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article stringlengths 4.36k 149k	summary stringlengths 32 3.35k	section_headings listlengths 1 91	keywords listlengths 0 141	year stringclasses 13 values	title stringlengths 20 281
The development of modern and affordable sequencing technologies has allowed the study of viral populations to an unprecedented depth . This is of particular interest for the study of within-host RNA viral populations , where variation due to error-prone polymerases can lead to immune escape , antiviral resistance and ...	Characterising genetic variation in viral populations can have important implications in terms of understanding how viruses evolve within infected hosts . Modern sequencing technologies allow genetic information to be obtained faster , more affordably , and in much greater quantities than before . This allows new exper...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "mathematics", "statistics", "genetics", "biology", "computational", "biology", "genetics", "and", "genomics" ]	2011	A Bayesian Approach to Analyse Genetic Variation within RNA Viral Populations
Lymphatic filariasis ( LF ) is a neglected tropical disease , and the Global Program to Eliminate LF delivers mass drug administration ( MDA ) to 500 million people every year . Adverse events ( AEs ) are common after LF treatment . To better understand the pathogenesis of AEs , we studied LF-patients from a treatment ...	Lymphatic filariasis ( LF ) is a disabling parasitic disease that affects millions of people in the developing world . The Global Programme to Eliminate Lymphatic Filariasis ( coordinated by the World Health Organization ) uses mass administration of antifilarial medications to cure infections , prevent disease , and r...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "body", "fluids", "clinical", "research", "design", "immune", "cells", "pathology", "and", "laboratory", "medicine", "immunology", "wolbachia"...	2019	Systems analysis-based assessment of post-treatment adverse events in lymphatic filariasis
The evolution of drug resistance has a profound impact on human health . Candida glabrata is a leading human fungal pathogen that can rapidly evolve resistance to echinocandins , which target cell wall biosynthesis and are front-line therapeutics for Candida infections . Here , we provide the first global analysis of m...	The evolution of drug resistance poses a severe threat to human health . Candida glabrata is a leading cause of mortality due to fungal infections worldwide . It can rapidly evolve resistance to drugs such as echinocandins , which target the fungal cell wall and are front-line therapeutics for Candida infections . We h...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "sequencing", "mycology", "genomics", "fungal", "evolution", "microbial", "evolution", "microbial", "pathogens", "biology", "evolutionary", "biology", "genomic", "evolution", "microbiology", "host-pathogen", "interaction", "genetics", "and", "genomics" ]	2012	Global Analysis of the Evolution and Mechanism of Echinocandin Resistance in Candida glabrata
Differences in the level , timing , or location of gene expression can contribute to alternative phenotypes at the molecular and organismal level . Understanding the origins of expression differences is complicated by the fact that organismal morphology and gene regulatory networks could potentially vary even between c...	For a gene to function properly , it must be active in the right place , at the right time , and in the right amount . Changes in any of these features can lead to observable differences between individuals and species and in some cases can lead to disease . We do not currently understand how the position , timing , an...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "developmental", "biology", "gene", "expression", "genetics", "regulatory", "networks", "biology", "computational", "biology", "pattern", "formation", "genetics", "and", "genomics", "evolutionary", "developmental", "biology" ]	2011	A Conserved Developmental Patterning Network Produces Quantitatively Different Output in Multiple Species of Drosophila
Lethal toxin ( LT ) is a critical virulence factor of Bacillus anthracis , the etiological agent of anthrax , whose pulmonary form is fatal in the absence of treatment . Inflammatory response is a key process of host defense against invading pathogens . We report here that intranasal instillation of a B . anthracis str...	Bacillus anthracis , the etiological agent of anthrax , can infect mammals either accidentally or as a potential consequence of a terrorism threat . Pulmonary infection is a life-threatening form of the disease , causing a near 100% mortality rate in the absence of appropriate therapy . Thus , it is important to unders...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/cellular", "microbiology", "and", "pathogenesis", "molecular", "biology/histone", "modification", "cell", "biology/leukocyte", "signaling", "and", "gene", "expression", "immunology/innate", "immunity", "infectious", "diseases/respiratory", "infections", "infectious", ...	2009	Anthrax Lethal Toxin Impairs IL-8 Expression in Epithelial Cells through Inhibition of Histone H3 Modification
Trypanosoma cruzi , the etiologic agent of Chagas Disease , is a major vector borne health problem in Latin America and an emerging infectious disease in the United States . We tested the efficacy of a multi-component DNA-prime/DNA-boost vaccine ( TcVac1 ) against experimental T . cruzi infection in a canine model . Do...	Immunization of dogs with DNA-prime/DNA-boost vaccine ( TcVac1 ) enhanced the Trypanosoma cruzi-specific type 1 antibody and CD8+ T cell responses that resulted in an early control of acute parasitemia and a moderate decline in pathological symptoms during chronic phase . Further improvement of vaccine-induced immunity...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "cardiovascular", "disorders/myopathies" ]	2011	Testing the Efficacy of a Multi-Component DNA-Prime/DNA-Boost Vaccine against Trypanosoma cruzi Infection in Dogs
In the last two decades , chikungunya virus ( CHIKV ) has rapidly expanded to several geographical areas , causing frequent outbreaks in sub-Saharan Africa , South East Asia , South America , and Europe . Therefore , the disease remains heavily neglected in Mozambique , and no recent study has been conducted . Between ...	Chikungunya virus ( CHIKV ) is an emerging arbovirus that remains heavily neglected in Mozambique , and no recent study has been conducted . Between January and September 2013 , four hundred acute febrile patients with no other evident cause of fever and attending a health center in a suburban area of Maputo city , Moz...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Serological Evidence of Chikungunya Virus among Acute Febrile Patients in Southern Mozambique
Candida auris is an emerging , multi-drug resistant , health care-associated fungal pathogen . Its predominant prevalence in hospitals and nursing homes indicates its ability to adhere to and colonize the skin , or persist in an environment outside the host—a trait unique from other Candida species . Besides being asso...	Candida auris has emerged as a major health concern to hospitalized patients and nursing home subjects . C . auris strains display multidrug resistance to current antifungal therapy and cause lethal infections . We have determined that C . auris harbors homologs of C . albicans Als cell surface proteins . The C . albic...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "flow", "cytometry", "graduates", "medicine", "and", "health", "sciences", "immune", "physiology", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "immune", "cells", "pathogens", "immunology", "microbiology", "alumni", "v...	2019	The NDV-3A vaccine protects mice from multidrug resistant Candida auris infection
Hair cells of the mammalian cochlea are specialized for the dynamic coding of sound stimuli . The transduction of sound waves into electrical signals depends upon mechanosensitive hair bundles that project from the cell's apical surface . Each stereocilium within a hair bundle is composed of uniformly polarized and tig...	Mammalian hearing depends on mechanosensory inner and outer hair cells within the inner ear that convert sound vibrations into electrical signals . While inner hair cells are the primary sensory receptors , outer hair cells improve auditory sensitivity . Although we know that sensory cells of the auditory , visual and ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "neuroscience", "developmental", "neuroscience", "cellular", "neuroscience", "biology", "sensory", "systems", "neuroscience" ]	2011	Eps8 Regulates Hair Bundle Length and Functional Maturation of Mammalian Auditory Hair Cells
TDP-43 , an RNA-binding protein that is primarily nuclear and important in splicing and RNA metabolism , is mislocalized from the nucleus to the cytoplasm of neural cells in amyotrophic lateral sclerosis ( ALS ) , and contributes to disease . We sought to investigate whether TDP-43 is mislocalized in infections with th...	TDP-43 is a widely expressed nuclear protein that shuttles between the nucleus and cytoplasm , and regulates many aspects of RNA processing , such as splicing , trafficking , stabilization , and miRNA production . In almost all cases of ALS , neuronal and glial TDP-43 is phosphorylated , cleaved , and mislocalized to t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "immunofluorescence", "staining", "hela", "cells", "biological", "cultures", "neuroscience", "cytoplasmic", "staining", "cell", "cultures", "cellular", "structures", "and", "organelles", "research", "and", "analysis", "methods", "specimen", "preparation",...	2019	TDP-43 proteinopathy in Theiler’s murine encephalomyelitis virus infection
Phagocytosis is an ancient mechanism central to both tissue homeostasis and immune defense . Both the identity of the receptors that mediate bacterial phagocytosis and the nature of the interactions between phagocytosis and other defense mechanisms remain elusive . Here , we report that Croquemort ( Crq ) , a Drosophil...	Phagocytosis is a first-line host defense mechanism against microbes . Interactions between phagocytosis and other immune mechanisms , such as the humoral response , however , remain elusive . Defective phagocytosis can lead to immune deficiencies and chronic auto-inflammation . Here , we show that Croquemort ( Crq ) ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "cell", "death", "medicine", "and", "health", "sciences", "immune", "cells", "vesicles", "pathology", "and", "laboratory", "medicine", "pathogens", "cell", "processes", "immunology", "microbiology", "staphylococcus", "aureus", "bacterial", "diseases", ...	2016	The Drosophila CD36 Homologue croquemort Is Required to Maintain Immune and Gut Homeostasis during Development and Aging
Leprosy Type-1 Reactions ( T1Rs ) are pathological inflammatory responses that afflict a sub-group of leprosy patients and result in peripheral nerve damage . Here , we employed a family-based GWAS in 221 families with 229 T1R-affect offspring with stepwise replication to identify risk factors for T1R . We discovered ,...	Leprosy still affects approximately 200 , 000 new victims each year . A major challenge of leprosy control is the prevention of permanent disability due to nerve damage . Nerve damage occurs if leprosy remains undiagnosed for extended periods or when patients undergo pathological inflammatory responses termed Type-1 Re...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "tropical", "diseases", "alleles", "long", "non-coding", "rnas", "ethnicities", "vietnamese", "people", "bacterial", "diseases", "mathematics", "statistics", "(mathematics)", "gastroenterology...	2017	A genome wide association study identifies a lncRna as risk factor for pathological inflammatory responses in leprosy
