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Seven rounds of mass drug administration ( MDA ) have been administered in Leogane , Haiti , an area hyperendemic for lymphatic filariasis ( LF ) . Sentinel site surveys showed that the prevalence of microfilaremia was reduced to <1% from levels as high as 15 . 5% , suggesting that transmission had been reduced . A sep...	Lymphatic filariasis ( LF ) is a mosquito-borne parasitic disease that affects an estimated 120 million people worldwide with over 1 billion at risk for infection . LF is considered to be a leading cause of permanent disability worldwide due to the clinical manifestations of the disease . A global effort was establishe...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology/global", "health", "public", "health", "and", "epidemiology/infectious", "diseases" ]	2010	A Community-Based Study of Factors Associated with Continuing Transmission of Lymphatic Filariasis in Leogane, Haiti
Much of our current understanding of the epidemiology of Ascaris lumbricoides infections in humans has been acquired by analyzing worm count data . These data are collected by treating infected individuals with anthelmintics so that worms are expelled intact from the gastrointestinal tract . Analysis of such data estab...	Numerous analyses have found that people infected with roundworm ( Ascaris lumbricoides ) are predisposed to harbor either many or few worms . Members of the same household also tend to harbor similar numbers of worms . These phenomena are called individual predisposition and household clustering respectively . In this...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/helminth", "infections", "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases", "mathematics/statistics" ]	2011	Individual Predisposition, Household Clustering and Risk Factors for Human Infection with Ascaris lumbricoides: New Epidemiological Insights
Following the 2010 cholera outbreak in Haiti , a plan was initiated to provide massive improvements to the sanitation and drinking water infrastructure in order to eliminate cholera from the island of Hispaniola by 2023 . Six years and a half billion dollars later , there is little evidence that any substantial improve...	After the introduction of toxigenic Vibrio cholerae O1 to the Caribbean nation of Haiti in 2010 , the country experienced the largest national cholera outbreak in recent history . With the help of the international community , over $500 , 000 , 000 USD was pledged to finance massive improvements in drinking water and s...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion", "Conclusion" ]	[ "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "water", "resources", "pathology", "and", "laboratory", "medicine", "pathogens", "vibrio", "immunology", "tropical", "diseases", "geographical", "locations", "microbiology", "health", ...	2017	Controlling cholera in the Ouest Department of Haiti using oral vaccines
Costs ( e . g . energetic expenditure ) and benefits ( e . g . food ) are central determinants of behavior . In ecology and economics , they are combined to form a utility function which is maximized to guide choices . This principle is widely used in neuroscience as a normative model of decision and action , but curre...	Behavior is made of decisions and actions . The decisions are based on the costs and benefits of potential actions , and the chosen actions are executed through the proper control of body segments . The corresponding processes are generally considered in separate theories of decision making and motor control , which ca...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "neuroscience", "biology", "neuroscience" ]	2012	A Model of Reward- and Effort-Based Optimal Decision Making and Motor Control
The protozoan parasite Leishmania causes leishmaniasis; a spectrum of diseases of which there are an estimated 1 million new cases each year . Current treatments are toxic , expensive , difficult to administer , and resistance to them is emerging . New therapeutics are urgently needed , however , screening the infectiv...	The protozoan parasite Leishmania causes a spectrum of diseases collectively known as leishmaniasis . The parasite is transmitted to humans by the bite of its vector , the sand fly , following which the parasite invades host white blood cells , particularly macrophages . Leishmaniasis is classified as a neglected tropi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biotechnology", "antimicrobials", "luciferase", "medicine", "and", "health", "sciences", "engineering", "and", "technology", "enzymes", "drugs", "microbiology", "enzymology", "antifungals", "parasitic", "diseases", "protozoan", "life", "cycles", "electromagnetic", "radiati...	2018	Development of NanoLuc-PEST expressing Leishmania mexicana as a new drug discovery tool for axenic- and intramacrophage-based assays
Snake envenomation is a serious public health threat in the rural areas of Asian and African countries . To date , the only proven treatment for snake envenomation is antivenom therapy . Cross-neutralization of heterologous venoms by antivenom raised against venoms of closely related species has been reported . The pre...	Snake envenomation is a serious public health threat in the rural areas of Asia and Africa . To date , the only proven treatment for snake envenomation is antivenom therapy . Owing to the difficulties in the diagnosis of the biting species , there is a need to develop polyvalent antivenoms that could cross-neutralize v...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "immunology", "biology", "toxicology", "immunoglobulins" ]	2012	Cross Neutralization of Afro-Asian Cobra and Asian Krait Venoms by a Thai Polyvalent Snake Antivenom (Neuro Polyvalent Snake Antivenom)
Antibody responses are thought to play an important role in control of Schistosoma infections , yet little is known about the phenotype and function of B cells in human schistosomiasis . We set out to characterize B cell subsets and B cell responses to B cell receptor and Toll-like receptor 9 stimulation in Gabonese sc...	Schistosomiasis affects over 200 million people and especially children in developing countries . It causes general hyporesponsiveness of the immune system , which until now has predominantly been described for various T cell subsets as well as dendritic cells . B cells in this context have not yet been investigated . ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "antibody-producing", "cells", "immune", "cells", "cytokines", "b", "cells", "immunity", "immunity", "to", "infections", "immunology", "biology", "immune", "response", "immune", "system" ]	2013	Alterations in Peripheral Blood B Cell Subsets and Dynamics of B Cell Responses during Human Schistosomiasis
The anterior inferotemporal cortex ( IT ) is the highest stage along the hierarchy of visual areas that , in primates , processes visual objects . Although several lines of evidence suggest that IT primarily represents visual shape information , some recent studies have argued that neuronal ensembles in IT code the sem...	To build meaningful representations of the external word , the stream of sensory information that reaches our senses is continuously processed and interpreted by the brain . Ultimately , such a processing allows the brain to arrange sensory ( e . g . , visual ) inputs into a hierarchy of categories ( such as animate an...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "visual", "system", "computational", "neuroscience", "sensory", "systems", "biology", "neuroscience", "coding", "mechanisms" ]	2013	Shape Similarity, Better than Semantic Membership, Accounts for the Structure of Visual Object Representations in a Population of Monkey Inferotemporal Neurons
Epistatic interactions between genes are a major factor in evolution . Hybrid necrosis is an example of a deleterious phenotype caused by epistatic interactions that is observed in many intra- and interspecific plant hybrids . A large number of hybrid necrosis cases share phenotypic similarities , suggesting a common u...	Hybridization brings together genetic material from different genomes . Sometimes , the novel combinations of genes are deleterious in the offspring , even though the genes were innocuous , or even beneficial , in their parents . Such “genetic incompatibilities” have been observed in crosses within and between species ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "plant", "biology", "evolutionary", "biology", "plants", "genetics", "and", "genomics" ]	2007	Autoimmune Response as a Mechanism for a Dobzhansky-Muller-Type Incompatibility Syndrome in Plants
The initiation , execution , and completion of complex locomotor behaviors are depending on precisely integrated neural circuitries consisting of motor pathways that activate muscles in the extremities and sensory afferents that deliver feedback to motoneurons . These projections form in tight temporal and spatial vici...	During embryonic development , growing axons establish intricate neural networks with their peripheral targets , a process that builds the basis for complex behaviors . While wiring up the proper circuits in peripheral limbs , for example , motor axons from the spinal cord and sensory axons from the dorsal root ganglia...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "developmental", "neuroscience", "axon", "guidance", "molecular", "development", "biology", "neuroscience" ]	2011	Npn-1 Contributes to Axon-Axon Interactions That Differentially Control Sensory and Motor Innervation of the Limb
Haploinsufficiency for Nipbl , a cohesin loading protein , causes Cornelia de Lange Syndrome ( CdLS ) , the most common “cohesinopathy” . It has been proposed that the effects of Nipbl-haploinsufficiency result from disruption of long-range communication between DNA elements . Here we use zebrafish and mouse models of ...	Limb malformations are a striking feature of Cornelia de Lange Syndrome ( CdLS ) , a multi-system birth defects disorder most commonly caused by haploinsufficiency for NIPBL . In addition to its role as a cohesin-loading factor , Nipbl also regulates gene expression , but how partial Nipbl deficiency causes limb defect...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "chromosome", "structure", "and", "function", "vertebrates", "animals", "dna", "transcription", "osteichthyes", "animal", "models", "developmental", "biology", "model", "organisms", "organism", "development", "molecular", "development", "morphogenesis", "limb", "development...	2014	Nipbl and Mediator Cooperatively Regulate Gene Expression to Control Limb Development
Synaptic degeneration is one of the earliest pathological correlates of prion disease , and it is a major determinant of the progression of clinical symptoms . However , the cellular and molecular mechanisms underlying prion synaptotoxicity are poorly understood . Previously , we described an experimental system in whi...	Prion diseases are a group of fatal neurodegenerative disorders that includes Creutzfeldt-Jakob disease and kuru in humans , and bovine spongiform encephalopathy in cattle . The infectious agent , or prion , that transmits these diseases is a naked protein molecule , the prion protein ( PrP ) , which is an altered form...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "animal", "diseases", "prions", "neuroscience", "animal", "prion", "diseases", "zoology", "neuronal", "dendrites", "mapk", "signaling", "cascades", "contractile", "proteins", "infectious", "diseases", "actins", "intracellular", "...	2018	Prions activate a p38 MAPK synaptotoxic signaling pathway
