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The live-attenuated TC-83 strain is the only licensed veterinary vaccine available to protect equids against Venezuelan equine encephalitis virus ( VEEV ) and to protect humans indirectly by preventing equine amplification . However , TC-83 is reactogenic due to its reliance on only two attenuating point mutations and ...	Venezuelan equine encephalitis virus ( VEEV ) is transmitted by mosquitoes and widely distributed in Central and South America , causing regular outbreaks in horses and humans . Often misdiagnosed as dengue , VEEV infection in humans can lead to lifelong neurological sequelae and is fatal in up to >80% of equine cases ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "viral", "vaccines", "virology", "emerging", "viral", "diseases", "biology", "microbiology" ]	2013	IRES-driven Expression of the Capsid Protein of the Venezuelan Equine Encephalitis Virus TC-83 Vaccine Strain Increases Its Attenuation and Safety
Buruli ulcer ( BU ) , one of 17 neglected tropical diseases , is a debilitating skin and soft tissue infection caused by Mycobacterium ulcerans . In tropical Africa , changes in land use and proximity to water have been associated with the disease . This study presents the first analysis of BU at the village level in s...	We studied the relationship between a neglected tropical disease , Buruli Ulcer ( BU ) , and landscape disturbance . We hypothesized that the increased presence of BU was related to landscape disturbance , especially alluvial mining , in endemic areas of the disease . We characterized recent cases of BU in southwestern...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Buruli Ulcer Disease and Its Association with Land Cover in Southwestern Ghana
Fluoroquinolones are a class of antibacterial agents used for leprosy treatment . Some new fluoroquinolones have been attracting interest due to their remarkable potency that is reportedly better than that of ofloxacin , the fluoroquinolone currently recommended for treatment of leprosy . For example , DC-159a , a rece...	Leprosy is now recognized as a disease curable by chemotherapy . Although the number of leprosy cases has dramatically decreased as a result of multidrug therapy , there are still more than 210 , 000 new cases reported worldwide every year . Recurrence is a major concern in the control of leprosy . Relapses are usually...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "mycobacterium", "leprae", "medicine", "and", "health", "sciences", "clinical", "research", "design", "tropical", "diseases", "plasmid", "construction", "bacterial", "diseases", "research", "design", "pharmaceutics", "neglected", "tropical", "diseases", "dna", "molecular"...	2016	DC-159a Shows Inhibitory Activity against DNA Gyrases of Mycobacterium leprae
The World Health Organization ( WHO ) has targeted yaws for global eradication . Eradication requires certification that all countries are yaws-free . While only 14 Member States currently report cases to WHO , many more are known to have a history of yaws and some of them may have ongoing transmission . We reviewed th...	Yaws is a disabling and disfiguring disease . When the World Health Organization ( WHO ) was established in 1948 , yaws was among the major public health problems that the new health agency chose to prioritize . In 2013 , it formally targeted yaws for global eradication . While only 14 Member States currently report ca...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "geomorphology", "medicine", "and", "health", "sciences", "wallis", "and", "futuna", "landforms", "topography", "tropical", "diseases", "geographical", "locations", "health", "care", "north", "america", "treponematoses", "bacterial", "diseases", "global", "health", "neg...	2018	Prioritizing surveillance activities for certification of yaws eradication based on a review and model of historical case reporting
Pathogenic mechanisms of Leptospira interrogans , the causal agent of leptospirosis , remain largely unknown . This is mainly due to the lack of tools for genetic manipulations of pathogenic species . In this study , we characterized a mutant obtained by insertion of the transposon Himar1 into a gene encoding a putativ...	The spirochetes , which include medically important pathogens such as the causative agents of Lyme disease , syphilis , and leptospirosis , constitute an evolutionarily unique group of bacteria . Leptospirosis is a zoonotic disease that causes a high rate of mortality and morbidity in humans and animals throughout the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "eubacteria", "microbiology" ]	2007	The OmpA-Like Protein Loa22 Is Essential for Leptospiral Virulence
Dengue virus ( DENV ) is the most prominent arbovirus worldwide , causing major epidemics in South-East Asia , South America and Africa . In 2010 , a major DENV-2 outbreak occurred in Gabon with cases of patients co-infected with chikungunya virus ( CHIKV ) . Although the innate immune response is thought to be of prim...	Dengue fever is the most important arthropod-borne viral disease worldwide , affecting 50 to 100 million individuals annually . The clinical picture associated with acute dengue virus ( DENV ) infections ranges from classical febrile illness to life-threatening disease . The innate immunity is the first line of defense...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "dengue", "virus", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "pathogens", "immunology", "microbiology", "alphaviruses", "cell", "differentiation", ...	2016	Longitudinal Analysis of Natural Killer Cells in Dengue Virus-Infected Patients in Comparison to Chikungunya and Chikungunya/Dengue Virus-Infected Patients
Insertional mutations leading to expansion of the octarepeat domain of the prion protein ( PrP ) are directly linked to prion disease . While normal PrP has four PHGGGWGQ octapeptide segments in its flexible N-terminal domain , expanded forms may have up to nine additional octapeptide inserts . The type of prion diseas...	Prion diseases are neurodegenerative disorders involving the prion protein , a normal component of the central nervous system . An unusual class of inherited mutations giving rise to prion disease involves elongation of the so-called octarepeat domain , near the protein's N-terminus . Research from our lab and others s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neurological", "disorders/prion", "diseases", "infectious", "diseases/prion", "diseases", "biophysics", "biophysics/protein", "folding" ]	2009	Early Onset Prion Disease from Octarepeat Expansion Correlates with Copper Binding Properties
The γ-aminobutyric acid type A receptor ( GABAA-R ) is a major inhibitory neuroreceptor that is activated by the binding of GABA . The structure of the GABAA-R is well characterized , and many of the binding site residues have been identified . However , most of these residues are obscured behind the C-loop that acts a...	Neurotransmitters convey signals from one neuron to the next and are indispensable to the functioning of the nervous system . These small molecules bind to receptors to exert their action . One of the most important neurotransmitters is γ-aminobutyric acid ( GABA ) , which binds to its type A receptor to exert an inhib...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "chemical", "bonding", "chemical", "characterization", "neurochemistry", "medicine", "and", "health", "sciences", "electrostatic", "bonding", "electricity", "radii", "electrophysiology", "neuroscience", "geometry", "simulation", "and", "modeling", "ion", "channels", "electr...	2016	An Electrostatic Funnel in the GABA-Binding Pathway
Axon ensheathment by specialized glial cells is an important process for fast propagation of action potentials . The rapid electrical conduction along myelinated axons is mainly due to its saltatory nature characterized by the accumulation of ion channels at the nodes of Ranvier . However , how these ion channels are t...	Myelination is an important process that enables fast propagation of action potential along the axons . Schwann cells ( SCs ) are the specialized glial cells that ensure the ensheathment of the corresponding axons in the Peripheral Nervous System . In order to do so , SCs and axons need to communicate to organize the m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "vesicles", "cell", "processes", "vertebrates", "electrophysiology", "neuroscience", "animals", "macroglial", "cells", "animal", "models", "osteichthyes", "developmental", "biology", "ion", "channels", "model", "organisms", "nerve"...	2016	Neuronal Ndrg4 Is Essential for Nodes of Ranvier Organization in Zebrafish
The initial steps in chlamydial infection involve adhesion and internalization into host cells and , most importantly , modification of the nascent inclusion to establish the intracellular niche . Here , we show that Chlamydia pneumoniae enters host cells via EGFR-dependent endocytosis into an early endosome with a pho...	Here , we show for the first time how Chlamydia pneumoniae an obligate intracellular pathogen establishes its intracellular niche . After EGFR-dependent endocytosis into host cells , the nascent chlamydial inclusion acquires early endosomal membrane identity and the Rab GTPases Rab4 , Rab5 and Rab7 , as well as the rec...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "vesicles", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "membrane", "proteins", "molecular", "motors", "sexually", "transmitted", "diseases", "chlamydia", "cellular", "structures", "and", "organelles"...	2017	Acquisition of Rab11 and Rab11-Fip2—A novel strategy for Chlamydia pneumoniae early survival
Alveolar echinococcosis ( AE ) is caused by the metacestode stage of Echinococcus multilocularis . Differential diagnosis with cystic echinococcosis ( CE ) caused by E . granulosus and AE is challenging . We aimed at improving diagnosis of AE on paraffin sections of infected human tissue by immunohistochemical testing ...	Echinococcosis is a life-threatening disease in humans that is caused by the larval stages of the tapeworms Echinococcus multilocularis and Echinococcus granulosus . The eggs of the parasites are released with faeces of canids , and humans are aberrantly infected . In humans , the larval stages of the parasites cause t...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "anatomical", "pathology", "surgical", "pathology", "diagnostic", "medicine", "pathology" ]	2012	Sensitive and Specific Immunohistochemical Diagnosis of Human Alveolar Echinococcosis with the Monoclonal Antibody Em2G11
India contributes ~60% to the global leprosy burden . The country implements 14-day community-based leprosy case detection campaigns ( LCDC ) periodically in all high endemic states . Paramedical staff screen the population and medical officers of primary health centres ( PHCs ) diagnose and treat leprosy cases . Sever...	India is the highest leprosy burden country in the world . Government of India’s National Leprosy Eradication Programme ( NLEP ) launched Leprosy Case Detection Campaign ( LCDC ) —an active community-based case detection campaign—in 2016 in all high burden areas to detect undiagnosed cases . Following these LCDC , a sm...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "nervous", "system", "tropical", "diseases", "geographical", "locations", "india", "sports", "and", "exercise", "medicine", "physical", "activity", "bacterial", "diseases", "signs", ...	2018	Does appreciative inquiry decrease false positive diagnosis during leprosy case detection campaigns in Bihar, India? An operational research study