The fungus Cryptococcus neoformans can undergo a-α bisexual and unisexual reproduction . Completion of both sexual reproduction modes requires similar cellular differentiation processes and meiosis . Although bisexual reproduction generates equal number of a and α progeny and is far more efficient than unisexual reprod...	Like many higher eukaryotes , the fungus Cryptococcus neoformans is known to undergo bisexual mating that involves α and a partners . Surprisingly , the α mating type is dominant in nature ( >99% ) . Unisexual reproduction was previously discovered in Cryptococcus and the mating type α allele enhances this sexual repro...	[ "Abstract", "Introduction", "Results", "Discussions", "Methods", "and", "materials" ]	[ "cell", "physiology", "cryptococcus", "neoformans", "medicine", "and", "health", "sciences", "cryptococcus", "pathology", "and", "laboratory", "medicine", "pathogens", "rna", "extraction", "microbiology", "sexual", "reproduction", "developmental", "biology", "fungi", "reg...	2017	Pheromone independent unisexual development in Cryptococcus neoformans
Aluminum ( Al ) toxicity is a primary limitation to crop productivity on acid soils , and rice has been demonstrated to be significantly more Al tolerant than other cereal crops . However , the mechanisms of rice Al tolerance are largely unknown , and no genes underlying natural variation have been reported . We screen...	While rice ( Oryza sativa ) is significantly more Al tolerant than other cereals , no genes underlying Al tolerance in rice have been reported . Using genome-wide association ( GWA ) and bi-parental QTL mapping , we investigated the genetic architecture of Al tolerance in rice . Japonica varieties were twice as Al tole...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "marker-assisted", "selection", "agricultural", "biotechnology", "agriculture" ]	2011	Genetic Architecture of Aluminum Tolerance in Rice (Oryza sativa) Determined through Genome-Wide Association Analysis and QTL Mapping
Combination therapies are often needed for effective clinical outcomes in the management of complex diseases , but presently they are generally based on empirical clinical experience . Here we suggest a novel application of search algorithms—originally developed for digital communication—modified to optimize combinatio...	This work describes methods that identify drug combinations that might alleviate the suffering caused by complex diseases . Our biological model systems are: physiological decline associated with aging , and selective killing of cancer cells . The novelty of this approach is based on a new application of methods from d...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "pharmacology/personalized", "medicine", "pharmacology", "computational", "biology/systems", "biology" ]	2008	Search Algorithms as a Framework for the Optimization of Drug Combinations
Elongator is a six subunit protein complex , conserved from yeast to humans . Mutations in the human Elongator homologue , hELP1 , are associated with the neurological disease familial dysautonomia . However , how Elongator functions in metazoans , and how the human mutations affect neural functions is incompletely und...	The efficiency of protein synthesis can be modulated by alterations of various components of the translation machinery . In translation , transfer RNAs act as adapter molecules that decode mRNA into protein and thereby play a central role in gene expression . In the tRNA maturation process , a subset of the normal nucl...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience/behavioral", "neuroscience", "genetics", "and", "genomics/animal", "genetics", "biochemistry/rna", "structure", "genetics", "and", "genomics/gene", "expression", "developmental", "biology/cell", "differentiation", "genetics", "and", "genomics/disease", "models", "...	2009	Defects in tRNA Modification Associated with Neurological and Developmental Dysfunctions in Caenorhabditis elegans Elongator Mutants
Infections with schistosomes and soil-transmitted helminths exert a considerable yet underappreciated economic and public health burden on afflicted populations . Accurate diagnosis is crucial for patient management , drug efficacy evaluations , and monitoring of large-scale community-based control programs . The diagn...	Infections with parasitic worms ( e . g . , Schistosoma mansoni , hookworm , roundworm , whipworm , and threadworm ) are still widespread in the developing world . Accurate diagnosis is important for better patient management and for monitoring of deworming programs . Unfortunately , methods to detect parasite eggs or ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology" ]	2010	Comparing Diagnostic Accuracy of Kato-Katz, Koga Agar Plate, Ether-Concentration, and FLOTAC for Schistosoma mansoni and Soil-Transmitted Helminths
Conventional patent-based drug development incentives work badly for the developing world , where commercial markets are usually small to non-existent . For this reason , the past decade has seen extensive experimentation with alternative R&D institutions ranging from private–public partnerships to development prizes ....	Open source drug discovery , a promising alternative avenue to conventional patent-based drug development , has so far remained elusive with few exceptions . A major stumbling block has been the absence of a critical mass of preexisting work that volunteers can improve through a series of granular contributions . This ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "computational", "biology/protein", "structure", "prediction", "computational", "biology/macromolecular", "structure", "analysis", "pharmacology/drug", "development", "biotechnology/small", "molecule", "chemistry" ]	2009	A Kernel for Open Source Drug Discovery in Tropical Diseases
Kaposi’s sarcoma herpesvirus ( KSHV ) is the etiologic agent of Kaposi’s sarcoma ( KS ) as well as two lymphoproliferative diseases , primary effusion lymphoma and multicentric Castleman’s disease . KSHV encodes viral proteins , such as K1 , that alter signaling pathways involved in cell survival . Expression of K1 has...	Infectious agents such as Kaposi’s sarcoma associated herpesvirus ( KSHV ) are etiologic agents of human cancer . KSHV-infected cells must survive various environmental stresses . Cells infected with KSHV express viral proteins that alter normal cellular processes to promote cell survival and viral persistence . We fou...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "physiology", "colorimetric", "assays", "medicine", "and", "health", "sciences", "cell", "viability", "testing", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "cell", "metabolism", "biochemical", "analysis", "viruses", "enzyme", "ass...	2016	The KSHV K1 Protein Modulates AMPK Function to Enhance Cell Survival
Human cytomegalovirus ( HCMV ) , a β-herpesvirus , has evolved many strategies to subvert both innate and adaptive host immunity in order to ensure its survival and propagation within the host . Induction of IL-8 is particularly important during HCMV infection as neutrophils , primarily attracted by IL-8 , play a key r...	The importance of herpesviruses is evident by their prevalence in the human population and the diverse range of diseases that they provoke . Their ability to establish latency provides a compelling example of how herpesviruses successfully evade the immune system and manipulate cellular biology . One promising approach...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "signal", "transduction", "virology", "host-pathogen", "interaction", "biology", "microbiology", "molecular", "cell", "biology" ]	2013	Human Cytomegalovirus Gene UL76 Induces IL-8 Expression through Activation of the DNA Damage Response
Many large-scale studies on intrinsically disordered proteins are implicitly based on the structural models deposited in the Protein Data Bank . Yet , the static nature of deposited models supplies little insight into variation of protein structure and function under diverse cellular and environmental conditions . Whil...	Intrinsically disordered proteins , proteins that exist as conformational ensembles without time-invariant residue positions , have emerged as an important and common class of proteins in all kingdoms of life . Disordered proteins are characterized by distinct amino acid preferences , distinct mechanisms of binding , d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/protein", "structure", "prediction", "computational", "biology" ]	2009	Influence of Sequence Changes and Environment on Intrinsically Disordered Proteins
Disrupted circadian rhythms and reduced sleep duration are associated with several human diseases , particularly obesity and type 2 diabetes , but until recently , little was known about the genetic factors influencing these heritable traits . We performed genome-wide association studies of self-reported chronotype ( m...	Numerous studies have identified links between too little or too much sleep and circadian misalignment with metabolic disorders such as obesity and type 2 diabetes . However , cause-and-effect is not easily determined , because of multiple confounding factors affecting both sleep patterns and disease risk . Using the f...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "sleep", "diabetes", "mellitus", "physiological", "processes", "endocrine", "disorders", "mathematics", "statistics", "(mathematics)", "genome", "analysis", "chronobiology", "type", "2", "di...	2016	Genome-Wide Association Analyses in 128,266 Individuals Identifies New Morningness and Sleep Duration Loci
Hepatitis C virus ( HCV ) infects over 170 million people worldwide and is the leading cause of chronic liver diseases , including cirrhosis , liver failure , and liver cancer . Available antiviral therapies cause severe side effects and are effective only for a subset of patients , though treatment outcomes have recen...	Hepatitis C virus ( HCV ) infects over 170 million people worldwide and is the leading cause of chronic liver diseases , including cirrhosis , liver failure , and liver cancer . New classes of directly-acting antiviral agents that target various HCV enzymes are being developed . Two such drugs that target the essential...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biochemistry", "infectious", "diseases", "medicinal", "chemistry", "chemistry", "biology", "chemical", "biology", "biophysics" ]	2012	The Molecular Basis of Drug Resistance against Hepatitis C Virus NS3/4A Protease Inhibitors
We present a technique applicable in any dynamical framework to identify control-robust subsets of an interacting system . These robust subsystems , which we call stable modules , are characterized by constraints on the variables that make up the subsystem . They are robust in the sense that if the defining constraints...	We show how to uncover the causal relationships between qualitative statements about the values of variables in ODE systems . We then show how these relationships can be used to identify subsystem behaviors that are robust to outside interventions . This informs potential system control strategies ( e . g . , in identi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "signaling", "networks", "animals", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "systems", "science", "mathematics", "network", "analysis", "experimental", "organism", "systems", "sequence", "motif", "analysis", "drosophila", "...	2018	Identifying (un)controllable dynamical behavior in complex networks