Infection with the Gram-negative bacterium Burkholderia pseudomallei is an important cause of community-acquired lethal sepsis in endemic regions in southeast Asia and northern Australia and is increasingly reported in other tropical areas . In animal models , production of interferon-gamma ( IFN-γ ) is critical for re...	The Gram-negative bacterium , Burkholderia pseudomallei , is a public health problem in southeast Asia and northern Australia and a Centers for Disease Control and Prevention listed Category B potential bioterrorism agent . It is the causative agent of melioidosis , and clinical manifestations vary from acute sepsis to...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "immunology/immunity", "to", "infections", "immunology/immune", "response" ]	2009	Phenotypic and Functional Characterization of Human Memory T Cell Responses to Burkholderia pseudomallei
In vibrios , the expression of virulence factors is often controlled by LuxR , the master quorum-sensing regulator . Here , we investigate the interplay between LuxR and σE , an alternative sigma factor , during the control of virulence-related gene expression and adaptations to temperature elevations in the zoonotic p...	Zoonotic Vibrio outbreaks are believed to be closely associated with increases in environmental temperature . The mechanisms underlying this phenomenon have not been defined . Here , we show that the expression of the V . alginolyticus exotoxin Asp and other quorum-sensing ( QS ) -regulated virulence factors are induce...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "classical", "mechanics", "pathology", "and", "laboratory", "medicine", "electrophoretic", "mobility", "shift", "assay", "gene", "regulation", "pathogens", "vibrio", "rna", "extraction", "mechanical", "stress", "dna", "molecular"...	2016	A σE-Mediated Temperature Gauge Controls a Switch from LuxR-Mediated Virulence Gene Expression to Thermal Stress Adaptation in Vibrio alginolyticus
G protein-coupled receptors ( GPCRs ) are the largest superfamily of signaling proteins . Their activation process is accompanied by conformational changes that have not yet been fully uncovered . Here , we carry out a novel comparative analysis of internal structural fluctuations across a variety of receptors from cla...	The biological functionality of several receptors and enzymes depends on their capability to sustain large-scale structural fluctuations and adopt different conformational states in response to ligand binding . This is the case for G protein-coupled receptors ( GPCRs ) , the largest superfamily of signaling proteins in...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Methods" ]	[ "cell", "physiology", "g-protein", "signaling", "receptor", "physiology", "protein", "structure", "protein", "structure", "databases", "molecular", "biology", "techniques", "g", "protein", "coupled", "receptors", "research", "and", "analysis", "methods", "amino", "acid"...	2017	Unifying view of mechanical and functional hotspots across class A GPCRs
Chikungunya virus ( CHIKV ) is the only causative agent of CHIKV fever with persistent arthralgia , and in some cases may lead to neurological complications which can be highly fatal , therefore it poses severe health issues in many parts of the world . CHIKV transmission can be mediated via the Aedes albopictus mosqui...	Chikungunya virus ( CHIKV ) , a re-emerging mosquito-borne virus , is the main cause of CHIKV fever , persistent arthralgia and serious neurological complications which can be highly fatal; therefore , it poses serious health threats worldwide . Unraveling the underappreciated aspects of mosquito cellular factors that ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Proteomics Profiling of Chikungunya-Infected Aedes albopictus C6/36 Cells Reveal Important Mosquito Cell Factors in Virus Replication
DNA double-strand breaks ( DSBs ) can be repaired by one of two major pathways—non-homologous end-joining ( NHEJ ) and homologous recombination ( HR ) —depending on whether cells are in G1 or S/G2 phase , respectively . However , the mechanisms of DSB repair during M phase remain largely unclear . In this study , we de...	DNA double-strand breaks ( DSBs ) are highly toxic to cells and often lead to genome instability and cell death . Organisms have several DSB repair mechanisms to prevent such instability . Proper choice of DSB repair pathways is highly regulated during the cell cycle . Inappropriate choice of the DSB repair pathway oft...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "dna", "damage", "biochemistry", "genetics", "biology", "and", "life", "sciences", "dna", "repair", "dna", "non-homologous", "end", "joining" ]	2014	Canonical Non-Homologous End Joining in Mitosis Induces Genome Instability and Is Suppressed by M-phase-Specific Phosphorylation of XRCC4
Borrelia burgdorferi transmission to the vertebrate host commences with growth of the spirochete in the tick gut and migration from the gut to the salivary glands . This complex process , involving intimate interactions of the spirochete with the gut epithelium , is pivotal to transmission . We utilized a yeast surface...	Lyme borreliosis , the most common vector-borne illness in Northeastern parts of USA , is caused by Borrelia burgdorferi sensu lato spirochetes , and transmitted by the Ixodes scapularis ticks . Currently there is no vaccine available to prevent Lyme borreliosis . A better understanding of tick proteins that interact w...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "borrelia", "infection", "fluorescence", "imaging", "medicine", "and", "health", "sciences", "animal", "models", "of", "disease", "vector-borne", "diseases", "microbiology", "animal", "models", "bacterial", "diseases", "fungi", "lyme", "disease", "model", "organisms", ...	2014	A Tick Gut Protein with Fibronectin III Domains Aids Borrelia burgdorferi Congregation to the Gut during Transmission
Biological systems are known to be both robust and evolvable to internal and external perturbations , but what causes these apparently contradictory properties ? We used Boolean network modeling and attractor landscape analysis to investigate the evolvability and robustness of the human signaling network . Our results ...	Biological systems are known to be robust and evolvable to internal mutations and external environmental changes . What causes these apparently contradictory properties ? This study shows that the human signaling network can be decomposed into two structurally distinct subgroups of links that provide both evolvability ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "biology", "and", "life", "sciences" ]	2014	Robustness and Evolvability of the Human Signaling Network
The infectious form of the parasitic nematode Strongyloides stercoralis is a developmentally arrested third-stage larva ( L3i ) , which is morphologically similar to the developmentally arrested dauer larva in the free-living nematode Caenorhabditis elegans . We hypothesize that the molecular pathways regulating C . el...	Human parasitic nematodes , including Strongyloides stercoralis , cause extensive morbidity in the developing world . The infectious form of S . stercoralis is a developmentally arrested third-stage larva ( L3i ) , which resumes development into a parasitic adult upon entering a host . The molecular mechanisms controll...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "insulin-dependent", "signal", "transduction", "invertebrates", "caenorhabditis", "microbiology", "animals", "parasitology", "dna", "transcription", "parasite", "physiology", "animal", "models", "caenorhabditis", "elegans", "model", "organisms", "research", "and", "analysis",...	2014	cGMP and NHR Signaling Co-regulate Expression of Insulin-Like Peptides and Developmental Activation of Infective Larvae in Strongyloides stercoralis
Cellular senescence , a state of irreversible cell cycle arrest , is thought to help protect an organism from cancer , yet also contributes to ageing . The changes which occur in senescence are controlled by networks of multiple signalling and feedback pathways at the cellular level , and the interplay between these is...	Ageing is characterised by a gradual loss of homeostasis within organs , which is known to be driven by the accumulation of senescent cells . Cellular senescence helps prevent cells from becoming cancerous , but their detrimental effect on organ function becomes debilitating once they accumulate . These cells are parti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "physiology", "cellular", "stress", "responses", "oxidative", "stress", "cell", "processes", "metabolic", "networks", "cell", "metabolism", "network", "analysis", "mitochondria", "bioenergetics", "cellular", "structures", "and", "organelles", "cell", "aging", "c...	2014	Dynamic Modelling of Pathways to Cellular Senescence Reveals Strategies for Targeted Interventions
Previous studies have shown that multivesicular bodies ( MVBs ) /endosomes-mediated vesicular trafficking may play key roles in plant immunity and cell death . However , the molecular regulation is poorly understood in rice . Here we report the identification and characterization of a MVBs-localized AAA ATPase LRD6-6 i...	Plants have evolved sophistical immunity system in fighting against pathogenic micro-organisms including bacteria , fungi and oomycetes . Upon perception of pathogens , the immune system activates rapid cell death , characterized as a form of hypersensitive response typically in and around the infection sites to restri...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "cell", "death", "plant", "anatomy", "medicine", "and", "health", "sciences", "enzymes", "cell", "processes", "immunology", "enzymology", "cell-mediated", "immunity", "plant", "physiology", "phosphatases", "cereal", "crops", "plant", "science", "rice", ...	2016	The Multivesicular Bodies (MVBs)-Localized AAA ATPase LRD6-6 Inhibits Immunity and Cell Death Likely through Regulating MVBs-Mediated Vesicular Trafficking in Rice
Prions are self-perpetuating aggregated proteins that are not limited to mammalian systems but also exist in lower eukaryotes including yeast . While much work has focused around chaperones involved in prion maintenance , including Hsp104 , little is known about factors involved in the appearance of prions . De novo ap...	Certain proteins that exist in functional unaggregated conformers can also form self-perpetuating infectious aggregates called prions . Here we investigate factors involved in the initial switch to the prion form . De novo appearance of the [PSI+] prion , which is the aggregated form of the Sup35 protein , is dramatica...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "biology/cellular", "death", "and", "stress", "responses", "genetics", "and", "genomics/functional", "genomics", "cell", "biology", "genetics", "and", "genomics/disease", "models", "genetics", "and", "genomics", "cell", "biology/cytoskeleton" ]	2011	Prion Formation and Polyglutamine Aggregation Are Controlled by Two Classes of Genes
Natural killer ( NK ) cells are innate lymphocytes that provide early host defense against intracellular pathogens , such as viruses . Although NK cell development , homeostasis , and proliferation are regulated by IL-15 , the influence of IL-15 receptor ( IL-15R ) -mediated signaling at the cellular level has not been...	Natural killer ( NK ) cells are innate immune cells that are important in our bodies' initial defenses against pathogens , like viruses . NK cells rapidly proliferate early during viral infections to provide an expanded pool of effector cells to suppress the infection . This proliferative response is driven by a cytoki...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Mechanistic Model of Natural Killer Cell Proliferative Response to IL-15 Receptor Stimulation
By means of meta-analysis of information from all relevant epidemiologic studies , we examined the hypothesis that Schistosoma infection in school-aged children ( SAC ) is associated with educational loss and cognitive deficits . This review was prospectively registered in the PROSPERO database ( CRD42016040052 ) . Med...	Empirical evidence for cognitive or educational benefits of anti-Schistosoma treatment is currently uncertain , despite the recommended practice of wide-scale deworming with praziquantel . We addressed this knowledge gap by synthesizing information from 30 relevant epidemiologic studies reporting on 38 , 992 children b...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "children", "cognitive", "neurology", "medicine", "and", "health", "sciences", "learning", "education", "helminths", "sociology", "social", "sciences", "neuroscience", "animals", "learning", "and", "memory", "pediatrics", "age", "groups", ...	2018	Cognitive deficits and educational loss in children with schistosome infection—A systematic review and meta-analysis
