its biconcave shape . The two main mechanical modifications are significant stiffenin...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biology" ]	2011	Multiscale Modeling of Red Blood Cell Mechanics and Blood Flow in Malaria
Many reproductive proteins from diverse taxa evolve rapidly and adaptively . These proteins are typically involved in late stages of reproduction such as sperm development and fertilization , and are more often functional in males than females . Surprisingly , many germline stem cell ( GSC ) regulatory genes , which ar...	Animals need to make gametes–sperm or eggs–in order to reproduce . Gametes are produced from a specialized tissue called the germline that is found within the testes or ovaries . These organs contain a small population of stem cells that are able to both self-renew and differentiate to generate gametes and are thus ess...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Drosophila bag of marbles Gene Interacts Genetically with Wolbachia and Shows Female-Specific Effects of Divergence
Social animals are capable of enhancing their awareness by paying attention to their neighbors , and prey found in groups can also confuse their predators . Both sides of these sensory benefits have long been appreciated , yet less is known of how the perception of events from the perspectives of both prey and predator...	Many social species coordinate their movements as they travel together , which is generally considered to be an adaptive behavior predominantly mediated by vision . Collective coordination lowers the individual’s chances of becoming separated from the group and can reduce the time spent in risky areas . More broadly , ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "velocity", "ecology", "and", "environmental", "sciences", "classical", "mechanics", "social", "sciences", "neuroscience", "cognitive", "psychology", "animal", "behavior", "vision", "zoology", "animal", "sociality", "behavior", "community", "ecology", "physics", "psycholo...	2016	A Sensory-Driven Trade-Off between Coordinated Motion in Social Prey and a Predator’s Visual Confusion
Rhinovirus ( RV ) , a single-stranded RNA picornavirus , is the most frequent cause of asthma exacerbations . We previously demonstrated in human bronchial epithelial cells that melanoma differentiation-associated gene ( MDA ) -5 and the adaptor protein for Toll-like receptor ( TLR ) -3 are each required for maximal RV...	Rhinovirus ( RV ) is the most frequent cause of acute respiratory tract infection in humans . RV has emerged as the most frequent pathogen associated with exacerbations of asthma . However , the mechanisms by which RV causes asthma flare-ups are not precisely known . We studied the requirements of two receptors which b...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "cytokines", "respiratory", "infections", "immunology", "pulmonology", "rhinovirus", "infection", "allergy", "and", "hypersensitivity", "asthma", "infectious", "diseases", "immune", "system", "clinical", "immunology", "immunity", "innate", "immunity", "viral", ...	2011	MDA5 and TLR3 Initiate Pro-Inflammatory Signaling Pathways Leading to Rhinovirus-Induced Airways Inflammation and Hyperresponsiveness
Ectromelia virus ( ECTV ) is an orthopoxvirus ( OPV ) that causes mousepox , the murine equivalent of human smallpox . C57BL/6 ( B6 ) mice are naturally resistant to mousepox due to the concerted action of innate and adaptive immune responses . Previous studies have shown that natural killer ( NK ) cells are a componen...	Ectromelia virus ( ECTV ) causes mousepox , a murine disease that is the equivalent of human smallpox . ECTV normally penetrates through the periphery but rapidly spreads through the lymphatic system to vital organs . In mousepox-sensitive strains of mice , ECTV infection culminates with either rapid death or overt sym...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viruses", "infectious", "diseases", "virology", "immunology", "mus", "(mouse)" ]	2008	A Role for NKG2D in NK Cell–Mediated Resistance to Poxvirus Disease
Recent advances in reconstruction and analytical methods for signaling networks have spurred the development of large-scale models that incorporate fully functional and biologically relevant features . An extended reconstruction of the human Toll-like receptor signaling network is presented herein . This reconstruction...	The human innate immune system , as the first line of defense against pathogens , is a vital component of our survival . One component of the innate immune system is the Toll-like receptor signaling network , which is responsible for transmitting activation signals from the outside of the cell to molecular machinery in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "immunology", "biochemistry/theory", "and", "simulation", "computational", "biology/signaling", "networks", "computational", "biology", "computational", "biology/systems", "biology" ]	2009	Identification of Potential Pathway Mediation Targets in Toll-like Receptor Signaling
In Brazil , case-fatality rates attributable to visceral leishmaniasis ( VL ) are high and knowledge of the risk factors associated with death may help reduce mortality . The aim of this study was to construct and validate a scoring system for prognosis of death from VL by using all cases reported in Brazil from 2007 t...	Visceral leishmaniasis ( VL ) is a fatal disease if not diagnosed and treated appropriately . In the present study , we investigated the risk factors associated with death caused by VL identifiable at the time of clinical suspicion . This study was conducted using all VL cases registered in Brazil during 2007 to 2011 ....	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "veterinary", "diseases", "zoonoses", "medicine", "and", "health", "sciences", "health", "risk", "analysis", "epidemiology", "leishmaniasis", "biology", "and", "life", "sciences", "protozoan", "infections", "parasitic", "diseases", "veterinary", "science", "health", "ca...	2014	Prognostic Factors and Scoring System for Death from Visceral Leishmaniasis: An Historical Cohort Study in Brazil
Understanding intratumor heterogeneity is clinically important because it could cause therapeutic failure by fostering evolutionary adaptation . To this end , we profiled the genome and epigenome in multiple regions within each of nine colorectal tumors . Extensive intertumor heterogeneity is observed , from which we i...	Cancer is heterogeneous disease; each tumor in different patients has different cancer genomes . Furthermore , another level of heterogeneity exists: even a single tumor harbors multiple genetically distinct subclones . This intratumor heterogeneity is presumably one of causes of therapeutic difficulty , and its unders...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "genome", "evolution", "cancer", "risk", "factors", "cancers", "and", "neoplasms", "cloning", "oncology", "mutation", "epigenetics", "dna", "molecular", "biology", "techniques", "dna", "methylation", "chromatin", "research", "a...	2016	Integrated Multiregional Analysis Proposing a New Model of Colorectal Cancer Evolution