Sensing invading pathogens early in infection is critical for establishing host defense . Two cytosolic RIG-like RNA helicases , RIG-I and MDA5 , are key to type I interferon ( IFN ) induction in response to viral infection . Mounting evidence suggests that another viral RNA sensor , protein kinase R ( PKR ) , may also...	Induction of type I interferon ( IFN ) during viral infection is a key step in the activation of innate host defense . Critical to this response is the ability to recognize viral nucleic acids in the host cell cytoplasm . Detection of viral RNA is mediated by RNA helicases , including RIG-I and MDA5 , which sense 5’-ph...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "phosphorylation", "medicine", "and", "health", "sciences", "luciferase", "poxviruses", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "enzymes", "pathogens", "messenger", "rna", "microbiology", "enzymology", "viruses", "rna", ...	2016	PKR Transduces MDA5-Dependent Signals for Type I IFN Induction
Statistical coupling analysis ( SCA ) is a method for analyzing multiple sequence alignments that was used to identify groups of coevolving residues termed “sectors” . The method applies spectral analysis to a matrix obtained by combining correlation information with sequence conservation . It has been asserted that th...	Statistical analyses of alignments of evolutionarily related protein sequences have been proposed as a method for obtaining information about protein structure and function . One such method , called statistical coupling analysis , identifies patterns of correlated mutations and uses them to find groups of coevolving r...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Protein Sectors: Statistical Coupling Analysis versus Conservation
Inflammasome activation is important for antimicrobial defense because it induces cell death and regulates the secretion of IL-1 family cytokines , which play a critical role in inflammatory responses . The inflammasome activates caspase-1 to process and secrete IL-1β . However , the mechanisms governing IL-1α release ...	The inflammasome , a multiprotein complex , is critical for host defense against bacterial infection . The inflammasome activates the host protease caspase-1 to process and secrete IL-1β . Another caspase , caspase-11 , can cause cell death and IL-1α release . The bacterial signals that trigger caspase-11 activation ar...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gram", "negative", "inflammation", "immune", "cells", "monocytes", "immunity", "innate", "immunity", "immune", "activation", "immune", "defense", "immunology", "immunity", "to", "infections", "biology", "microbiology", "host-pathogen", "interaction", "bacterial", "pathog...	2013	Caspase-11 Activation in Response to Bacterial Secretion Systems that Access the Host Cytosol
Disparate enveloped viruses initiate infection by fusing with endosomes . However , the highly diverse and dynamic nature of endosomes impairs mechanistic studies of fusion and identification of sub-cellular sites supporting the nucleocapsid release . We took advantage of the extreme stability of avian retrovirus-recep...	Endosomal trafficking and regulation of retrovirus fusion is poorly understood , due in part to heterogeneity of viral particles and their asynchronous entry into an endocytic pathway . Here , we used an avian retrovirus that enters host cells in a receptor- and low pH-dependent manner . This feature allowed capturing ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2012	Synchronized Retrovirus Fusion in Cells Expressing Alternative Receptor Isoforms Releases the Viral Core into Distinct Sub-cellular Compartments
DNA:RNA hybrid formation is emerging as a significant cause of genome instability in biological systems ranging from bacteria to mammals . Here we describe the genome-wide distribution of DNA:RNA hybrid prone loci in Saccharomyces cerevisiae by DNA:RNA immunoprecipitation ( DRIP ) followed by hybridization on tiling mi...	RNA processing factors are mutated in human cancers , inherited developmental disorders and neurodegenerative syndromes . Defects in RNA processing have been associated with increased levels of mutations and DNA damage in part via the formation of DNA:RNA hybrids . Although it is likely that specific regions of the gen...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "model", "organisms", "cell", "biology", "genetics", "biology", "and", "life", "sciences", "genomics", "molecular", "cell", "biology", "research", "and", "analysis", "methods" ]	2014	Genome-Wide Profiling of Yeast DNA:RNA Hybrid Prone Sites with DRIP-Chip
Regulation and maintenance of protein synthesis are vital to all organisms and are thus key targets of attack and defense at the cellular level . Here , we mathematically analyze protein synthesis for its sensitivity to the inhibition of elongation factor EF-Tu and/or ribosomes in dependence of the system’s tRNA and co...	We predict and analyze the response of differently composed protein synthesis systems to the inhibition of elongation factor EF-Tu and/or ribosomes . The study reveals a strong interdependency of a protein synthesis system’s composition and its susceptibility to inhibition . This interdependency defines a generic mecha...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "antimicrobials", "transfer", "rna", "medicine", "and", "health", "sciences", "toxins", "pathology", "and", "laboratory", "medicine", "drugs", "microbiology", "toxicology", "toxic", "agents", "protein", "synthesis", "antibiotics", "mitochondria", "pharmacology", "bioenerg...	2019	Efficiency of protein synthesis inhibition depends on tRNA and codon compositions
Stomata , microscopic pores in leaf surfaces through which water loss and carbon dioxide uptake occur , are closed in response to drought by the phytohormone abscisic acid ( ABA ) . This process is vital for drought tolerance and has been the topic of extensive experimental investigation in the last decades . Although ...	Guard cells , located in pairs on the surface of plant leaves , circumscribe microscopic pores called stomata , through which plants take up gaseous carbon dioxide that will be fixed by photosynthesis into sugars . However , plants also inevitably lose water vapor to the atmosphere through open stomata . Under drought ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "plant", "anatomy", "stem", "anatomy", "guard", "cells", "enzymes", "plant", "cell", "biology", "ions", "enzymology", "signaling", "networks", "anions", "stomata", "phosphatases", "plant", "science", "network", "analysis", "physical", "chemistry", "computer", "and", ...	2017	A new discrete dynamic model of ABA-induced stomatal closure predicts key feedback loops
Protein-protein interactions ( PPIs ) are of central importance for many areas of biological research . Several complementary high-throughput technologies have been developed to study PPIs . The wealth of information that emerged from these technologies led to the first maps of the protein interactomes of several model...	Protein–protein interactions ( PPI ) occur when two or more proteins bind together to form large molecular machines . The importance of PPIs led to the development of multitude technologies to detect them , and to the first maps of the protein interactomes . One important challenge in biology is to understand how prote...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[]	2013	Reverse PCA, a Systematic Approach for Identifying Genes Important for the Physical Interaction between Protein Pairs
The levels of methyl-CpG–binding protein 2 ( MeCP2 ) are critical for normal post-natal development and function of the nervous system . Loss of function of MeCP2 , a transcriptional regulator involved in chromatin remodeling , causes classic Rett syndrome ( RTT ) as well as other related conditions characterized by au...	Rett syndrome ( RTT ) is a progressive neurodevelopmental disorder that affects girls early in childhood and is caused by mutations in the MECP2 gene . Loss of MeCP2 function can also lead to clinically distinct conditions characterized by autism , learning disability , and mental retardation . Remarkably , increased l...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/genetics", "of", "disease", "neurological", "disorders" ]	2008	Genetic Modifiers of MeCP2 Function in Drosophila
Accurate and reliable predictions of infectious disease dynamics can be valuable to public health organizations that plan interventions to decrease or prevent disease transmission . A great variety of models have been developed for this task , using different model structures , covariates , and targets for prediction ....	Public health agencies such as the US Centers for Disease Control and Prevention would like to have as much information as possible when planning interventions intended to reduce and prevent the spread of infectious disease . For instance , accurate and reliable predictions of the timing and severity of the influenza s...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "influenza", "seasons", "probability", "distribution", "mathematics", "forecasting", "statistics", "(mathematics)", "discrete", "mathematics", "combinatorics", "research", "and", "analysis", "methods", "public", "and", "occupational"...	2018	Prediction of infectious disease epidemics via weighted density ensembles
Late gene transcription in herpesviruses is dependent on viral DNA replication in cis but the mechanistic basis for this linkage remains unknown . DNA replication results in demethylated DNA , topological changes , removal of proteins and recruitment of proteins to promoters . One or more of these effects of DNA replic...	Herpesviruses exhibit both latent and lytic replication cycles . Gammaherpesviruses such as Kaposi’s sarcoma-associated herpesvirus and Epstein Barr virus undergo lytic replication when they reactivate from latency . During this process , when infectious virions are produced , an orderly cascade of gene expression occu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods", "DNA", "and", "RNA", "isolation", "and", "analysis" ]	[ "medicine", "and", "health", "sciences", "functional", "genomics", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "dna", "transcription", "viruses", "dna", "replication", "dna", "viruses", "dna", "epigenetics", "dna", "methylation", "chromati...	2018	Continuous DNA replication is required for late gene transcription and maintenance of replication compartments in gammaherpesviruses
The evolution of proteins is one of the fundamental processes that has delivered the diversity and complexity of life we see around ourselves today . While we tend to define protein evolution in terms of sequence level mutations , insertions and deletions , it is hard to translate these processes to a more complete pic...	Proteins are the molecular workers of the cell . They are formed from a string of amino acids which folds into an elaborate three-dimensional structure . While there is a relationship between a protein's sequence and its structure this relationship is highly complex and not fully understood . Protein structures tend to...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	Exploring Fold Space Preferences of New-born and Ancient Protein Superfamilies
The T cell immunoglobulin mucin 3 ( Tim-3 ) receptor is highly expressed on HIV-1-specific T cells , rendering them partially “exhausted” and unable to contribute to the effective immune mediated control of viral replication . To elucidate novel mechanisms contributing to the HTLV-1 neurological complex and its classic...	The retrovirus , Human T lymphotropic virus type 1 ( HTLV-1 ) infects 10–20 million people worldwide . The majority of infected individuals are asymptomatic; however , approximately 3% develop the debilitating neurological disease , HTLV-1-associated myelopathy/tropical spastic paraparesis ( HAM/TSP ) . There is also c...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "immune", "cells", "clinical", "immunology", "immunity", "t", "cells", "immunity", "to", "infections", "immunology", "viral", "diseases", "immune", "response" ]	2011	HTLV-1 Tax Specific CD8+ T Cells Express Low Levels of Tim-3 in HTLV-1 Infection: Implications for Progression to Neurological Complications