Prdm16 determines the bidirectional fate switch of skeletal muscle/brown adipose tissue ( BAT ) and regulates the thermogenic gene program of subcutaneous white adipose tissue ( SAT ) in mice . Here we show that miR-133a , a microRNA that is expressed in both BAT and SATs , directly targets the 3′ UTR of Prdm16 . The e...	Global obesity and associated health issues have raised the significance of adipocyte biology . Adipose tissues are classified as brown and white adipose . White adipose tissues store lipids , leading to overweight , obesity , insulin resistance and Type2 diabetes . In contrast , brown adipose tissues use lipid storage...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "signal", "transduction", "rna", "interference", "stem", "cells", "gene", "expression", "signaling", "pathways", "biology", "molecular", "cell", "biology", "cell", "fate", "determination", "adult", "stem", "cells" ]	2013	miR-133a Regulates Adipocyte Browning In Vivo
Bdellovibrio are predatory bacteria that have evolved to invade virtually all Gram-negative bacteria , including many prominent pathogens . Upon invasion , prey bacteria become rounded up into an osmotically stable niche for the Bdellovibrio , preventing further superinfection and allowing Bdellovibrio to replicate ins...	Bdellovibrio bacteriovorus is a small predatory bacterium that invades other bacteria including pathogens of humans and animals . Bdellovibrio digest the pathogens from within , growing at their expense . Bdellovibrio do not attack human , plant or animal cells and so could be applied as “living antibiotics” . Here we ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "proteins", "biology", "microbiology" ]	2012	Specialized Peptidoglycan Hydrolases Sculpt the Intra-bacterial Niche of Predatory Bdellovibrio and Increase Population Fitness
In many plant species , conflicts between divergent elements of the immune system , especially nucleotide-binding oligomerization domain-like receptors ( NLR ) , can lead to hybrid necrosis . Here , we report deleterious allele-specific interactions between an NLR and a non-NLR gene cluster , resulting in not one , but...	In many plant species , conflicts between divergent elements of the immune system can cause hybrids to express autoimmunity , a generally deleterious syndrome known as hybrid necrosis . We are investigating multiple hybrid necrosis cases in Arabidopsis thaliana that are caused by allele-specific interactions between di...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "genome-wide", "association", "studies", "plant", "anatomy", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "brassica", "alleles", "genetic", "mapping", "plant", "science", "model", "organisms", "signs", "and", "symptoms", "expe...	2019	RPW8/HR repeats control NLR activation in Arabidopsis thaliana
To explore the efficacy of ivermectin in the treatment of serologically diagnosed cases of Strongyloides stercoralis ( S . stercoralis ) infection in an Aboriginal community and to describe factors that may influence the outcome of treatment . Longitudinal study of a group of 92 individuals with serologically diagnosed...	In this study we examine the treatment of the intestinal worm infection Strongyloides stercoralis , a soil transmitted helminth that is common in the developing world and in the Aboriginal communities of northern Australia . Oral ivermectin is generally accepted as the treatment of choice for this condition . We screen...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Type 2 Diabetes Mellitus Is Associated with Strongyloides stercoralis Treatment Failure in Australian Aboriginals
The development of arsenical and diamidine resistance in Trypanosoma brucei is associated with loss of drug uptake by the P2 purine transporter as a result of alterations in the corresponding T . brucei adenosine transporter 1 gene ( TbAT1 ) . Previously , specific TbAT1 mutant type alleles linked to melarsoprol treatm...	Human African trypanosomiasis ( HAT ) manifests as a chronic infection caused by Trypanosoma brucei gambiense , or as a more acute form due to T . b . rhodesiense . Both manifestations occur in Uganda and melarsoprol use against the former was jeopardised in the 1990s as reports of reduced efficacy increased to the poi...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases", "infectious", "diseases/neglected", "tropical", "diseases", "infectious", "diseases/antimicrobials", "and", "drug", "resistance", "infectious", "diseases/protozoal", "infections" ]	2009	Genotypic Status of the TbAT1/P2 Adenosine Transporter of Trypanosoma brucei gambiense Isolates from Northwestern Uganda following Melarsoprol Withdrawal
Chikungunya virus ( CHIKV ) and clinically-related arboviruses cause large epidemics with serious economic and social impact . As clinical symptoms of CHIKV infections are similar to several flavivirus infections , good detection methods to identify CHIKV infection are desired for improved treatment and clinical manage...	Chikungunya virus ( CHIKV ) causes Chikungunya fever in humans . The symptoms , particularly joint pain , can be severe and long lasting , and outbreaks can have serious socioeconomic impact . CHIKV is a mosquito-borne alphavirus that co-exists geographically with other mosquito-borne flaviviruses such as dengue virus ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "medicine", "and", "health", "sciences", "emerging", "infectious", "diseases", "virology", "biology", "and", "life", "sciences", "microbiology" ]	2015	Sero-Prevalence and Cross-Reactivity of Chikungunya Virus Specific Anti-E2EP3 Antibodies in Arbovirus-Infected Patients
Schistosomiasis is one of the most widely distributed parasitic diseases in the world . Schistosoma japonicum , a zoonotic parasite with a wide range of mammalian hosts , is one of the major pathogens of this disease . Although numerous studies on schistosomiasis japonica have been performed using laboratory animal mod...	The zoonotic parasite Schistosoma japonicum is one of the major pathogens of schistosomiasis and can parasitize a wide range of mammals . Although numerous schistosome transcriptional profiling studies have been performed using laboratory animal models , the differences in the global gene expression profiles of worms f...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[]	2015	Comparative Analysis of Transcriptional Profiles of Adult Schistosoma japonicum from Different Laboratory Animals and the Natural Host, Water Buffalo
Rac1 is a founding member of the Rho-GTPase family and a key regulator of membrane remodeling . In the context of apoptotic cell corpse engulfment , CED-10/Rac1 acts with its bipartite guanine nucleotide exchange factor , CED-5/Dock180-CED-12/ELMO , in an evolutionarily conserved pathway to promote phagocytosis . Here ...	When cargo is internalized from the cell surface by endocytosis , it enters a series of intracellular organelles called endosomes . Endosomes sort cargo , such that some cargos are sent to the lysosome for degradation , while others are recycled to the plasma membrane . Small GTPase proteins ( Rabs ) are well-known mas...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "model", "organisms", "genetics", "biology", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2012	CED-10/Rac1 Regulates Endocytic Recycling through the RAB-5 GAP TBC-2
We compared the performance of two new commercial tests for the detection of dengue NS1 protein during the clinical phase of dengue virus ( DENV ) infection—an immunochromatographic test allowing rapid detection of the NS1 antigen , Dengue NS1 Ag STRIP ( Bio-Rad Laboratories - Marnes La Coquette , France ) , and a two-...	Dengue is a viral disease transmitted by mosquitoes that is endemic in more than 100 countries in tropical areas , threatening over 2 . 5 billion people . It causes a wide range of symptoms and has severe forms . In reference laboratories , dengue disease is confirmed by virus isolation or genome detection during the a...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "virology/diagnosis", "public", "health", "and", "epidemiology/infectious", "diseases", "virology/emerging", "viral", "diseases" ]	2008	Evaluation of Two New Commercial Tests for the Diagnosis of Acute Dengue Virus Infection Using NS1 Antigen Detection in Human Serum
Parasites of the Leishmania genus can rapidly alter several macrophage ( MØ ) signalling pathways in order to tame down the innate immune response and inflammation , therefore favouring their survival and propagation within their mammalian host . Having recently reported that Leishmania and bacterial LPS generate a sig...	Leishmania developed several methods to seize control of macrophage signalling pathways in an effort to inactivate their killing abilities . One effective method utilized by the parasite is the activation of host protein tyrosine phosphatases , specifically SHP-1 . This increased phosphatase activity contributes to the...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "cell", "biology/leukocyte", "signaling", "and", "gene", "expression", "cell", "biology/cell", "signaling", "infectious", "diseases/neglected", "tropical", "diseases", "immunology/innate", "immunity", "infectious", "diseases/protozoal", "infections", "microbiology/parasitology", ...	2008	Leishmania-Induced IRAK-1 Inactivation Is Mediated by SHP-1 Interacting with an Evolutionarily Conserved KTIM Motif
Members of the major candidate phylum Dependentiae ( a . k . a . TM6 ) are widespread across diverse environments from showerheads to peat bogs; yet , with the exception of two isolates infecting amoebae , they are only known from metagenomic data . The limited knowledge of their biology indicates that they have a long...	Little is known about the biology of bacteria in the candidate phylum Dependentiae , despite being widespread in nature . Here , we describe a novel isolate of this phylum , Chromulinavorax destructans , which infects an abundant aquatic predatory protist , Spumella elongata . Chromulinavorax destructans is an obligate...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "flow", "cytometry", "taxonomy", "viral", "transmission", "and", "infection", "microbiology", "phylogenetics", "data", "management", "protozoans", "phylogenetic", "analysis", "genome", "analysis", "research", "and", "analysis", "methods", "computer", "and", "information",...	2019	Chromulinavorax destructans, a pathogen of microzooplankton that provides a window into the enigmatic candidate phylum Dependentiae
Giardia passes through two stages during its life cycle , the trophozoite and the cyst . Cyst formation involves the synthesis of cyst wall proteins ( CWPs ) and the transport of CWPs into encystation-specific vesicles ( ESVs ) . Active vesicular trafficking is essential for encystation , but the molecular machinery dr...	The encystation process is crucial for survival and transmission of Giardia lamblia to new hosts . During this process , vesicular trafficking and the cytoskeleton play important roles . In eukaryotic cells , intracellular transport is regulated by proteins , including Rab-GTPases and SNAREs , which regulate vesicle fo...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "cell", "biology/chemical", "biology", "of", "the", "cell", "immunology/antigen", "processing", "and", "recognition", "chemistry/biochemistry", "microbiology/immunity", "to", "infections", "cell", "biology/morphogenesis", "and", "cell", "biology", "cell", "biology/cell", "g...	2010	Rab11 and Actin Cytoskeleton Participate in Giardia lamblia Encystation, Guiding the Specific Vesicles to the Cyst Wall