During RNA virus infection , the adaptor protein MAVS recruits TRAF3 and TRAF6 to form a signalosome , which is critical to induce the production of type I interferons ( IFNs ) and proinflammatory cytokines . While activation of the MAVS/TRAF3/TRAF6 signalosome is well studied , the negative regulation of the signaloso...	Extensive studies have demonstrated redundant roles of multiple antiviral signaling pathways in host defense against viral infection . However , the strategies viruses have evolved to efficiently antagonize the complementary effect of alternative IFNs-inducing signaling remain largely unknown . Here we report that RNA ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "vesicular", "stomatitis", "virus", "antiviral", "immune", "response", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "molecular", "probe", "techniques", "pathogens", "immunology", "mic...	2018	Induction of OTUD1 by RNA viruses potently inhibits innate immune responses by promoting degradation of the MAVS/TRAF3/TRAF6 signalosome
Listeria monocytogenes is a pathogenic bacterium that moves within infected cells and spreads directly between cells by harnessing the cell's dendritic actin machinery . This motility is dependent on expression of a single bacterial surface protein , ActA , a constitutively active Arp2 , 3 activator , and has been wide...	Cells tightly regulate the branched actin networks involved in motility , division , and other important cellular functions through localized activation of the Arp2 , 3 protein , which nucleates new actin filaments off the sides of existing ones . The pathogenic bacterium , Listeria monocytogenes , expresses its own Ar...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/systems", "biology", "cell", "biology/cytoskeleton" ]	2009	An Experimental and Computational Study of the Effect of ActA Polarity on the Speed of Listeria monocytogenes Actin-based Motility
Chemotaxis is fundamentally important , but the sources of gradients in vivo are rarely well understood . Here , we analyse self-generated chemotaxis , in which cells respond to gradients they have made themselves by breaking down globally available attractants , using both computational simulations and experiments . W...	Cells move in response to chemical gradients . This is chemotaxis , a fundamental process that is crucial for embryonic development , immune response , and the progression of cancer . How the environment dictates cell movement has been studied extensively , but most studies do not account for how cells alter the enviro...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "physiology", "cell", "motility", "dictyosteliomycota", "directed", "cell", "migration", "developmental", "biology", "receptor", "physiology", "model", "organisms", "chemotaxis", "assay", "bioassays", "and", "physiological", "analysis", "population", "biology", "r...	2016	Self-Generated Chemoattractant Gradients: Attractant Depletion Extends the Range and Robustness of Chemotaxis
Leishmaniasis is a disease caused by protozoan parasites of genus Leishmania . The frequent involvement of Leishmania tropica in human leishmaniasis has been recognized only recently . Similarly as L . major , L . tropica causes cutaneous leishmaniasis in humans , but can also visceralize and cause systemic illness . T...	Several hundred million people are exposed to the risk of leishmaniasis , a disease caused by intracellular protozoan parasites of several Leishmania species and transmitted by phlebotomine sand flies . In humans , L . tropica causes cutaneous form of leishmaniasis with painful and long-persisting lesions in the site o...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "immunology", "microbiology", "host-pathogen", "interaction", "parasitic", "diseases", "parasitology", "parastic", "protozoans", "model", "organisms", "leishmania", "neglected", "tropical", "diseases", "infectious", "diseases", "biology", "leishmaniasis", "genetic...	2012	Genetics of Host Response to Leishmania tropica in Mice – Different Control of Skin Pathology, Chemokine Reaction, and Invasion into Spleen and Liver
Type 1 diabetes ( T1D ) is an autoimmune disease in which pancreatic beta cells are killed by infiltrating immune cells and by cytokines released by these cells . Signaling events occurring in the pancreatic beta cells are decisive for their survival or death in diabetes . We have used RNA sequencing ( RNA–seq ) to ide...	Pancreatic beta cells are destroyed by the immune system in type 1 diabetes mellitus , causing insulin dependence for life . Candidate genes for diabetes contribute to this process by acting both at the immune system and , as we suggest here , at the pancreatic beta cell level . We have utilized a novel technology , RN...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "genome", "analysis", "tools", "diabetic", "endocrinology", "endocrinology", "biology", "genomics", "diabetes", "and", "endocrinology", "genetics", "and", "genomics" ]	2012	The Human Pancreatic Islet Transcriptome: Expression of Candidate Genes for Type 1 Diabetes and the Impact of Pro-Inflammatory Cytokines
Buruli ulcer ( BU ) is a severe necrotizing human skin disease caused by Mycobacterium ulcerans . Clinically , presentation is a sum of these diverse pathogenic hits subjected to critical immune-regulatory mechanisms . Among them , autophagy has been demonstrated as a cellular process of critical importance . Since mic...	Buruli ulcer ( BU ) is a neglected tropical disease caused by Mycobacterium ulcerans . Because the exact trigger is still under investigation , current treatment options rely mostly on the surgical excision of the affected site . There is therefore a pressing demand for improved risk prediction and tailored treatment a...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "cell", "death", "medicine", "and", "health", "sciences", "autophagic", "cell", "death", "fungal", "genetics", "cell", "processes", "tropical", "diseases", "variant", "genotypes", "genetic", "mapping", "bacterial", "diseases", "genetic", "predisposition", "neglected", ...	2016	Genetic Variation in Autophagy-Related Genes Influences the Risk and Phenotype of Buruli Ulcer
Animal cells initiate cytokinesis in parallel with anaphase onset , when an actomyosin ring assembles and constricts through localized activation of the small GTPase RhoA , giving rise to a cleavage furrow . Furrow formation relies on positional cues provided by anaphase spindle microtubules ( MTs ) , but how such cues...	During mitosis , the separation of duplicated chromosomes and subsequent cytokinesis ( cell division ) are tightly coupled processes . Cytokinesis must occur not only after chromosomes have separated but also in the physical space between the chromosomes , so that each daughter cell inherits the appropriate genetic mat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/cell", "growth", "and", "division", "cell", "biology/chemical", "biology", "of", "the", "cell" ]	2009	Plk1 Self-Organization and Priming Phosphorylation of HsCYK-4 at the Spindle Midzone Regulate the Onset of Division in Human Cells
Variation in DNA methylation is being increasingly associated with health and disease outcomes . Although DNA methylation is hypothesized to be a mechanism by which both genetic and non-genetic factors can influence the regulation of gene expression , little is known about the extent to which DNA methylation at specifi...	The study of monozygotic ( MZ ) and dizygotic ( DZ ) twins provides an opportunity for exploring the extent to which heritable and environmental factors contribute to phenotypic variation in human populations . We exploit the twin study design to explore the factors influencing epigenetic variation between individuals ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "population", "genetics", "habits", "twins", "developmental", "biology", "epigenetics", "dna", "population", "biology", "smoking", "habits", "dna", "methylation", "chromatin", "sex", "chromosomes", "genetic", ...	2018	Characterizing genetic and environmental influences on variable DNA methylation using monozygotic and dizygotic twins
The genetic factors that give rise to variation in susceptibility to environmental toxins remain largely unexplored . Studies on genetic variation in susceptibility to environmental toxins are challenging in human populations , due to the variety of clinical symptoms and difficulty in determining which symptoms causall...	Although physiological effects of environmental toxins are well documented , we know little about the genetic factors that determine individual variation in susceptibility to toxins . Such information is difficult to obtain in human populations due to heterogeneity in genetic background and environmental exposure , and...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "genetic", "networks", "toxins", "heavy", "metals", "pathology", "and", "laboratory", "medicine", "rna", "interference", "animals", "toxicology", "toxic", "agents", "lead", "(element)", "animal", "models", "tox...	2017	A Drosophila model for toxicogenomics: Genetic variation in susceptibility to heavy metal exposure
Some studies of Saccharomyces cerevisiae and mammals have shown that RIO protein kinases ( RIOKs ) are involved in ribosome biogenesis , cell cycle progression and development . However , there is a paucity of information on their functions in parasitic nematodes . We aimed to investigate the function of RIOK-1 encodin...	Parasitic nematodes cause serious global health problems and enormous economic losses . Control of these parasites is difficult due to their complicated life cycle and the lack of knowledge of their developmental biology at the molecular level . Protein kinases are key molecules regulating a range of biological process...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biology", "and", "life", "sciences" ]	2014	Toward Understanding the Functional Role of Ss-riok-1, a RIO Protein Kinase-Encoding Gene of Strongyloides stercoralis
During Dec-2013 , a chikungunya virus ( CHIKV ) outbreak was first detected in the French-West Indies . Subsequently , the virus dispersed to other Caribbean islands , continental America and many islands in the Pacific Ocean . Previous estimates of the attack rate were based on declaration of clinically suspected case...	Chikungunya virus ( CHIKV ) is an emerging mosquito-borne arbovirus responsible of a large outbreak since December 2013 in the Americas from French islands in the Caribbean . Documentation of the epidemic was based on the survey of clinically suspected cases , providing limited information on the incidence of the disea...	[ "Abstract", "Introduction", "Materials", "&", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "pathogens", "tropical", "diseases", "geographical", "locations", "microbiology", "blood", "groups", "alphaviruses", "health...	2017	Epidemiology of Chikungunya Virus Outbreaks in Guadeloupe and Martinique, 2014: An Observational Study in Volunteer Blood Donors
Bursaphelenchus xylophilus is the nematode responsible for a devastating epidemic of pine wilt disease in Asia and Europe , and represents a recent , independent origin of plant parasitism in nematodes , ecologically and taxonomically distinct from other nematodes for which genomic data is available . As well as being ...	Bursaphelenchus xylophilus is an important plant pathogen , responsible for an epidemic of pine wilt disease in Asia and Europe . B . xylophilus has acquired the ability to parasitise plants independently from other economically important nematodes and has a complex life cycle that includes fungal feeding and a stage a...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results/Discussion" ]	[ "genome", "sequencing", "plant", "science", "genomics", "plant", "biology", "plant", "pathogens", "plant", "pathology", "biology", "evolutionary", "biology", "comparative", "genomics", "genetics", "and", "genomics" ]	2011	Genomic Insights into the Origin of Parasitism in the Emerging Plant Pathogen Bursaphelenchus xylophilus