Mutations in the human survival motor neuron 1 ( SMN ) gene are the primary cause of spinal muscular atrophy ( SMA ) , a devastating neuromuscular disorder . SMN protein has a well-characterized role in the biogenesis of small nuclear ribonucleoproteins ( snRNPs ) , core components of the spliceosome . Additional tissu...	Spinal Muscular Atrophy ( SMA ) is a prevalent childhood neuromuscular disease , which in its most common form causes death by the age of two . One in fifty Americans is a carrier for SMA , making this genetic disease a serious health concern . SMA is caused by loss of function mutations in the survival motor neuron 1 ...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "biomacromolecule-ligand", "interactions", "invertebrates", "animal", "genetics", "molecular", "complexes", "neuroscience", "animals", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "molecular", "genetics", "drosophila", "r...	2014	SMA-Causing Missense Mutations in Survival motor neuron (Smn) Display a Wide Range of Phenotypes When Modeled in Drosophila
Equine arteritis virus ( EAV ) is the causative agent of equine viral arteritis ( EVA ) , a respiratory , systemic , and reproductive disease of horses and other equid species . Following natural infection , 10–70% of the infected stallions can become persistently infected and continue to shed EAV in their semen for pe...	A variable proportion of EAV infected stallions ( 10–70% ) may become persistently infected and continuously shed the virus exclusively in their semen after recovery from acute infection . Previous studies in our laboratory have shown that stallions with the CD3+ T lymphocyte susceptibility phenotype to in vitro EAV in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "sequencing", "techniques", "cell", "motility", "medicine", "and", "health", "sciences", "immune", "cells", "body", "fluids", "immunology", "vertebrates", "animals", "mammals", "membrane", "proteins", "sequence", "motif", "analysis", "molecular", "bi...	2016	Allelic Variation in CXCL16 Determines CD3+ T Lymphocyte Susceptibility to Equine Arteritis Virus Infection and Establishment of Long-Term Carrier State in the Stallion
The X chromosome constitutes a unique genomic environment because it is present in one copy in males , but two copies in females . This simple fact has motivated several theoretical predictions with respect to how standing genetic variation on the X chromosome should differ from the autosomes . Unmasked expression of d...	Theory provides contrasting predictions with respect to the relative magnitude of standing genetic variation on the X chromosome and the autosomes . While most classic population genetics theory suggests a dearth of variation on the X chromosome , theory which concerns selection operating differently in males and femal...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Sex-specific Trans-regulatory Variation on the Drosophila melanogaster X Chromosome
Inhibitory pathways are an essential component in the function of the neocortical microcircuitry . Despite the relatively small fraction of inhibitory neurons in the neocortex , these neurons are strongly activated due to their high connectivity rate and the intricate manner in which they interconnect with pyramidal ce...	The neocortex of the mammalian brain contains many more excitatory neurons than inhibitory neurons , yet inhibitory neurons are essential components of neocortical circuitry . Inhibitory neurons form dense and intricate connections with excitatory neurons , which are mainly pyramidal cells . One prominent pathway forme...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience", "neuroscience/sensory", "systems" ]	2010	Brief Bursts Self-Inhibit and Correlate the Pyramidal Network
Diverse mechanisms for DNA-protein recognition have been elucidated in numerous atomic complex structures from various protein families . These structural data provide an invaluable knowledge base not only for understanding DNA-protein interactions , but also for developing specialized methods that predict the DNA-bind...	DNA-binding proteins represent only a small fraction of proteins encoded in genomes , yet they play a critical role in a variety of biological activities . Identifying these proteins and understanding how they function are important issues . The structures of solved DNA protein complexes of different protein families p...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/protein", "structure", "prediction", "biophysics/biomacromolecule-ligand", "interactions", "computational", "biology/macromolecular", "sequence", "analysis", "computational", "biology/protein", "homology", "detection" ]	2009	A Threading-Based Method for the Prediction of DNA-Binding Proteins with Application to the Human Genome
The soil transmitted helminths are a group of parasitic worms responsible for extensive morbidity in many of the world’s most economically depressed locations . With growing emphasis on disease mapping and eradication , the availability of accurate and cost-effective diagnostic measures is of paramount importance to gl...	With a growing emphasis on the mapping and elimination of soil transmitted helminth ( STH ) infections , the need for optimal and specific diagnostic methods is increasing . While PCR-based diagnostic methods for the detection of these parasitic organisms exist , these assays make use of sub-optimal target sequences . ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "sequencing", "techniques", "invertebrates", "animals", "necator", "americanus", "ascaris", "ascaris", "lumbricoides", "molecular", "biology", "techniques", "strongyloides", "stercoralis", "research", "and", "analysis", "methods", "ancylostoma", "sequence", "analysis", "str...	2016	Improved PCR-Based Detection of Soil Transmitted Helminth Infections Using a Next-Generation Sequencing Approach to Assay Design
Large-scale white matter pathways crisscrossing the cortex create a complex pattern of connectivity that underlies human cognitive function . Generative mechanisms for this architecture have been difficult to identify in part because little is known in general about mechanistic drivers of structured networks . Here we ...	White matter tracts crisscrossing the human cortex are linked in a complex pattern that constrains human thought and behavior . Why the human brain displays the complex pattern that it does is a fascinating open question . Progress in uncovering generative mechanisms for this architecture requires greater knowledge abo...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "statistical", "mechanics", "nervous", "system", "applied", "mathematics", "neuroscience", "systems", "science", "mathematics", "statistics", "(mathematics)", "computational", "neuroscience", "neuroimaging", "complex", "systems", "computer", "and", "information", "sciences", ...	2014	Resolving Structural Variability in Network Models and the Brain
Glucose is the preferred carbon and energy source in prokaryotes , unicellular eukaryotes , and metazoans . However , excess of glucose has been associated with several diseases , including diabetes and the less understood process of aging . On the contrary , limiting glucose ( i . e . , calorie restriction ) slows agi...	Lowering caloric intake by limiting glucose ( the preferred carbon and energy source ) increases life span in various species . Excess glucose can have deleterious effects , but it is not clear whether this is due to the caloric contribution of glucose or to some other effect . Glucose sensed by the cells activates sig...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/cellular", "death", "and", "stress", "responses", "cell", "biology/microbial", "physiology", "and", "metabolism", "cell", "biology/gene", "expression", "cell", "biology/cell", "signaling" ]	2009	Pro-Aging Effects of Glucose Signaling through a G Protein-Coupled Glucose Receptor in Fission Yeast
Stress granules ( SGs ) are membrane-less dynamic structures consisting of mRNA and protein aggregates that form rapidly in response to a wide range of environmental cellular stresses and viral infections . They act as storage sites for translationally silenced mRNAs under stress conditions . During viral infection , S...	Exposure of cells to environmental stresses , such as heat shock and viral infection , induces a cellular response leading to the formation of Stress Granules ( SGs ) composed of stalled translation initiation complexes ( RNA-binding proteins and mRNA ) . The subsequent inhibition of host translation participates to ce...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "nuclear", "staining", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "gene", "regulation", "pathogens", "messenger", "rna", "immunology", "microbiology", "viral...	2016	Rabies Virus Infection Induces the Formation of Stress Granules Closely Connected to the Viral Factories
Voluntarily shifting attention to a location of the visual field improves the perception of events that occur there . Regions of frontal cortex are thought to provide the top-down control signal that initiates a shift of attention , but because of the temporal limitations of functional brain imaging , the timing and se...	To extract important details about objects in the environment , people must focus their attention on a specific location in space at any given moment . Research using functional magnetic resonance imaging ( fMRI ) has suggested that regions of the frontal and parietal lobes work together to control our ability to direc...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "neuroscience" ]	2008	Electrical Neuroimaging Reveals Timing of Attentional Control Activity in Human Brain
The bivalent killed oral cholera vaccine ( OCV ) provides 65% cumulative protection over five years . It remains unknown whether a boosting regimen can maintain protection in previously immunized populations . This study examines the immunogenicity and safety of an OCV regimen given five years following initial dosing ...	The five year efficacy results of the bivalent , killed whole cell oral cholera vaccine ( WC OCV ) was shown to offer 65% protection in cholera endemic Kolkata . Further search strategies focused on natural boosting of immunity , since this trial assessed protection in a population that has endemic cholera at high rate...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	An Open Label Non-inferiority Trial Assessing Vibriocidal Response of a Killed Bivalent Oral Cholera Vaccine Regimen following a Five Year Interval in Kolkata, India
Copy number variation ( CNV ) is rife in eukaryotic genomes and has been implicated in many human disorders , particularly cancer , in which CNV promotes both tumorigenesis and chemotherapy resistance . CNVs are considered random mutations but often arise through replication defects; transcription can interfere with re...	Evolutionary theory asserts that adaptive mutations , which improve cellular fitness in challenging environments , occur at random and cannot be controlled by the cell . The mutation mechanisms involved are of widespread importance , governing diverse processes from the acquisition of resistance during chemotherapy to ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "alkaloids", "chemical", "compounds", "formaldehyde", "molecular", "probe", "techniques", "carbohydrates", "galactose", "organic", "compounds", "fungi", "model", "organisms", "experimental", "organism", "systems", "copy", "number", "variation", "molecular", "biology", "te...	2017	Environmental change drives accelerated adaptation through stimulated copy number variation