In many brain regions , inhibition is mediated by numerous classes of specialized interneurons , but within the rodent dorsal lateral geniculate nucleus ( dLGN ) , a single class of interneuron is present . dLGN interneurons inhibit thalamocortical ( TC ) neurons and regulate the activity of TC neurons evoked by retina...	Within the visual thalamus , a single type of inhibitory interneuron regulates activity evoked by retinal ganglion cells and controls the visual signals that reach the cortex . Here , we find that neuromodulation , of the sort thought to occur when an animal is attending to a task , regulates the firing mode of these i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience", "neuroscience/sensory", "systems" ]	2010	Cholinergic Activation of M2 Receptors Leads to Context-Dependent Modulation of Feedforward Inhibition in the Visual Thalamus
The Atlixco municipality , Puebla State , at a mean altitude of 1840 m , was selected for a study of Fasciola hepatica infection in schoolchildren in Mexico . This area presents permanent water collections continuously receiving thaw water from Popocatepetl volcano ( 5426 m altitude ) through the community supply chann...	A human fascioliasis endemic area is described for the first time in North America . In Atlixco , Puebla State , Mexico , prevalences of 2 . 94–13 . 33% by F . hepatica were found in 865 6–14-year-old schoolchildren by FasciDIG coproantigen test and Lumbreras rapid sedimentation technique , and quantitatively assessed ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2013	Fascioliasis and Intestinal Parasitoses Affecting Schoolchildren in Atlixco, Puebla State, Mexico: Epidemiology and Treatment with Nitazoxanide
Burkholderia pseudomallei is a soil-dwelling bacterium and the causative agent of melioidosis . Isolation of B . pseudomallei from clinical samples is the “gold standard” for the diagnosis of melioidosis; results can take 3–7 days to produce . Alternatively , antibody-based tests have low specificity due to a high perc...	Burkholderia pseudomallei is an environmental bacterium and the cause of melioidosis . Culture of patient samples is the “gold standard” diagnostic test , but may take up to 7 days to complete . Melioidosis has a 10–40% case fatality rate depending on the geographic location . Delays in diagnosis could lead to administ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "gram", "negative", "diagnostic", "medicine", "emerging", "infectious", "diseases", "medical", "microbiology", "global", "health", "biology", "microbiology", "public", "health", "bacterial", "pathogens" ]	2014	Development of a Prototype Lateral Flow Immunoassay (LFI) for the Rapid Diagnosis of Melioidosis
In endemic communities , zoonotic tungiasis , a severe skin disease caused by penetrating female sand fleas , is a public health hazard causing significant human and animal morbidity . No validated drugs are currently available for treatment of animal tungiasis . Due to the reservoir in domestic animals , integrated ma...	Infection with the sand flea Tunga penetrans causes severe disease in humans and animals . There are no validated drugs for treatment of animal tungiasis preventing implementation of integrated tungiasis control interventions targeting human and animal infections . A field trial was conducted to evaluate the effects of...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion", "Conclusions" ]	[ "invertebrates", "livestock", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "vertebrates", "animals", "mammals", "dogs", "health", "care", "signs", "and", "symptoms", "pharmaceutics", "materials", "science", "fleas", "materials",...	2016	Successful Treatment of Severe Tungiasis in Pigs Using a Topical Aerosol Containing Chlorfenvinphos, Dichlorphos and Gentian Violet
WRN-1 is the Caenorhabditis elegans homolog of the human Werner syndrome protein , a RecQ helicase , mutations of which are associated with premature aging and increased genome instability . Relatively little is known as to how WRN-1 functions in DNA repair and DNA damage signaling . Here , we take advantage of the gen...	Werner syndrome is a premature aging syndrome associated with genomic instability . The protein linked to Werner syndrome , WRN , has both helicase and exonuclease activities and is thought to be involved in DNA repair , including the resolution of replication fork arrest as well as in telomere maintenance . However , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/germ", "cells", "cell", "biology/cellular", "death", "and", "stress", "responses", "cell", "biology/cell", "signaling", "developmental", "biology/aging", "biochemistry/replication", "and", "repair" ]	2010	The Caenorhabditis elegans Werner Syndrome Protein Functions Upstream of ATR and ATM in Response to DNA Replication Inhibition and Double-Strand DNA Breaks
Infection-related acute kidney injury ( AKI ) is an important preventable cause of morbidity and mortality in the tropical region . The prevalence and outcome of kidney involvement , especially AKI , in scrub typhus is not known . We investigated all patients with undiagnosed fever and multisystem involvement for scrub...	A large number of patients present to Indian hospitals with acute febrile illness and multisystem involvement . Acute kidney injury is an important component . Clinical manifestations do not allow distinction between infectious etiologies with overlapping presentations . Many of the cases remain undiagnosed and therefo...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "bacterial", "diseases", "infectious", "diseases", "clinical", "epidemiology", "epidemiology", "nephrology", "acute", "renal", "failure", "rickettsia" ]	2014	Scrub Typhus Is an Under-recognized Cause of Acute Febrile Illness with Acute Kidney Injury in India
To evade the host immune system , several pathogens periodically change their cell-surface epitopes . In the African trypanosomes , antigenic variation is achieved by tightly regulating the expression of a multigene family encoding a large repertoire of variant surface glycoproteins ( VSGs ) . Immune evasion relies on ...	The surface of Trypanosoma brucei , a unicellular parasite that lives in the bloodstream of its mammalian host , is coated with glycoprotein ( VSG ) molecules . To evade elimination by the immune system , this parasite replaces its coat with one tailored from another glycoprotein variant . Even though there are hundred...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "cell", "biology", "microbiology", "molecular", "biology", "genetics", "and", "genomics" ]	2008	A Histone Methyltransferase Modulates Antigenic Variation in African Trypanosomes
Mucociliary clearance is one of the major lines of defense of the respiratory system . The mucus layer coating the pulmonary airways is moved along and out of the lung by the activity of motile cilia , thus expelling the particles trapped in it . Here we compare ex vivo measurements of a Newtonian flow induced by cilia...	Mucociliary clearance is the first line of defense of the human pulmonary airways . Mucus transporting debris , particles , microorganisms and pollutants is carried away by the coordinated motion of cilia beating at the surface of the airway epithelium . We present here an experimental , mathematical and numerical stud...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "velocity", "medicine", "and", "health", "sciences", "body", "fluids", "classical", "mechanics", "fluid", "mechanics", "mechanical", "stress", "viscosity", "materials", "science", "materials", "physics", "cellular", "structures", "and", "organelles", "chemical", "proper...	2017	A new index for characterizing micro-bead motion in a flow induced by ciliary beating: Part I, experimental analysis
In mammals , several genetic pathways have been characterized that govern engagement of multipotent embryonic progenitors into the myogenic program through the control of the key myogenic regulatory gene Myod . Here we demonstrate the involvement of Six homeoproteins . We first targeted into a Pax3 allele a sequence en...	The onset of skeletal muscle formation is controlled by complex gene regulatory networks . By manipulation of these genetic pathways in the mouse embryo , we have examined the interplay between genes encoding the transcriptional regulator Pax3; the major myogenic determination proteins Myf5 , Mrf4 , and Myod; as well a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "cell", "biology", "genetics", "developmental", "biology", "biology" ]	2013	Six Homeoproteins Directly Activate Myod Expression in the Gene Regulatory Networks That Control Early Myogenesis
Bacillus anthracis infects hosts as a spore , germinates , and disseminates in its vegetative form . Production of anthrax lethal and edema toxins following bacterial outgrowth results in host death . Macrophages of inbred mouse strains are either sensitive or resistant to lethal toxin depending on whether they express...	In this study , we show that anthrax lethal toxin activation of Nlrp1b in toxin-sensitive mouse macrophages imparts resistance to infection . Inbred and congenic mice harboring macrophage-sensitizing Nlrp1b alleles control bacterial growth and dissemination independent of infection route or effects on germination effic...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/cellular", "microbiology", "and", "pathogenesis", "microbiology/innate", "immunity", "immunology/innate", "immunity", "infectious", "diseases/bacterial", "infections", "microbiology/cellular", "microbiology", "and", "pathogenesis" ]	2010	Inflammasome Sensor Nlrp1b-Dependent Resistance to Anthrax Is Mediated by Caspase-1, IL-1 Signaling and Neutrophil Recruitment
Cryptococcus neoformans encounters a low oxygen environment when it enters the human host . Here , we show that the conserved Ras1 ( a small GTPase ) and Cdc24 ( the guanine nucleotide exchange factor for Cdc42 ) play an essential role in cryptococcal growth in hypoxia . Suppressor studies indicate that PTP3 functions ...	When Cryptococcus neoformans , an environmental fungal pathogen , enters the human host , it encounters a low oxygen condition . The well conserved Ras1 and Cdc24 proteins are known for their key roles in maintenance of the actin cytoskeletal integrity in eukaryotic cells . In this work , we show a unique role of RAS1 ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cryptococcosis", "cellular", "stress", "responses", "medicine", "and", "health", "sciences", "cell", "processes", "microbiology", "fungal", "physiology", "gene", "function", "developmental", "biology", "fungi", "cell", "growth", "fungal", "diseases", "microbial", "grow...	2014	Molecular Mechanisms of Hypoxic Responses via Unique Roles of Ras1, Cdc24 and Ptp3 in a Human Fungal Pathogen Cryptococcus neoformans
Visceral leishmaniasis ( VL ) , caused by infection with Leishmania donovani complex , remains a major public health problem in endemic regions of South Asia , East Africa , and Brazil . If untreated , symptomatic VL is usually fatal . Rapid field diagnosis relies principally on demonstration of anti-Leishmania antibod...	Visceral leishmaniasis ( VL ) is caused by infection with parasites of the Leishmania donovani complex , spread by the bite of blood-sucking sandflies , especially in South Asia , East Africa , and Brazil . If untreated , symptomatic VL leads to systemic pathologies and is usually fatal . Up to approximately 400 , 000 ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "diagnostic", "medicine", "leishmaniasis", "biology", "microbiology", "parasitic", "diseases", "parasitology" ]	2013	Comparison of Visceral Leishmaniasis Diagnostic Antigens in African and Asian Leishmania donovani Reveals Extensive Diversity and Region-specific Polymorphisms