While several studies have investigated general properties of the genetic architecture of natural variation in gene expression , few of these have considered natural , outbreeding populations . In parallel , systems biology has established that a general feature of biological networks is that they are scale-free , rend...	Numerous studies have shown that many genomic polymorphisms contributing to phenotypic variation are located outside of protein coding regions , suggesting that they act by modulating gene expression . Furthermore , phenotypes are seldom explained by individual genes , but rather emerge from networks of interacting gen...	[ "Abstract", "Introduction", "Results", "Discussion", "Conclusion", "Materials", "and", "methods" ]	[ "genetic", "networks", "population", "genetics", "mathematics", "network", "analysis", "molecular", "biology", "techniques", "population", "biology", "discrete", "mathematics", "combinatorics", "research", "and", "analysis", "methods", "computer", "and", "information", "s...	2017	Gene co-expression network connectivity is an important determinant of selective constraint
The N-Myc oncoprotein is a critical factor in neuroblastoma tumorigenesis which requires additional mechanisms converting a low-level to a high-level N-Myc expression . N-Myc protein is stabilized when phosphorylated at Serine 62 by phosphorylated ERK protein . Here we describe a novel positive feedback loop whereby N-...	The class III histone deacetylase SIRT1 is repressed by tumor suppressor genes and exerts divergent effects on tumorigenesis depending on its down-stream targets . Small molecule SIRT1 inhibitors have shown promising anti-cancer effects both in vitro and in vivo . Here we identified SIRT1 as a gene directly up-regulate...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "medicine", "neurological", "tumors", "gene", "expression", "genetics", "biology", "cancers", "and", "neoplasms", "genetics", "and", "genomics", "dna", "transcription" ]	2011	SIRT1 Promotes N-Myc Oncogenesis through a Positive Feedback Loop Involving the Effects of MKP3 and ERK on N-Myc Protein Stability
CBP and the related p300 protein are widely used transcriptional co-activators in metazoans that interact with multiple transcription factors . Whether CBP/p300 occupies the genome equally with all factors or preferentially binds together with some factors is not known . We therefore compared Drosophila melanogaster CB...	Development of an embryo into different cell types relies on regulation of gene expression , whereby genes are coordinately turned on or off . CBP and the related p300 protein are central regulators of gene expression in animal cells . These co-activator proteins facilitate gene activation by a multitude of transcripti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "genetics", "gene", "regulation", "dna", "transcription", "histone", "modification", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "molecular", "development", "molecular", "genetics", "pattern", "formation", ...	2012	Preferential Genome Targeting of the CBP Co-Activator by Rel and Smad Proteins in Early Drosophila melanogaster Embryos
In mice , Quaking ( Qk ) is required for myelin formation; in humans , it has been associated with psychiatric disease . QK regulates the stability , subcellular localization , and alternative splicing of several myelin-related transcripts , yet little is known about how QK governs these activities . Here , we show tha...	Myelin is a lipid-rich structure that insulates neuronal axons , facilitating electrical conductance and protecting neurons from degeneration . Myelin comprises multiple compact layers of phospholipid bilayer and specific myelin proteins that occupy distinct positions within the structure . In the central nervous syste...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/neuronal", "and", "glial", "cell", "biology", "molecular", "biology/rna-protein", "interactions", "genetics", "and", "genomics/gene", "expression", "molecular", "biology/mrna", "stability", "molecular", "biology/rna", "splicing", "biochemistry/biomacromolecule-...	2011	Quaking Regulates Hnrnpa1 Expression through Its 3′ UTR in Oligodendrocyte Precursor Cells
The ability of spiking neurons to synchronize their activity in a network depends on the response behavior of these neurons as quantified by the phase response curve ( PRC ) and on coupling properties . The PRC characterizes the effects of transient inputs on spike timing and can be measured experimentally . Here we us...	Synchronization of neuronal spiking in the brain is related to cognitive functions , such as perception , attention , and memory . It is therefore important to determine which properties of neurons influence their collective behavior in a network and to understand how . A prominent feature of many cortical neurons is s...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "circuit", "models", "mathematics", "neural", "networks", "computational", "neuroscience", "single", "neuron", "function", "biology", "computational", "biology", "neuroscience", "nonlinear", "dynamics" ]	2012	Impact of Adaptation Currents on Synchronization of Coupled Exponential Integrate-and-Fire Neurons
Targeted environmental and ecosystem management remain crucial in control of dengue . However , providing detailed environmental information on a large scale to effectively target dengue control efforts remains a challenge . An important piece of such information is the extent of the presence of potential dengue vector...	Providing detailed environmental information on a large scale to effectively target dengue control efforts remains a challenge . In this paper we present the design and implementation of a pipeline to detect outdoor open containers which constitute potential dengue vector breeding sites from geotagged images and to cre...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "neural", "networks", "statistics", "geographical", "locations", "visual", "object", "recognition", "social", "sciences", "neuroscience", "animals", "learning", "and", "memory", "perception", "regression", "analysi...	2019	Large scale detailed mapping of dengue vector breeding sites using street view images
Metagenomic studies characterize both the composition and diversity of uncultured viral and microbial communities . BLAST-based comparisons have typically been used for such analyses; however , sampling biases , high percentages of unknown sequences , and the use of arbitrary thresholds to find significant similarities...	Metagenomics uses DNA or RNA sequences isolated directly from the environment to determine what viruses or microorganisms exist in natural communities and what metabolic activities they encode . Typically , metagenomic sequences are compared to annotated sequences in public databases using the BLAST search tool . Our m...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/metagenomics", "ecology/environmental", "microbiology", "marine", "and", "aquatic", "sciences/bioinformatics" ]	2009	The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes
The human Y-chromosome does not recombine across its male-specific part and is therefore an excellent marker of human migrations . It also plays an important role in male fertility . However , its evolution is difficult to fully understand because of repetitive sequences , inverted repeats and the potentially large rol...	The Y chromosome is extraordinary in many respects; it is non-recombining along most of its length , it carries many testis-expressed genes that are often found in palindromes and thus in several copies , and it is generally highly repetitive with very few unique genes . Its evolutionary process is not well understood ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "taxonomy", "deletion", "mutation", "insertion", "mutation", "population", "genetics", "mutation", "phylogenetics", "data", "management", "phylogenetic", "analysis", "dna", "population", "biology", "gene", "conversion", "haplogroups", "computer", "and", "information", "sc...	2017	Analysis of 62 hybrid assembled human Y chromosomes exposes rapid structural changes and high rates of gene conversion
Vibrio cholerae , the agent of cholera , is a motile non-invasive pathogen that colonizes the small intestine ( SI ) . Most of our knowledge of the processes required for V . cholerae intestinal colonization is derived from enumeration of wt and mutant V . cholerae recovered from orogastrically infected infant mice . T...	Vibrio cholerae is a highly motile bacterium that causes the diarrheal disease cholera . Despite our extensive knowledge of the genes and processes that enable this non-invasive pathogen to colonize the small intestine , there is limited knowledge of the pathogen's fine localization within the intestine . Here , we use...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "animal", "models", "of", "infection", "biology", "and", "life", "sciences", "microbiology" ]	2014	Insights into Vibrio cholerae Intestinal Colonization from Monitoring Fluorescently Labeled Bacteria
The genetic architecture of many phenotypic traits is such that genes often contribute to multiple traits , and mutations in these genes can therefore affect multiple phenotypes . These pleiotropic interactions often manifest as tradeoffs between traits where improvement in one property entails a cost in another . The ...	One of the most fundamental tradeoffs in evolutionary biology is between survival and reproduction . Many parasites experience distinct selective pressures during different stages of their life cycles; mutations arising during one stage may be beneficial , but come at a cost during another . For example , many viruses ...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "computer", "and", "information", "sciences", "evolutionary", "processes", "virology", "genetics", "biology", "and", "life", "sciences", "molecular", "evolution", "microbiology", "computational", "biology", "evolutionary", "biology", "biophysics", "evolutionary", "genetics"...	2014	Payoffs, Not Tradeoffs, in the Adaptation of a Virus to Ostensibly Conflicting Selective Pressures
Two central biophysical laws describe sensory responses to input signals . One is a logarithmic relationship between input and output , and the other is a power law relationship . These laws are sometimes called the Weber-Fechner law and the Stevens power law , respectively . The two laws are found in a wide variety of...	One of the first measurements an experimentalist makes to understand a sensory system is to explore the relation between input signal and the systems response amplitude . Here , we show using mathematical models that this measurement can give important clues about the possible mechanism of sensing . We use models that ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "systems", "biology", "biophysics", "biology", "and", "life", "sciences" ]	2014	Logarithmic and Power Law Input-Output Relations in Sensory Systems with Fold-Change Detection
Herpes simplex virus 1 ( HSV-1 ) establishes life-long latent infection within sensory neurons , during which viral lytic gene expression is silenced . The only highly expressed viral gene product during latent infection is the latency-associated transcript ( LAT ) , a non-protein coding RNA that has been strongly impl...	Like all herpesviruses , herpes simplex virus 1 ( HSV-1 ) persistently infects an individual for their entire life . This persistent—or latent—virus is maintained as silenced DNA within the nuclei of sensory neurons , from which only the virus latency-associated transcript RNA is abundantly transcribed . Periodically ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "luciferase", "enzymes", "enzymology", "microbiology", "neuroscience", "mammalian", "genomics", "microbial", "genetics", "microbial", "genomics", "viral", "genomics", "animal", "cells", "proteins", "oxidoreductases", "gene", "expression", "viral", "replication", "animal", ...	2016	The HSV-1 Latency-Associated Transcript Functions to Repress Latent Phase Lytic Gene Expression and Suppress Virus Reactivation from Latently Infected Neurons
The adaptive immune response to vaccination or infection can lead to the production of specific antibodies to neutralize the pathogen or recruit innate immune effector cells for help . The non-neutralizing role of antibodies in stimulating effector cell responses may have been a key mechanism of the protection observed...	Antibodies are one of the central mechanisms that the human immune system uses to eliminate infection: an antibody can recognize a pathogen or infected cell using its Fab region while recruiting additional immune cells through its Fc that help destroy the offender . This mechanism may have been key to the reduced risk ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Machine Learning Methods Enable Predictive Modeling of Antibody Feature:Function Relationships in RV144 Vaccinees