In eukaryotes , Dom34 upregulates translation by securing levels of activatable ribosomal subunits . We found that in the yeast Saccharomyces cerevisiae and the human fungal pathogen Candida albicans , Dom34 interacts genetically with Pmt1 , a major isoform of protein O-mannosyltransferase . In C . albicans , lack of D...	Fungi respond to damages of their glycostructures in their cell wall by transcriptional upregulation of genes that specify compensatory activities . Upon block of protein N-glycosylation , the human fungal pathogen Candida albicans increases transcription of PMT1 encoding a major isoform of protein O-mannosyltransferas...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "and", "Materials" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "nucleases", "enzymes", "pathogens", "messenger", "rna", "microbiology", "dna-binding", "proteins", "enzymology", "nucleotides", "fungi", "model", "organisms", "untranslated", "regions"...	2016	Dom34 Links Translation to Protein O-mannosylation
MnmE , which is involved in the modification of the wobble position of certain tRNAs , belongs to the expanding class of G proteins activated by nucleotide-dependent dimerization ( GADs ) . Previous models suggested the protein to be a multidomain protein whose G domains contact each other in a nucleotide dependent man...	MnmE is an evolutionary conserved G protein that is involved in modification of the wobble U position of certain tRNAs to suppress translational wobbling . Despite high homology between its G domain and the small G protein Ras , MnmE displays entirely different regulatory properties to that of many molecular switch-typ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biophysics/experimental", "biophysical", "methods", "biochemistry/macromolecular", "assemblies", "and", "machines", "biochemistry/experimental", "biophysical", "methods" ]	2009	Kissing G Domains of MnmE Monitored by X-Ray Crystallography and Pulse Electron Paramagnetic Resonance Spectroscopy
Careful monitoring for recrudescence of Wuchereria bancrofti infection is necessary in communities where mass drug administration ( MDA ) for the elimination of lymphatic filariasis ( LF ) as a public health problem has been stopped . During the post-MDA period , transmission assessment surveys ( TAS ) are recommended ...	To ensure elimination of lymphatic filariasis , efficient surveillance methods are needed . While some available methods rely on the detection of Wuchereria bancrofti microfilaria , antigen or antibody in human blood samples , molecular xenomonitoring can identify parasite DNA in vector mosquitoes . We collected the ma...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "geographical", "locations", "tropical", "diseases", "parasitic", "diseases", "animals", "filariasis", "neglected", "tropical", "diseases", "molecular", "biology", "techniques", "insect", "vectors", "zoology", "lym...	2018	Molecular xenomonitoring for Wuchereria bancrofti in Culex quinquefasciatus in two districts in Bangladesh supports transmission assessment survey findings
Comparisons of DNA sequences between Neandertals and present-day humans have shown that Neandertals share more genetic variants with non-Africans than with Africans . This could be due to interbreeding between Neandertals and modern humans when the two groups met subsequent to the emergence of modern humans outside Afr...	One of the key discoveries from the analysis of the Neandertal genome is that Neandertals share more genetic variants with non-Africans than with Africans . This observation is consistent with two hypotheses: interbreeding between Neandertals and modern humans after modern humans emerged out of Africa or population str...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "haplotypes", "mathematics", "genetic", "polymorphism", "statistics", "statistical", "methods", "population", "genetics", "biology", "evolutionary", "biology", "gene", "flow", "evolutionary", "genetics" ]	2012	The Date of Interbreeding between Neandertals and Modern Humans
Cell penetrating peptides ( CPPs ) are those peptides that can transverse cell membranes to enter cells . Once inside the cell , different CPPs can localize to different cellular components and perform different roles . Some generate pore-forming complexes resulting in the destruction of cells while others localize to ...	Cell penetrating peptides ( CPPs ) are peptides that can potentially transport other functional molecules across cellular membranes and therefore serve a role as drug delivery vehicles . The properties of a given peptide that make it cell penetrating are unclear , and the rapid screening of potential CPPs aids research...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "algorithms", "computer", "science", "biology", "computational", "biology", "molecular", "cell", "biology" ]	2011	Prediction of Cell Penetrating Peptides by Support Vector Machines
Appropriate nutrient response is essential for growth and reproduction . Under favorable nutrient conditions , the C . elegans nuclear receptor DAF-12 is activated by dafachronic acids , hormones that commit larvae to reproductive growth . Here , we report that in addition to its well-studied role in controlling develo...	Animals adjust their internal biological processes in response to their environments . In this study , we report that in a nutrient rich environment the free-living nematode , Caenorhabditis elegans , induces an energy-generating metabolic pathway to govern its reproductive growth by activating the nuclear receptor , D...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Nuclear Receptor DAF-12 Regulates Nutrient Metabolism and Reproductive Growth in Nematodes
Schistosomiasis is endemic to several parts of the world . Among the species that affect humans , Schistosoma mansoni is one of the most common causes of illness . In regions where schistosomiasis mansoni is endemic , reinfection is responsible for the emergence of hepatosplenic schistosomiasis ( HSS ) with portal hype...	Among the species of Schistosoma that infect humans Schistosoma mansoni is one of the most common causes of illness . In the areas where schistosomiasis mansoni is endemic , around 10% of infected individuals develop hepatosplenic schistosomiasis ( HSS ) with portal hypertension . Portal hypertension may promotes an im...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "medicine", "and", "health", "sciences", "diagnostic", "radiology", "ultrasound", "imaging", "helminths", "cardiovascular", "anatomy", "tropical", "diseases", "fibrosis", "parasitic", "diseases", "animals", "liver", ...	2017	Pulmonary shunts in severe hepatosplenic schistosomiasis: Diagnosis by contrast echocardiography and their relationship with abdominal ultrasound findings
Arabidopsis seeds rapidly release hydrophilic polysaccharides from the seed coat on imbibition . These form a heavy mucilage layer around the seed that makes it sink in water . Fourteen natural Arabidopsis variants from central Asia and Scandinavia were identified with seeds that have modified mucilage release and floa...	Seeds of the model plant Arabidopsis release sticky mucilage on imbibition that is constituted of complex polysaccharides . In this study , we have identified and characterised natural Arabidopsis variants that do not release mucilage and found that their seeds float . The accumulation of unreleased polysaccharides in ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "science", "plant", "evolution", "plant", "genetics", "biology", "plant", "physiology" ]	2014	Local Evolution of Seed Flotation in Arabidopsis
Due to the omnipresent risk of epidemics , insect societies have evolved sophisticated disease defences at the individual and colony level . An intriguing yet little understood phenomenon is that social contact to pathogen-exposed individuals reduces susceptibility of previously naive nestmates to this pathogen . We te...	Close social contact facilitates pathogen transmission in societies , often causing epidemics . In contrast to this , we show that limited transmission of a fungal pathogen in ant colonies can be beneficial for the host , because it promotes “social immunisation” of healthy group members . We found that ants exposed to...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "mycology", "zoology", "immunity", "immunology", "biology", "evolutionary", "biology", "microbiology" ]	2012	Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies
Kaposi’s sarcoma-associated herpesvirus ( KSHV ) is the etiologic agent of Kaposi’s sarcoma ( KS ) . It is endemic in a number of sub-Saharan African countries with infection rate of >50% . The high prevalence of HIV-1 coupled with late presentation of advanced cancer staging make KS the leading cancer in the region wi...	Kaposi’s sarcoma-associated herpesvirus ( KSHV ) is endemic in sub-Saharan Africa and cause Kaposi’s sarcoma ( KS ) . KS is one of the most common cancer among HIV-1 patients in this region . Despite anti-retroviral treatment , prognosis for KS is poor with high mortality often due to presentation of late cancer stage ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "carbohydrate", "metabolism", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "cancers", "and", "neoplasms", "microbiology", "glucose", "metabolism", "retroviruses", "oncology", "immunodeficiency", "viruses", "viruses", ...	2018	RNA-Seq of Kaposi’s sarcoma reveals alterations in glucose and lipid metabolism
Metronidazole , a 5-nitroimidazole drug , has been the gold standard for several decades in the treatment of infections with microaerophilic protist parasites , including Entamoeba histolytica . For activation , the drug must be chemically reduced , but little is known about the targets of the active metabolites . Appl...	The protist parasites Entamoeba histolytica , Trichomonas vaginalis , and Giardia intestinalis grow in environments with low oxygen concentration . Infections with these parasites are commonly treated with metronidazole , a nitroimidazole drug that must be reduced for activation , resulting in several toxic metabolites...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "biochemistry", "infectious", "diseases", "pharmacology", "microbiology", "paramecium", "etc)", "ciliates", "(tetrahymena" ]	2007	Nitroimidazole Action in Entamoeba histolytica: A Central Role for Thioredoxin Reductase
Enterotoxigenic Escherichia coli ( ETEC ) encoding heat-stable enterotoxin ( ST ) alone or with heat-labile enterotoxin ( LT ) cause moderate-to-severe diarrhea ( MSD ) in developing country children . The Global Enteric Multicenter Study ( GEMS ) identified ETEC encoding ST among the top four enteropathogens . Since t...	Enterotoxigenic Escherichia coli ( “ETEC” ) were found to be one of the four most consistently important agents that cause moderate-to-severe diarrhea among children <5 years of age in a large case-control study , the Global Enteric Multicenter Study , performed in four countries in sub-Saharan Africa and three in Sout...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "bacteriology", "medicine", "and", "health", "sciences", "toxins", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "enterotoxins", "pili", "and", "fimbriae", "toxic", "agents", "toxicology", "vaccines", "diarrhea", "preventive", ...	2019	Colonization factors among enterotoxigenic Escherichia coli isolates from children with moderate-to-severe diarrhea and from matched controls in the Global Enteric Multicenter Study (GEMS)
Besides being building blocks for protein synthesis , amino acids serve a wide variety of cellular functions , including acting as metabolic intermediates for ATP generation and for redox homeostasis . Upon amino acid deprivation , free uncharged tRNAs trigger GCN2-ATF4 to mediate the well-characterized transcriptional...	In order for mammalian cells to live and function , amino acids are required for protein synthesis and the generation of metabolic intermediates . An imbalance or deficiency of amino acids often triggers an “amino acid response” ( AAR ) to allow cells to adapt to their environment . However , it remains unclear whether...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Comprehensive Profiling of Amino Acid Response Uncovers Unique Methionine-Deprived Response Dependent on Intact Creatine Biosynthesis