Nidoviruses with large genomes ( 26 . 3–31 . 7 kb; ‘large nidoviruses’ ) , including Coronaviridae and Roniviridae , are the most complex positive-sense single-stranded RNA ( ssRNA+ ) viruses . Based on genome size , they are far separated from all other ssRNA+ viruses ( below 19 . 6 kb ) , including the distantly rela...	Research in virology is driven towards the characterization of a limited number of socioeconomically important pathogens , mostly those infecting humans . Yet , characterization of other viruses may advance our understanding of these topical pathogens and the fundamentals of virology . Here we describe the discovery of...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viral", "classification", "emerging", "viral", "diseases", "viral", "enzymes", "microbiology", "viral", "genera", "unassigned", "to", "a", "family", "rna", "viruses", "comparative", "genomics", "biology", "viral", "replication", "complex", "viral", "replication", "vi...	2011	Discovery of the First Insect Nidovirus, a Missing Evolutionary Link in the Emergence of the Largest RNA Virus Genomes
Bacterial cells use chromosome-associated division inhibitors to help coordinate the processes of DNA replication and segregation with cytokinesis . SlmA from Escherichia coli , a member of the tetracycline repressor ( TetR ) –like protein family , is one example of this class of regulator . It blocks the assembly of t...	The tetracycline repressor ( TetR ) –like protein family is broadly distributed among bacteria . These factors typically regulate the expression of genes coding for drug resistance pumps . When they bind drug molecules , the repressors undergo a conformational change that releases them from their specific DNA-binding s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "chromosome", "structure", "and", "function", "microbiology", "escherichia", "coli", "prokaryotic", "models", "model", "organisms", "cell", "division", "cytokinesis", "molecular", "genetics", "microbial", "growth", "and", "development", "chromosome", "biology", "biology",...	2013	Identification of the SlmA Active Site Responsible for Blocking Bacterial Cytokinetic Ring Assembly over the Chromosome
Mass drug administration ( MDA ) programmes against Onchocerca volvulus use ivermectin ( IVM ) which targets microfilariae ( MF ) , the worm's offspring . Most infected individuals are hyporesponsive and present regulated immune responses despite high parasite burden . Recently , with MDA programmes , the existence of ...	Onchocerciasis affects over 37 million people in poor communities . Infected individuals usually present a generalized form which is characterized by low inflammation , tightly-controlled immune responses and high parasite burden . In contrast , patients with chronic dermatitis ( sowda ) have reduced parasite loads and...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "cytokines", "clinical", "immunology", "immunity", "immunity", "to", "infections", "immunology", "biology", "parasitic", "diseases", "onchocerciasis", "immunomodulation", "immune", "response", "immune", "system" ]	2014	Immunoepidemiological Profiling of Onchocerciasis Patients Reveals Associations with Microfilaria Loads and Ivermectin Intake on Both Individual and Community Levels
Maf1 was initially identified as a transcriptional repressor of RNA pol III-transcribed genes , yet little is known about its other potential target genes or its biological function . Here , we show that Maf1 is a key downstream target of PTEN that drives both its tumor suppressor and metabolic functions . Maf1 express...	Obesity is a strong risk factor for human cancers , yet the biological basis for this is unclear . In addition to aberrant growth , abnormal lipid synthesis is a hallmark of cancer cells . Our results have identified a novel role for Maf1 in suppressing both lipid biogenesis and tumor formation . Maf1 elicits these bio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "signal", "transduction", "cell", "biology", "biology", "and", "life", "sciences", "cell", "processes", "molecular", "cell", "biology", "molecular", "biology" ]	2014	Maf1 Is a Novel Target of PTEN and PI3K Signaling That Negatively Regulates Oncogenesis and Lipid Metabolism
The evolutionary benefit of viral genome segmentation is a classical , yet unsolved question in evolutionary biology and RNA genetics . Theoretical studies anticipated that replication of shorter RNA segments could provide a replicative advantage over standard size genomes . However , this question has remained elusive...	Genome segmentation , the splitting of a linear genome into two or more segments , is a major evolutionary transition from independent towards complementing transmission of genetic information . Many viruses with RNA as genetic material have segmented genomes , but the molecular forces behind genome segmentation are un...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/evolutionary", "modeling", "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "virology/virus", "evolution", "and", "symbiosis" ]	2011	Viral Genome Segmentation Can Result from a Trade-Off between Genetic Content and Particle Stability
Recent studies have noted extensive inconsistencies in gene start sites among orthologous genes in related microbial genomes . Here we provide the first documented evidence that imposing gene start consistency improves the accuracy of gene start-site prediction . We applied an algorithm using a genome majority vote ( G...	The genetic code tells us precisely how a DNA sequence will be translated into a protein . However , it is more difficult to identify where translation will start and stop in the entire length of an organism's genome sequence . Computer software can predict where the start sites are , and this is successful most of the...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "genome", "analysis", "tools", "genomics", "gene", "prediction", "biology", "computational", "biology", "comparative", "genomics" ]	2011	Genome Majority Vote Improves Gene Predictions
Influenza A viruses may cross species barriers and transmit to humans with the potential to cause pandemics . Interplay of human- ( PB2 627K ) and avian-like ( PB2 627E ) influenza polymerase complexes with unknown host factors have been postulated to play a key role in interspecies transmission . Here , we have identi...	Adaptive mutations in the polymerase complex , such as PB2 E627K and PB2 D701N play a crucial role in influenza virus interspecies transmission . We have shown earlier that PB2 D701N promotes nuclear entry of PB2 by enhanced importin-α binding in mammalian cells ( Gabriel et al . , PLoS Pathogens 2008; Gabriel et al . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "biology", "microbiology" ]	2012	Human-like PB2 627K Influenza Virus Polymerase Activity Is Regulated by Importin-α1 and -α7
Mitochondrial DNA ( mtDNA ) variation can affect phenotypic variation; therefore , knowing its distribution within and among individuals is of importance to understanding many human diseases . Intra-individual mtDNA variation ( heteroplasmy ) has been generally assumed to be random . We used massively parallel sequenci...	DNA mutations are expected to be formed randomly , thus any reproducible pattern of DNA somatic mutations across multiple individuals or even across organs within each individual is highly unexpected . Using next generation sequencing of multiple tissues from the same individuals we found several somatic mutations in m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Recurrent Tissue-Specific mtDNA Mutations Are Common in Humans
Bartonellae are facultative intracellular bacteria and are highly adapted to their mammalian host cell niches . Straw-colored fruit bats ( Eidolon helvum ) are commonly infected with several bartonella strains . To elucidate the genetic diversity of these bartonella strains , we analyzed 79 bartonella isolates from str...	Bats , with over 1000 recognized species , represent about 20% of all classified mammalian species worldwide . These mammals have a wide range of ecologies and life-history traits , and are now widely recognized as important reservoirs of many pathogens . Bartonella species have been found distributed in a wide range o...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Classification of Bartonella Strains Associated with Straw-Colored Fruit Bats (Eidolon helvum) across Africa Using a Multi-locus Sequence Typing Platform
Regulatory T cells expressing the transcription factor Foxp3 play indispensable roles for the induction and maintenance of immunological self-tolerance and immune homeostasis . Genome-wide mRNA expression studies have defined canonical signatures of T cell subsets . Changes in steady-state mRNA levels , however , often...	Regulatory T cells expressing the nuclear protein Foxp3 are essential for the control of immune responses towards self and foreign antigens . Genome-wide gene expression studies have defined canonical signatures of T cell subsets . However , changes in mRNA levels often do not reflect those of corresponding proteins du...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "immunology", "biology" ]	2013	Distinct Translational Control in CD4+ T Cell Subsets
The adult Taenia solium , the pork tapeworm , usually lives as a single worm in the small intestine of humans , its only known definitive host . Mechanisms of genetic variation in T . solium are poorly understood . Using three microsatellite markers previously reported [1] , this study explored the genetic variability ...	Taenia solium , the pork tapeworm , is a major cause of epilepsy in developing countries . Although it has been deemed a potentially eradicable pathogen , it remains prevalent in rural communities . This two-part study aims to evaluate the utility of three microsatellite markers previously reported , to identify parasi...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "population", "genetics", "vertebrates", "parasitic", "diseases", "animals", "mammals", "microsatellite", "loci", "tongue", "gene", "types", "molecular", "biology", "techniques", "population", "biology", "genotyping", "genetic", ...	2017	Genetic variability of Taenia solium cysticerci recovered from experimentally infected pigs and from naturally infected pigs using microsatellite markers
A recent experimental study investigating patients with lone atrial fibrillation identified six novel mutations in the KCNA5 gene . The mutants exhibited both gain- and loss-of-function of the atrial specific ultra-rapid delayed rectifier K+ current , IKur . The aim of this study is to elucidate and quantify the functi...	In a recent study , six mutations resulting in either gain-of-function or loss-of-function in the ultra-rapid delayed rectifier potassium current IKur , were identified to be associated with atrial fibrillation ( AF ) . However , the causative link between the mutant IKur ( either gain- or loss-of-function ) and AF gen...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "action", "potentials", "membrane", "potential", "electrophysiology", "neuroscience", "pharmacology", "waves", "cardiology", "tissue", "distribution", "arrhythmia", "atrial", "fibrillation", "behavior", "chemistry", "pharmacokinetics",...	2017	In silico assessment of genetic variation in KCNA5 reveals multiple mechanisms of human atrial arrhythmogenesis
The topology of the gene-regulatory network has been extensively analyzed . Now , given the large amount of available functional genomic data , it is possible to go beyond this and systematically study regulatory circuits in terms of logic elements . To this end , we present Loregic , a computational method integrating...	Gene expression is controlled by various gene regulatory factors . Those factors work cooperatively forming a complex regulatory circuit genome wide . Corruptions of regulatory cooperativity may lead to abnormal gene expression activity such as cancer . Traditional experimental methods , however , can only identify sma...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Loregic: A Method to Characterize the Cooperative Logic of Regulatory Factors