Complex eukaryotic promoters normally contain multiple cis-regulatory sequences for different transcription factors ( TFs ) . The binding patterns of the TFs to these sites , as well as the way the TFs interact with each other and with the RNA polymerase ( RNAp ) , lead to combinatorial problems rarely understood in de...	The paper proposes and validates experimentally a model for the fine-graded regulation of a gene , called Or59b , coding for an olfactory receptor in Drosophila . The model is based on statistical thermodynamical theory , theory that so far has been mostly used for prokaryotes . In order to apply it to our more complex...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "gene", "regulation", "animals", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "experimental", "organism", "systems", "epigenetics", "chromatin", "drosophila", "research", "and", "analysis", "methods", "transcriptional", "control",...	2019	Thermodynamic model of gene regulation for the Or59b olfactory receptor in Drosophila
Transcript degradation is a widespread and important mechanism for regulating protein abundance . Two major regulators of transcript degradation are RNA Binding Proteins ( RBPs ) and microRNAs ( miRNAs ) . We computationally explored whether RBPs and miRNAs cooperate to promote transcript decay . We defined five RBP mo...	Transcript degradation represents an important mechanism of regulation used in diverse biological processes , including during development to eliminate maternally inherited transcripts , in adult tissues to define cell lineages , and as part of signaling pathways to down-regulate unneeded transcripts . RNA binding prot...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "gene", "regulation", "molecular", "genetics", "biology", "computational", "biology" ]	2013	Computational Assessment of the Cooperativity between RNA Binding Proteins and MicroRNAs in Transcript Decay
Several critical events dictate the successful establishment of nascent vasculature in yolk sac and in the developing embryos . These include aggregation of angioblasts to form the primitive vascular plexus , followed by the proliferation , differentiation , migration , and coalescence of endothelial cells . Although t...	An essential step during early embryonic development is to establish elaborate vascular networks that provide nutrients to ensure the proper growth of the embryos . This process , known as angiogenesis , requires coordinated regulation of cell proliferation , migration , and differentiation in endothelial cells , which...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "physiology", "biology", "anatomy", "and", "physiology", "molecular", "cell", "biology" ]	2013	Transcriptional Corepressors HIPK1 and HIPK2 Control Angiogenesis Via TGF-β–TAK1–Dependent Mechanism
A clear contradiction exists between cytotoxic in-vitro studies demonstrating effectiveness of Gemcitabine to curtail pancreatic cancer and in-vivo studies failing to show Gemcitabine as an effective treatment . The outcome of chemotherapy in metastatic stages , where surgery is no longer viable , shows a 5-year surviv...	There are few treatment options for advanced pancreatic cancer . The chemotherapeutic drug Gemcitabine is routinely used , yet 95% of patients die within 5 years of diagnosis . Surprisingly , Gemcitabine experiments with pancreatic tumor cells in the laboratory dish show that most cells will be killed by this drug . It...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2013	Predictive Modeling of In Vivo Response to Gemcitabine in Pancreatic Cancer
Identifying clusters of acute paracoccidioidomycosis cases could potentially help in identifying the environmental factors that influence the incidence of this mycosis . However , unlike other endemic mycoses , there are no published reports of clusters of paracoccidioidomycosis . A retrospective cluster detection test...	Paracoccocidioidomycosis is acquired through inhalation of spores released from filamentous forms of Paracoccidioides brasiliensis presumably present in the soil of endemic areas . However , successful isolation of the fungus from these areas has been rare , making it difficult to determine the fungus's ecological nich...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "ecology/environmental", "microbiology" ]	2010	First Description of a Cluster of Acute/Subacute Paracoccidioidomycosis Cases and Its Association with a Climatic Anomaly
Rhizopus oryzae is the primary cause of mucormycosis , an emerging , life-threatening infection characterized by rapid angioinvasive growth with an overall mortality rate that exceeds 50% . As a representative of the paraphyletic basal group of the fungal kingdom called “zygomycetes , ” R . oryzae is also used as a mod...	Rhizopus oryzae is a widely dispersed fungus that can cause fatal infections in people with suppressed immune systems , especially diabetics or organ transplant recipients . Antibiotic therapy alone is rarely curative , particularly in patients with disseminated infection . We sequenced the genome of a pathogenic R . o...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology/microbial", "evolution", "and", "genomics", "infectious", "diseases/fungal", "infections", "computational", "biology/comparative", "sequence", "analysis", "microbiology/microbial", "evolution", "and", "genomics", "evolutionary", "biology/genomics", "genet...	2009	Genomic Analysis of the Basal Lineage Fungus Rhizopus oryzae Reveals a Whole-Genome Duplication
Human Cytomegalovirus ( HCMV ) infection induces several metabolic activities that are essential for viral replication . Despite the important role that this metabolic modulation plays during infection , the viral mechanisms involved are largely unclear . We find that the HCMV UL38 protein is responsible for many aspec...	Viruses are parasites that usurp the energy and molecular building blocks of their hosts to support their replication . In the past few years , numerous studies have shown that a wide variety of viruses induce cellular metabolic activities that are essential for successful infection . However , the viral mechanisms res...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "physiology", "carbohydrate", "metabolism", "medicine", "and", "health", "sciences", "protein", "metabolism", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "cell", "metabolism", "glucose", "metabolism", "viruses", "physiological", "pro...	2019	The Human Cytomegalovirus UL38 protein drives mTOR-independent metabolic flux reprogramming by inhibiting TSC2
Sexually attractive characteristics are often thought to reflect an individual's condition or reproductive potential , but the underlying molecular mechanisms through which they do so are generally unknown . Insulin/insulin-like growth factor signaling ( IIS ) is known to modulate aging , reproduction , and stress resi...	In nature , a myriad of specialized traits have evolved that are used for intraspecific communication and mate choice . We postulated that certain traits may have evolved to be attractive by virtue of their accurate representation of molecular pathways that are critical for determining evolutionary fitness . Insulin si...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "insulin", "animal", "behavior", "sexual", "selection", "evolutionary", "biology", "physiology", "endocrine", "system", "pheromones", "biology", "anatomy", "and", "physiology", "evolutionary", "processes", "endocrine", "physiology" ]	2012	Insulin Signaling Mediates Sexual Attractiveness in Drosophila
Despite rapid advances in genomic technology , our ability to account for phenotypic variation using genetic information remains limited for many traits . This has unfortunately resulted in limited application of genetic data towards preventive and personalized medicine , one of the primary impetuses of genome-wide ass...	While previous genome-wide association studies have implicated numerous loci associated with complex traits , such loci typically account for a very small proportion of phenotypic variation . However , a recent study using height as a model trait has illustrated that common single nucleotide polymorphisms can explain a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "genome", "analysis", "tools", "mathematics", "statistics", "genetics", "biology", "genomics", "biostatistics", "statistical", "methods", "genetics", "and", "genomics" ]	2011	Beyond Missing Heritability: Prediction of Complex Traits
To functionally link coronary artery disease ( CAD ) causal genes identified by genome wide association studies ( GWAS ) , and to investigate the cellular and molecular mechanisms of atherosclerosis , we have used chromatin immunoprecipitation sequencing ( ChIP-Seq ) with the CAD associated transcription factor TCF21 i...	While coronary artery disease ( CAD ) is due in part to environmental and metabolic factors , about half of the risk is genetically predetermined . Genome-wide association studies in human populations have identified approximately 150 sites in the genome that appear to be associated with CAD . The mechanisms by which m...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Characterization of TCF21 Downstream Target Regions Identifies a Transcriptional Network Linking Multiple Independent Coronary Artery Disease Loci
Trichinella spiralis expresses paramyosin ( Ts-Pmy ) as a defense mechanism . Ts-Pmy is a functional protein with binding activity to human complement C8 and C9 and thus plays a role in evading the attack of the host’s immune system . In the present study , the binding activity of Ts-Pmy to human complement C1q and its...	Trichinellosis is one of the most important food-borne parasitic zoonoses worldwide . The key factor for Trichinella spiralis to survive in its host is evading from the attacks by the immune defense system . Our previous study revealed that paramyosin from Trichinella spiralis ( Ts-Pmy ) played a role in evading host i...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Trichinella spiralis Paramyosin Binds Human Complement C1q and Inhibits Classical Complement Activation
Growth rate is a near-universal selective pressure across microbial species . High growth rates require hundreds of metabolic enzymes , each with different nonlinear kinetics , to be precisely tuned within the bounds set by physicochemical constraints . Yet , the metabolic behaviour of many species is characterized by ...	The microbial genome encodes for a large network of enzyme-catalyzed reactions . The reaction rates depend on concentrations of enzymes and metabolites , which in turn depend on those rates . Cells face a number of biophysical constraints on enzyme expression , for example due to a limited membrane area or cytosolic vo...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "organismal", "evolution", "protein", "metabolism", "enzymes", "metabolic", "networks", "enzymology", "microbiology", "network", "analysis", "enzyme", "metabolism", "microbial", "evolution", "membrane", "metabolism", "enzyme", "kinetics", "cellular", "structures", "and", ...	2019	The number of active metabolic pathways is bounded by the number of cellular constraints at maximal metabolic rates
Extracellular RNA is becoming increasingly recognized as a signaling molecule . Virally derived double stranded ( ds ) RNA released into the extracellular space during virus induced cell lysis acts as a powerful inducer of classical type I interferon ( IFN ) responses; however , the receptor that mediates this response...	Nearly all viruses produce dsRNA during their replication cycle . This molecule is not normally found in a healthy host cell and thus functions as a flag , alerting the host to a viral infection . Cells can die by lysis during virus infections , and the intracellular dsRNA is then released into the extracellular space ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/viral", "infections", "virology/host", "antiviral", "responses", "immunology/immunity", "to", "infections", "immunology/innate", "immunity" ]	2010	An Accessory to the ‘Trinity’: SR-As Are Essential Pathogen Sensors of Extracellular dsRNA, Mediating Entry and Leading to Subsequent Type I IFN Responses