Seasonal influenza surveillance is usually carried out by sentinel general practitioners ( GPs ) who compile weekly reports based on the number of influenza-like illness ( ILI ) clinical cases observed among visited patients . This traditional practice for surveillance generally presents several issues , such as a dela...	This study suggests how web-based surveillance data can provide an epidemiological signal capable of detecting the temporal trends of influenza-like illness without relying on a specific case definition . The proposed framework was able to forecast quite accurately the ILI trend of the forthcoming influenza season base...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "european", "union", "pathology", "and", "laboratory", "medicine", "statistics", "influenza", "geographical", "locations", "ireland", "mathematics", "forecasting", "signs", "and", "symptoms", "infectious", "disease", "control", "...	2019	Unsupervised extraction of epidemic syndromes from participatory influenza surveillance self-reported symptoms
Acquisition of iron is necessary for the replication of nearly all bacterial pathogens; however , iron of vertebrate hosts is mostly sequestered by heme and bound to hemoglobin within red blood cells . In Bacillus anthracis , the spore-forming agent of anthrax , the mechanisms of iron scavenging from hemoglobin are unk...	Iron is an essential nutrient used by almost all organisms . Bacterial pathogens must acquire iron in order to grow inside mammalian hosts . The host , however , limits the availability of free iron , thereby providing an effective defense strategy against infection . In response , bacteria have evolved clever ways to ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "infectious", "diseases", "microbiology" ]	2008	Bacillus anthracis Secretes Proteins That Mediate Heme Acquisition from Hemoglobin
The repeated rDNA array gives rise to the nucleolus , an organelle that is central to cellular processes as varied as stress response , cell cycle regulation , RNA modification , cell metabolism , and genome stability . The rDNA array is also responsible for the production of more than 70% of all cellular RNAs ( the ri...	The repeated ribosomal DNA ( rDNA ) array gives rise to the nucleolus , an organelle that is involved in key cellular processes such as stress response , cell cycle regulation , RNA modification , and production of more than 70% of all cellular RNAs ( the ribosomal RNAs ) . This critical genome element has remained una...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "pseudogenes", "human", "genomics", "genome", "analysis", "gene", "types", "energy-producing", "organelles", "mitochondria", "bioenergetics", "cell", "nucleus", "cellular", "structures", "and", "organelles", "nucleolus", "genome", "complexity", "proteins", "gene", "expres...	2018	The long-range interaction map of ribosomal DNA arrays
Endocytosis is an essential process by which cells internalize a piece of plasma membrane and material from the outside . In cells with turgor , pressure opposes membrane deformations , and increases the amount of force that has to be generated by the endocytic machinery . To determine this force , and calculate the sh...	Cells use endocytosis to intake molecules and to recycle components of their membrane . Even in its simplest form , endocytosis involves a large number of proteins with often redundant functions that are organized into a microscopic force-producing “machine” . Knowing how much force is needed to induce a membrane invag...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Membrane Mechanics of Endocytosis in Cells with Turgor
Lassa virus ( LASV ) is a causative agent of hemorrhagic fever in West Africa . In recent years , it has been imported several times to Europe and North America . The method of choice for early detection of LASV in blood is RT-PCR . Therefore , the European Network for Diagnostics of ‘Imported’ Viral Diseases ( ENIVD )...	A proficiency test panel for molecular diagnostic of Lassa virus provides objective evidence of testing quality of International diagnostic laboratories . Since there are no commercial assays available , it is very important to assess the quality of diagnostic test used as well as evaluate detection sensitivity and spe...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results" ]	[]	2015	International External Quality Assessment Study for Molecular Detection of Lassa Virus
Trinucleotide repeat expansions are the genetic cause of numerous human diseases , including fragile X mental retardation , Huntington disease , and myotonic dystrophy type 1 . Disease severity and age of onset are critically linked to expansion size . Previous mouse models of repeat instability have not recreated larg...	Many neurological and/or neuromuscular diseases , such as myotonic dystrophy , Huntington disease , and fragile X mental retardation are caused by an increase in the size of a repeated DNA sequence within a specific gene . These repetitive DNA sequences are prone to expansion , increasing in size when transmitted from ...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "mus", "(mouse)", "molecular", "biology", "genetics", "and", "genomics", "neurological", "disorders" ]	2007	CTG Trinucleotide Repeat “Big Jumps”: Large Expansions, Small Mice
Memory storage in the brain relies on mechanisms acting on time scales from minutes , for long-term synaptic potentiation , to days , for memory consolidation . During such processes , neural circuits distinguish synapses relevant for forming a long-term storage , which are consolidated , from synapses of short-term st...	The ability to form memories of the past is a main feature of the brain . Memories are formed by learning . However , the biological mechanisms for learning , which change the synaptic weights by synaptic plasticity , act on a different time scale ( minutes ) than those that lead to memory consolidation ( days ) . Expe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Synaptic Scaling Enables Dynamically Distinct Short- and Long-Term Memory Formation
The mechanosensitive channel of large conductance ( MscL ) is capable of transducing mechanical stimuli such as membrane tension into an electrochemical response . MscL provides a widely-studied model system for mechanotransduction and , more generally , for how bilayer mechanical properties regulate protein conformati...	A fundamental property of living cells is their ability to detect mechanical stimuli . Microbes , in particular , often transition between different chemical environments , leading to osmotic shock and concurrent changes in membrane tension . The tension of microbial cell membranes is detected and controlled by membran...	[ "Abstract", "Introduction", "Results", "Discussion", "Models", "and", "Methods" ]	[ "physics", "interdisciplinary", "physics", "biology", "computational", "biology", "molecular", "cell", "biology", "biophysics" ]	2013	Connection between Oligomeric State and Gating Characteristics of Mechanosensitive Ion Channels
Recent discoveries of direct acting antivirals against Hepatitis C virus ( HCV ) have raised hopes of effective treatment via combination therapies . Yet rapid evolution and high diversity of HCV populations , combined with the reality of suboptimal treatment adherence , make drug resistance a clinical and public healt...	Hepatitis C virus ( HCV ) affects approximately 170 million people world-wide and chronic infections can lead to cirrhosis and liver cancer . New combination therapies of direct acting antivirals have achieved remarkably high cure rates in clinical trials . However , high mutation rates and high diversity of HCV popula...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Rational Design and Adaptive Management of Combination Therapies for Hepatitis C Virus Infection
Eukaryotic cells assemble viscoelastic networks of crosslinked actin filaments to control their shape , mechanical properties , and motility . One important class of actin network is nucleated by the Arp2/3 complex and drives both membrane protrusion at the leading edge of motile cells and intracellular motility of pat...	Networks of actin filaments provide the force that drives eukaryotic cell movement . In a model system for this kind of force generation , a spherical bead coated with an actin nucleating protein builds and rockets around on an actin “comet tail , ” much like the tails observed in some cellular systems . How does a sph...	[ "Abstract", "Introduction", "Results", "Discussion", "Conclusions", "Materials", "and", "Methods" ]	[ "biophysics/theory", "and", "simulation", "cell", "biology/cytoskeleton" ]	2009	In Silico Reconstitution of Actin-Based Symmetry Breaking and Motility
Coxiella burnetii is an intracellular bacterial pathogen that causes human Q fever , an acute flu-like illness that can progress to chronic endocarditis and liver and bone infections . Humans are typically infected by aerosol-mediated transmission , and C . burnetii initially targets alveolar macrophages wherein the pa...	Q fever , caused by the intracellular bacterial pathogen Coxiella burnetii , is an aerosol-transmitted infection that can develop into life-threatening chronic infections such as endocarditis . The pathogen preferentially grows within alveolar macrophages in a phagolysosome-like compartment termed the parasitophorous v...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "phosphorylation", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "vacuoles", "intracellular", "pathogens", "gene", "regulation", "pathogens", "microbiology", "immunoprecipitation", "cellular", "structures", "and", "organelles", "bact...	2016	Vasodilator-Stimulated Phosphoprotein Activity Is Required for Coxiella burnetii Growth in Human Macrophages
Approximately 200 million people worldwide harbour parasitic flatworm infections that cause schistosomiasis . A single drug—praziquantel ( PZQ ) —has served as the mainstay pharmacotherapy for schistosome infections since the 1980s . However , the relevant in vivo target ( s ) of praziquantel remain undefined . Here , ...	Praziquantel is the major drug used to treat people infected with parasitic worms that cause the neglected tropical disease schistosomiasis . Despite being in widespread clinical use , it is surprising that scientists have not identified how praziquantel works to kill pathogenic schistosomes . This lack of pathobiologi...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "developmental", "biology/stem", "cells", "cell", "biology/cell", "signaling", "physiology/pattern", "formation", "developmental", "biology/pattern", "formation", "physiology/neurodevelopment", "physiology/cell", "signaling", "pharmacology" ]	2009	A Novel Biological Activity of Praziquantel Requiring Voltage-Operated Ca2+ Channel β Subunits: Subversion of Flatworm Regenerative Polarity
Recent evidence suggests that many malignancies , including breast cancer , are driven by a cellular subcomponent that displays stem cell-like properties . The protein phosphatase and tensin homolog ( PTEN ) is inactivated in a wide range of human cancers , an alteration that is associated with a poor prognosis . Becau...	Healthy adult tissues are maintained through the regulated proliferation of a subset of cells known as tissue stem and progenitor cells . Many cancers , including breast cancer , also are thought to arise from and be maintained by a small population of cells that display stem cell-like properties . These so-called “can...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology", "oncology/breast", "cancer", "cell", "biology/cell", "signaling" ]	2009	Regulation of Mammary Stem/Progenitor Cells by PTEN/Akt/β-Catenin Signaling