Infection with Mycobacterium ulcerans is characterised by tissue necrosis and immunosuppression due to mycolactone , the necessary and sufficient virulence factor for Buruli ulcer disease pathology . Many of its effects are known to involve down-regulation of specific proteins implicated in important cellular processes...	Buruli ulcer is a progressive necrotic skin lesion caused by infection with the human pathogen Mycobacterium ulcerans . Mycolactone , a small compound produced by the mycobacterium , is the root cause of the disease pathology , but until now there has been no unifying mechanism explaining why . We have been using a mod...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "blood", "cells", "cell", "physiology", "bacteriology", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "small", "molecules", "endothelial", "cells", "immunology", ...	2014	The Pathogenic Mechanism of the Mycobacterium ulcerans Virulence Factor, Mycolactone, Depends on Blockade of Protein Translocation into the ER
Characterizing how genomic sequence interacts with trans-acting regulatory factors to implement a program of gene expression in eukaryotic organisms is critical to understanding genome function . One means by which patterns of gene expression are achieved is through the differential packaging of DNA into distinct types...	Epigenetic packaging of DNA sequence into chromatin is a major force in shaping the function of complex genomes . Different types of chromatin have distinct effects on gene expression , and thus chromatin state imparts distinct features on the associated genomic DNA . Our study focuses on the transition between two opp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/epigenetics", "molecular", "biology/chromatin", "structure" ]	2009	The Impact of Local Genome Sequence on Defining Heterochromatin Domains
Duplex-comb ( D ) is one of three major loci affecting comb morphology in the domestic chicken . Here we show that the two Duplex-comb alleles , V-shaped ( DV ) and Buttercup ( DC ) , are both associated with a 20 Kb tandem duplication containing several conserved putative regulatory elements located 200 Kb upstream ...	There are three major variant comb types found in the domestic chicken; Rose-comb , Pea-comb and Duplex-comb . Within the Duplex-comb there are two distinct types , V-shaped and Buttercup . Previous experiments have shown that these two Duplex-comb types represent different alleles at a single locus . We have mapped th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	A Genomic Duplication is Associated with Ectopic Eomesodermin Expression in the Embryonic Chicken Comb and Two Duplex-comb Phenotypes
Topoisomerase 3α , a class I topoisomerase , consists of a TOPRIM domain , an active centre and a variable number of zinc-finger domains ( ZFDs ) at the C-terminus , in multicellular organisms . Whereas the functions of the TOPRIM domain and the active centre are known , the specific role of the ZFDs is still obscure ....	DNA Topoisomerases are essential for transcription , DNA repair and DNA replication due to their function to break and change the topological state of DNA molecules . Topoisomerase 3α is especially important for DNA repair as it is able to process different DNA recombination and repair intermediates . The protein can b...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "chemical", "compounds", "plant", "growth", "and", "development", "brassica", "organic", "compounds", "developmental", "biology", "plant", "science", "model", "organisms", "tyrosine", "experimental", "organism", "systems", "amino", "acids", "dna", "embryos", "plants", ...	2018	The topoisomerase 3α zinc-finger domain T1 of Arabidopsis thaliana is required for targeting the enzyme activity to Holliday junction-like DNA repair intermediates
Mitochondrial DNA ( mtDNA ) is highly polymorphic at the population level , and specific mtDNA variants affect mitochondrial function . With emerging evidence that mitochondrial mechanisms are central to common human diseases , it is plausible that mtDNA variants contribute to the “missing heritability” of several comp...	There is a growing body of evidence indicating that mitochondrial dysfunction , a result of genetic variation in the mitochondrial genome , is a critical component in the aetiology of a number of complex traits . Here , we take advantage of recent technical and methodological advances to examine the role of common mito...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences" ]	2014	Recent Mitochondrial DNA Mutations Increase the Risk of Developing Common Late-Onset Human Diseases
Ten outbreaks of poliomyelitis caused by pathogenic circulating vaccine-derived polioviruses ( cVDPVs ) have recently been reported in different regions of the world . Two of these outbreaks occurred in Madagascar . Most cVDPVs were recombinants of mutated poliovaccine strains and other unidentified enteroviruses of sp...	Following intense vaccination campaigns with Sabin's trivalent live-attenuated oral poliovirus vaccine , poliomyelitis caused by wild polioviruses has disappeared from large parts of the world . However , poliomyelitis outbreaks due to pathogenic circulating vaccine-derived polioviruses ( cVDPVs ) have recently been re...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/virulence", "factors", "and", "mechanisms", "virology/virus", "evolution", "and", "symbiosis", "molecular", "biology/recombination", "neurological", "disorders/infectious", "diseases", "of", "the", "nervous", "system", "molecular", "biology/molecular", "evolution", ...	2009	Recombination between Polioviruses and Co-Circulating Coxsackie A Viruses: Role in the Emergence of Pathogenic Vaccine-Derived Polioviruses
A remarkable aspect of the interaction of Cryptococcus neoformans with mammalian hosts is a consistent increase in capsule volume . Given that many aspects of the interaction of C . neoformans with macrophages are also observed with amoebae , we hypothesized that the capsule enlargement phenomenon also had a protozoan ...	A key event in C . neoformans pathogenesis is capsule enlargement in mammalian hosts . Historically , this phenomenon was attributed to high CO2 and iron deprivation but the magnitude of capsular enlargement observed in vivo cannot be consistently replicated in vitro . This paper reports that C . neoformans responds to...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2011	Phospholipids Trigger Cryptococcus neoformans Capsular Enlargement during Interactions with Amoebae and Macrophages
Successful mass drug administration ( MDA ) campaigns have brought several countries near the point of Lymphatic Filariasis ( LF ) elimination . A diagnostic tool is needed to determine when the prevalence levels have decreased to a point that MDA campaigns can be discontinued without the threat of recrudescence . A si...	Lymphatic filariasis ( LF ) , a mosquito-borne parasitic disease , is a candidate for elimination largely because of the success of mass drug administration ( MDA ) campaigns , in which entire at-risk populations are given a once-yearly regimen of single-dose treatment with two medications . As a result , a diagnostic ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "neglected", "tropical", "diseases", "parasitic", "diseases" ]	2012	A Multicenter Evaluation of Diagnostic Tools to Define Endpoints for Programs to Eliminate Bancroftian Filariasis
Genome-wide association studies ( GWAS ) yielded significant advances in defining the genetic architecture of complex traits and disease . Still , a major hurdle of GWAS is narrowing down multiple genetic associations to a few causal variants for functional studies . This becomes critical in multi-phenotype GWAS where ...	Nowadays , the availability of cheaper and accurate assays to quantify multiple ( endo ) phenotypes in large population cohorts allows multi-trait studies . However , these studies are limited by the lack of flexible models integrated with efficient computational tools for genome-wide multi SNPs-traits analyses . To ov...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computer", "science", "mathematics", "statistics", "computerized", "simulations", "statistical", "methods" ]	2013	GUESS-ing Polygenic Associations with Multiple Phenotypes Using a GPU-Based Evolutionary Stochastic Search Algorithm
In the past few years , case-control studies of common diseases have shifted their focus from single genes to whole exomes . New sequencing technologies now routinely detect hundreds of thousands of sequence variants in a single study , many of which are rare or even novel . The limitation of classical single-marker as...	Inexpensive , high-throughput sequencing has transformed the field of case-control association studies . For the first time , it may be possible to identify the genetic underpinnings of complex diseases , by sequencing the DNA of hundreds ( even thousands ) of cases and controls and comparing patterns of DNA sequence v...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome", "analysis", "tools", "genomics", "genetic", "association", "studies", "genetics", "biology", "computational", "biology", "genetics", "and", "genomics", "human", "genetics" ]	2013	A Hybrid Likelihood Model for Sequence-Based Disease Association Studies
The liver fluke Opisthorchis viverrini infects several million people in Southeast Asia . Adult flukes live in the bile ducts of humans , where they cause hepatobiliary pathology , including cholangiocarcinoma . Here , we investigated the potential of extracellular vesicles ( EVs ) secreted by the fluke and defined rec...	Cholangiocarcinoma ( CCA ) is a significant public health problem in countries throughout Southeast Asia . In these areas CCA has a strong association with chronic infection with the food-borne liver fluke Opisthorchis viverrini . Current control of the infection relies on chemotherapy and health education , however th...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "serum", "invertebrates", "medicine", "and", "health", "sciences", "immune", "physiology", "body", "fluids", "helminths", "immunology", "bile", "vertebrates", "animals", "mammals", "trematodes", "preventive", "medicine", "vaccines", "immunologic", "adjuvants", ...	2019	Vaccination of hamsters with Opisthorchis viverrini extracellular vesicles and vesicle-derived recombinant tetraspanins induces antibodies that block vesicle uptake by cholangiocytes and reduce parasite burden after challenge infection
Prior studies have shown that 2′-O methyltransferase activity of flaviviruses , coronaviruses , and poxviruses promotes viral evasion of Ifit1 , an interferon-stimulated innate immune effector protein . Viruses lacking 2′-O methyltransferase activity exhibited attenuation in primary macrophages that was rescued in cell...	We recently showed that a West Nile virus ( WNV ) mutant in NS5 ( WNV-E218A ) lacking 2′-O methyltransferase activity was attenuated in primary macrophages but replicated well in cells lacking type I interferon ( IFN ) signaling or expression of Ifit1 , an IFN-stimulated gene . Here , we follow-up these studies by exam...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viral", "classification", "immunity", "to", "infections", "immunology", "microbiology", "host-pathogen", "interaction", "rna", "viruses", "immune", "defense", "animal", "models", "of", "infection", "virulence", "factors", "and", "mechanisms", "viral", "immune", "evasio...	2012	2′-O Methylation of the Viral mRNA Cap by West Nile Virus Evades Ifit1-Dependent and -Independent Mechanisms of Host Restriction In Vivo
Radial glial cells ( RGCs ) are distinctive neural stem cells with an extraordinary slender bipolar morphology and dual functions as precursors and migration scaffolds for cortical neurons . Here we show a novel mechanism by which the Lis1-Nde1 complex maintains RGC functions through stabilizing the dystrophin/dystrogl...	The processes of neurogenesis and neuronal migration within the developing cerebral cortex must be tightly orchestrated to enable ordered generation and transportation of neurons to designated cortical layers . The mechanism by which these two processes are integrated remains elusive . Radial glial cells , the major ne...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "developmental", "biology", "genetics", "biology", "molecular", "cell", "biology", "neuroscience", "genetics", "and", "genomics" ]	2011	Three-Dimensional Regulation of Radial Glial Functions by Lis1-Nde1 and Dystrophin Glycoprotein Complexes