In metazoans , the mechanism by which DNA is synthesized during homologous recombination repair of double-strand breaks is poorly understood . Specifically , the identities of the polymerase ( s ) that carry out repair synthesis and how they are recruited to repair sites are unclear . Here , we have investigated the ro...	DNA polymerases are required during both DNA replication and various types of DNA repair . DNA double-strand breaks are frequently repaired by homologous recombination , a conservative process in which DNA is copied into the break site from a similar template . The specific polymerases that operate during homologous re...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "drosophila", "melanogaster", "model", "organisms", "molecular", "cell", "biology", "transposons", "cell", "biology", "chromosome", "biology", "nucleic", "acids", "genetics", "molecular", "genetics", "biology", "molecular", "biology", "genetics", "an...	2012	Competition between Replicative and Translesion Polymerases during Homologous Recombination Repair in Drosophila
Bacterial Microcompartments ( BMCs ) are proteinaceous organelles that encapsulate critical segments of autotrophic and heterotrophic metabolic pathways; they are functionally diverse and are found across 23 different phyla . The majority of catabolic BMCs ( metabolosomes ) compartmentalize a common core of enzymes to ...	In metabolism , molecules with “high-energy” bonds ( e . g . , ATP and Acetyl~CoA ) are critical for both catabolic and anabolic processes . Accordingly , the retention of these bonds during biochemical transformations is incredibly important . The phosphotransacylase ( Pta ) enzyme catalyzes the conversion between acy...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "crystal", "structure", "chemical", "compounds", "phosphates", "enzymes", "condensed", "matter", "physics", "enzymology", "enzyme", "metabolism", "crystallography", "cellular", "structures", "and", "organelles", "enzyme", "chemistry", "solid", "state", "physics", "protein...	2016	The Structural Basis of Coenzyme A Recycling in a Bacterial Organelle
Over the last few years , experimental data on the fluctuations in gene activity between individual cells and within the same cell over time have confirmed that gene expression is a “noisy” process . This variation is in part due to the small number of molecules taking part in some of the key reactions that are involve...	Recent experimental data showing fluctuations in gene activity between individual cells and within the same cell over time confirm that gene expression is a “noisy” process . This variation is partly due to the small number of molecules involved in gene expression . One consequence is that protein production often occu...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "cell", "biology", "computational", "biology", "computational", "biology/systems", "biology" ]	2008	Nonidentifiability of the Source of Intrinsic Noise in Gene Expression from Single-Burst Data
There exists significant interest in developing statistical and computational tools for inferring ‘who infected whom’ in an infectious disease outbreak from densely sampled case data , with most recent studies focusing on the analysis of whole genome sequence data . However , genomic data can be poorly informative of t...	Reconstructing the history of transmission events in an infectious disease outbreak provides valuable information for informing infection control policy . Recent years have seen considerable progress in the development of statistical tools for the inference of such transmission trees from outbreak data , with a major f...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "coronaviruses", "pathology", "and", "laboratory", "medicine", "statistics", "pathogens", "sars", "coronavirus", "microbiology", "viruses", "statistical", "data", "probability", "distribution", "mathematics", "rna", "viruses", "gen...	2019	Bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact data
Understanding the mechanistic basis of transcriptional regulation has been a central focus of molecular biology since its inception . New high-throughput chromatin immunoprecipitation experiments have revealed that most regulatory proteins bind thousands of sites in mammalian genomes . However , the functional signific...	Gene expression is controlled , in large part , by regulatory proteins called transcription factors that bind specific sites in the genome . A major focus of molecular biology has been understanding how these transcription factors interact with the cell's transcriptional machinery , the genome , and with each other to ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/genomics", "computational", "biology/transcriptional", "regulation" ]	2010	A Quantitative Model of Transcriptional Regulation Reveals the Influence of Binding Location on Expression
During meiosis , programmed double strand breaks ( DSBs ) are repaired preferentially between homologs to generate crossovers that promote proper chromosome segregation at Meiosis I . In many organisms , there are two strand exchange proteins , Rad51 and the meiosis-specific Dmc1 , required for interhomolog ( IH ) bias...	Sexual reproduction requires the formation of haploid gametes by a highly conserved , specialized cell division called meiosis . Failures in meiotic chromosome segregation lead to chromosomally imbalanced gametes that cause infertility and birth defects such as Trisomy 21 in humans . Meiotic crossovers , initiated by p...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "phosphorylation", "meiosis", "cell", "cycle", "and", "cell", "division", "cell", "processes", "chromatids", "dna", "homologous", "recombination", "chromosome", "biology", "proteins", "recombinant", "proteins", "biochemistry", "cell", "biology", "post-translational", "mod...	2016	Mek1 Down Regulates Rad51 Activity during Yeast Meiosis by Phosphorylation of Hed1
Over one billion people are infected with soil-transmitted helminths ( STH ) , i . e . Ascaris lumbricoides , hookworm and Trichuris trichiura . For estimating drug efficacy and monitoring anthelminthic drug resistance , accurate diagnostic methods are critical . FECPAKG2 is a new remote-diagnostic tool used in veterin...	About 1 . 5 billion people are infected with soil-transmitted helminths ( Ascaris lumbricoides , hookworm and Trichuris trichiura ) . Since morbidity correlates with the number of worms harbored by an infected individual , WHO aims to reduce moderate and heavy infections in pre- and school-aged children by 2020 . The c...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "helminths", "tropical", "diseases", "hookworms", "geographical", "locations", "parasitic", "diseases", "animals", "ascaris", "ascaris", "lumbricoides", "veterinary", "diagnostics", "tanzania", "internet", "neglected...	2018	Diagnostic comparison between FECPAKG2 and the Kato-Katz method for analyzing soil-transmitted helminth eggs in stool
Merkel cell carcinoma ( MCC ) is a relatively uncommon but highly lethal form of skin cancer . A majority of MCC tumors carry DNA sequences derived from a newly identified virus called Merkel cell polyomavirus ( MCV or MCPyV ) , a candidate etiologic agent underlying the development of MCC . To further investigate the ...	For more than 50 years it has been known that some polyomavirus types can induce cancer in experimental animals . However , associations between the various polyomaviruses known to chronically infect most humans and the development of cancer have been difficult to uncover . Last year , DNA from a new human polyomavirus...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/viruses", "and", "cancer" ]	2009	Quantitation of Human Seroresponsiveness to Merkel Cell Polyomavirus
We report here the sequencing and analysis of the genome of the nitrogen-fixing endophyte , Klebsiella pneumoniae 342 . Although K . pneumoniae 342 is a member of the enteric bacteria , it serves as a model for studies of endophytic , plant-bacterial associations due to its efficient colonization of plant tissues ( inc...	Bacterial endophytes are capable of inhabiting the living tissues of plants without causing them significant harm . Klebsiella pneumoniae 342 ( Kp342 ) is a model for this plant host-bacterial association , in part due to its capacity to colonize in high numbers the interior of plants including wheat and maize , two of...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/plant-biotic", "interactions", "genetics", "and", "genomics/comparative", "genomics", "genetics", "and", "genomics/genome", "projects", "genetics", "and", "genomics/disease", "models", "biotechnology/bioengineering", "infectious", "diseases/respiratory", "infections",...	2008	Complete Genome Sequence of the N2-Fixing Broad Host Range Endophyte Klebsiella pneumoniae 342 and Virulence Predictions Verified in Mice
Tandem direct duplications are a common feature of the genomes of eukaryotes ranging from yeast to human , where they comprise a significant fraction of copy number variations . The prevailing model for the formation of tandem direct duplications is non-allelic homologous recombination ( NAHR ) . Here we report the iso...	The recent explosion of genome sequence data has greatly increased the need to understand the forces that shape eukaryotic genomes . A common feature of higher plant genomes is the presence of large numbers of duplications , often occurring as tandem repeats of thousands of base pairs . Despite the importance of gene d...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "plant", "science", "biology", "genomics" ]	2013	Generation of Tandem Direct Duplications by Reversed-Ends Transposition of Maize Ac Elements
Fascioliasis is a worldwide parasitic disease of domestic animals caused by helminths of the genus Fasciola . In many parts of the world , particularly in poor rural areas where animal disease is endemic , the parasite also infects humans . Adult parasites reside in the bile ducts of the host and therefore diagnosis of...	Fascioliasis is a food-borne human disease caused by helminth parasites of the genus Fasciola . It is a global disease of domestic animals but its increased recognition as a major zoonosis has led to the World Health Organization including fascioliasis on the list of important human parasitic diseases . Current diagnos...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2013	The Diagnosis of Human Fascioliasis by Enzyme-Linked Immunosorbent Assay (ELISA) Using Recombinant Cathepsin L Protease
Metalloproteases ( MPs ) have demonstrated roles in immune modulation . In some cases , these enzymes are produced by parasites to influence host immune responses such that parasite infection is facilitated . One of the best examples of parasite-mediated immune modulation is the matrix metalloprotease ( MMP ) leishmano...	Parasitic flatworms , or digenetic trematodes , cause a wide range of diseases of both medical and agricultural importance . Nearly all species of digenea require specific species of snail for their larval development and transmission . The factors underpinning snail host specificity and how they dictate infection esta...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "medicine", "and", "health", "sciences", "helminths", "enzymes", "metalloproteases", "immunology", "enzymology", "parasitic", "diseases", "animals", "parasitology", "serine", "proteases", "developmental", "biology", ...	2018	A metalloprotease produced by larval Schistosoma mansoni facilitates infection establishment and maintenance in the snail host by interfering with immune cell function