Sporulation is an ancient developmental process that involves the formation of a highly resistant endospore within a larger mother cell . In the model organism Bacillus subtilis , sporulation-specific sigma factors activate compartment-specific transcriptional programs that drive spore morphogenesis . σG activity in th...	The bacterial spore-forming pathogen Clostridium difficile is a leading cause of nosocomial infections in the United States and represents a significant threat to healthcare systems around the world . As an obligate anaerobe , C . difficile must form spores in order to survive exit from the gastrointestinal tract . Acc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Regulation of Clostridium difficile Spore Formation by the SpoIIQ and SpoIIIA Proteins
Axon-guidance by Slit-Roundabout ( Robo ) signaling at the midline initially guides growth cones to synaptic targets and positions longitudinal axon tracts in discrete bundles on either side of the midline . Following the formation of commissural tracts , Slit is found also in tracts of the commissures and longitudinal...	Early during embryogenesis , the Slit ligand is present only at the midline of the nerve cord . It binds its receptor Robo on growth cones of axons and guides axons such that they form a series of axon tracts called longitudinal tracts on either side of the midline . It has been proposed that Slit regulates axon guidan...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "enzymes", "enzymology", "neuroscience", "developmental", "biology", "signs", "and", "symptoms", "immunoprecipitation", "nerve", "fibers", "embryos", "research", "and", "analysis", "m...	2017	Post-guidance signaling by extracellular matrix-associated Slit/Slit-N maintains fasciculation and position of axon tracts in the nerve cord
The ability to tolerate Candida albicans , a human commensal of the gastrointestinal tract and vagina , implicates that host defense mechanisms of resistance and tolerance cooperate to limit fungal burden and inflammation at the different body sites . We evaluated resistance and tolerance to the fungus in experimental ...	This study disentangles resistance and tolerance components of murine and human C . albicans vaginal infection and introduces the challenging notion of a disease due to a defective tolerance mechanism . Vulvovaginal candidiasis ( VVC ) and recurrent VVC ( RVVC ) are two forms of disease that affect a large number of ot...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "genetics", "immunology", "biology", "microbiology" ]	2013	IL-22 and IDO1 Affect Immunity and Tolerance to Murine and Human Vaginal Candidiasis
As with many viruses , rabies virus ( RABV ) infection induces type I interferon ( IFN ) production within the infected host cells . However , RABV has evolved mechanisms by which to inhibit IFN production in order to sustain infection . Here we show that RABV infection of dendritic cells ( DC ) induces potent type I I...	Rabies virus ( RABV ) is a neurotropic RNA virus responsible for the deaths of the at least 40 , 000 to 70 , 000 individuals globally each year . However , the innate immune response induced by both wildtype and vaccine strains of RABV is not well understood . In this study , we assessed the pattern recognition recepto...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/vaccines", "virology", "virology/host", "antiviral", "responses", "virology/immune", "evasion", "virology/host", "invasion", "and", "cell", "entry" ]	2010	Rabies Virus Infection Induces Type I Interferon Production in an IPS-1 Dependent Manner While Dendritic Cell Activation Relies on IFNAR Signaling
Postzygotic single-nucleotide mosaicisms ( pSNMs ) have been extensively studied in tumors and are known to play critical roles in tumorigenesis . However , the patterns and origin of pSNMs in normal organs of healthy humans remain largely unknown . Using whole-genome sequencing and ultra-deep amplicon re-sequencing , ...	Genomic mosaicism led by postzygotic mutation is the major cause of cancers and many non-cancer developmental disorders . Theoretically , postzygotic mutations should be accumulated during the developmental process of healthy individuals , but the genome-wide characterization of postzygotic mosaicisms across many organ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "liver", "variant", "genotypes", "genetic", "mapping", "oncology", "mutation", "developmental", "biology", "epigenetics", "dna", "chromatin", "dna", "methylation", "chromosome", "biology", "gene", "expression", "chromatin", "modi...	2018	Distinctive types of postzygotic single-nucleotide mosaicisms in healthy individuals revealed by genome-wide profiling of multiple organs
Exonization of Alu elements is a major mechanism for birth of new exons in primate genomes . Prior analyses of expressed sequence tags show that almost all Alu-derived exons are alternatively spliced , and the vast majority of these exons have low transcript inclusion levels . In this work , we provide genomic and expe...	New exons have been created and added to existing functional genes during eukaryotic genome evolution . Alu elements , a class of primate-specific retrotransposons , are a major source of new exons in primates . However , recent analyses of expressed sequence tags suggest that the vast majority of Alu-derived exons are...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/alternative", "splicing", "genetics", "and", "genomics/gene", "expression", "evolutionary", "biology/genomics" ]	2008	Diverse Splicing Patterns of Exonized Alu Elements in Human Tissues
Prophylactic interventions such as vaccine allocation are some of the most effective public health policy planning tools . The supply of vaccines , however , is limited and an important challenge is to optimally allocate the vaccines to minimize epidemic impact . This resource allocation question ( which we refer to as...	Annual vaccination campaigns continue to be one of the prime measures which help alleviate the burden of seasonal influenza . Due to production and logistic constraints , there is a need for prioritization policies associated with vaccine deployment . While there is general consensus on age-based or risk-based prioriti...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "influenza", "applied", "mathematics", "immunology", "social", "sciences", "human", "mobility", "simulation", "and", "modeling", "vaccines", "preventive", "medicine", "algorithms", "mathematics", "infectious", "disease", "control",...	2019	Optimizing spatial allocation of seasonal influenza vaccine under temporal constraints
Despite recent advances in our ability to detect adaptive evolution involving the cis-regulation of gene expression , our knowledge of the molecular mechanisms underlying these adaptations has lagged far behind . Across all model organisms , the causal mutations have been discovered for only a handful of gene expressio...	Evolutionary adaptation is the process that has given rise to the ubiquitous , yet remarkable , fit between all living organisms and their environments . The molecular mechanisms of these adaptations have been a subject of great interest , but we still know very little about their mechanisms , particularly in the case ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	The Molecular Mechanism of a Cis-Regulatory Adaptation in Yeast
The interferon ( IFN ) system represents the first line of defense against a wide range of viruses . Virus infection rapidly triggers the transcriptional induction of IFN-β and IFN Stimulated Genes ( ISGs ) , whose protein products act as viral restriction factors by interfering with specific stages of virus life cycle...	The antiviral functions of interferons ( IFNs ) are mediated by the IFN-induced proteins , encoded by the IFN Stimulated Genes ( ISGs ) . Because ISGs are virus-specific , we performed a high throughput genetic screen to identify novel antiviral ISGs against Sendai virus ( SeV ) , a respirovirus of the Paramyxoviridae ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "death", "autophagic", "cell", "death", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "molecular", "probe", "techniques", "hela", "cells", "pathogens", "cell", "processes", "biological", "cultures", "microbiology", "imm...	2018	A new mechanism of interferon’s antiviral action: Induction of autophagy, essential for paramyxovirus replication, is inhibited by the interferon stimulated gene, TDRD7
As populations spread into new territory , environmental heterogeneities can shape the population front and genetic composition . We focus here on the effects of an important building block of heterogeneous environments , isolated obstacles . With a combination of experiments , theory , and simulation , we show how iso...	Geographical structure influences the dynamics of the expansion of populations into new habitats and the relative importance of the evolutionary forces of mutation , selection , genetic drift , and gene flow . While populations often spread and evolve in highly complex environments , simplified scenarios allow one to u...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	How Obstacles Perturb Population Fronts and Alter Their Genetic Structure
Leprosy is a chronic inflammatory disease caused by Mycobacterium leprae that mainly affects the skin and peripheral nervous system , leading to a high disability rate and social stigma . Previous studies have shown a contribution of genes encoding products of the lectin pathway of complement in the modulation of the s...	Leprosy is considered a neglected disease and still a public health problem in many countries where it was not yet eliminated , leading to a high disability rate and social stigma . The molecular mechanisms of M . leprae infection and immune evasion are still poorly known , raising the need for studies that may contrib...	[ "Abstract", "Introduction", "Material", "and", "methods", "Results", "Discussion" ]	[ "mycobacterium", "leprae", "medicine", "and", "health", "sciences", "variant", "genotypes", "tropical", "diseases", "alleles", "genetic", "mapping", "bacterial", "diseases", "neglected", "tropical", "diseases", "molecular", "biology", "techniques", "bacteria", "research",...	2017	Association of a new FCN3 haplotype with high ficolin-3 levels in leprosy
Aedes control interventions are considered the cornerstone of dengue control programmes , but there is scarce evidence on their effect on disease . We set-up a cluster randomized controlled trial in Santiago de Cuba to evaluate the entomological and epidemiological effectiveness of periodical intra- and peri-domiciliar...	This is the first cluster randomized controlled trial providing evidence on the effect of applying residual insecticide treatment and deploying insecticide treated curtains on clinical dengue case incidence . In a context of intensive routine control activities , low Aedes infestation and moderate transmission , we did...	[ "Abstract", "Introduction", "Methodology", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "geographical", "locations", "randomized", "controlled", "trials", "animals", "north", "america", "clinical", "medicine", "pharmacology", "infectious", "disease", "control", "caribbean", "insect", "vectors", "zoolo...	2017	The additional benefit of residual spraying and insecticide-treated curtains for dengue control over current best practice in Cuba: Evaluation of disease incidence in a cluster randomized trial in a low burden setting with intensive routine control
From gastrulation to late organogenesis animal development involves many genetic and bio-mechanical interactions between epithelial and mesenchymal tissues . Ectodermal organs , such as hairs , feathers and teeth are well studied examples of organs whose development is based on epithelial-mesenchymal interactions . The...	The genes and signalling pathways involved in ectodermal organ development ( teeth , hair , mammary glands , etc . ) are relatively well studied . However , the bio-mechanical processes by which these organs grow and change shape from an early primordium ( an epithelial bud similar among different organs ) is far less ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "classical", "mechanics", "cell", "cycle", "and", "cell", "division", "cell", "processes", "mechanical", "stress", "epithelial", "cells", "damage", "mechanics", "digestive", "system", "dentition", "animal", "cells", "deformatio...	2018	Differential tissue growth and cell adhesion alone drive early tooth morphogenesis: An ex vivo and in silico study