Bacterial efflux pumps transport small molecules from the cytoplasm or periplasm outside the cell . Efflux pump activity is typically increased in multi-drug resistant ( MDR ) pathogens; chemicals that inhibit efflux pumps may have potential for antibiotic development . Using an in-cell screen , we identified three eff...	Bacteria evolved molecular machines called efflux pumps to export toxic chemicals , including antibiotics encountered in the environment . Multi-drug resistant ( MDR ) bacteria use efflux pumps to rapidly transport clinical antibiotics out of the cell and thereby increase the dosage at which they tolerate antibiotics ....	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "antimicrobials", "periplasm", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "pathogens", "drugs", "immunology", "microbiology", "carbohydrates", "salmonellosis", "organ...	2018	A cell-based infection assay identifies efflux pump modulators that reduce bacterial intracellular load
The transmission of schistosomiasis japonica in a local setting is still poorly understood in the lake regions of the People's Republic of China ( P . R . China ) , and its transmission patterns are closely related to human , social and economic factors . We aimed to apply the integrated approach of artificial neural n...	Schistosomiasis japonica is one of the serious infectious diseases causing problems in public health in People's Republic of China ( P . R . China ) . The prevalence of schistosomiasis japonica is easily rebounding in the lake regions due to unique environmental settings . By considering the importance in assessing the...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "biochemical", "simulations", "infectious", "diseases", "public", "health", "and", "epidemiology", "parasitic", "diseases", "epidemiology", "environmental", "epidemiology", "neglected", "tropical", "diseases", "biology", "computational", "biology", "spatial", "e...	2013	Transmission Risks of Schistosomiasis Japonica: Extraction from Back-propagation Artificial Neural Network and Logistic Regression Model
The high-risk Human Papillomavirus ( HPV ) E6 oncoproteins are characterised by the presence of a class I PDZ-binding motif ( PBM ) on their extreme carboxy termini . The PBM is present on the E6 proteins derived from all cancer-causing HPV types , but can also be found on some related non-cancer-causing E6 proteins . ...	The cancer-causing Human Papillomavirus ( HPV ) E6 oncoproteins have a unique carboxy terminal PDZ binding motif ( PBM ) , which interacts with a number of different cellular PDZ domain-containing substrates . The PBM has important functions in both the viral life cycle and in HPV-induced malignancy . In this study we ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "affinity", "chromatography", "pathogens", "microbiology", "viruses", "hpv-18", "oncology", "dna", "viruses", "human", "papillomavirus", "glutathione", "chromatography", "research", "an...	2016	Analysis of Multiple HPV E6 PDZ Interactions Defines Type-Specific PDZ Fingerprints That Predict Oncogenic Potential
Schistosomiasis continues to be one of the most prevalent parasitic diseases in the world . Despite the existence of a highly effective antischistosome drug , the disease is spreading into new areas , and national control programs do not arrive to complete their tasks particularly in low endemic areas . The availabilit...	Schistosomiasis is a neglected disease affecting more than 200 million people globally , especially in sub-Saharan Africa . The mainstay of control of schistosomiasis is Praziquantel , but the mass administration of this drug is unsustainable due to the high rates of re-infection after treatment . These high rates of r...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "biology" ]	2013	Immunoprotection of Mice against Schistosomiasis Mansoni Using Solubilized Membrane Antigens
Coronaviruses induce in infected cells the formation of double membrane vesicles , which are the sites of RNA replication . Not much is known about the formation of these vesicles , although recent observations indicate an important role for the endoplasmic reticulum in the formation of the mouse hepatitis coronavirus ...	Coronaviruses are the causative agents of many respiratory and enteric infections in humans and animals . As with all viruses , virtually all of the steps of their infection cycle depend on host cellular factors . As the first and most crucial step after their entry into cells , coronaviruses assemble their replication...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/viral", "replication", "and", "gene", "regulation" ]	2008	Mouse Hepatitis Coronavirus RNA Replication Depends on GBF1-Mediated ARF1 Activation
Circadian clocks organize the precise timing of cellular and behavioral events . In Drosophila , circadian clocks consist of negative feedback loops in which the clock component PERIOD ( PER ) represses its own transcription . PER phosphorylation is a critical step in timing the onset and termination of this feedback ....	The molecular mechanism that governs organization of physiology and behavior into 24-h rhythms is a conserved transcriptional feedback process that is strikingly similar across distinct phyla . Notably , cyclic phosphorylation of negative feedback regulators is critical to time molecular rhythms . Indeed , mutation of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "neuroscience", "drosophila", "genetics", "and", "genomics" ]	2008	Dominant-Negative CK2α Induces Potent Effects on Circadian Rhythmicity
SHANK genes code for scaffold proteins located at the post-synaptic density of glutamatergic synapses . In neurons , SHANK2 and SHANK3 have a positive effect on the induction and maturation of dendritic spines , whereas SHANK1 induces the enlargement of spine heads . Mutations in SHANK genes have been associated with a...	Autism spectrum disorders ( ASD ) are a heterogeneous group of neurodevelopmental disorders . Mutations altering genes involved in the junction between brain cells have been repeatedly associated in ASD . For example , SHANK1 , SHANK2 and SHANK3 emerged as one family of genes that are associated with ASD . However , li...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "biology", "and", "life", "sciences", "human", "genetics" ]	2014	Meta-analysis of SHANK Mutations in Autism Spectrum Disorders: A Gradient of Severity in Cognitive Impairments
Here we introduce a quantitative structure-driven computational domain-fusion method , which we used to predict the structures of proteins believed to be involved in regulation of the subtilin pathway in Bacillus subtilis , and used to predict a protein-protein complex formed by interaction between the proteins . Homol...	Because proteins so frequently function in coordination with other proteins , identification and characterization of the interactions among proteins are essential for understanding how proteins work . Computational methods for identification of protein-protein interactions have been limited by the degree to which prote...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "computational", "biology/macromolecular", "structure", "analysis", "cell", "biology/cell", "signaling", "biochemistry/bioinformatics", "biochemistry/macromolecular", "assemblies", "and", "machines", "computational", "biology", "genetics", "and", "genomics/bioinformatics" ]	2009	SpaK/SpaR Two-component System Characterized by a Structure-driven Domain-fusion Method and in Vitro Phosphorylation Studies
Background/Objectives: Parasites of the subgenus Leishmania ( Viannia ) cause varying clinical symptoms ranging from cutaneous leishmaniases ( CL ) with single or few lesions , disseminated CL ( DL ) with multiple lesions to disfiguring forms of mucocutaneous leishmaniasis ( MCL ) . In this population genetics study , ...	Cutaneous leishmaniasis ( CL ) constitutes a significant public health problem in all federal states of Brazil . Most cases are caused by parasites of the subgenus Leishmania ( Viannia ) which can cause a variety of clinical symptoms ranging from single or few lesions , disseminated CL with multiple lesions , to disfig...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2013	Population Structure and Evidence for Both Clonality and Recombination among Brazilian Strains of the Subgenus Leishmania (Viannia)
Dengue fever is among the most widespread vector-borne infectious diseases . The primary vector of dengue is the Aedes aegypti mosquito . Ae . aegypti is prevalent in the tropics and sub-tropics and is closely associated with human habitats outside its native range of Africa . While long established in the southeastern...	Dengue fever is a vector-borne disease that has dramatically increased in frequency and severity in recent decades , affecting over half of the world's population . The primary vector of dengue is Aedes aegypti . Breeding populations of this mosquito were reported for the first time in California in summer 2013 , and t...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "evolutionary", "ecology", "medicine", "and", "health", "sciences", "ecology", "viral", "transmission", "and", "infection", "infectious", "disease", "epidemiology", "virology", "epidemiology", "vector", "biology", "genetics", "biology", "and", "life", "sciences", "popul...	2014	Origin of the Dengue Fever Mosquito, Aedes aegypti, in California
Saliva is an essential part of activities such as speaking , masticating and swallowing . Enzymes in salivary fluid protect teeth and gums from infectious diseases , and also initiate the digestion process . Intracellular calcium ( Ca2+ ) plays a critical role in saliva secretion and regulation . Experimental measureme...	We construct a mathematical model of Ca2+ and IP3 oscillations in HSY cells , a salivary ductal cell line from human parotid . The model reproduces the experimental data that exhibit coupled oscillations of [Ca2+] and [IP3] with the peak of each Ca2+ spike being followed by the peak of an IP3 spike . Recently , it was ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "liver", "body", "fluids", "mathematical", "models", "saliva", "photolysis", "simulation", "and", "modeling", "physiological", "processes", "cellular", "structures", "and", "organelles", "research", "and", "analysis", "methods", ...	2017	A mathematical model of calcium dynamics in HSY cells
The evolution of complex organismal traits is obvious as a historical fact , but the underlying causes—including the role of natural selection—are contested . Gould argued that a random walk from a necessarily simple beginning would produce the appearance of increasing complexity over time . Others contend that selecti...	Over billions of years , life has evolved into the extraordinarily diverse and complex organisms that populate the Earth today . Although evolution often proceeds toward increasing complexity , more complex traits do not necessarily make organisms more fit . So when and why is greater complexity favored ? One hypothesi...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "ecology", "ecology", "and", "environmental", "sciences", "coevolution", "ecology", "evolutionary", "modeling", "biology", "and", "life", "sciences", "computational", "biology", "evolutionary", "biology", "evolutionary", "emergence", "evolutionary", "process...	2014	Coevolution Drives the Emergence of Complex Traits and Promotes Evolvability