Experimental studies have shown that some proteins exist in two alternative native-state conformations . It has been proposed that such bi-stable proteins can potentially function as evolutionary bridges at the interface between two neutral networks of protein sequences that fold uniquely into the two different native ...	Proteins are essential molecules for performing a majority of functions in all biological systems . These functions often depend on the three-dimensional structures of proteins . Here , we investigate a fundamental question in molecular evolution: how can proteins acquire new advantageous structures via mutations while...	[ "Abstract", "Introduction", "Discussion", "Methods" ]	[ "evolutionary", "selection", "protein", "folding", "divergent", "evolution", "biophysics", "simulations", "forms", "of", "evolution", "theoretical", "biology", "biology", "evolutionary", "theory", "biophysics", "adaptation", "biophysic", "al", "simulations", "natural", "s...	2012	Evolutionary Dynamics on Protein Bi-stability Landscapes can Potentially Resolve Adaptive Conflicts
In insects and other animals , intraspecific communication between individuals of the opposite sex is mediated in part by chemical signals called sex pheromones . In most moth species , male moths rely heavily on species-specific sex pheromones emitted by female moths to identify and orient towards an appropriate matin...	Like many animal species , moths use chemical signals called sex pheromones to communicate with conspecific individuals of the opposite sex in the context of reproduction . Typically , male moths depend on sex pheromones emitted by conspecific females to identify and locate their mates . Therefore , the behavioral pref...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "chemical", "ecology", "ecology", "gene", "identification", "and", "analysis", "genetics", "olfactory", "system", "molecular", "genetics", "biology", "sensory", "systems", "neuroethology", "neuroscience", "genetics", "and", "genomics" ]	2011	A Single Sex Pheromone Receptor Determines Chemical Response Specificity of Sexual Behavior in the Silkmoth Bombyx mori
Stable and robust oscillations in the concentration of adenosine 3′ , 5′-cyclic monophosphate ( cAMP ) are observed during the aggregation phase of starvation-induced development in Dictyostelium discoideum . In this paper we use mathematical modelling together with ideas from robust control theory to identify two fact...	The molecular network , which underlies the oscillations in the concentration of adenosine 3′ , 5′-cyclic monophosphate ( cAMP ) during the aggregation phase of starvation-induced development in Dictyostelium discoideum , achieves remarkable levels of robust performance in the face of environmental variations and cellu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "eukaryotes", "computational", "biology" ]	2007	Stochastic Noise and Synchronisation during Dictyostelium Aggregation Make cAMP Oscillations Robust
Cellular adaptation to stress is essential to ensure organismal survival . NRF2/NFE2L2 is a key determinant of xenobiotic stress responses , and loss of negative regulation by the KEAP1-CUL3 proteasome system is implicated in several chemo- and radiation-resistant cancers . Advantageously using C . elegans alongside hu...	Chronic exposure to environmental stressors throughout life ( “the exposome” ) has been tied to several cancers in humans . Cellular adaptation to stress is essential to ensure organismal survival , and NRF2 is an exceptionally well-studied and key determinant of cellular stress responses that plays complex roles in ca...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "cellular", "stress", "responses", "rna", "interference", "caenorhabditis", "enzymes", "gene", "regulation", "cell", "processes", "enzymology", "animals", "animal", "models", "caenorhabditis", "elegans", "model", "organisms", "experimental", "organism", "...	2017	WDR23 regulates NRF2 independently of KEAP1
Of all biochemically characterized metabolic reactions formalized by the IUBMB , over one out of four have yet to be associated with a nucleic or protein sequence , i . e . are sequence-orphan enzymatic activities . Few bioinformatics annotation tools are able to propose candidate genes for such activities by exploitin...	The discovery of the various metabolic functions catalyzed by enzymes encoded by the genes from the exponentially increasing number of sequenced genomes is one of the main focuses of bioinformatics tools today . However , most of these tools rely on already identified enzyme-coding gene or protein sequence information ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biochemistry", "genomics", "biology", "computational", "biology", "metabolism", "genetics", "and", "genomics" ]	2012	The CanOE Strategy: Integrating Genomic and Metabolic Contexts across Multiple Prokaryote Genomes to Find Candidate Genes for Orphan Enzymes
Understanding the structure and function of complex gene regulatory networks using classical genetic assays is an error-prone procedure that frequently generates ambiguous outcomes . Even some of the best-characterized gene networks contain interactions whose validity is not conclusively proven . Founded on dynamic exp...	Gene regulatory networks underlie all key processes that enable a cell to maintain long-term homeostasis in a changing environment . Understanding the structure and function of complex gene networks is an experimentally difficult and error-prone procedure . Mechanistic mathematical modeling promises to alleviate these ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetic", "networks", "chemical", "compounds", "gene", "regulation", "organic", "compounds", "dna", "transcription", "fungi", "model", "organisms", "network", "analysis", "genome", "analysis", "acidic", "amino", "acids", "amino", "acids", "research", "and", "analysis...	2016	Elucidation of Genetic Interactions in the Yeast GATA-Factor Network Using Bayesian Model Selection
The malarial parasite Plasmodium falciparum possesses a functional thioredoxin and glutathione system comprising the dithiol-containing redox proteins thioredoxin ( Trx ) and glutaredoxin ( Grx ) , as well as plasmoredoxin ( Plrx ) , which is exclusively found in Plasmodium species . All three proteins belong to the th...	Protection from oxidative stress and efficient redox regulation are essential for malarial parasites which have to grow and multiply rapidly in various environments . As shown by glucose-6 phosphate dehydrogenase deficiency , a genetic variation protecting from malaria , the parasite–host cell unit is very susceptible ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "biochemistry/protein", "chemistry" ]	2009	Identification of Proteins Targeted by the Thioredoxin Superfamily in Plasmodium falciparum
Maintaining genome stability in the germline is thought to be an evolutionarily ancient role of the p53 family . The sole Caenorhabditis elegans p53 family member CEP-1 is required for apoptosis induction in meiotic , late-stage pachytene germ cells in response to DNA damage and meiotic recombination failure . In an un...	Germ cell apoptosis helps to ensure that only healthy germ cells contribute to the next generation . The C . elegans p53 family member CEP-1 plays an important role in inducing apoptosis in damaged germ cells . CEP-1 protein is maximally expressed in late-stage pachytene cells , which are the only cells of the germline...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "death", "animal", "models", "caenorhabditis", "elegans", "model", "organisms", "apoptotic", "signaling", "radiobiology", "signaling", "in", "cellular", "processes", "ras", "signaling", "biology", "molecular", "biology", "signal", "transduction", "cell", "biolog...	2011	Regulation of Caenorhabditis elegans p53/CEP-1–Dependent Germ Cell Apoptosis by Ras/MAPK Signaling
The Ku complex binds non-specifically to DNA breaks and ensures repair via NHEJ . However , Ku is also known to bind directly to telomeric DNA ends and its presence there is associated with telomere capping , but avoiding NHEJ . How the complex discriminates between a DNA break and a telomeric extremity remains unknown...	The Ku complex binds to and mediates the rejoining of two DNA ends that were generated by a double-stranded DNA break in the genome . However , Ku is known to be present at telomeres as well . If it would induce end-to-end joining there , it would create chromosome end-fusions that inevitably will lead to gross chromos...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "chemical", "compounds", "chromosome", "structure", "and", "function", "molecular", "probe", "techniques", "dna-binding", "proteins", "galactose", "carbohydrates", "organic", "compounds", "telomeres", "dna", "replication", "dna", "molecular", "biology", "techniques", "res...	2016	Ku Binding on Telomeres Occurs at Sites Distal from the Physical Chromosome Ends
The genus Onchocerca encompasses parasitic nematodes including Onchocerca volvulus , causative agent of river blindness in humans , and the zoonotic Onchocerca lupi infecting dogs and cats . In dogs , O . lupi adult worms cause ocular lesions of various degrees while humans may bear the brunt of zoonotic onchocercosis ...	The genus Onchocerca ( Spirurida , Onchocercidae ) includes Onchocerca volvulus , which is estimated to infect at least 37 million people globally , and zoonotic Onchocerca lupi in carnivores . Infection by O . lupi has been reported in dogs and cats from several European countries and recently also in the U . S . and ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "onchocerca", "volvulus", "diagnostic", "radiology", "ultrasound", "imaging", "helminths", "vertebrates", "parasitic", "diseases", "dogs", "onchocerca", "animals", "mammals", "nematode", "infectio...	2018	Evaluation of oxfendazole in the treatment of zoonotic Onchocerca lupi infection in dogs
Genetically diverse pathogens ( such as Human Immunodeficiency virus type 1 , HIV-1 ) are frequently stratified into phylogenetically or immunologically defined subtypes for classification purposes . Computational identification of such subtypes is helpful in surveillance , epidemiological analysis and detection of nov...	There are nine different subtypes of the main group of HIV-1 , each originating as a distinct subepidemic of HIV-1 . The distribution of subtypes is often unique to a given geographic region of the world and constitutes a useful epidemiological and surveillance resource . The effects of viral subtype on disease progres...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "computer", "science/applications", "computational", "biology/comparative", "sequence", "analysis", "virology/immunodeficiency", "viruses", "computational", "biology/evolutionary", "modeling", "mathematics/statistics" ]	2009	An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1
Visceral leishmaniasis ( VL ) control in the Indian subcontinent is currently based on case detection and treatment , and on vector control using indoor residual spraying ( IRS ) . The use of long-lasting insecticidal nets ( LN ) has been postulated as an alternative or complement to IRS . Here we tested the impact of ...	Visceral leishmaniasis ( VL ) is a vector-borne disease causing at least 60 , 000 deaths each year amongst an estimated half million cases , and until recently there have been no significant initiatives to reduce this burden . However , in 2005 , the governments of India , Bangladesh and Nepal signed a memorandum of un...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases" ]	2010	Effect of Village-wide Use of Long-Lasting Insecticidal Nets on Visceral Leishmaniasis Vectors in India and Nepal: A Cluster Randomized Trial