Biological regulatory systems face a fundamental tradeoff: they must be effective but at the same time also economical . For example , regulatory systems that are designed to repair damage must be effective in reducing damage , but economical in not making too many repair proteins because making excessive proteins carr...	Many systems in the cell work to keep homeostasis , or balance . For example , damage repair systems make special repair proteins to resolve damage . These systems typically have many biochemical parameters such as biochemical rate constants , and it is not clear how much of the huge parameter space is filled by actual...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "systems", "biology", "theoretical", "biology", "evolutionary", "modeling", "biology", "evolutionary", "theory", "evolutionary", "biology", "computational", "biology" ]	2013	Evolutionary Tradeoffs between Economy and Effectiveness in Biological Homeostasis Systems
In sub-Saharan Africa , invasive nontyphoidal Salmonella ( iNTS ) infections with serovars S . Enteritidis , S . Typhimurium and I 4 , [5] , 12:i:- are widespread in children < 5 years old . Development of an efficacious vaccine would provide an important public health tool to prevent iNTS disease in this population . ...	Non-typhoidal Salmonella enterica ( NTS ) serovars Enteritidis and Typhimurium ( including monophasic variant I 4 , [5] , 12:i:- ) are significant causes of invasive bacterial disease amongst infants and toddlers in sub-Saharan Africa , and currently , there are no approved NTS vaccines . We have demonstrated previousl...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "vaccines", "preventive", "medicine", "bacterial", "diseases", "immunologic", "adjuvant...	2018	Immunogenicity and efficacy following sequential parenterally-administered doses of Salmonella Enteritidis COPS:FliC glycoconjugates in infant and adult mice
The rate at which genomes adapt to environmental changes and the prevalence of adaptive processes in molecular evolution are two controversial issues in current evolutionary genetics . Previous attempts to quantify the genome-wide rate of adaptation through amino-acid substitution have revealed a surprising diversity o...	The rate at which species adapt to environmental changes is a controversial topic . The theory predicts that adaptation is easier in large than in small populations , and the genomic studies of model organisms have revealed a much higher adaptive rate in large population-sized flies than in small population-sized human...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2016	Adaptive Protein Evolution in Animals and the Effective Population Size Hypothesis
The human opportunistic pathogen Bacillus cereus belongs to the B . cereus group that includes bacteria with a broad host spectrum . The ability of these bacteria to colonize diverse hosts is reliant on the presence of adaptation factors . Previously , an IVET strategy led to the identification of a novel B . cereus pr...	Iron is an essential compound for almost all living organisms , taking part in basic cellular homeostasis . Preventing access to iron sources for invading pathogens is one of the defense systems used by hosts to avoid pathogen colonization . To counteract this , pathogens have developed mechanisms to acquire nutrient i...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "microbiology/microbial", "physiology", "and", "metabolism", "microbiology/innate", "immunity", "biochemistry/biomacromolecule-ligand", "interactions", "infectious", "diseases/bacterial", "infections", "microbiology/microbial", "growth", "and", "development", "microbiology/cellular", ...	2009	IlsA, A Unique Surface Protein of Bacillus cereus Required for Iron Acquisition from Heme, Hemoglobin and Ferritin
Homologous recombination events between circular chromosomes , occurring during or after replication , can generate dimers that need to be converted to monomers prior to their segregation at cell division . In Escherichia coli , chromosome dimers are converted to monomers by two paralogous site-specific tyrosine recomb...	Bacteria with circular chromosome and active homologous recombination systems have to resolve chromosomal dimers before segregation at cell division . In Escherichia coli , the Xer site-specific recombination system , composed of two recombinases and a specific chromosomal site ( dif ) , is involved in the correct inhe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/bioinformatics", "molecular", "biology/recombination", "genetics", "and", "genomics" ]	2010	Evidence for a Xer/dif System for Chromosome Resolution in Archaea
An age-dependent association between variation at the FTO locus and BMI in children has been suggested . We meta-analyzed associations between the FTO locus ( rs9939609 ) and BMI in samples , aged from early infancy to 13 years , from 8 cohorts of European ancestry . We found a positive association between additional m...	Variation at the FTO locus is reliably associated with BMI and adiposity-related traits , but little is still known about the effects of variation at this gene , particularly in children . We have examined a large collection of samples for which both genotypes at rs9939609 and multiple measurements of BMI are available...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/complex", "traits" ]	2011	Association between Common Variation at the FTO Locus and Changes in Body Mass Index from Infancy to Late Childhood: The Complex Nature of Genetic Association through Growth and Development
Evolution of biological sensory systems is driven by the need for efficient responses to environmental stimuli . A paradigm among prokaryotes is the chemotaxis system , which allows bacteria to navigate gradients of chemoattractants by biasing their run-and-tumble motion . A notable feature of chemotaxis is adaptation:...	Biological sensory pathways are presumed to evolve for the processing of environmental information , yet quantitative evidence is scant . Chemotaxis allows bacteria to sense chemical gradients but their ecological distribution , e . g . whether natural gradients sensed by E . coli change slowly or rapidly in space and ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "velocity", "cell", "motility", "medicine", "and", "health", "sciences", "classical", "mechanics", "chemical", "compounds", "pathology", "and", "laboratory", "medicine", "engineering", "and", "technology", "pathogens", "biological", "locomotion", "biomechanics", "organic"...	2016	The Role of Adaptation in Bacterial Speed Races

Subsets and Splits

No community queries yet

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