Gene duplications within the conserved Hox cluster are rare in animal evolution , but in Lepidoptera an array of divergent Hox-related genes ( Shx genes ) has been reported between pb and zen . Here , we use genome sequencing of five lepidopteran species ( Polygonia c-album , Pararge aegeria , Callimorpha dominula , Ca...	We have examined gene duplication in a set of ancient genes used in patterning of animal embryos: the Hox genes . These genes code for proteins that bind DNA and switch on or off other genes , and they are very similar between distantly related animal species . Butterflies and moths , however , have additional Hox gene...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "arthropoda", "invertebrates", "developmental", "biology", "genomics", "genome", "evolution", "moths", "and", "butterflies", "genetics", "biology", "and", "life", "sciences", "comparative", "genomics", "molecular", "evolution", "computational", "biology", "evolutionary", ...	2014	Ancient Expansion of the Hox Cluster in Lepidoptera Generated Four Homeobox Genes Implicated in Extra-Embryonic Tissue Formation
PKR-like endoplasmic reticulum ( ER ) kinase ( PERK ) is an ER-associated stress sensor protein which phosphorylates eukaryotic initiation factor 2α ( eIF2α ) to induce translation attenuation in response to ER stress . PERK is also a regulator of lipogenesis during adipocyte differentiation through activation of the c...	HCMV , a β-herpesvirus , is a significant pathogen which infects most of the human population by puberty . Primary HCMV infection can be unnoticed in healthy people , but can be life threatening for the immunocompromised and it is the most important cause of congenital infection in the developed world , frequently lead...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology", "biology", "microbiology" ]	2013	PKR-Like Endoplasmic Reticulum Kinase Is Necessary for Lipogenic Activation during HCMV Infection
Genetic robustness , or fragility , is defined as the ability , or lack thereof , of a biological entity to maintain function in the face of mutations . Viruses that replicate via RNA intermediates exhibit high mutation rates , and robustness should be particularly advantageous to them . The capsid ( CA ) domain of the...	The HIV-1 capsid protein ( CA ) is absolutely essential for viral replication and there is , therefore , intense evolutionary pressure for HIV-1 CA to conserve its functions . However , HIV-1 CA is also a key target of the host immune response , which should provide evolutionary pressure to diversify CA sequence . Gene...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunodeficiency", "viruses", "virology", "biology", "microbiology" ]	2013	Extreme Genetic Fragility of the HIV-1 Capsid
Epstein-Barr Virus ( EBV ) is an oncogenic γ-herpesvirus that capably establishes both latent and lytic modes of infection in host cells and causes malignant diseases in humans . Nuclear antigen 2 ( EBNA2 ) -mediated transcription of both cellular and viral genes is essential for the establishment and maintenance of th...	Epstein-Barr Virus ( EBV ) infects human B cells to establish a permanent infection in hosts , which can cause diseases ranging from infectious mononucleosis to a broad spectrum of human malignancies . The conversion of human primary B cells into indefinitely proliferating lymphoblastoid cell lines ( LCLs ) by in vitro...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "virology", "biology", "microbiology", "viral", "diseases" ]	2012	The Nuclear Chaperone Nucleophosmin Escorts an Epstein-Barr Virus Nuclear Antigen to Establish Transcriptional Cascades for Latent Infection in Human B Cells
Type 2 Diabetes ( T2D ) is a highly prevalent chronic metabolic disease with strong co-morbidity with obesity and cardiovascular diseases . There is growing evidence supporting the notion that a crosstalk between mitochondria and the insulin signaling cascade could be involved in the etiology of T2D and insulin resista...	It has been shown that the crosstalk between insulin signaling and the mitochondria may be involved in the etiology of type 2 diabetes . In order to characterize the molecular basis of this crosstalk , we mined and filtered several interaction databases of different natures , including protein–protein interactions , ge...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "genome-wide", "association", "studies", "genomics", "functional", "genomics", "genetics", "biology", "computational", "biology", "metabolic", "networks", "signaling", "networks", "genetics", "and", "genomics" ]	2012	Identification of Novel Type 2 Diabetes Candidate Genes Involved in the Crosstalk between the Mitochondrial and the Insulin Signaling Systems
Yersinia pestis causes pneumonic plague , a disease characterized by inflammation , necrosis and rapid bacterial growth which together cause acute lung congestion and lethality . The bacterial type III secretion system ( T3SS ) injects 7 effector proteins into host cells and their combined activities are necessary to e...	In this work , we studied the mechanism whereby bacteria manipulate innate immune responses by controlling host cell death . Yersinia pestis , the causative agent of plague , requires effector Yops of the Type III Secretion System ( T3SS ) to evade the innate immune system during infection . We show that Yersinia induc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gram", "negative", "emerging", "infectious", "diseases", "immunity", "innate", "immunity", "microbial", "pathogens", "immune", "defense", "host-pathogen", "interaction", "biology", "microbiology", "bacterial", "pathogens" ]	2013	Early Apoptosis of Macrophages Modulated by Injection of Yersinia pestis YopK Promotes Progression of Primary Pneumonic Plague
Bacillus anthracis causes three forms of anthrax: inhalational , gastrointestinal , and cutaneous . Anthrax is characterized by both toxemia , which is caused by secretion of immunomodulating toxins ( lethal toxin and edema toxin ) , and septicemia , which is associated with bacterial encapsulation . Here we report tha...	Anthrax is caused by Bacillus anthracis , a bacterial pathogen that forms spores , dormant bacteria that are highly resistant to destruction . Infections initiate from the introduction of spores into airways or damaged skin , or from the consumption of contaminated food . Within the host , spores germinate , then bacte...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion", "Supporting", "Information" ]	[ "mus", "(mouse)", "infectious", "diseases", "microbiology", "eubacteria" ]	2007	Primary Involvement of Pharynx and Peyer's Patch in Inhalational and Intestinal Anthrax
Despite a high current standard of care in antiretroviral therapy for HIV , multidrug-resistant strains continue to emerge , underscoring the need for additional novel mechanism inhibitors that will offer expanded therapeutic options in the clinic . We report a new class of small molecule antiretroviral compounds that ...	Although the current standard of care for Human Immunodeficiency Virus ( HIV ) is high , viral resistance has emerged to every drug currently in the clinic , in some cases rendering the entire class ineffective for patients . A new class of antiretroviral drugs would be effective against strains of HIV-1 that are resis...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "virology/virion", "structure,", "assembly,", "and", "egress", "virology/immunodeficiency", "viruses", "virology/viral", "replication", "and", "gene", "regulation", "virology/antivirals,", "including", "modes", "of", "action", "and", "resistance" ]	2010	HIV Capsid is a Tractable Target for Small Molecule Therapeutic Intervention
Screening of herbal remedies for Cl− channel inhibition identified Krisanaklan , a herbal extract used in Thailand for treatment of diarrhea , as an effective antidiarrheal in mouse models of secretory diarrheas with inhibition activity against three Cl− channel targets . Krisanaklan fully inhibited cholera toxin-induc...	Secretory diarrhea is a major health challenge in developing countries . Causative agents include bacteria , as in cholera , and viruses , as in childhood rotaviral diarrhea . Though oral rehydration solution ( ORS ) has reduced mortality from diarrhea four-fold in the last three decades , its efficacy is limited , par...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "biology" ]	2014	Antidiarrheal Efficacy and Cellular Mechanisms of a Thai Herbal Remedy
Silene latifolia is a dioecious plant with heteromorphic sex chromosomes that have originated only ∼10 million years ago and is a promising model organism to study sex chromosome evolution in plants . Previous work suggests that S . latifolia XY chromosomes have gradually stopped recombining and the Y chromosome is und...	The mammalian sex chromosomes originated from an ancestral pair of autosomes about 150 million years ago and the Y chromosome subsequently degenerated , losing most of its genes . During this process , a phenomenon called dosage compensation evolved to compensate for the gene loss on the Y chromosome and to equalize ex...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "sequence", "analysis", "genome", "expression", "analysis", "plant", "science", "genomics", "genome", "evolution", "evolutionary", "biology", "plant", "evolution", "plant", "biology", "plant", "genomics", "biology", "computational", "biology", "comparative", "genomics", ...	2012	Rapid De Novo Evolution of X Chromosome Dosage Compensation in Silene latifolia, a Plant with Young Sex Chromosomes
Microsatellites have been found to be useful in determining genetic diversities of various medically-important parasites which can be used as basis for an effective disease management and control program . In Asia and Africa , the identification of different geographical strains of Schistosoma japonicum , S . haematobi...	Schistosomiasis is one of the important neglected tropical diseases endemic in 78 countries throughout the world . The disease is caused by the parasitic worms known as schistosomes . In the Philippines , S . japonicum is the causative agent of the disease . The prevalence of the disease varies in endemic areas , sugge...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "biogeography", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "pathology", "and", "laboratory", "medicine", "helminths", "population", "genetics", "parasitic", "diseases", "animals", "microsatellite",...	2017	Geographic strain differentiation of Schistosoma japonicum in the Philippines using microsatellite markers
Improving accuracy in genetic studies would greatly accelerate understanding the genetic basis of complex diseases . One approach to achieve such an improvement for risk variants identified by the genome wide association study ( GWAS ) approach is to incorporate previously known biology when screening variants across t...	Integrating multiple types of -omics data is a rapidly growing research area due in part to the increasing amount of diverse and publicly accessible data . In this study , we demonstrated that integration of genetic association and protein interaction data using a network diffusion approach measurably improves reproduc...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "genetic", "networks", "protein", "interactions", "pathology", "and", "laboratory", "medicine", "neurodegenerative", "diseases", "protein", "interaction", "networks", "immunology", "signs", ...	2018	One for all and all for One: Improving replication of genetic studies through network diffusion

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