Hospitalization of the elderly for invasive pneumococcal disease is frequently accompanied by the occurrence of an adverse cardiac event; these are primarily new or worsened heart failure and cardiac arrhythmia . Herein , we describe previously unrecognized microscopic lesions ( microlesions ) formed within the myocard...	Hospitalization for community-acquired pneumonia carries a documented risk for adverse cardiac events . These occur during infection and contribute to elevated mortality rates in convalescent individuals up to 1 year thereafter . We describe a previously unrecognized pathogenic mechanism by which Streptococcus pneumoni...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "gram", "positive", "bacteria", "acute", "cardiovascular", "problems", "heart", "failure", "infectious", "diseases", "bacterial", "diseases", "medicine", "and", "health", "sciences", "arrhythmia", "cell", "biology", "biology", "and", "life", "sciences", ...	2014	Streptococcus pneumoniae Translocates into the Myocardium and Forms Unique Microlesions That Disrupt Cardiac Function
The term “motor neuron disease” encompasses a spectrum of disorders in which motor neurons are the primary pathological target . However , in both patients and animal models of these diseases , not all motor neurons are equally vulnerable , in that while some motor neurons are lost very early in disease , others remain...	The term “motor neuron disease” refers to a group of disorders , causing progressive paralysis of affected patients due to the degeneration of motor neurons cells which control voluntary movements . Importantly , not all motor neurons appear to be affected in the same way , with those that control the face being affect...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "neuromuscular", "junctions", "nervous", "system", "neurodegenerative", "diseases", "animal", "models", "of", "disease", "electrophysiology", "neuroscience", "animals", "motor", "neurons", "animal", "models", "dros...	2017	Comparison of independent screens on differentially vulnerable motor neurons reveals alpha-synuclein as a common modifier in motor neuron diseases
Renal carriage and shedding of leptospires is characteristic of carrier or maintenance animal hosts . Sporadic reports indicate that after infection , humans may excrete leptospires for extended periods . We hypothesized that , like mammalian reservoir hosts , humans develop asymptomatic leptospiruria in settings of hi...	Leptospirosis is a bacterial disease commonly transmitted from animals to humans . The more than 200 types of spiral-shaped bacteria ( spirochetes ) in the genus Leptospira are classified as pathogenic , intermediately pathogenic , or saprophytic ( meaning not causing infection in any mammal ) based on their ability to...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/bacterial", "infections", "microbiology/applied", "microbiology", "microbiology/environmental", "microbiology", "microbiology" ]	2010	Asymptomatic Renal Colonization of Humans in the Peruvian Amazon by Leptospira
Day length is a key environmental cue regulating the timing of major developmental transitions in plants . For example , in perennial plants such as the long-lived trees of the boreal forest , exposure to short days ( SD ) leads to the termination of meristem activity and bud set ( referred to as growth cessation ) . T...	Day length is a critical and robust environmental cue utilised by plants to modulate their patterns of growth to adapt to changing seasonal conditions . In perennial plants such as long-lived trees of the boreal forest , reduction in day length ( short day signal/SD ) induces the cessation of growth prior to the advent...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "science", "plant", "growth", "and", "development", "plant", "biology", "biology" ]	2011	Short Day–Mediated Cessation of Growth Requires the Downregulation of AINTEGUMENTALIKE1 Transcription Factor in Hybrid Aspen
Taenia solium cysticercosis is a neglected parasitic zoonosis occurring in many developing countries . Socio-cultural determinants related to its control remain unclear . Studies in Africa have shown that the underuse of sanitary facilities and the widespread occurrence of free-roaming pigs are the major risk factors f...	Livestock owners from small scale farms are most vulnerable for Neglected Zoonotic Diseases ( NZD ) in developing countries and their risk behavior leads to more intense and complex transmission patterns . Studies in Africa have shown that the underuse of sanitary facilities and the widespread occurrence of free-roamin...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Why Latrines Are Not Used: Communities’ Perceptions and Practices Regarding Latrines in a Taenia solium Endemic Rural Area in Eastern Zambia
Model-based analysis of fMRI data is an important tool for investigating the computational role of different brain regions . With this method , theoretical models of behavior can be leveraged to find the brain structures underlying variables from specific algorithms , such as prediction errors in reinforcement learning...	In recent years , model-based fMRI has emerged as a powerful technique in psychology and neuroscience . With this method , computational models of behavior can be leveraged to identify where , whether and how different algorithms are implemented in the brain . Yet this approach seems to have an Achilles heel in that th...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Is Model Fitting Necessary for Model-Based fMRI?
The outer membrane of Gram-negative bacteria functions as a permeability barrier that protects these bacteria against harmful compounds in the environment . Most nutrients pass the outer membrane by passive diffusion via pore-forming proteins known as porins . However , diffusion can only satisfy the growth requirement...	The sequestration of essential nutrient metals is a first line of defense used by vertebrates to limit the growth of invading pathogens , a process termed “nutritional immunity . ” As a part of this defense mechanism , neutrophils and other cells produce massive amounts of calprotectin , a protein that limits bacterial...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Zinc Piracy as a Mechanism of Neisseria meningitidis for Evasion of Nutritional Immunity
Transforming growth factor-beta ( TGF-β ) , a multifunctional cytokine regulating several immunologic processes , is expressed by virtually all cells as a biologically inactive molecule termed latent TGF-β ( LTGF-β ) . We have previously shown that TGF-β activity increases during influenza virus infection in mice and s...	Transforming growth factor-beta ( TGF-β ) is a multifunctional protein that serves as a global regulator of immunity by controlling the initiation and resolution of inflammatory responses . A pathogen that can regulate TGF-β activation could promote an immune-privileged state for itself within its host . Indeed , multi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/virulence", "factors", "and", "mechanisms", "pathology/pathophysiology", "virology/animal", "models", "of", "infection", "virology", "virology/mechanisms", "of", "resistance", "and", "susceptibility,", "including", "host", "genetics" ]	2010	Transforming Growth Factor-β: Activation by Neuraminidase and Role in Highly Pathogenic H5N1 Influenza Pathogenesis
A large number of experiments have asked to what degree human reaching movements can be understood as being close to optimal in a statistical sense . However , little is known about whether these principles are relevant for other classes of movements . Here we analyzed movement in a task that is similar to surfing or s...	There is a growing body of work demonstrating that humans are close to statistically optimal in both their perception of the world and their actions on it . That is , we seem to combine information from our sensors with the constraints and costs of moving to minimize our errors and effort . Most of the evidence for thi...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "neuroscience/motor", "systems", "computer", "science/systems", "and", "control", "theory", "neuroscience/theoretical", "neuroscience" ]	2009	Bayesian Integration and Non-Linear Feedback Control in a Full-Body Motor Task
Canine distemper virus ( CDV ) vaccination confers long-term protection against CDV reinfection . To investigate the utility of CDV as a polyvalent vaccine vector for Leishmania , we generated recombinant CDVs , based on an avirulent Yanaka strain , that expressed Leishmania antigens: LACK , TSA , or LmSTI1 ( rCDV–LACK...	More than 1 million new cases of leishmaniasis occur throughout the world every year . Leishmaniasis typically presents as one of two clinical forms , either cutaneous or visceral . Dogs harboring Leishmania act as reservoirs , and are closely associated with human infections in South America and southern Europe . Ther...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Efficacy of Recombinant Canine Distemper Virus Expressing Leishmania Antigen against Leishmania Challenge in Dogs
Ebola viruses are highly lethal human pathogens that have received considerable attention in recent years due to an increasing re-emergence in Central Africa and a potential for use as a biological weapon . There is no vaccine or treatment licensed for human use . In the past , however , important advances have been ma...	Being highly pathogenic for humans and monkeys and the subject of former weapons programs makes Ebola virus one of the most feared pathogens worldwide today . Due to a lack of licensed pre- and post-exposure intervention , our current response depends on rapid diagnostics , proper isolation procedures , and supportive ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Supporting", "Information" ]	[ "viruses", "animals", "infectious", "diseases", "virology" ]	2007	Effective Post-Exposure Treatment of Ebola Infection
Borders are important as they demarcate developing tissue into distinct functional units . A key challenge is the discovery of mechanisms that can convert morphogen gradients into tissue borders . While mechanisms that produce ultrasensitive cellular responses provide a solution , how extracellular morphogens drive suc...	During development , morphogen gradients play a crucial role in transforming a uniform field of cells into regions with distinct cell identities ( marked by the expression of specific genes ) . Finding mechanisms that convert morphogen gradients into sharp borders of gene expression , however , remains a challenge . Ce...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "physics", "systems", "biology", "developmental", "biology", "computer", "science", "mathematics", "applied", "mathematics", "biology", "computational", "biology", "computerized", "simulations", "biophysics", "neuroscience", "nonlinear", "dynamics" ]	2014	A BMP-FGF Morphogen Toggle Switch Drives the Ultrasensitive Expression of Multiple Genes in the Developing Forebrain
Genome-wide association studies ( GWAS ) have identified >500 common variants associated with quantitative metabolic traits , but in aggregate such variants explain at most 20–30% of the heritable component of population variation in these traits . To further investigate the impact of genotypic variation on metabolic t...	Abnormal serum levels of various metabolites , including measures relevant to cholesterol , other fats , and sugars , are known to be risk factors for cardiovascular disease and type 2 diabetes . Identification of the genes that play a role in generating such abnormalities could advance the development of new treatment...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome-wide", "association", "studies", "genome", "sequencing", "genomics", "genetic", "polymorphism", "genetic", "association", "studies", "genetics", "population", "genetics", "biology", "human", "genetics", "genetics", "of", "disease", "genetic", "drift" ]	2014	Re-sequencing Expands Our Understanding of the Phenotypic Impact of Variants at GWAS Loci