Research on human motor adaptation has often focused on how people adapt to self-generated or externally-influenced errors . Trial-by-trial adaptation is a person’s response to self-generated errors . Externally-influenced errors applied as catch-trial perturbations are used to calculate a person’s perturbation adaptat...	By observing the learning rate of a person making a movement under new conditions , researchers can better understand how the nervous system handles uncertainty . Patients suffering from motor deficits or using prostheses will often display different motor abilities that can be observed as changes in error correction r...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "learning", "medicine", "and", "health", "sciences", "engineering", "and", "technology", "statistics", "nervous", "system", "applied", "mathematics", "signal", "processing", "social", "sciences", "neuroscience", "learning", "and", "memory", "noise", "reduction", "simula...	2018	Conventional analysis of trial-by-trial adaptation is biased: Empirical and theoretical support using a Bayesian estimator
Yellow fever virus ( YFV ) is a vector-borne flavivirus endemic to Africa and Latin America . Ninety per cent of the global burden occurs in Africa where it is primarily transmitted by Aedes spp , with Aedes aegypti the main vector for urban yellow fever ( YF ) . Mosquito life cycle and viral replication in the mosquit...	In this article , we describe the development of a model to quantify the seasonal dynamics of yellow fever virus ( YFV ) transmission across Africa . YFV is a flavivirus transmitted , within Africa , primarily by Aedes spp where it causes an estimated 78 , 000 deaths a year despite the presence of a safe and effective ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "death", "rates", "invertebrates", "medicine", "and", "health", "sciences", "population", "dynamics", "geographical", "locations", "vector-borne", "diseases", "animals", "seasons", "population", "biology", "insect", "vectors", "africa", "infectious", "diseases", "aedes", ...	2018	The seasonal influence of climate and environment on yellow fever transmission across Africa
With few exceptions , current methods for short read mapping make use of simple seed heuristics to speed up the search . Most of the underlying matching models neglect the necessity to allow not only mismatches , but also insertions and deletions . Current evaluations indicate , however , that very different error mode...	The successful mapping of high-throughput sequencing ( HTS ) reads to reference genomes largely depends on the accuracy of both the sequencing technologies and reference genomes . Current mapping algorithms focus on mapping with mismatches but largely neglect insertions and deletions—regardless of whether they are caus...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/bioinformatics", "computational", "biology/genomics", "computational", "biology" ]	2009	Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures
Gamma-herpesviruses colonise lymphocytes . Murid Herpesvirus-4 ( MuHV-4 ) infects B cells via epithelial to myeloid to lymphoid transfer . This indirect route entails exposure to host defences , and type I interferons ( IFN-I ) limit infection while viral evasion promotes it . To understand how IFN-I and its evasion bo...	Gamma-herpesviruses establish chronic infections and cause cancers . They achieve this by immune evasion . Immune responses nonetheless suppress infection to a degree . By understanding how immune responses and viral evasion come together we can potentially control infection and prevent disease . MuHV-4 provides an acc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "nuclear", "staining", "respiratory", "infections", "spleen", "immunology", "microbiology", "viral", "structure", "pulmonology", "research", "and", "analysis", "methods...	2016	Type I Interferons Direct Gammaherpesvirus Host Colonization
North American triple reassortant swine ( TRS ) influenza A viruses have caused sporadic human infections since 2005 , but human-to-human transmission has not been documented . These viruses have six gene segments ( PB2 , PB1 , PA , HA , NP , and NS ) closely related to those of the 2009 H1N1 pandemic viruses . Therefo...	North American triple reassortant swine ( TRS ) influenza A viruses have caused sporadic human infections , but human-to-human transmission has not been established . We wished to elucidate potential human health threats posed by the TRS viruses and to identify determinants of virulence in the TRS and closely related 2...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "of", "infection", "veterinary", "diseases", "virulence", "factors", "and", "mechanisms", "viral", "transmission", "and", "infection", "virology", "zoonotic", "diseases", "biology", "microbiology", "veterinary", "science", "animal", "influenza" ]	2012	Pathogenicity and Transmissibility of North American Triple Reassortant Swine Influenza A Viruses in Ferrets
The interchromosomal organization of a subset of human chromosomes ( #1 , 4 , 11 , 12 , 16 , 17 , and 18 ) was examined in G1 and S phase of human WI38 lung fibroblast and MCF10A breast epithelial cells . Radial positioning of the chromosome territories ( CTs ) was independent of gene density , but size dependent . Whi...	During interphase , chromosomes occupy discrete bodies within the cell nucleus termed chromosome territories ( CT ) . The organization of CT and the genes within them have been implicated in genomic regulation . Numerous reports suggest that specific interchromosomal interactions enable distally located genes to cluste...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computer", "and", "information", "sciences", "computer", "modeling", "systems", "science", "cell", "biology", "biology", "and", "life", "sciences", "computerized", "simulations", "systems", "analysis" ]	2014	Cell Type Specific Alterations in Interchromosomal Networks across the Cell Cycle
Circadian timing largely modifies efficacy and toxicity of many anticancer drugs . Recent findings suggest that optimal circadian delivery patterns depend on the patient genetic background . We present here a combined experimental and mathematical approach for the design of chronomodulated administration schedules tail...	Treatment timing within the 24-h timescale , that is , circadian ( circa , about; dies , day ) timing , can change by several fold the tolerability and antitumor efficacy of anticancer agents both in experimental models and in cancer patients . Chronotherapeutics aims at improving the tolerability and/or the efficacy o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "applied", "mathematics", "cancer", "treatment", "oncology", "mathematical", "computing", "mathematics", "theoretical", "biology", "chemotherapy", "and", "drug", "treatment", "biology", "systems", "biology", "biochemical", "simulations", "computer", "science", ...	2011	A Combined Experimental and Mathematical Approach for Molecular-based Optimization of Irinotecan Circadian Delivery
Antibodies have long been shown to play a critical role in naturally acquired immunity to malaria , but it has been suggested that Plasmodium-specific antibodies in humans may not be long lived . The cellular mechanisms underlying B cell and antibody responses are difficult to study in human infections; therefore , we ...	Malaria causes considerable human suffering resulting from associated high mortality , morbidity and reduced economic productivity in endemic areas . Current control methods are thwarted by a multiplicity of problems including rapidly developing resistance for anti-malarial drugs and insecticide-treated nets , and huge...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/protozoal", "infections", "infectious", "diseases/tropical", "and", "travel-associated", "diseases", "immunology/immunity", "to", "infections" ]	2009	Functional Memory B Cells and Long-Lived Plasma Cells Are Generated after a Single Plasmodium chabaudi Infection in Mice
Although molecular chaperones are essential components of protein homeostatic machinery , their mechanism of action and impact on adaptation and evolutionary dynamics remain controversial . Here we developed a physics-based ab initio multi-scale model of a living cell for population dynamics simulations to elucidate th...	Molecular chaperones or heat-shock proteins are essential components of protein homeostatic machinery in all three domains of life , whose role is not only to prevent protein aggregation but also catalyze the protein folding process by decreasing the energetic barrier for folding . Importantly , chaperones have often b...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	Catalysis of Protein Folding by Chaperones Accelerates Evolutionary Dynamics in Adapting Cell Populations
American visceral leishmaniasis ( AVL ) is an emerging disease in the state of São Paulo , Brazil . Its geographical expansion and the increase in the number of human cases has been linked to dispersion of Lutzomyia longipalpis into urban areas . To produce more accurate risk maps we investigated the geographic distrib...	Information on the geographical distribution , dispersal mechanisms and dispersion route of insect-borne diseases can help to identify ongoing transmission areas , new risk areas and guide surveillance and control activities . Lutzomyia longipalpis , the principal vector of American visceral leishmaniasis disease in th...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Distribution of Lutzomyia longipalpis Chemotype Populations in São Paulo State, Brazil
Giardia intestinalis is one of the most common diarrhea-related parasites in humans , where infection ranges from asymptomatic to acute or chronic disease . G . intestinalis consists of eight genetically distinct genotypes or assemblages , designated A–H , and assemblages A and B can infect humans . Giardiasis has been...	Giardia intestinalis is a protozoan parasite found world-wide and it is a major cause of diarrhea in humans and other mammals . The genetic variability within G . intestinalis is high with eight distinct genotypes or assemblages ( A-H ) . Here we performed sequence-based multilocus genotyping of around 200 human Giardi...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "giardiasis", "parasitic", "diseases" ]	2011	Multilocus Genotyping of Human Giardia Isolates Suggests Limited Zoonotic Transmission and Association between Assemblage B and Flatulence in Children
During prion infections of the central nervous system ( CNS ) the cellular prion protein , PrPC , is templated to a conformationally distinct form , PrPSc . Recent studies have demonstrated that the Sprn gene encodes a GPI-linked glycoprotein Shadoo ( Sho ) , which localizes to a similar membrane environment as PrPC an...	In prion infections of the nervous system the cellular prion protein , PrPC , changes to a distinct form , PrPSc . Recent studies have demonstrated that another glycoprotein Shadoo ( Sho ) , which occupies a similar membrane environment as PrPC , is reduced in the brains of rodents with terminal prion disease . Our ana...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "chemistry", "biology", "veterinary", "science" ]	2011	Down-Regulation of Shadoo in Prion Infections Traces a Pre-Clinical Event Inversely Related to PrPSc Accumulation
Methylation of histone H3 lysine 4 ( H3K4me ) is an evolutionarily conserved modification whose role in the regulation of gene expression has been extensively studied . In contrast , the function of H3K4 acetylation ( H3K4ac ) has received little attention because of a lack of tools to separate its function from that o...	In the nucleus of mammals and yeast , DNA is packaged by forming complexes with histone proteins in a structure called the nucleosome , the basic building block of chromatin . The tails of the histones protrude from the nucleosome and can be marked on many amino acid residues by chemical modifications such as methylati...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/histone", "modification", "molecular", "biology/chromatin", "structure", "molecular", "biology/transcription", "initiation", "and", "activation" ]	2011	H3 Lysine 4 Is Acetylated at Active Gene Promoters and Is Regulated by H3 Lysine 4 Methylation

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