Mucormycosis—an emergent , deadly fungal infection—is difficult to treat , in part because the causative species demonstrate broad clinical antifungal resistance . However , the mechanisms underlying drug resistance in these infections remain poorly understood . Our previous work demonstrated that one major agent of mu...	The emerging infection mucormycosis causes high mortality in part because the major causative fungi , including Mucor circinelloides , are resistant to most clinically available antifungal drugs . We previously discovered an RNA interference-based resistance mechanism , epimutation , through which M . circinelloides de...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "rna", "interference", "nucleobases", "drugs", "microbiology", "antifungals", "nucleotides", "mutation", "uracils", "genome", "analysis", "pharmacology", "epigenetics", "molecular", "biology", "techniques", "nucleot...	2019	Broad antifungal resistance mediated by RNAi-dependent epimutation in the basal human fungal pathogen Mucor circinelloides
Telomeres are nucleoprotein complexes that protect the ends of linear chromosomes from incomplete replication , degradation and detection as DNA breaks . Mammalian telomeres are protected by shelterin , a multiprotein complex that binds the TTAGGG telomeric repeats and recruits a series of additional factors that are e...	Chromosome ends are capped by specialized structures called telomeres , which protect chromosomes from deterioration , incomplete replication and end-to-end fusion . Defects in telomere structure and/or function may have a strong impact on human health , leading to premature aging and a variety of diseases including ca...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	AKTIP/Ft1, a New Shelterin-Interacting Factor Required for Telomere Maintenance
Using forward genetics , we have identified the genes mutated in two classes of zebrafish fin mutants . The mutants of the first class are characterized by defects in embryonic fin morphogenesis , which are due to mutations in a Laminin subunit or an Integrin alpha receptor , respectively . The mutants of the second cl...	There are a large number of human genetic syndromes with limb and digit deformities . It has been shown that the genes underlying these syndromes are well conserved in evolution , and most perform the same role even in the fins of fish . One such human syndrome is Fraser Syndrome , characterized by a number of defects ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/embryology", "dermatology/pediatric", "skin", "diseases,", "including", "genetic", "diseases", "developmental", "biology", "cell", "biology/developmental", "molecular", "mechanisms", "cell", "biology/extra-cellular", "matrix" ]	2010	Genetic Analysis of Fin Development in Zebrafish Identifies Furin and Hemicentin1 as Potential Novel Fraser Syndrome Disease Genes
Although considerable evidence supports that misfolded prion protein ( PrPSc ) is the principal component of “prions” , underpinning both transmissibility and neurotoxicity , clear consensus around a number of fundamental aspects of pathogenesis has not been achieved , including the time of appearance of neurotoxic spe...	Although evidence clearly supports that misfolded prion protein ( PrPSc ) is the principal component of “prions” , underpinning both transmissibility and neurotoxicity , consensus is lacking around the time of appearance and biochemical profile of neurotoxic species during disease evolution . Employing an electrophysio...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "brain", "electrophysiology", "vertebrates", "electrophysiology", "mice", "neuroscience", "animals", "mammals", "materials", "science", "bioassays", "and", "physiological", "analysis", "oligomers", "research", "and", "analysis", "m...	2019	Early existence and biochemical evolution characterise acutely synaptotoxic PrPSc
Fungal cells change shape in response to environmental stimuli , and these morphogenic transitions drive pathogenesis and niche adaptation . For example , dimorphic fungi switch between yeast and hyphae in response to changing temperature . The basidiomycete Cryptococcus neoformans undergoes an unusual morphogenetic tr...	Changes in cell shape underlie fungal pathogenesis by allowing immune evasion and dissemination . Aspergillus and Candida albicans hyphae drive tissue penetration . Histoplasma capsulatum and C . albicans yeast growth allows evasion and dissemination . As major virulence determinants , morphogenic transitions are exten...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "walls", "cryptococcus", "neoformans", "medicine", "and", "health", "sciences", "cryptococcus", "pathology", "and", "laboratory", "medicine", "pathogens", "cell", "cycle", "and", "cell", "division", "population", "genetics", "ploidy", "microbiology", "cell", "...	2018	The Cryptococcus neoformans Titan cell is an inducible and regulated morphotype underlying pathogenesis
MHC class II ( MHCII ) genes are transactivated by the NOD-like receptor ( NLR ) family member CIITA , which is recruited to SXY enhancers of MHCII promoters via a DNA-binding “enhanceosome” complex . NLRC5 , another NLR protein , was recently found to control transcription of MHC class I ( MHCI ) genes . However , det...	Major histocompatibility complex class I ( MHCI ) molecules are central to immunity and immunological disorders , and constitute a major obstacle in organ transplantation . It is therefore vital to gain insight into the regulation of their expression . NLRC5 was recently found to regulate MHCI gene transcription . Howe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	NLRC5 Exclusively Transactivates MHC Class I and Related Genes through a Distinctive SXY Module
Post-therapeutic follow-up is essential to confirm cure and to detect early treatment failures in patients affected by sleeping sickness ( HAT ) . Current methods , based on finding of parasites in blood and cerebrospinal fluid ( CSF ) and counting of white blood cells ( WBC ) in CSF , are imperfect . New markers for t...	The reduction of the number of lumbar punctures performed during the follow-up of patients affected by sleeping sickness ( HAT ) is considered a research priority . Follow-up , consisting of the examination of cerebrospinal fluid ( CSF ) for presence of parasites and for the number of leukocytes , is necessary to asses...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "parastic", "protozoans", "medicine", "infectious", "diseases", "trypanosoma", "neglected", "tropical", "diseases", "protozoology", "biology", "microbiology" ]	2013	Neopterin Is a Cerebrospinal Fluid Marker for Treatment Outcome Evaluation in Patients Affected by Trypanosoma brucei gambiense Sleeping Sickness
Melioidosis , caused by the Gram-negative bacterium Burkholderia pseudomallei , is an emerging cause of pneumonia-derived sepsis in the tropics . The gut microbiota supports local mucosal immunity and is increasingly recognized as a protective mediator in host defenses against systemic infection . Here , we aimed to ch...	Melioidosis is a common cause of community-acquired pneumonia and sepsis in Asia . The causative agent , Burkholderia pseudomallei , is listed as a potential bioterror weapon . The intestinal microbiota has been suggested to be a modulator of innate immune defenses against bacterial infections . Here we investigated in...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "antimicrobials", "medicine", "and", "health", "sciences", "gut", "bacteria", "microbiome", "immune", "cells", "melioidosis", "drugs", "immunology", "microbiology", "animal", "models", "bacterial", "diseases", "model", "organisms", "antibiotics", "expe...	2017	The gut microbiota as a modulator of innate immunity during melioidosis
Neural signals are characterized by rich temporal and spatiotemporal dynamics that reflect the organization of cortical networks . Theoretical research has shown how neural networks can operate at different dynamic ranges that correspond to specific types of information processing . Here we present a data analysis fram...	In neuroscience , researchers are often interested in the modulations of specific signal components ( e . g . , oscillations in a particular frequency band ) , that have to be extracted from a background of both rhythmic and non-rhythmic activity . As the interfering background signals often have higher amplitude than ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "fourier", "analysis", "medicine", "and", "health", "sciences", "engineering", "and", "technology", "signal", "processing", "brain", "random", "variables", "neuroscience", "covariance", "simulation", "and", "modeling", "mathematics", "brain", "mapping", "white", "noise"...	2017	Dynamic decomposition of spatiotemporal neural signals
Compelling behavioral evidence suggests that humans can make optimal decisions despite the uncertainty inherent in perceptual or motor tasks . A key question in neuroscience is how populations of spiking neurons can implement such probabilistic computations . In this article , we develop a comprehensive framework for o...	Most of our daily actions are subject to uncertainty . Behavioral studies have confirmed that humans handle this uncertainty in a statistically optimal manner . A key question then is what neural mechanisms underlie this optimality , i . e . how can neurons represent and compute with probability distributions . Previou...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience", "neuroscience/theoretical", "neuroscience", "neuroscience/sensory", "systems", "computational", "biology/computational", "neuroscience" ]	2011	Spike-Based Population Coding and Working Memory
Haploinsufficiency , a dominant phenotype caused by a heterozygous loss-of-function mutation , has been rarely observed . However , high-dimensional single-cell phenotyping of yeast morphological characteristics revealed haploinsufficiency phenotypes for more than half of 1 , 112 essential genes under optimal growth co...	Diploid organisms harboring a wild-type gene and a loss-of-function mutation are called heterozygotes . They are expected to have weak or no individual phenotypes because the mutation is compensated for by the intact allele . The dominant inheritance of phenotypes in heterozygotes is an exceptional phenomenon called ha...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "methods", "and", "resources", "multivariate", "analysis", "fungi", "model", "organisms", "mathematics", "statistics", "(mathematics)", "genome", "analysis", "experimental", "organism", "systems", "molecular", "biology", "techniques", "mutagenesis", "and", "gene", "deleti...	2018	High-dimensional single-cell phenotyping reveals extensive haploinsufficiency
Cortical computations are critically dependent on interactions between pyramidal neurons ( PNs ) and a menagerie of inhibitory interneuron types . A key feature distinguishing interneuron types is the spatial distribution of their synaptic contacts onto PNs , but the location-dependent effects of inhibition are mostly ...	Establishing how inhibitory neurons shape the computing functions of neural circuits is crucial to understanding both normal function and dysfunction in the human brain . It has been known for over a century that different classes of inhibitory interneurons project to different sub-regions of the neurons they contact –...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "neuroscience", "single", "neuron", "function", "biology", "computational", "biology" ]	2012	Location-Dependent Effects of Inhibition on Local Spiking in Pyramidal Neuron Dendrites
Pathogenic bacteria such as Listeria and Yersinia gain initial entry by binding to host target cells and stimulating their internalization . Bacterial uptake entails successive , increasingly strong associations between receptors on the surface of bacteria and hosts . Even with genetically identical cells grown in the ...	Uptake of bacteria by mammalian cells is highly variable within a population of host cells and between host cell types . A detailed but unwieldy mechanistic model describing individual host-pathogen receptor binding events is captured by a simple power-law dependence on the concentration of the host receptors . The pow...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	A Power-Law Dependence of Bacterial Invasion on Mammalian Host Receptors

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